bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference
Authors: Zerrouk Naouel , Miagoux Quentin , Dispot Aurelien , Elati Mohamed , Niarakis Anna 
Published: October 2020

AbstractRheumatoid arthritis (RA) is a systemic autoimmune disease that affects the synovial joints of the body. Rheumatoid arthritis fibroblast-like synoviocytes (RA FLS) are central players in the disease pathogenesis, as they are involved in the secretion of cytokines and proteolytic enzymes, exhibit invasive traits, high rate of self-proliferation and an apoptosis-resistant phenotype. We aim at characterizing transcription factors (TFs) that are master regulators in RA FLS and could potentially explain phenotypic traits. We make use of differentially expressed genes in synovial tissue from patients suffering from RA and osteoarthritis (OA) to infer a TF co-regulatory network, using dedicated software. The co-regulatory network serves as a reference to analyze microarray and single-cell RNA-seq data from isolated RA FLS. We identified five master regulators specific to RA FLS, namely BATF, POU2AF1, STAT1, LEF1 and IRF4. TF activity of the identified master regulators was also estimated with the use of two additional, independent software. The identified TFs contribute to the regulation of inflammation, proliferation and apoptosis, as indicated by the comparison of their differentially expressed target genes with hallmark molecular signatures derived from the Molecular Signatures Database (MSigDB). Our results show that TFs influence could be used to identify putative master regulators of phenotypic traits and suggest novel, druggable targets for experimental validation.
Mechanical behavior of frozen soil improved with sulphoaluminate cement and its microscopic mechanism
Authors: Yin Zhenhua , Zhang Hu , Zhang Jianming , Chai Mingtang 
Published: October 2020

AbstractThe foundation of constructions built in the permafrost areas undergo considerable creeping or thawing deformation because of the underlying ice-rich permafrost. Soil improvement may be of advantage in treating ice-rich permafrost at shallow depth. Sulphoaluminate cement was a potential material to improve frozen soil. Simultaneously, two other cements, ordinary Portland cement and Magnesium phosphate cement were selected as the comparison. The mechanical behavior of modified frozen soil was studied with thaw compression tests and unconfined compression strength tests. Meanwhile, the microscopic mechanism was explored by field emission scanning electron microscopy, particle size analysis and X-ray diffractometry. The results showed Sulphoaluminate cement was useful in reducing the thaw compression deformation and in enhancing the strength of the frozen soil. The improvement of the mechanical behavior depended mainly on two aspects: the formation of structural mineral crystals and the agglomeration of soil particles. The two main factors contributed to the improvement of mechanical properties simultaneously. The thicker AFt crystals result in a higher strength and AFt plays an important role in improving the mechanical properties of frozen soils.The study verified that Sulphoaluminate cement was an excellent stabilizer to improve ice-rich frozen soils.
Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm
Authors: Ting Ngoot-Chin , Sherbina Katrina , Khoo Jia-Shiun , Kamaruddin Katialisa , Chan Pek-Lan , Chan Kuang-Lim , Halim Mohd Amin Ab , Sritharan Kandha , Yaakub Zulkifli , Mayes Sean , Massawe Festo , Chang Peter L. , Nuzhdin Sergey V. , Sambanthamurthi Ravigadevi , Singh Rajinder 
Published: October 2020

AbstractEvaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted fromE. oleifera×E. guineensisinterspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.
Renal fibrosis detected by diffusion-weighted magnetic resonance imaging remains unchanged despite treatment in subjects with renovascular disease
Authors: Ferguson Christopher M. , Eirin Alfonso , Abumoawad Abdelrhman , Saad Ahmed , Jiang Kai , Hedayat Ahmad F. , Misra Sanjay , Glockner James , Textor Stephen C. , Lerman Lilach O. 
Published: October 2020

AbstractTissue fibrosis is an important index of renal disease progression. Diffusion-weighted magnetic resonance imaging’s (DWI-MRI) apparent diffusion coefficient (ADC) reveals water diffusion is unobstructed by microstructural alterations like fibrosis. We hypothesized that ADC may indicate renal injury and response to therapy in patients with renovascular disease (RVD). RVD patients were treated with medical therapy (MT) and percutaneous transluminal renal angioplasty (MT + PTRA) (n = 11, 3 bilaterally, n = 14 kidneys) or MT (n = 9). ADC and renal hypoxia (R2*) by blood-oxygen-level-dependent MRI were studied before (n = 27) and 3 months after (n = 20) treatment. Twelve patients underwent renal biopsies. Baseline ADC values were correlated with changes in eGFR, serum creatinine (SCr), systolic blood pressure (SBP), renal hypoxia, and renal vein levels of pro-inflammatory marker tumor necrosis-factor (TNF)-α. Renal oxygenation, eGFR, and SCr improved after MT + PTRA. ADC inversely correlated with the histological degree of renal fibrosis, but remained unchanged after MT or MT + PTRA. Basal ADC values correlated modestly with change in SBP, but not in renal hypoxia, TNF-α levels, or renal function. Lower ADC potentially reflects renal injury in RVD patients, but does not change in response to medical or interventional therapy over 3 months. Future studies need to pinpoint indices of kidney recovery potential.
Computational analysis of eugenol inhibitory activity in lipoxygenase and cyclooxygenase pathways
Authors: das Chagas Pereira de Andrade Francisco , Mendes Anderson Nogueira 
Published: October 2020

AbstractChronic inflammation is triggered by numerous diseases such as osteoarthritis, Crohn's disease and cancer. The control of the pro-inflammatory process can prevent, mitigate and/or inhibit the evolution of these diseases. Therefore, anti-inflammatory drugs have been studied as possible compounds to act in these diseases. This paper proposes a computational analysis of eugenol in relation to aspirin and diclofenac and analyzing the ADMET profile and interactions with COX-2 and 5-LOX enzymes, important enzymes in the signaling pathway of pro-inflammatory processes. Through the analysis of ADMET in silico, it was found that the pharmacokinetic results of eugenol are similar to NSAIDs, such as diclofenac and aspirin. Bioinformatics analysis using coupling tests showed that eugenol can bind to COX-2 and 5-LOX. These results corroborate with different findings in the literature that demonstrate anti-inflammatory activity with less gastric irritation, bleeding and ulcerogenic side effects of eugenol. The results of bioinformatics reinforce studies that try to propose eugenol as an anti-inflammatory compound that can act in the COX-2/5-LOX pathways, replacing some NSAIDs in different diseases.
Efficacy of fungicides in controlling rice blast and dirty panicle diseases in Thailand
Authors: Kongcharoen Nattapatphon , Kaewsalong Nipon , Dethoup Tida 
Published: October 2020

AbstractIn this study, the fungicidal activities of the fungicides azoxystrobin, difenoconazole + propiconazole, carbendazim, flutriafol, fluopyram + tebuconazole, mancozeb and thiophanate-methyl against rice blast and dirty panicle pathogens were evaluated under laboratory and field conditions. Mancozeb exhibited the highest level of fungicidal activity against the blast pathogenPyricularia oryzae, with an EC50value of 0.25 parts per million (ppm). The combination of two fungicides, fluopyram + tebuconazole, showed the strongest fungicidal effect againstBipolaris oryzaeandCurvularia lunata, with EC50values of 0.587 ppm and 0.435 ppm,respectively. Meanwhile, carbendazim and flutriafol demonstrated the best level of fungicidal activity againstFusarium incarnatum, with the lowest EC50values of 0.211 ppm and 0.214 ppm,respectively. The results showed that the fungicides, triazole and strobilurin, had significant effects against rice blast and dirty panicle diseases. The combination of fluopyram + tebuconazole, when applied twice, was the most effective in reducing dirty panicle disease by up to 60% and increasing rice yield by 29% more than the untreated control. Fluopyram + tebuconazole, difenoconazole + propiconazole, flutriafol and azoxystrobin achieved stronger fungicidal activity against rice blast disease, reducing its severity by 32–33% when applied twice by foliar spraying. However, carbendazim, mancozeb and thiophanate-methyl had low to moderate fungicidal activity against both rice diseases in this study.
Habitat preferences of Southern Ground-hornbills in the Kruger National Park: implications for future conservation measures
Authors: Combrink Leigh , Combrink Hendrik J. , Botha André J. , Downs Colleen T. 
Published: October 2020

AbstractUnderstanding how a species utilises its habitat, and the processes that give rise to its movements and patterns of space use, is critical for its conservation. Southern Ground-hornbills Bucorvus leadbeateri are listed as Endangered in South Africa, as a result of habitat loss and persecution. The National Species Recovery Plan lists reintroductions as a suitable conservation action, but highlights “understanding the exact habitat requirements of Southern Ground-hornbills” as a knowledge gap. In this study, we used tracking data from six Southern Ground-hornbill groups (a total of 37,060 GPS locations) in the Kruger National Park to investigate their seasonal home range differences and habitat preferences. We used first-passage time analysis to determine the scale at which Southern Ground-hornbills concentrate their foraging efforts and whether specific movement behaviours were linked to habitat types. We found marked differences in seasonal home ranges, with all groups showing a range contraction during the breeding season. Grassland and open woodland habitat types were used throughout the year in accordance with their availability within the territory, with grassland, open woodland and dense thicket being favoured habitats for foraging. Our habitat preference results, based on longitudinal GPS data, allowed us to determine ideal habitat ratios (grassland:open woodland:low shrubland of 1.00:6.10:0.09 ha) to assist with the selection of suitable reintroduction sites for Southern Ground-hornbills. With an increasing number of species being threatened with extinction, reintroductions into suitable habitats may be a useful conservation mitigation measure. However, our findings highlight the importance of a thorough understanding of a species’ movement and space use prior to the selection of areas for reintroduction to ensure the establishment and sustainability of these species at these sites.
Molecular targets for diagnostic and intraoperative imaging of pancreatic ductal adenocarcinoma after neoadjuvant FOLFIRINOX treatment
Authors: Vuijk F. A. , de Muynck L. D. A. N. , Franken L. C. , Busch O. R. , Wilmink J. W. , Besselink M. G. , Bonsing B. A. , Bhairosingh S. S. , Kuppen P. J. K. , Mieog J. S. D. , Sier C. F. M. , Vahrmeijer A. L. , Verheij J. , Fariňa-Sarasqueta A. , Swijnenburg R. J. 
Published: October 2020

AbstractNeoadjuvant systemic treatment is increasingly being integrated in the standard treatment of pancreatic ductal adenocarcinoma (PDAC) patients to improve oncological outcomes. Current available imaging techniques remain unreliable in assessing response to therapies, as they cannot distinguish between (vital) tumor tissue and therapy induced fibrosis (TIF). Consequently, resections with tumor positive margins and subsequent early post-operative recurrences occur and patients eligible for potential radical resection could be missed. To optimize patient selection and monitor results of neoadjuvant treatment, PDAC-specific diagnostic and intraoperative molecular imaging methods are required. This study aims to evaluate molecular imaging targets for PDAC after neoadjuvant FOLFIRINOX treatment. Expression of integrin αvβ6, carcinoembryonic antigen cell adhesion molecule 5 (CEACAM5), mesothelin, prostate-specific membrane antigen (PSMA), urokinase-type plasminogen activator receptor, fibroblast activating receptor, integrin α5 subunit and epidermal growth factor receptor was evaluated using immunohistochemistry. Immunoreactivity was determined using the semiquantitative H-score. Resection specimens from patients after neoadjuvant FOLFIRINOX treatment containing PDAC (n = 32), tumor associated pancreatitis (TAP) and TIF (n = 15), normal pancreas parenchyma (NPP) (n = 32) and tumor positive (n = 24) and negative (n = 56) lymph nodes were included. Integrin αvβ6, CEACAM5, mesothelin and PSMA stainings showed significantly higher expression in PDAC compared to TAP and NPP. No expression of αvβ6, CEACAM5 and mesothelin was observed in TIF. Integrin αvβ6 and CEACAM5 allow for accurate metastatic lymph node detection. Targeting integrin αvβ6, CEA, mesothelin and PSMA has the potential to distinguish vital PDAC from fibrotic tissue after neoadjuvant FOLFIRINOX treatment. Integrin αvβ6 and CEACAM5 detect primary tumors and tumor positive lymph nodes.
Electrode-free visual prosthesis/exoskeleton control using augmented reality glasses in a first proof-of-technical-concept study
Authors: Hazubski Simon , Hoppe Harald , Otte Andreas 
Published: October 2020

AbstractIn the field of neuroprosthetics, the current state-of-the-art method involves controlling the prosthesis with electromyography (EMG) or electrooculography/electroencephalography (EOG/EEG). However, these systems are both expensive and time consuming to calibrate, susceptible to interference, and require a lengthy learning phase by the patient. Therefore, it is an open challenge to design more robust systems that are suitable for everyday use and meet the needs of patients. In this paper, we present a new concept of complete visual control for a prosthesis, an exoskeleton or another end effector using augmented reality (AR) glasses presented for the first time in a proof-of-concept study. By using AR glasses equipped with a monocular camera, a marker attached to the prosthesis is tracked. Minimal relative movements of the head with respect to the prosthesis are registered by tracking and used for control. Two possible control mechanisms including visual feedback are presented and implemented for both a motorized hand orthosis and a motorized hand prosthesis. Since the grasping process is mainly controlled by vision, the proposed approach appears to be natural and intuitive.
Fabrication of piezoelectric poly(l-lactic acid)/BaTiO3 fibre by the melt-spinning process
Authors: Oh Hyun Ju , Kim Do-Kun , Choi Young Chan , Lim Seung-Ju , Jeong Jae Bum , Ko Jae Hoon , Hahm Wan-Gyu , Kim Sang-Woo , Lee Yongju , Kim Hyeok , Yeang Byeong Jin 
Published: October 2020

AbstractPoly(l-lactic acid) (PLLA) based piezoelectric polymers are gradually becoming the substitute for the conventional piezoelectric ceramic and polymeric materials due to their low cost and biodegradable, non-toxic, piezoelectric and non-pyroelectric nature. To improve the piezoelectric properties of melt-spun poly(l-lactic acid) (PLLA)/BaTiO3, we optimized the post-processing conditions to increase the proportion of the β crystalline phase. The α → β phase transition behaviour was determined by two-dimensional wide-angle x-ray diffraction and differential scanning calorimetry. The piezoelectric properties of PLLA/BaTiO3 fibres were characterised in their yarn and textile form through a tapping method. From these results, we confirmed that the crystalline phase transition of PLLA/BaTiO3 fibres was significantly enhanced under the optimised post-processing conditions at a draw ratio of 3 and temperature of 120 °C during the melt-spinning process. The results indicated that PLLA/BaTiO3 fibres could be a one of the material for organic-based piezoelectric sensors for application in textile-based wearable piezoelectric devices.
Eruptive Spitz nevus, a striking example of benign metastasis
Authors: Raghavan Shyam S. , Kapler Elisa S. , Dinges Martin M. , Bastian Boris C. , Yeh Iwei 
Published: October 2020

AbstractMetastasis is generally considered a characteristic of malignant tumors. Herein, we describe a patient with more than one hundred discrete Spitz nevi scattered all over her skin. Molecular analysis from three of the lesions identified a ROS1 fusion oncogene with identical genomic breakpoints, indicating that the nevi arose from a single transformed melanocyte and then disseminated throughout the integument. The demonstration of widespread distribution of a benign tumor with limited proliferative capability indicates that metastatic dissemination is not contingent on full malignant transformation. Thus, eruptive Spitz nevus is a striking example of benign metastasis, demonstrating that metastasis can occur before malignant transformation.
Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace
Authors: Brander Søren , Horvath Istvan , Ipsen Johan Ø. , Peciulyte Ausra , Olsson Lisbeth , Hernández-Rollán Cristina , Nørholm Morten H. H. , Mossin Susanne , Leggio Leila Lo , Probst Corinna , Thiele Dennis J. , Johansen Katja S. 
Published: October 2020

AbstractLytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
Analysis of a multiple-quantum-dots embedded ring structure for potential optically-controlled quantum switch or spin filter
Authors: He Zelong , Zhao Xinwei , Chen Kongfa , Bai Jiyuan , Guo Yong 
Published: October 2020

AbstractWe theoretically study the average current through a ring embedded with multiple quantum dots in each arm subjected to a time-dependent external field. A current resonance band can be observed in a six-quantum-dot system. In the presence of a time-dependent external field, mutual transformation occurs between the resonance band and antiresonance band, indicating an effective optically-controlled quantum switch can be realized in a wider quantum dot’s energy regime. As the Zeeman effect is introduced, the conversion between 100 and − 100% for spin polarization $$p$$
p
can be realized by adjusting the frequency of time-dependent external field, suggesting a physical scheme of an optically-controlled spin filter. The present work sheds lights onto the design and quantum computation of future nano-devices.
Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity
Authors: Börlin Marine , Claisse Olivier , Albertin Warren , Salin Franck , Legras Jean-Luc , Masneuf-Pomarede Isabelle 
Published: October 2020

AbstractSaccharomyces cerevisiaeis the main actor of wine fermentation but at present, still little is known about the factors impacting its distribution in the vineyards. In this study, 23 vineyards and 7 cellars were sampled over 2 consecutive years in the Bordeaux and Bergerac regions. The impact of geography and farming system and the relation between grape and vat populations were evaluated using a collection of 1374S. cerevisiaemerlot grape isolates and 289 vat isolates analyzed at 17 microsatellites loci. A very high genetic diversity ofS. cerevisiaestrains was obtained from grape samples, higher in conventional farming system than in organic one. The geographic appellation and the wine estate significantly impact theS. cerevisiaepopulation structure, whereas the type of farming system has a weak global effect. When comparing cellar and vineyard populations, we evidenced the tight connection between the two compartments, based on the high proportion of grape isolates (25%) related to the commercial starters used in the cellar and on the estimation of bidirectional geneflows between the vineyard and the cellar compartments.
The tissue specific regulation of miR22 expression in the lung and brain by ribosomal protein L29
Authors: Ali Mohammad Ishaque , Li Linrui , Li Lexing , Yao Lun , Liu Jie , Gu Wei , Huang Shuguang , Wang Bingyu , Liu Guoquan 
Published: October 2020

AbstractEndogenous miR22 is associated with a diverse range of biological processes through post-translational modification of gene expression and its deregulation results in various diseases including cancer. Its expression is usually tissue or cell-specific, however, the reasons behind this tissue or cell specificity are not clearly outlined till-date. Therefore, our keen interest was to investigate the mechanisms of tissue or cell-specific expression of miR22. In the current study, miR22 expression showed a tissues-specific difference in the poly(I:C) induced inflammatory mouse lung and brain tissues. The cell-specific different expression of miR22 was also observed in inflammatory glial cells and endothelial cells. The pattern of RPL29 expression was also similar to miR22 in these tissues and cells under the same treatment. Interestingly, the knockdown of RPL29 exerted an inhibitory effect on miR22 and its known transcription factors including Fos-B and c-Fos. Fos-B and c-Fos were also differentially expressed in the two cell lines transfected with poly(I:C). The knockdown of c-Fos also exerted its negative effects on miR22 expression in both cells. These findings suggest that RPL29 might have regulatory roles on tissue or cell-specific expression of miR22 through the transcription activities of c-Fos and also possibly through Fos-B.