bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of cytoplasmic organelles via in-resin CLEM using an osmium-resistant far-red protein
Authors: Tanida Isei , Kakuta Soichiro , Oliva Trejo Juan Alejandro , Uchiyama Yasuo 
Published: July 2020

AbstractPost-fixation with osmium tetroxide staining and the embedding of Epon are robust and essential treatments that are used to preserve and visualize intracellular membranous structures during electron microscopic analyses. These treatments, however, can significantly diminish the fluorescent intensity of most fluorescent proteins in cells, which creates an obstacle for the in-resin correlative light-electron microscopy (CLEM) of Epon-embedded cells. In this study, we used a far-red fluorescent protein that retains fluorescence after osmium staining and Epon embedding to perform an in-resin CLEM of Epon-embedded samples. The fluorescence of this protein was detected in 100 nm thin sections of the cells in Epon-embedded samples after fixation with 2.5% glutaraldehyde and post-fixation with 1% osmium tetroxide. We performed in-resin CLEM of the mitochondria in Epon-embedded cells using a mitochondria-localized fluorescent protein. Using this protein, we achieved in-resin CLEM of the Golgi apparatus and the endoplasmic reticulum in thin sections of the cells in Epon-embedded samples. To our knowledge, this is the first reported use of a far-red fluorescent protein retains its fluorescence after osmium staining and Epon-embedding, and it represents the first achievement of in-resin CLEM of both the Golgi apparatus and the endoplasmic reticulum in Epon-embedded samples.
A new functional JAZ degron sequence in strawberry JAZ1 revealed by structural and interaction studies on the COI1–JA-Ile/COR–JAZs complexes
Authors: Garrido-Bigotes Adrián , Valenzuela-Riffo Felipe , Torrejón Marcela , Solano Roberto , Morales-Quintana Luis , Figueroa Carlos R. 
Published: July 2020

AbstractThe phytohormone jasmonoyl-isoleucine (JA-Ile) regulates fundamental plant processes as developmental and defense responses. JA-Ile mediates the interaction between the F-box protein COI1 (part of the SCFCOI1 E3 ubiquitin ligase) and a JAZ repressor leading to early jasmonate responses. The Arabidopsis JAZ1 protein contains the canonical LPIARR degron sequence, which is responsible for the stabilization of the AtCOI1-JA-Ile-AtJAZ1 complex. In strawberry (Fragaria × ananassa) JAZ family was described at the transcriptional level during fruit development but the information about the interaction mode of this complex is still scarce at the molecular level. To gain insight into the strawberry JA-Ile receptor complex, we evaluated the interaction at the structural level, and protein models were built and analyzed for FaCOI1 and FaJAZ1, FaJAZ8.1, and FaJAZ10. The interaction between FaCOI1 and FaJAZ1, FaJAZ8.1 and FaJAZ10 were explored using several ligands, through molecular docking and molecular dynamics (MD) simulations, finding the strongest interaction with (+)-7-iso-JA-Ile than other ligands. Additionally, we tested interactions between FaCOI1 and FaJAZs by yeast two-hybrid assays in the presence of coronatine (COR, a JA-Ile mimic). We detected strong COR-dependent interactions between FaCOI1 and FaJAZ1. Interestingly, FaJAZ1 contains a new non-canonical (IPMQRK) functional degron sequence, in which Arg and Lys are the key residues for maintaining the interaction of the FaCOI1–COR–FaJAZ1 complex as we observed in mutated versions of the FaJAZ1 degron. Phylogenetic analysis showed that the IPMQRK degron is only present in orthologs belonging to the Rosoideae but not in other Rosaceae subfamilies. Together, this study uncovers a new degron sequence in plants, which could be required to make an alternative and functional JA-Ile perception complex in strawberry.
Digit ratio (2D:4D) in women and men with lung cancer
Authors: Kasielska-Trojan Anna , Manning J. T. , Antczak A. , Dutkowska A. , Kuczyński W. , Sitek A. , Antoszewski B. 
Published: July 2020

AbstractA prenatal sex steroid environment of high prenatal testosterone and low prenatal oestrogen inhibits lung development and may predispose individuals to be vulnerable to lung disease in later life. Therefore, the aim of this report was to investigate whether there is an association between right and left 2D:4D (biomarker of prenatal sex steroids exposure) and primary lung cancer in women and men. Also, we considered the relationship between right–left 2D:4D (Δ2D:4D, a negative correlate of high prenatal testosterone and low prenatal oestrogen) and the age of lung cancer diagnosis. The study included 109 patients (61 men) with lung cancer and 197 controls (78 men). In the study we found that: (i) women with lung cancer have lower 2D:4D compared to controls (the effect was independent of smoking), (ii) among women with cancer, age at diagnosis was positively related to 2D:4D, i.e. women with masculinized 2D:4D present earlier with the cancer than women with feminized 2D:4D, (iii) among men with lung cancer, those with the most aggressive form (small-cell lung cancer) had masculinized (low) Δ2D:4D compared to those with the less aggressive form (non-small cell lung cancer). The data suggests that masculinized right 2D:4D and Δ2D:4D are associated with a predisposition to lung cancer and/or the more aggressive forms of lung cancer.
Establishment and validation of highly accurate formalin-fixed paraffin-embedded quantitative proteomics by heat-compatible pressure cycling technology using phase-transfer surfactant and SWATH-MS
Authors: Uchida Yasuo , Sasaki Hayate , Terasaki Tetsuya 
Published: July 2020

AbstractThe purpose of this study was to establish a quantitative proteomic method able to accurately quantify pathological changes in the protein expression levels of not only non-membrane proteins, but also membrane proteins, using formalin-fixed paraffin-embedded (FFPE) samples. Protein extraction from FFPE sections of mouse liver was increased 3.33-fold by pressure cycling technology (PCT) and reached the same level as protein extraction from frozen sections. After PCT-assisted processing of FFPE liver samples followed by SWATH-MS-based comprehensive quantification, the peak areas of 88.4% of peptides agreed with those from matched fresh samples within a 1.5-fold range. For membrane proteins, this percentage was remarkably increased from 49.1 to 93.8% by PCT. Compared to the conventional method using urea buffer, the present method using phase-transfer surfactant (PTS) buffer at 95 °C showed better agreement of peptide peak areas between FFPE and fresh samples. When our method using PCT and PTS buffer at 95 °C was applied to a bile duct ligation (BDL) disease model, the BDL/control expression ratios for 80.0% of peptides agreed within a 1.2-fold range between FFPE and fresh samples. This heat-compatible FFPE-PCT-SWATH proteomics technology using PTS is suitable for quantitative studies of pathological molecular mechanisms and biomarker discovery utilizing widely available FFPE samples.
Candle flame soot sizing by planar time-resolved laser-induced incandescence
Authors: Verdugo Ignacio , Cruz Juan José , Álvarez Emilio , Reszka Pedro , Figueira da Silva Luís Fernando , Fuentes Andrés 
Published: July 2020

AbstractSoot emissions from flaming combustion are relevant as a significant source of atmospheric pollution and as a source of nanomaterials. Candles are interesting targets for soot characterization studies since they burn complex fuels with a large number of carbon atoms, and yield stable and repeatable flames. We characterized the soot particle size distributions in a candle flame using the planar two-color time-resolved laser induced incandescence (2D-2C TiRe-LII) technique, which has been successfully applied to different combustion applications, but never before on a candle flame. Soot particles are heated with a planar laser sheet to temperatures above the normal flame temperatures. The incandescent soot particles emit thermal radiation, which decays over time when the particles cool down to the flame temperature. By analyzing the temporal decay of the incandescence signal, soot particle size distributions within the flame are obtained. Our results are consistent with previous works, and show that the outer edges of the flame are characterized by larger particles ($$\approx 60\,\hbox {nm}$$≈60nm), whereas smaller particles ($$\approx 25\,\hbox {nm}$$≈25nm) are found in the central regions. We also show that our effective temperature estimates have a maximum error of 100 K at early times, which decreases as the particles cool.
Influence of amorphous cellulose on mechanical, thermal, and hydrolytic degradation of poly(lactic acid) biocomposites
Authors: Wan Ishak Wan Hafizi , Rosli Noor Afizah , Ahmad Ishak 
Published: July 2020

AbstractEco-friendly materials such as poly(lactic acid) (PLA) and cellulose are gaining considerable interest as suitable substitutes for petroleum-based plastics. Therefore, amorphous cellulose (AC) was fabricated as a new reinforcing material for PLA biocomposites by modifying a microcrystalline cellulose (MCC) structure via milling. In this study, the mechanical properties, thermal properties, and degradability of PLA were analysed to compare the effects of both MCC and AC on PLA. The tensile and impact properties improved at an optimum value with AC at 8 wt% and 4 wt% fibre loading, respectively. Notably, a scanning electron micrograph analysis revealed improved AC fibre–matrix adhesion, compared with MCC fibre–matrix adhesion, as well as excellent interaction between AC and PLA. Both MCC and AC improved the hydrolytic degradation of PLA. Moreover, the biocomposites with AC exhibited superior degradation when the incorporation of AC improved the water absorption efficiency of PLA. These findings can expand AC applications and improve sustainability.
Classification and characterization of electromagnetic materials
Authors: Aladadi Yosef T. , Alkanhal Majeed A. S. 
Published: July 2020

AbstractIn this paper, we present an efficient method to classify complex electromagnetic materials. This method is based on the directional interaction of incident circularly polarized waves with the materials being tested. The presented method relies on an algorithm that classifies the test materials to one of the following categories: isotropic, chiral, bi-isotropic, symmetric anisotropic or general bianisotropic. The transmitted and reflected fields of right-handed and left-handed circularly polarized waves normally incident from three orthogonal orientations are utilized to determine the reflection/transmission coefficients and complex refractive indices. Both analytical and numerical solutions are used to compute fields of the circularly polarized waves from the arbitrary complex material slab. The complex materials are discriminated accordingly and then classified under an appropriate category. Additionally, new results for material characterization by extracting the scalar/tensorial parameters of bi-isotropic and gyrotropic materials are presented.
Pulmonary paracoccidioidomycosis in AhR deficient hosts is severe and associated with defective Treg and Th22 responses
Authors: de Araújo Eliseu Frank , Preite Nycolas Willian , Veldhoen Marc , Loures Flávio Vieira , Calich Vera Lúcia Garcia 
Published: July 2020

AbstractAhR is a ligand-activated transcription factor that plays an important role in the innate and adaptive immune responses. In infection models, it has been associated with host responses that promote or inhibit disease progression. In pulmonary paracoccidioidomycosis, a primary fungal infection endemic in Latin America, immune protection is mediated by Th1/Th17 cells and disease severity with predominant Th2/Th9/Treg responses. Because of its important role at epithelial barriers, we evaluate the role of AhR in the outcome of a pulmonary model of paracoccidioidomycosis. AhR−/− mice show increased fungal burdens, enhanced tissue pathology and mortality. During the infection, AhR−/− mice have more pulmonary myeloid cells with activated phenotype and reduced numbers expressing indoleamine 2,3 dioxygenase 1. AhR-deficient lungs have altered production of cytokines and reduced numbers of innate lymphoid cells (NK, ILC3 and NCR IL-22). The lungs of AhR−/− mice showed increased presence Th17 cells concomitant with reduced numbers of Th1, Th22 and Foxp3+ Treg cells. Furthermore, treatment of infected WT mice with an AhR-specific antagonist (CH223191) reproduced the main findings obtained in AhR−/− mice. Collectively our data demonstrate that in pulmonary paracoccidioidomycosis AhR controls fungal burden and excessive tissue inflammation and is a possible target for antifungal therapy.
Effect of microstructure change on permeability of flax-fiber reinforced silty clay soaked with zinc-ion solution
Authors: Ma Qiang , Xiang Jun-chen , Wu Nian-ze , Xiao Heng-lin 
Published: July 2020

AbstractWith the application of fiber-reinforcement technology, the mechanical properties of silty clay are improved with fiber reinforcement. However, the variation of permeability coefficient and other parameters of flax-fiber reinforced silty clay have not been sufficiently studied. In this study, the permeability of flax-fiber reinforced silty clay soaked with zinc-contaminated solution under different osmotic pressure was tested by a flexible-wall permeameter, and the effects of zinc-ion concentration and confining pressure on the permeability of flax-fiber reinforced silty clay were studied. Genius XRF was employed to detect the types and quantity of metal elements in the specimens, thereafter, the reasons for the change of permeability were explained from chemical and microscopic perspective. The results showed that the permeability coefficient of flax-fiber reinforced silty clay decreased significantly with the increase of zinc-ion concentration in a low concentration (about 1–10 mg L−1). While in a high concentration (about 100 mg L−1), the permeability coefficient of flax-fiber reinforced silty clay changed little with the increase of zinc-ion concentration. While the flax-fiber reinforced silty clay was not soaked with zinc-ion solution, the permeability coefficient of the specimen increased with the increase of confining pressure. However, when the flax-fiber reinforced silty clay was soaked with zinc-contaminated solution, the permeability coefficient first decreased and then tended to be constant with the increase of confining pressure. With the increase of confining pressure, the porosity of flax-fiber reinforced silty clay decreased, and with the increase of zinc-ion concentration, the porosity of flax-fiber reinforced silty clay first increased and then decreased.
Global patterns of parasite diversity in cephalopods
Authors: Tedesco Perla , Bevilacqua Stanislao , Fiorito Graziano , Terlizzi Antonio 
Published: July 2020

AbstractWe compiled an updated global catalogue of parasites in cephalopods. Data were used to assess changes in taxonomic distinctness of parasites over two centuries and across the world’s oceans, to quantify turnover and nestedness components of parasite β-diversity, and to attempt estimating their γ-diversity at a global scale. A total of 309 parasites infecting 164 cephalopods were found. We hypothesize that this diversity counts for less than half the potential parasite richness in this molluscan taxon. Taxonomic breadth of parasites was significantly above expectations from null models for Mediterranean Sea and NE Atlantic Ocean, whereas the opposite occurred for NW Pacific Ocean, where a few closely related genera characterized the parasite pool. β-diversity of parasites was very high and dominated by turnover, except for the Atlantic Ocean where a nested pattern among sub-basins emerged. Taxonomic relatedness of parasite species remained substantially unchanged through time, but species replacements largely occurred over the last two centuries. Our findings highlighted potential hotspots of taxonomic distinctness in cephalopod parasites, geographic regions deserving future research, and the need for a deeper understanding of the magnitude of marine parasite diversity, their biogeography, and their role in marine ecosystems. Our global overview may represent a baseline step for future advances in this direction.
The behaviour of sea snakes (Emydocephalus annulatus) shifts with the tides
Authors: Goiran Claire , Brown Gregory P. , Shine Richard 
Published: July 2020

AbstractTidal cycles are known to affect the ecology of many marine animals, but logistical obstacles have discouraged behavioural studies on sea snakes in the wild. Here, we analyse a large dataset (1,445 observations of 126 individuals) to explore tidally-driven shifts in the behaviour of free-ranging turtle-headed sea snakes (Emydocephalus annulatus, Hydrophiinae) in the Baie des Citrons, New Caledonia. Snakes tended to move into newly-inundated areas with the rising tide, and became more active (e.g. switched from inactivity to mate-searching and courting) as water levels rose. However, the relative use of alternative habitat types was largely unaffected by tidal phase.
Nanosensors based on LSPR are able to serologically differentiate dengue from Zika infections
Authors: Versiani Alice F. , Martins Estefânia M. N. , Andrade Lidia M. , Cox Laura , Pereira Glauco C. , Barbosa-Stancioli Edel F. , Nogueira Mauricio L. , Ladeira Luiz O. , da Fonseca Flávio G. 
Published: July 2020

AbstractThe Flaviviridae virus family was named after the Yellow-fever virus, and the latin term flavi means “of golden color”. Dengue, caused by Dengue virus (DENV), is one of the most important infectious diseases worldwide. A sensitive and differential diagnosis is crucial for patient management, especially due to the occurrence of serological cross-reactivity to other co-circulating flaviviruses. This became particularly important with the emergence of Zika virus (ZIKV) in areas were DENV seroprevalence was already high. We developed a sensitive and specific diagnostic test based on gold nanorods (GNR) functionalized with DENV proteins as nanosensors. These were able to detect as little as one picogram of anti-DENV monoclonal antibodies and highly diluted DENV-positive human sera. The nanosensors could differentiate DENV-positive sera from other flavivirus-infected patients, including ZIKV, and were even able to distinguish which DENV serotype infected individual patients. Readouts are obtained in ELISA-plate spectrophotometers without the need of specific devices.
NIR multiphoton ablation of cancer cells, fluorescence quenching and cellular uptake of dansyl-glutathione-coated gold nanoparticles
Authors: Buonerba Antonio , Lapenta Rosita , Donniacuo Anna , Licasale Magda , Vezzoli Elena , Milione Stefano , Capacchione Carmine , Tecce Mario Felice , Falqui Andrea , Piacentini Roberto , Grassi Claudio , Grassi Alfonso 
Published: July 2020

AbstractTheranostics based on two-photon excitation of therapeutics in the NIR region is an emerging and powerful tool in cancer therapy since this radiation deeply penetrates healthy biological tissues and produces selective cell death. Aggregates of gold nanoparticles coated with glutathione corona functionalized with the dansyl chromophore (a-DG-AuNPs) were synthesized and found efficient nanodevice for applications in photothermal therapy (PTT). Actually the nanoparticle aggregation enhances the quenching of radiative excitation and the consequent conversion into heat. The a-DG-AuNPs are readily internalized in Hep G2 where the chromophore acts as both antenna and transducer of the NIR radiation under two-photons excitation, determining efficient cell ablation via photothermal effect.
Muographic monitoring of the volcano-tectonic evolution of Mount Etna
Authors: Lo Presti D. , Riggi F. , Ferlito C. , Bonanno D. L. , Bonanno G. , Gallo G. , La Rocca P. , Reito S. , Romeo G. 
Published: July 2020

AbstractAt Mount Etna volcano, the focus point of persistent tectonic extension is represented by the Summit Craters. A muographic telescope has been installed at the base of the North-East Crater from August 2017 to October 2019, with the specific aim to find time related variations in the density of volcanic edifice. The results are significant, since the elaborated images show the opening and evolution of different tectonic elements; in 2017, a cavity was detected months before the collapse of the crater floor and in 2018 a set of underground fractures was identified, at the tip of which, in June 2019, a new eruptive vent started its explosive activity, still going on (February, 2020). Although this is the pilot experiment of the project, the results confirm that muography could be a turning point in the comprehension of the plumbing system of the volcano and a fundamental step forward to do mid-term (weeks/months) predictions of eruptions. We are confident that an increment in the number of telescopes could lead to the realization of a monitoring system, which would keep under control the evolution of the internal dynamic of the uppermost section of the feeding system of an active volcano such as Mount Etna.
Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling
Authors: Chen Kuang-Yui , Bush Kelly , Klein Rachel Herndon , Cervantes Vanessa , Lewis Nichole , Naqvi Aasim , Carcaboso Angel M. , Lechpammer Mirna , Knoepfler Paul S. 
Published: July 2020

AbstractHistone H3.3 mutations are a hallmark of pediatric gliomas, but their core oncogenic mechanisms are not well-defined. To identify major effectors, we used CRISPR-Cas9 to introduce H3.3K27M and G34R mutations into previously H3.3-wildtype brain cells, while in parallel reverting the mutations in glioma cells back to wildtype. ChIP-seq analysis broadly linked K27M to altered H3K27me3 activity including within super-enhancers, which exhibited perturbed transcriptional function. This was largely independent of H3.3 DNA binding. The K27M and G34R mutations induced several of the same pathways suggesting key shared oncogenic mechanisms including activation of neurogenesis and NOTCH pathway genes. H3.3 mutant gliomas are also particularly sensitive to NOTCH pathway gene knockdown and drug inhibition, reducing their viability in culture. Reciprocal editing of cells generally produced reciprocal effects on tumorgenicity in xenograft assays. Overall, our findings define common and distinct K27M and G34R oncogenic mechanisms, including potentially targetable pathways.
Nano-imaging trace elements at organelle levels in substantia nigra overexpressing α-synuclein to model Parkinson’s disease
Authors: Lemelle Laurence , Simionovici Alexandre , Colin Philippe , Knott Graham , Bohic Sylvain , Cloetens Peter , Schneider Bernard L. 
Published: July 2020

AbstractSub-cellular trace element quantifications of nano-heterogeneities in brain tissues offer unprecedented ways to explore at elemental level the interplay between cellular compartments in neurodegenerative pathologies. We designed a quasi-correlative method for analytical nanoimaging of the substantia nigra, based on transmission electron microscopy and synchrotron X-ray fluorescence. It combines ultrastructural identifications of cellular compartments and trace element nanoimaging near detection limits, for increased signal-to-noise ratios. Elemental composition of different organelles is compared to cytoplasmic and nuclear compartments in dopaminergic neurons of rat substantia nigra. They exhibit 150–460 ppm of Fe, with P/Zn/Fe-rich nucleoli in a P/S-depleted nuclear matrix and Ca-rich rough endoplasmic reticula. Cytoplasm analysis displays sub-micron Fe/S-rich granules, including lipofuscin. Following AAV-mediated overexpression of α-synuclein protein associated with Parkinson’s disease, these granules shift towards higher Fe concentrations. This effect advocates for metal (Fe) dyshomeostasis in discrete cytoplasmic regions, illustrating the use of this method to explore neuronal dysfunction in brain diseases.