bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frontier orbitals and quasiparticle energy levels in ionic liquids
Authors: Kahk Juhan Matthias , Kuusik Ivar , Kisand Vambola , Lovelock Kevin R. J. , Lischner Johannes 
Published: October 2020

AbstractIonic liquids play an important role in many technological applications and a detailed understanding of their frontier molecular orbitals is required to optimize interfacial barriers, reactivity and stability with respect to electron injection and removal. In this work, we calculate quasiparticle energy levels of ionic liquids using first-principles many-body perturbation theory within the GW approximation and compare our results to various mean-field approaches, including semilocal and hybrid density-functional theory and Hartree–Fock. We find that the mean-field results depend qualitatively and quantitatively on the treatment of exchange–correlation effects, while GW calculations produce results that are in excellent agreement with experimental photoelectron spectra of gas phase ion pairs and ionic liquids. These results establish the GW approach as a valuable tool for understanding the electronic structures of ionic liquids.
A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage
Authors: Hasegawa Masumi , Hosaka Toshiaki , Kojima Keiichi , Nishimura Yosuke , Nakajima Yu , Kimura-Someya Tomomi , Shirouzu Mikako , Sudo Yuki , Yoshizawa Susumu 
Published: October 2020

AbstractMicrobial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.
Quantitative proteomic comparison of myofibroblasts derived from bone marrow and cornea
Authors: Saikia Paramananda , Crabb Jack S. , Dibbin Luciana L. , Juszczak Madison J. , Willard Belinda , Jang Geeng-Fu , Shiju Thomas Michael , Crabb John W. , Wilson Steven E. 
Published: October 2020

AbstractMyofibroblasts are fibroblastic cells that function in wound healing, tissue repair and fibrosis, and arise from bone marrow (BM)-derived fibrocytes and a variety of local progenitor cells. In the cornea, myofibroblasts are derived primarily from stromal keratocytes and from BM-derived fibrocytes after epithelial-stromal and endothelial-stromal injuries. Quantitative proteomic comparison of mature alpha-smooth muscle actin (α-SMA)+ myofibroblasts (verified by immunocytochemistry for vimentin, α-SMA, desmin, and vinculin) generated from rabbit corneal fibroblasts treated with transforming growth factor (TGF) beta-1 or generated directly from cultured BM treated with TGF beta-1 was pursued for insights into possible functional differences. Paired cornea-derived and BM-derived α-SMA+ myofibroblast primary cultures were generated from four New Zealand white rabbits and confirmed to be myofibroblasts by immunocytochemistry. Paired cornea- and BM-derived myofibroblast specimens from each rabbit were analyzed by LC MS/MS iTRAQ technology using an Orbitrap Fusion Lumos Tribrid mass spectrometer, the Mascot search engine, the weighted average quantification method and the UniProt rabbit and human databases. From 2329 proteins quantified with ≥ 2 unique peptides from ≥ 3 rabbits, a total of 673 differentially expressed (DE) proteins were identified. Bioinformatic analysis of DE proteins with Ingenuity Pathway Analysis implicate progenitor-dependent functional differences in myofibroblasts that could impact tissue development. Our results suggest BM-derived myofibroblasts may be more prone to the formation of excessive cellular and extracellular material that are characteristic of fibrosis.
The relationship between fleas and small mammals in households of the Western Yunnan Province, China
Authors: Yin Jia-Xiang , Cheng Xiao-Ou , Luo Yun-Yan , Zhao Qiu-Fang , Wei Zhao-Fei , Xu Dan-Dan , Wang Meng-Di , Zhou Yun , Wang Xiu-Fang , Liu Zheng-Xiang 
Published: October 2020

AbstractThe Yunnan province has one of the most serious outbreaks of the plague epidemic in China. Small mammals and fleas are risk factors for the occurrence of plague in commensal plague foci. Understanding the relationship between fleas and small mammals will help control fleas and prevent the onset of the plague. Four hundred and twenty-one small mammals, belonging to 9 species, were captured. Of these, 170 small mammals (40.4%) were found infested with fleas. A total of 992 parasitic fleas (including 5 species) were collected. The number of Leptopsylla segnis and Xenopsylla cheopis accounted for 91.03% (903/992). The final multiple hurdle negative binomial regression model showed that when compared with Rattus tanezumi, the probability of flea infestation with Mus musculus as well as other host species decreased by 58% and 99%, respectively, while the number of flea infestations of the other host species increased by 4.71 folds. The probability of flea prevalence in adult hosts increased by 74%, while the number of fleas decreased by 76%. The number of flea infestations in small male mammals increased by 62%. The number of fleas in small mammals weighing more than 59 g has been multiplied by about 4. R. tanezumi is the predominant species in households in the west Yunnan province, while L.segnis and X. cheopis were dominant parasitic fleas. There is a strong relationship between the abundance of fleas and the characteristics of small mammals (e.g. Species, age, sex, and body weight).
Rosettes integrity protects Plasmodium vivax of being phagocytized
Authors: Albrecht Letusa , Lopes Stefanie C. P. , da Silva Ana Beatriz Iung Enembreck , Barbosa Vanessa , Almeida Rodrigo P. , Siqueira André M. , Leite Juliana Almeida , Bittencourt Najara C. , dos Santos Hellen Geremias , Bourgard Catarina , Garcia Luiz Fernando Cardoso , Kayano Ana Carolina A. V. , Soares Irene S. , Russell Bruce , Rénia Laurent , Lacerda Marcus V. G. , Costa Fabio T. M. 
Published: October 2020

AbstractPlasmodium vivax is the most prevalent cause of malaria outside of Africa. P. vivax biology and pathogenesis are still poorly understood. The role of one highly occurring phenotype in particular where infected reticulocytes cytoadhere to noninfected normocytes, forming rosettes, remains unknown. Here, using a range of ex vivo approaches, we showed that P. vivax rosetting rates were enhanced by plasma of infected patients and that total immunoglobulin M levels correlated with rosetting frequency. Moreover, rosetting rates were also correlated with parasitemia, IL-6 and IL-10 levels in infected patients. Transcriptomic analysis of peripheral leukocytes from P. vivax-infected patients with low or moderated rosetting rates identified differentially expressed genes related to human host phagocytosis pathway. In addition, phagocytosis assay showed that rosetting parasites were less phagocyted. Collectively, these results showed that rosette formation plays a role in host immune response by hampering leukocyte phagocytosis. Thus, these findings suggest that rosetting could be an effective P. vivax immune evasion strategy.
Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae)
Authors: Hsieh Yi-Chiang , Chang Chung-Te , Chung Jeng-Der , Hwang Shih-Ying 
Published: October 2020

AbstractDemographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.
Gallic acid nanoflower immobilized membrane with peroxidase-like activity for m-cresol detection
Authors: Dadi Seyma , Celik Cagla , Ocsoy Ismail 
Published: October 2020

AbstractWe report fabrication of new generation nanoflowers (NFs) using gallic acid (GA) and copper (II) ions (Cu2+) acted as an organic and inorganic component, respectively with effective peroxidase mimic activities in solution and on filter membrane. Unlike the typical protein NFs synthesis mechanism, gallic acid NFs (GA-NFs) was formed via coordination reaction between carboxyl groups of GA and Cu2+. The different morphologies of the GA-NFs were acquired based upon whether the carboxyl groups in gallic acid are active or not. The peroxidase mimic activity of the GA-NFs relied on the Fenton reaction in the presence of hydrogen peroxide (H2O2) was tested towards m-cresol as a function of concentration of the GA-NFs, m-cresol, H2O2 and reaction time. Under the optimized conditions, the oxidative coupling of m-cresol with 4-aminoantipyrine (4-AAP) was catalyzed by the GA-NFs dispersed in solution and adsorbed on filter paper to form an antipyrine dye and it was visually and spectrophotometrically recorded. The m-cresol with range of 0.05–0.5 mM was detected in 10 min and 15 min by using the GA-NFs in solution and on filter paper, respectively. We demonstrated that the NFs can be produced from non-protein molecules and GA-NFs can be used as a promising nanocatalyst for a variety of applications.
Paclitaxel exposure downregulates miR-522 expression and its downregulation induces paclitaxel resistance in ovarian cancer cells
Authors: Miyamoto Mayuko , Sawada Kenjiro , Nakamura Koji , Yoshimura Akihiko , Ishida Kyoso , Kobayashi Masaki , Shimizu Aasa , Yamamoto Misa , Kodama Michiko , Hashimoto Kae , Kimura Tadashi 
Published: October 2020

AbstractPaclitaxel resistance is a critical challenge in ovarian cancer treatment. This study aimed to identify microRNAs (miRNAs) that modulate paclitaxel resistance for use as potential therapeutic targets in such settings. Paclitaxel-resistant cell lines were established using two ovarian cancer cell lines: SKOV3ip1 and HeyA8. The evaluation of miRNA polymerase chain reaction (PCR) arrays indicated that the expression of miR-522-3p was downregulated in paclitaxel-resistant cells. The restoration of miR-522-3p sensitized the resistant cells to paclitaxel, and its downregulation desensitized the parental cells. Using PCR arrays, we focused on E2F2, with the luciferase reporter assay revealing that it was a direct target for miR-522-3p. The paclitaxel-resistant cells showed stronger E2F2 expression than the parental cells, while E2F2 inhibition sensitized the resistant cells to paclitaxel. Forced E2F2 expression in the parental cells led to the acquisition of paclitaxel resistance, while miR-522-3p inhibited E2F2 expression and was associated with retinoblastoma protein phosphorylation attenuation, which resulted in G0/G1 arrest. The effects of miR-522-3p and E2F2 in ovarian cancer were examined using public databases, revealing that low miR-522-3p expression and high E2F2 expression were associated with significantly poorer overall survival. In conclusion, miR-522-3p attenuated the degree of paclitaxel resistance in vitro through the downregulation of E2F2; miR-522-3p supplementation may be a therapeutic target for paclitaxel-resistant ovarian cancer.
Ideal memcapacitors and meminductors are overunity devices
Authors: Jeltsema Dimitri , van der Schaft Arjan 
Published: October 2020

AbstractIt is rigorously proved that ideal memcapacitors and meminductors are not passive or cyclo-passive devices. Equivalently, this implies that there exist excitation profiles that allow to extract more energy from the device than it is supplied with; so that their energy conversion efficiency exceeds 100%. This means that ideal memcapacitors and meminductors violate the First Law of thermodynamics, and thus are non-physical as they constitute so-called overunity systems. An illustrative mechanical analogue is provided for which such an excitation profile is explicitly constructed. Hence ideal memcapacitors and meminductors are mathematical artefacts, and the question arises what this implies for the properties of non-ideal memcapacitors and meminductors (or, memcapacitive systems and meminductive systems), which do satisfy the First Law.
Multicompartment modeling of protein shedding kinetics during vascularized tumor growth
Authors: Machiraju Gautam B. , Mallick Parag , Frieboes Hermann B. 
Published: October 2020

AbstractIdentification of protein biomarkers for cancer diagnosis and prognosis remains a critical unmet clinical need. A major reason is that the dynamic relationship between proliferating and necrotic cell populations during vascularized tumor growth, and the associated extra- and intra-cellular protein outflux from these populations into blood circulation remains poorly understood. Complementary to experimental efforts, mathematical approaches have been employed to effectively simulate the kinetics of detectable surface proteins (e.g., CA-125) shed into the bloodstream. However, existing models can be difficult to tune and may be unable to capture the dynamics of non-extracellular proteins, such as those shed from necrotic and apoptosing cells. The models may also fail to account for intra-tumoral spatial and microenvironmental heterogeneity. We present a new multi-compartment model to simulate heterogeneously vascularized growing tumors and the corresponding protein outflux. Model parameters can be tuned from histology data, including relative vascular volume, mean vessel diameter, and distance from vasculature to necrotic tissue. The model enables evaluating the difference in shedding rates between extra- and non-extracellular proteins from viable and necrosing cells as a function of heterogeneous vascularization. Simulation results indicate that under certain conditions it is possible for non-extracellular proteins to have superior outflux relative to extracellular proteins. This work contributes towards the goal of cancer biomarker identification by enabling simulation of protein shedding kinetics based on tumor tissue-specific characteristics. Ultimately, we anticipate that models like the one introduced herein will enable examining origins and circulating dynamics of candidate biomarkers, thus facilitating marker selection for validation studies.
Metabolic profiling of Candida clinical isolates of different species and infection sources
Authors: Oliver Josidel Conceição , Laghi Luca , Parolin Carola , Foschi Claudio , Marangoni Antonella , Liberatore Andrea , Dias Amanda Latercia Tranches , Cricca Monica , Vitali Beatrice 
Published: October 2020

AbstractCandida species are the most common cause of opportunistic fungal infections. Rapid identification and novel approaches for the characterization of these fungi are of great interest to improve the diagnosis and the knowledge about their pathogenic properties. This study aimed to characterize clinical isolates of Candida spp. by proteomics (MALDI-TOF MS) and metabolomics (1H-NMR), and to correlate their metabolic profiles with Candida species, source of infection and different virulence associated parameters. In particular, 49 Candida strains from different sources (blood, n = 15; vagina, n = 18; respiratory tract, n = 16), belonging mainly to C. albicans complex (61%), C. glabrata (20%) and C. parapsilosis (12%) species were used. Several extracellular and intracellular metabolites showed significantly different concentrations among isolates recovered from different sources of infection, as well as among different Candida species. These metabolites were mainly related to the glycolysis or gluconeogenesis, tricarboxylic acid cycle, nucleic acid synthesis and amino acid and lipid metabolism. Moreover, we found specific metabolic fingerprints associated with the ability to form biofilm, the antifungal resistance (i.e. caspofungin and fluconazole) and the production of secreted aspartyl proteinase. In conclusion, 1H-NMR-based metabolomics can be useful to deepen Candida spp. virulence and pathogenicity properties.
Characterization of the weathered basement rocks in the Dongping field from the Qaidam Basin, Western China: significance as gas reservoirs
Authors: Yang Wei , Wang Jiangong , Ma Feng , Zhang Yongshu , Bai Yadong , Sun Xiujian , Li Hongzhe , Zhang Jing , Wang Pu 
Published: October 2020

AbstractReservoir quality is a critical risk factor in basement reservoirs. Researches into basement reservoirs by petrographic analysis combined with X-ray diffraction, log identification, electron microscopy, field emission scanning electron microscopy, porosity and pulse-decay permeability and core analysis have provided insights into the characterization of the commonality, diversity and difference of the weathered basement rocks as gas reservoirs in the Dongping field. Geological structures, lithology and near-surface processes control the reservoir physical property together. From Wellblock Dp 3 to Wellblock Dp 17, the high uplift gradually transforms into the low slope area towards the center of basin, with the lithology changing as well, which results in different degrees of fracture development in the bedrock in different wellblocks. The basement lithologies are granite, granitic gneiss, and limestone with slate in Wellblock Dp3, Dp1 and Dp17, respectively. Though they all provide effective reservoir space for gas accumulation, the productivity of nature gas shows significant differences. Fractures are the main store space in the three wellblocks. The development of fractures gives rise to secondary porosity around them because of physical weathering and chemical dissolution, but they generate many inhomogeneous fractures and secondary solution pores, whether on the planar distribution or in vertical. In Wellblock Dp3, high angle fractures were generated under the action of structural stress mechanism, with a large number of secondary pores. The porosity is between 0.1 and 23.2%. In Wellblock Dp 1, low angle fractures were the main storage space, with plenty of solution pores mainly in melanocratic minerals. The porosity is between 0.1 and 18.8%. In Wellblock Dp 17, where short and dense fractures developed, the porosity is between 0.1 and 10.3%. The data indicate that the granite in the uplift in Wellblock Dp3 has better reservoir properties due to the stronger physical weathering and chemical dissolution. As the porosity gradually decreases towards the slope and low-lying area, the more favorable exploration area should be the uplift and slope area in the depression area. However, the effective caprock developed locally in Wellblock Dp3, which affected the gas accumulation. Meanwhile, the reservoirs’ petrophysical properties showed distintive variation with different depths in different wellblocks. High productivity layers are under the 200 m, 100 m and 200 m depths from the top of the basement rocks in Wellblock Dp 3, Wellblock Dp 1 and Wellblock Dp 17, respectively. This suggestion in this study will be of significance for guiding oil and gas exploration in front of the Altun Mountains.
MicroRNA-708 targeting ZNF549 regulates colon adenocarcinoma development through PI3K/AKt pathway
Authors: Zhao Zhidong , Qin Xianju 
Published: October 2020

AbstractColon adenocarcinoma (COAD) is the most common type of gastrointestinal cancer and is still the third leading cause of cancer-related mortality worldwide. Therefore, finding new and promising drugs to eradicate cancer may be a feasible method to treat COAD patients. Cys2-His2 zinc finger proteins (ZFPs) is one of the largest transcription factor family and many of them are highly involved in regulation of cell differentiation, proliferation, apoptosis, and neoplastic transformation. In this study, we identified a tumor-inhibiting factor, ZNF549, which expressed lowly in COAD tissues and COAD cell lines (HT29, HCT116, SW480, LoVo, and SW620). Overexpression of ZNF549 inhibit the ability of COAD cell proliferation and migration. On the contrary, decreasing the ZNF549 expression level promote the ability of COAD cell proliferation and migration. Through bioinformatics analysis, we found that ZNF549 was a potential target of hsa-miR-708-5p (miR-708-5p). Furthermore, we verified the possibility of miR-708-5p targeting the ZNF549 gene, and miR-708-5p inhibited the expression of ZNF549 by luciferase reporter assays, qRT-PCR and western blot assays. Moreover, the relationship between miR-708-5p and phosphatidylinositol 3-kinase/AKt (PI3K/AKt) signal pathway was elucidated. Overexpression and inhibition of miR-708-5p resulted in increased and decreased expression of p-AKt and p-PI3K in HCT116 cells, respectively. RT-qPCR and western blot assays results demonstrated that miR-708-5p regulated COAD cells development by promoting the process of Epithelial-mesenchymal transition (EMT) through PI3K/AKt signaling pathway. In summary, our findings demonstrated that ZNF549, the target gene of miR-708-5p, functions as a tumor suppressor to inhibit COAD cell lines proliferation and migration through regulate the PI3K/AKt signal pathway.