bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring robustness of brain networks in autism spectrum disorder with Ricci curvature
Authors: Simhal Anish K. , Carpenter Kimberly L. H. , Nadeem Saad , Kurtzberg Joanne , Song Allen , Tannenbaum Allen , Sapiro Guillermo , Dawson Geraldine 
Published: July 2020

AbstractOllivier–Ricci curvature is a method for measuring the robustness of connections in a network. In this work, we use curvature to measure changes in robustness of brain networks in children with autism spectrum disorder (ASD). In an open label clinical trials, participants with ASD were administered a single infusion of autologous umbilical cord blood and, as part of their clinical outcome measures, were imaged with diffusion MRI before and after the infusion. By using Ricci curvature to measure changes in robustness, we quantified both local and global changes in the brain networks and their potential relationship with the infusion. Our results find changes in the curvature of the connections between regions associated with ASD that were not detected via traditional brain network analysis.
Effect of BNP on risk assessment in cardiac surgery patients, in addition to EuroScore II
Authors: Suc Gaspard , Estagnasie Philippe , Brusset Alain , Procopi Niki , Squara Pierre , Nguyen Lee S. 
Published: July 2020

AbstractPatients’ prognostication around cardiac surgery is key to better assess risk–benefit balance. Preoperative brain natriuretic peptide (BNP) biomarker has been associated with mortality after cardiac surgery, but its added value with EuroScore 2 remains to be confirmed. In a prospective registry cohort of 4,980 patients undergoing cardiac surgery, the prognostic performance of EuroScore 2 and preoperative BNP was assessed regarding postoperative in-hospital mortality. Discrimination feature was evaluated using receiver-operator-characteristics analysis with area under curve (AUROC). Calibration feature was assessed using Hosmer–Lemeshow test. Multivariable analysis was performed to assess the association between covariates and in-hospital mortality. In-hospital mortality was 3.7%. The AUROC of EuroScore 2 was 0.82 (95% confidence interval (95%CI) 0.79–0.85, p < 0.0001). The AUROC of BNP was 0.66 (95%CI 0.62–0.70, p < 0.0001). The combined model with an AUROC of 0.67 (95%CI 0.63–0.71, p = 0.0001) did not yield better AUROC than EuroScore 2 alone (p < 0.0001 in disfavor of the combined model), nor BNP alone (p = 0.79). In multivariable analysis, EuroScore 2 remained independently associated with mortality (adj.OR of 1.12 (1.10–1.14), p < 0.0001), but BNP was not. Preoperative BNP was not an independent risk factor of postoperative mortality and did not add prognostic information, as compared to EuroScore 2 alone.Clinical trial registry Registry for the Improvement of Postoperative OutcomeS in Cardiac and Thoracic surgEry (RIPOSTE) database (NCT03209674).
Mesoporous ZnAl2Si10O24 nanofertilizers enable high yield of Oryza sativa L.
Authors: Naseem Fizza , Zhi Yang , Farrukh Muhammad Akhyar , Hussain Fayyaz , Yin Zongyou 
Published: July 2020

AbstractControllable release of nutrients in soil can overcome the environmental problems associated with conventional fertilizer. Here we synthesized mesoporous nanocomposite of Zinc aluminosilicate (ZnAl2Si10O24) via co-precipitation method. Oryza sativa L. husk was used as source of silica for making the synthesis process green and economical. The nanocomposite was subsequently loaded with urea to achieve the demand of simultaneous and slow delivery of both zinc and urea. The structural characterization of nanocomposite was done by FTIR, XRD, TGA, BET, SEM/EDX and TEM. The release of urea and zinc was investigated with UV–Vis spectrophotometry and atomic absorption spectroscopy, respectively, up to 14 days. It was noted that urea holding capacity of mesoporous ZnAl2Si10O24 nanocomposite over long period of time was increased as compared to bulk aluminosilicates, due to its high surface area (193.07 m2 g−1) and small particle size of (64 nm). Urea release was found highest in first 24 h because of excess of adsorption on nanocomposite and least at 14th day. Fertilizer efficiency was checked on Oryza sativa L. in comparison with commercial urea and results showed significantly higher yield in case of urea loaded ZnAl2Si10O24 nanocomposite.
High nitrogen solubility in stishovite (SiO2) under lower mantle conditions
Authors: Fukuyama Ko , Kagi Hiroyuki , Inoue Toru , Kakizawa Sho , Shinmei Toru , Hishita Shunichi , Takahata Naoto , Sano Yuji 
Published: July 2020

AbstractNitrogen is a crucial volatile element in the early Earth’s evolution and the origin of life. Despite its importance, nitrogen’s behavior in the Earth's interior remains poorly understood. Compared to other volatile elements, nitrogen is depleted in the Earth’s atmosphere (the so-called “missing nitrogen”), calling for a hidden deep reservoir. To investigate nitrogen’s behavior in the deep Earth including how the reservoir formed, high-pressure and high-temperature experiments were conducted at 28 GPa and 1,400–1,700 °C. To reproduce the conditions in the lower mantle, the redox was controlled using a Fe–FeO buffer. We observed that depending on the temperature conditions, stishovite can incorporate up to 90–404 ppm nitrogen, experimentally demonstrating that stishovite has the highest nitrogen solubility among the deep mantle minerals. Stishovite is the main mineral component of subducted nitrogen-rich sedimentary rocks and eroded continental crust that are eventually transported down to the lower mantle. Our results suggest that nitrogen could have been continuously transported into the lower mantle via subduction, ever since plate tectonics began.
Suppression of chorismate synthase, which is localized in chloroplasts and peroxisomes, results in abnormal flower development and anthocyanin reduction in petunia
Authors: Zhong Shiwei , Chen Zeyu , Han Jinyi , Zhao Huina , Liu Juanxu , Yu Yixun 
Published: July 2020

AbstractIn plants, the shikimate pathway generally occurs in plastids and leads to the biosynthesis of aromatic amino acids. Chorismate synthase (CS) catalyses the last step of the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate, but the role of CS in the metabolism of higher plants has not been reported. In this study, we found that PhCS, which is encoded by a single-copy gene in petunia (Petunia hybrida), contains N-terminal plastidic transit peptides and peroxisomal targeting signals. Green fluorescent protein (GFP) fusion protein assays revealed that PhCS was localized in chloroplasts and, unexpectedly, in peroxisomes. Petunia plants with reduced PhCS activity were generated through virus-induced gene silencing and further characterized.PhCSsilencing resulted in reduced CS activity, severe growth retardation, abnormal flower and leaf development and reduced levels of folate and pigments, including chlorophylls, carotenoids and anthocyanins. A widely targeted metabolomics analysis showed that most primary and secondary metabolites were significantly changed in pTRV2-PhCS-treated corollas. Overall, the results revealed a clear connection between primary and specialized metabolism related to the shikimate pathway in petunia.
Deterministic culturing of single cells in 3D
Authors: Jain Rohil , Chittiboyina Shirisha , Chang Chun-Li , Lelièvre Sophie A. , Savran Cagri A. 
Published: July 2020

AbstractModels using 3D cell culture techniques are increasingly accepted as the most biofidelic in vitro representations of tissues for research. These models are generated using biomatrices and bulk populations of cells derived from tissues or cell lines. We present an alternate method to culture individually selected cells in relative isolation from the rest of the population under physiologically relevant matrix conditions. Matrix gel islands are spotted on a cell culture dish to act as support for receiving and culturing individual single cells; a glass capillary-based microfluidic setup is used to extract each desired single cell from a population and seed it on top of an island. Using examples of breast and colorectal cancers, we show that individual cells evolve into tumors or aspects of tumors displaying different characteristics of the initial cancer type and aggressiveness. By implementing a morphometry assay with luminal A breast cancer, we demonstrate the potential of the proposed approach to study phenotypic heterogeneity. Results reveal that intertumor heterogeneity increases with time in culture and that varying degrees of intratumor heterogeneity may originate from individually seeded cells. Moreover, we observe that a positive relationship exists between fast growing tumors and the size and heterogeneity of their nuclei.
Correlation of magnetic and magnetoresistive properties of nanoporous Co/Pd thin multilayers fabricated on anodized TiO2 templates
Authors: Nguyen Thi Ngoc Anh , Kasiuk Julia , Wu Wen-Bin , Fedotova Julia , Przewoźnik Janusz , Kapusta Czesław , Kupreeva Olga , Lazarouk Serguei , Cao Thi Thanh Hai , Nguyen Thi Thanh Thuy , Dinh Hung Manh , Do Khanh Tung , Nguyen Thanh Huong , Vu Hong Ky , Vu Dinh Lam , Åkerman Johan 
Published: July 2020

AbstractIn this study, we consider a technological approach to obtain a high perpendicular magnetic anisotropy of the Co/Pd multilayers deposited on nanoporous TiO2 templates of different types of surface morphology. It is found that the use of templates with homogeneous and smoothed surface relief, formed on silicon wafers, ensures conservation of perpendicular anisotropy of the deposited films inherent in the continuous multilayers. Also, their magnetic hardening with doubling of the coercive field is observed. However, inhomogeneous magnetic ordering is revealed in the porous films due to the occurrence of magnetically soft regions near the pore edges and/or inside the pores. Modeling of the field dependences of magnetization and electrical resistance indicates that coherent rotation is the dominant mechanism of magnetization reversal in the porous system instead of the domain-wall motion typical of the continuous multilayers, while their magnetoresistance is determined by electron-magnon scattering, similarly to the continuous counterpart. The preservation of spin waves in the porous films indicates a high uniformity of the magnetic ordering in the fabricated porous systems due to a sufficiently regular pores array introduced into the films, despite the existence of soft-magnetic regions. The results are promising for the design and fabrication of future spintronic devices.
High throughput single cell analysis of mitochondrial heteroplasmy in mitochondrial diseases
Authors: Maeda Ryotaro , Kami Daisuke , Maeda Hideki , Shikuma Akira , Gojo Satoshi 
Published: July 2020

AbstractMitochondrial heteroplasmy, which fundamentally means intracellular heterogeneity of mitochondrial DNA (mtDNA), has been measured in a group of cells, regardless of intercellular heterogeneity. Ordinal methods for mitochondrial heteroplasmy cannot discriminate between an intercellular homogenic population composed of cells with similar intracellular heterogeneity for mtDNA and an intercellular heterogenic population composed of cells with different rates of mutated mtDNA. A high-throughput method to determine mitochondrial heteroplasmy in a single cell was developed by using droplet digital PCR with TaqMan polymerase in this study. This technique revealed that there are three different cell populations of cultured fibroblasts derived from patients with mitochondrial disease carrying a mutation in the mtDNA; cells with homoplasmy of either mutated or healthy mtDNA; and cells mixed with mutated and healthy mtDNA. The presence of intercellular heterogeneity, even in uniformed cultured fibroblasts, suggests that heterogeneity should exist among different kinds of cells. The diagnosis of intercellular heterogeneity with respect to mitochondrial heteroplasmy by this methodology could provide novel insight into developing a treatment strategy for mitochondrial diseases.
Asymmetrical response of California electricity demand to summer-time temperature variation
Authors: Kumar Rohini , Rachunok Benjamin , Maia-Silva Debora , Nateghi Roshanak 
Published: July 2020

AbstractCurrent projections of the climate-sensitive portion of residential electricity demand are based on estimating the temperature response of the mean of the demand distribution. In this work, we show that there is significant asymmetry in the summer-time temperature response of electricity demand in the state of California, with high-intensity demand demonstrating a greater sensitivity to temperature increases. The greater climate sensitivity of high-intensity demand is found not only in the observed data, but also in the projections in the near future (2021–2040) and far future periods (2081–2099), and across all (three) utility service regions in California. We illustrate that disregarding the asymmetrical climate sensitivity of demand can lead to underestimating high-intensity demand in a given period by 37–43%. Moreover, the discrepancy in the projected increase in the climate-sensitive portion of demand based on the 50th versus 90$${th}$$th quantile estimates could range from 18 to 40% over the next 20 years.
HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks
Authors: Timmons Patrick Brendan , Hewage Chandralal M. 
Published: July 2020

AbstractThe growing prevalence of resistance to antibiotics motivates the search for new antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane-active peptides which function as part of the innate host defence system, and form a promising avenue in antibiotic drug research. Some antimicrobial peptides exhibit toxicity against eukaryotic membranes, typically characterised by hemolytic activity assays, but currently, the understanding of what differentiates hemolytic and non-hemolytic peptides is limited. This study leverages advances in machine learning research to produce a novel artificial neural network classifier for the prediction of hemolytic activity from a peptide’s primary sequence. The classifier achieves best-in-class performance, with cross-validated accuracy of$$85.7\%$$85.7%and Matthews correlation coefficient of 0.71. This innovative classifier is available as a web server athttps://research.timmons.eu/happenn, allowing the research community to utilise it for in silico screening of peptide drug candidates for high therapeutic efficacies.
Identification of circRNA-associated ceRNA network in BMSCs of OVX models for postmenopausal osteoporosis
Authors: Wang Huichao , Zhou Kaifeng , Xiao Fangzhu , Huang Zhongyue , Xu Jun , Chen Guangnan , Liu Youwen , Gu Huijie 
Published: July 2020

AbstractCircular RNAs (circRNAs) serve as competing endogenous RNAs (ceRNAs) and indirectly regulate gene expression through shared microRNAs (miRNAs). However, the potential circRNAs functioning as ceRNAs in osteoporosis remain unclear. The bone marrow mesenchymal stem cells (BMSCs) were isolated from ovariectomy (OVX) mice and controls. We systematically analyzed RNA‐seq and miRNA‐microarray data, miRNA‐target interactions, and prominently coexpressed gene pairs to identify aberrantly expressed circRNAs, miRNAs, and messenger RNAs (mRNAs) between the OVX mice and controls. A total of 45 circRNAs, 22 miRNAs, and 548 mRNAs were significantly dysregulated (fold change > 1.5; p < 0.05). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted for differentially expressed mRNAs, and subsequently a circRNA‐associated ceRNA network involved in osteoporosis was constructed. We identified two ceRNA regulatory pathways in this osteoporosis mouse model—novel circRNA 0020/miR-206-3p/Nnmt and circRNA 3832/miR-3473e/Runx3, which were validated by real-time PCR. This is the first study to elucidate the circRNA-associated ceRNA network in OVX and control mice using deep RNA-seq and RNA-microarray analysis. The data further expanded the understanding of circRNA-associated ceRNA networks, and the regulatory functions of circRNAs, miRNAs and mRNAs in the pathogenesis and pathology of osteoporosis.
Miniaturized magnetic stir bars for controlled agitation of aqueous microdroplets
Authors: Gires Pierre-Yves , Thampi Mithun , Weiss Matthias 
Published: July 2020

AbstractControlled stirring of tiny volumes of aqueous fluids is of particular importance in the life sciences, e.g. in the context of microfluidic and lab-on-chip applications. Local stirring not only accelerates fluid mixing and diffusion-limited processes, but it also allows for adding controlled active noise to the fluid. Here we report on the synthesis and characterization of magnetic nano-stir bars (MNBs) with which these features can be achieved in a straightforward fashion. We also demonstrate the applicability of MNBs to cell extract droplets in microfluidic channels and we show that they can introduce active noise to cell extracts as evidenced by altered fluctuations of ensembles of cytoskeletal filaments.
Normal aging changes in the choroidal angioarchitecture of the macula
Authors: Nivison-Smith Lisa , Khandelwal Neha , Tong Janelle , Mahajan Sarakashi , Kalloniatis Michael , Agrawal Rupesh 
Published: July 2020

AbstractThe choroidal vascularity index (CVI) has been shown to be sensitive in detecting changes in choroidal angioarchitecture in a range of ocular diseases. However, changes in CVI in association with normal physiological aging and spatial distribution remains to be determined. This is significant as a range of ocular conditions with choroidal degeneration are associated with aging. In this study, we assessed CVI for 106 healthy eyes from 106 individuals (range 21–78 years old, ~ 20 individuals/decade) at 15 eccentricities across the macula (0, 230 µm, 460 µm, 690 µm, 1,150 µm, 1,380 µm and 2,760 µm from the fovea in the superior and inferior direction). Total choroidal area, luminal area and stromal area were all significantly decreased with age (p < 0.001 for all parameters). CVI was also significantly decreased with age (p < 0.01) and eccentricity. Fitting of quadratic regression curves to CVI as a function of age yielded a good fit for all eccentricities (r2 = 0.55–0.80) and suggested a decrease in CVI from the ages of 33–43 years at a rate of 0.7–2.7% per decade. CVI was lower in the inferior versus superior retina at matching eccentricities and a significant difference in age-related decline of CVI with eccentricity only occurred in inferior locations. These findings suggest choroidal angioarchitecture declines from the 4th decade of life with potential eccentricity differences in the inferior and superior retina. Considering the number of age-related diseases with choroidal dysfunction, these results provide foundational knowledge to understand choroidal involvement in these diseases.
Gregariousness in the giant sloth Lestodon (Xenarthra): multi-proxy approach of a bonebed from the Last Maximum Glacial of Argentine Pampas
Authors: Tomassini Rodrigo L. , Montalvo Claudia I. , Garrone Mariana C. , Domingo Laura , Ferigolo Jorge , Cruz Laura E. , Sanz-Pérez Dánae , Fernández-Jalvo Yolanda , Cerda Ignacio A. 
Published: July 2020

AbstractMegamammals constituted an important component in the Pleistocene faunal communities of South America. Paleobiological and paleoecological studies involving different megamammal taxa have increased significantly in the last years, but there are still several poorly-known issues of its life history. In this work, we analyze an assemblage composed of 13 individuals of different ontogenetic stages, and possibly different sex, belonging to the giant ground slothLestodon armatus(Xenarthra, Folivora), recovered from Playa del Barco site (Pampean Region, Argentina). A dating of 19,849 years Cal BP allows assigning this assemblage to a period of the MIS (Marine Isotope Stage) 2 related to the end of the Last Glacial Maximum. Based on multiple lines of research (e.g. taphonomy, paleopathology, osteohistology, isotopy), we interpret the origin of the assemblage and diverse paleobiological and paleoecological aspects (e.g. social behavior, ontogenetic changes, sexual dimorphism, diseases, resource and habitat use, trophic relationships) ofL. armatus. Evidence suggests that the assemblage was formed by a local single event of catastrophic mortality, which affected different members of a social group. This record represents the first accurate evidence of gregariousness for this ground sloth, providing new data on a poorly-known behavior among extinct Folivora.
Disease-related cellular protein networks differentially affected under different EGFR mutations in lung adenocarcinoma
Authors: Nishimura Toshihide , Nakamura Haruhiko , Yachie Ayako , Hase Takeshi , Fujii Kiyonaga , Koizumi Hirotaka , Naruki Saeko , Takagi Masayuki , Matsuoka Yukiko , Furuya Naoki , Kato Harubumi , Saji Hisashi 
Published: July 2020

AbstractIt is unclear how epidermal growth factor receptor EGFR major driver mutations (L858R or Ex19del) affect downstream molecular networks and pathways. This study aimed to provide information on the influences of these mutations. The study assessed 36 protein expression profiles of lung adenocarcinoma (Ex19del, nine; L858R, nine; no Ex19del/L858R, 18). Weighted gene co-expression network analysis together with analysis of variance-based screening identified 13 co-expressed modules and their eigen proteins. Pathway enrichment analysis for the Ex19del mutation demonstrated involvement of SUMOylation, epithelial and mesenchymal transition, ERK/mitogen-activated protein kinase signalling via phosphorylation and Hippo signalling. Additionally, analysis for the L858R mutation identified various pathways related to cancer cell survival and death. With regard to the Ex19del mutation, ROCK, RPS6KA1, ARF1, IL2RA and several ErbB pathways were upregulated, whereas AURK and GSKIP were downregulated. With regard to the L858R mutation, RB1, TSC22D3 and DOCK1 were downregulated, whereas various networks, including VEGFA, were moderately upregulated. In all mutation types, CD80/CD86 (B7), MHC, CIITA and IFGN were activated, whereas CD37 and SAFB were inhibited. Costimulatory immune-checkpoint pathways by B7/CD28 were mainly activated, whereas those by PD-1/PD-L1 were inhibited. Our findings may help identify potential therapeutic targets and develop therapeutic strategies to improve patient outcomes.
Evaluation and management of fungal-infected carrot seeds
Authors: Zhang Xue , Wang Ruiting , Ning Hailong , Li Wenxia , Bai Yunlong , Li Yonggang 
Published: July 2020

AbstractCarrot (Daucus carota L.), which is one of the 10 most important vegetable crops worldwide, is an edible root vegetable desired for its taste as well as its medicinal uses. However, a fungus isolated from carrot seeds was observed to substantially decrease the germination rate. The isolate was identified as Alternaria alternata based on morphological and molecular characteristics as well as a phylogenetic tree. The maximum seed infection rate of selected carrot cultivars was approximately 60%, with the main infection site just underneath the seed shell. Additionally, the germination rate of infected seeds decreased by 28.7%. However, the seed infection rate varied among the examined carrot cultivars. Regarding the effects of chemical fungicides, the optimal treatment involved immersing seeds in amistar top suspension concentrate (SC) (effective concentration of 0.65 g/L) for 6 h, which effectively killed the fungi inside the carrot seeds. The results of this study provide a theoretical basis for the development of efficient methods for preventing the infection of carrot seeds by specific fungi and increasing the germination rate and vigour index.