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A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress

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journal of Molecular Cell Biology 2019年第10期11卷 829-844页

作者： Antonella Di Liddo camila de Oliveira Freitas Machado Sandra fischer Stefanie Ebersberger Andreas WHeumliller julia EWeigand Michaela Muller-McNicoll Kathi Zarnack Buchmann Institute for Molecular Life Sciences Goethe University FrankfurtFrankfurt am MainGermany Institute of Cell Biology and Neuroscience Goethe University FrankfurtFrankfurt am MainGermany Institute for Cardiovascular Regeneration Goethe University FrankfurtFrankfurt am MainGermany Department of Biology Technical University DarmstadtGermany Institute of Molecular Biology(IMB) MainzGermany

Hypoxia is associated with several diseases,including *** that are deprived of adequate oxygen supply trigger tran-scriptional and post-transcriptional responses,which control cellular pathways such as angiogenesis,proliferation,and metabolic *** RNAs(circRNAs)are a novel class of mainly non-coding RNAs,which have been implicated in multiple cancers and attract increasing attention as potential ***,we characterize the circRNA signatures of three different cancer cell lines from cervical(HeLa),breast(MCF-7),and lung(A549)cancer under *** order to reliably detect circRNAs,we integrate available tools with custom approaches for quantification and statistical analysis?Using this consolidated computational pipeline,we identify?12000 circRNAs in the three cancer *** molecular characteristics point to an involvement of complementary RNA sequences as well as trans-acting factors in circRNA biogenesis,such as the RNA-binding protein HNRNPC-Notably,we detect a number of circRNAs that are more abundant than their linear *** addition,64 circRNAs significantly change in abundance upon hypoxia,in most cases in a cell type-specific *** summary,we present a comparative circRNA profiling in human cancer cell lines,which promises novel insights into the biogenesis and function of circRNAs under hypoxic stress.

关键词： circular RNA computational pipeline differential expression cancer cells hypoxia RNA-Seq

Preparation of the Rutin-SBA-16 Drug Delivery System

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journal of Biomaterials and Nanobiotechnology 2020年第1期11卷 1-13页

作者： j.liana camila fischer karnopp Teofilo Fernando Mazon Cardoso Daniel Araujo Goncalves Aline Regina Hellman Carollo Gustavo Rocha de Castro Adriana Pereira Duarte Marco Antonio Utrera Martines Institute of Chemistry Federal University of Mato Grosso do SulCidade UniversitariaCampo GrandeMSBrazil Faculty of Pharmaceutical Sciences Food and NutritionFederal University of Mato Grosso do SulCidade UniversitariaCampo GrandeMSBrazil Department of Chemistry Minas Gerais State UniversityItuiutabaMGBrazil Institute of Biosciences Sao Paulo State UniversityBotucatuSPBrazil

This study sets out a scheme for a controlled release delivery system using SBA-16 as a carrier matrix and Rutin as a drug (Rutin-SBA-16). Physicochemical characterizations were performed to confirm the structure of the SBA-16 for post-synthesis by scanning electron microscopy (SEM), Transmission Electron Microscopy (TEM) and X-ray Diffraction (XRD). The presence of Rutin-SBA-16 was confirmed by Fourier-transform infrared spectroscopy (FTIR) and Nitrogen adsorption-desorption isotherms at 77 K. The dissolution kinetics was evaluated by the Zero Order, First Order and Higuchi models, and Rutin quantification was carried out by High Performance Liquid Chromatography (HPLC). The best impregnation time, which was 8 hours, adsorbing 284 μg Rutin per mg of silica, and the maximum degree of dissolution occurred in a period of 20 - 25 h. The release kinetics of the Rutin was called Higuchi, and showed high linearity, with a correlation coefficient (R2) of 0.999 compared with 0.905 and 0.980 of the zero order and first order models respectively. The study shows the benefits of Rutin-SBA-16 as a drug delivery system.

关键词： Rutin Controlled Release Systems Kinetic Study Mesoporous Silica Flavonoid

Analysis of Compression Resistance and Oil Adsorption Capacity of Cellulose/NaOH Cryogels

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journal of Renewable Materials 2019年第3期7卷 227-234页

作者： Lídia K.Lazzari Vitória B.Zampieri Ademir j.Zattera camila Baldasso Center for Exact Sciences and Technologies-University of Caxias do Sul.1130 Francisco Getúlio Vargas Street Caxias do Sul95070-560Brazil

This work aimed at analyzing the petroleum adsorption capacity and the compressive strength of cellulose cryogels produced with the addition of 4 and 8%(w/w)sodium hydroxide(NaOH).Cryogels were produced from a 1.5%(m/m)suspension of cellulose microfibers,which originated from Pinus elliotti,in distilled *** addition of NaOH increased the compression strength of cryogel by 30% when compared to cryogel without the *** to the 50% decrease in volume,the cryogel FLNB-8h(8%NaOH)has its petroleum adsorption capacity decreased in average by 58%,whereas the FLNB-4(4%NaOH)cryogel had it only by 14%.The cellulose suspension which provided the best results for the properties of the cryogels tested had a 4%concentration of NaOH.

关键词： Cryogel cellulose NaOH adsorption compression resistance

Optical closure of parameterized bio-optical relationships

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Chinese journal of Oceanology and Limnology 2014年第2期32卷 480-489页

作者：贺双颜 fischer jürgen SCHAALE Michael 贺明霞 Institute for Space Sciences Freie Universitt Berlin Ocean Remote Sensing Institute Ocean University of China Ocean College Zhejiang University

An optical closure study on bio-optical relationships was carried out using radiative transfer model matrix operator method developed by Freie Universitat Berlin. As a case study, the optical closure of bio-optical relationships empirically parameterized with in situ data for the East China Sea was examined. Remote-sensing reflectance （Rrs） was computed from the inherent optical properties predicted by these biooptical relationships and compared with published in situ data. It was found that the simulated Rrs was overestimated for turbid water. To achieve optical closure, bio-optical relationships for absorption and scattering coefficients for suspended particulate matter were adjusted. Furthermore, the results show that the Fournier and Forand phase functions obtained from the adjusted relationships perform better than the Petzold phase function. Therefore, before bio-optical relationships are used for a local sea area, the optical closure should be examined.

关键词： optical closure ocean color remote sensing bio-optical relationship

The carbon fluxes in different successional stages:modelling the dynamics of tropical montane forests in South Ecuador

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Forest Ecosystems 2017年第2期4卷 143-153页

作者： sebastian paulick claudia dislich jürgen homeier rico fischer andreas huth Department of Ecological Modelling Helmholtz Centre for Environmental Research-UFZPermoserstr1504318 LeipzigGermany Georg-August-University Gottingen Plant EcologyUntere KarspOle 237073 GottingenGermany University of Osnabriick Institute of Environmental Systems ResearchBarbarastr1249076 OsnabruckGermany iDiv German Centre for Integrative Biodiversity Research(iDiv)Halle-Jena-LeipzigDeutscher Platz 5e04103 LeipzigGermany

Background： Tropical forests play an important role in the global carbon（C） ***, tropical montane forests have been studied less than tropical lowland forests, and their role in carbon storage is not well *** forests are highly endangered due to logging, land-use and climate *** objective was to analyse how the carbon balance changes during forest ***： In this study, we used a method to estimate local carbon balances that combined forest inventory data with process-based forest *** utilised such a forest model to study the carbon balance of a tropical montane forest in South Ecuador, comparing two topographical slope positions（ravines and lower slopes vs upper slopes and ridges）.Results： The simulation results showed that the forest acts as a carbon sink with a maximum net ecosystem exchange（NEE） of 9.3 Mg C？（ha？yr）-1during its early successional stage（0–100 years）.In the late successional stage, the simulated NEE fluctuated around zero and had a variation of 0.77 Mg C？（ha？yr）–*** simulated variability of the NEE was within the range of the field *** discovered several forest attributes（e.g., basal area or the relative amount of pioneer trees） that can serve as predictors for NEE for young forest stands（0–100 years） but not for those in the late successional stage（500–1,000 years）.In case of young forest stands these correlations are high, especially between stand basal area and ***： In this study, we used an Ecuadorian study site as an example of how to successfully link a forest model with forest inventory data, for estimating stem-diameter distributions, biomass and aboveground net primary *** conclude, this study shows that process-based forest models can be used to investigate the carbon balance of tropical montane *** this model it is possible to find hidden relationships between forest attributes and forest carbon *** relationships promote a better understandin

关键词： Forest model Tropical montane forest Forest succession Carbon balance Forest productivity FORMIND

Performance evaluation of operational atmospheric correction algorithms over the East China Seas

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Chinese journal of Oceanology and Limnology 2017年第1期35卷 1-22页

作者： HE Shuangyan[l,2,3] HE Mingxia fischer jurgen Ocean Remote Sensing Institute Ocean University of China Qingdao 266003 China Institute for Space Sciences Freie Universitdt Berlin Berlin D-12165 Germany Ocean College Zhejiang University Hangzhou 310058 China

To acquire high-quality operational data products for Chinese in-orbit and scheduled ocean color sensors, the performances of two operational atmospheric correction(AC) algorithms(ESA MEGS 7.4.1 and NASA Sea DAS 6.1) were evaluated over the East China Seas(ECS) using MERIS data. The spectral remote sensing reflectance R_(rs)(λ), aerosol optical thickness(AOT), and ?ngstr?m exponent(α) retrieved using the two algorithms were validated using in situ measurements obtained between May 2002 and October 2009. Match-ups of R_(rs), AOT, and α between the in situ and MERIS data were obtained through strict exclusion criteria. Statistical analysis of R_(rs)(λ) showed a mean percentage difference(MPD) of 9%–13% in the 490–560 nm spectral range, and significant overestimation was observed at 413 nm(MPD>72%). The AOTs were overestimated(MPD>32%), and although the ESA algorithm outperformed the NASA algorithm in the blue-green bands, the situation was reversed in the red-near-infrared bands. The value of α was obviously underestimated by the ESA algorithm(MPD=41%) but not by the NASA algorithm(MPD=35%). To clarify why the NASA algorithm performed better in the retrieval of α, scatter plots of the α single scattering albedo(SSA) density were prepared. These α-SSA density scatter plots showed that the applicability of the aerosol models used by the NASA algorithm over the ECS is better than that used by the ESA algorithm, although neither aerosol model is suitable for the ECS region. The results of this study provide a reference to both data users and data agencies regarding the use of operational data products and the investigation into the improvement of current AC schemes over the ECS.

关键词： validation remote sensing reflectance aerosol optical thickness ocean color atmospheric correction remote sensing

Immunology of a unique biological structure:the Echinococcus laminated layer

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Protein & Cell 2023年第2期14卷 87-104页

作者： Álvaro Díaz Anabella ABarrios Leticia Grezzi camila Mouhape Stephen j.jenkins judith E.Allen Cecilia Casaravilla Área Inmunología Departamento de Biociencias(Facultad de Química)and Cátedra de InmunologíaInstituto de Química Biológica(Facultad de Ciencias)Universidad de la RepúblicaMontevideoUruguay Centre for Inflammation Research Queen's Medical Research InstituteUniversity of EdinburghEdinburghEH89JUUK Lydia Becker Institute of Immunology and Inflammation School of Biological SciencesUniversity of ManchesterManchester Academic Health Sciences CentreManchesterM139NQUK

The larval stages of the cestode parasites belonging to the genus Echinococcus grow within internal organs of humans and a range of animal *** resulting diseases,collectively termed echinococcoses,include major neglected tropical diseases of humans and *** larvae are outwardly protected by the laminated layer(LL),an acellular structure that is unique to this *** LL is based on a fibrillar meshwork made up of mucins,which are decorated by galactose-rich *** addition,in the species cluster termed *** sensu lato,the LL features nano-deposits of the calcium salt of myo-inositol hexakisphosphate(Insp_(6)).The main purpose of our article is to update the immunobiology of the *** recent advances in this area are(i)the demonstration of LL“debris”at the infection site and draining lymph nodes,(ii)the characterization of the decoy activity of calcium Inp6 with respect to complement,(iii)the evidence that the LL mucin carbohydrates interact specifically with a lectin receptor expressed in Kupffer cells(Clec4F),and(iv)the characterization of what appear to be receptor-independent effects of LL particles on dendritic cells and *** information is missing on the immunology of this intriguing structure:we discuss gaps in knowledge and propose possible avenues for research.

关键词： mucin complement Echinococcus macrophage dendritic cell Clec4F

Experimental proof of joule heating-induced switched-back regions in OLEDs

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Light(Science & Applications) 2020年第1期9卷 1951-1960页

作者： Anton Kirch Axel fischer Matthias Liero jurgen Fuhrmann Annegret Glitzky Sebastian Reineke Dresden Integrated Center for Applied Physics and Photonic Materials(IAPP)and Institute of Applied Physics Technische Universitat DresdenNothnitzer StraBe 6101187 DresdenGermany Weierstrass Institute Berlin MohrenstraBe 3910117 BerlinGermany

Organic light-emitting diodes(OLEDs)have become a major pixel technology in the display sector,with products spanning the entire range of current panel *** ability to freely scale the active area to large and random surfaces paired with flexible substrates provides additional application scenarios for OLEDs in the general lighting,automotive,and signage *** applications require higher brightness and,thus,current density operation compared to the specifications needed for general *** extended transparent electrodes pose a significant ohmic resistance,OLEDs suffering from joule self-heating exhibit spatial inhomogeneities in electrical potential,current density,and hence *** this article,we provide experimental proof of the theoretical prediction that OLEDs will display regions of decreasing luminance with increasing driving *** a two-dimensional OLED model,we can conclude that these regions are switched back locally in voltage as well as current due to insufficient lateral thermal ***,we demonstrate this effect in lab-scale devices and derive that it becomes more severe with increasing pixel size,which implies its significance for large-area,high-brightness use cases of ***,these non-linear switching effects cannot be ignored with respect to the long-term operation and stability of OLEDs;in particular,they might be important for the understanding of sudden-death scenarios.

关键词： OLEDs switched proof

催化:古老却富有挑战性的石墨烯基材料(英文)

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催化学报 2014年第6期35卷 792-797页

作者： Ljubisa R.Radovic camila Mora-Vilches Adolfo j.A.Salgado-Casanova Department of Chemical Engineering University of Concepción Concepción Chile Department of Energy & Mineral Engineering Penn State University University Park PA USA

An assessment is offered regarding the progress made, and the remaining challenges, in the field of carbocatalysis. The fundamental principles that govern the preparation and performance of sp2-hybridized carbon materials in heterogeneous catalysis have been known for decades, and the level of understanding of key issues – especially the importance of textural and ion-exchange properties (i.e., surface area, pore size distribution, and proton transfer) – remains quite satisfactory. The opportunities for novel catalytic materials – especially graphene nanosheets and carbon nanotubes– are tremendous, especially when it comes to taking advantage of their structural order, such that electron transfer can be both better understood and controlled to enhance catalytic activity and selectivity.

关键词：碳材料石墨催化剂个旧基础碳纳米管多相催化离子交换