bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving orthotopic mouse models of patient-derived breast cancer brain metastases by a modified intracarotid injection method
Authors: Liu Zongming , Wang Yanzhi , Kabraji Sheheryar , Xie Shaozhen , Pan Peichen , Liu Zhenning , Ni Jing , Zhao Jean J. 
Published: January 2019

AbstractBreast cancer brain metastasis (BCBM) remains a major clinical problem. Approximately 10–16% of patients with breast cancer develop brain metastases (BCBM). However, no systemic therapy has gained regulatory approval for the specific treatment of BCBM and this remains an area of persistent, unmet medical need. Rapid, predictive and clinically-relevant animal models are critical to study the biology of brain metastases and to identify effective therapeutic approaches for patients with BCBM. Here, we describe a method for efficient establishment of orthotopic mouse models of patient-derived brain metastases via an improved intracarotid injection protocol that permits tumor cell growth in the unique brain microenvironment without compromising the blood-brain barrier (BBB). We demonstrate that our newly improved models of patient-derived brain metastases recapitulate the histologic, molecular, and genetic characteristics of their matched patient tumor specimens and thus represent a potentially powerful tool for pre-clinical and translational research.
5-Fluorouracil Induces Enteric Neuron Death and Glial Activation During Intestinal Mucositis via a S100B-RAGE-NFκB-Dependent Pathway
Authors: Costa Deiziane V. S. , Bon-Frauches Ana C. , Silva Angeline M. H. P. , Lima-Júnior Roberto C. P. , Martins Conceição S. , Leitão Renata F. C. , Freitas Gutierrez B. , Castelucci Patricia , Bolick David T. , Guerrant Richard L. , Warren Cirle A. , Moura-Neto Vivaldo , Brito Gerly A. C. 
Published: January 2019

Abstract5-Fluorouracil (5-FU) is an anticancer agent whose main side effects include intestinal mucositis associated with intestinal motility alterations maybe due to an effect on the enteric nervous system (ENS), but the underlying mechanism remains unclear. In this report, we used an animal model to investigate the participation of the S100B/RAGE/NFκB pathway in intestinal mucositis and enteric neurotoxicity caused by 5-FU (450 mg/kg, IP, single dose). 5-FU induced intestinal damage observed by shortened villi, loss of crypt architecture and intense inflammatory cell infiltrate as well as increased GFAP and S100B co-expression and decreased HuC/D protein expression in the small intestine. Furthermore, 5-FU increased RAGE and NFκB NLS immunostaining in enteric neurons, associated with a significant increase in the nitrite/nitrate, IL-6 and TNF-α levels, iNOS expression and MDA accumulation in the small intestine. We provide evidence that 5-FU induces reactive gliosis and reduction of enteric neurons in a S100B/RAGE/NFκB-dependent manner, since pentamidine, a S100B inhibitor, prevented 5-FU-induced neuronal loss, enteric glia activation, intestinal inflammation, oxidative stress and histological injury.
Incidental findings on brain MRI among Chinese at the age of 55–65 years: the Taizhou Imaging Study
Authors: Li Shuyuan , Fang Fang , Cui Mei , Jiang Yanfeng , Wang Yingzhe , Kong Xuhui , Tian Weizhong , Fan Min , Yuan Ziyu , Chen Jinhua , Yang Qi , Xue Fuzhong , Wang Jiucun , Lu Ming , Wang Xiaofeng , Chen Xingdong , Jin Li , Ye Weimin 
Published: January 2019

AbstractAsymptomatic brain abnormalities are common incidental findings on brain MRI in the elderly population and can be regarded as imaging markers of early stroke and dementia. We initiated the Taizhou Imaging Study (TIS) to examine the prevalence and correlates of incidental findings using brain MRI among an elderly population residing in a rural area of China. A total of 562 individuals, at the age of 55 to 65 years, participated in the TIS study with a response rate of 90%. The prevalence of lacunes, white matter hyperintensity (WMH), cerebral microbleeds (CMB), perivascular space, and intracranial arterial stenosis was 26.69%, 10.68%, 18.51%, 27.76%, and 12.81%, respectively. Age and hypertension were the major correlates of these incidental findings. Per each year increase in age, the risks of WMH and CMB increased by 15% and 14%. Compared to individuals with normal blood pressure, individuals with hypertension had an increased risk of all incidental findings, with the adjusted odds ratios of 2.28 to 5.45. Correlations of age, gender and body mass index with brain gray matter fraction were also observed. The high prevalence of these findings indicates a need of preventative strategy to help prevent future stroke and dementia in this population.
Role of Water on the Rotational Dynamics of the Organic Methylammonium Cation: A First Principles Analysis
Authors: Hoehn Ross D. , Francisco Joseph S. , Kais Sabre , Kachmar Ali 
Published: January 2019

AbstractUnderstanding the degradation mechanisms of lead-halide perovskites (CH3NH3PbI3) under exposure to liquid/aerosol water is an essential problem within the photovoltaic community. Herein we investigate both the static and the dynamic properties of the methylammonuim cation (MA) as it coordinates with invading water molecules (MA.(H2O)n, n = 1, 2, 3, 4) using both stationary state quantum mechanics and first principle molecular dynamics simulations. Various solvation structures of MA were characterized by their stabilization energies, dipoles, and Maximally-Localized Wannier Function (MLWF) centers. Calculation – and analysis – of vibrational shifts in the IR spectral region were performed for hydrated complexes; the locations of $${\bf{N}}{{\bf{H}}}_{{\bf{3}}}^{{\boldsymbol{+}}}$$
N

H

3

+

stretching vibrations allude to significant hydrogen bonding between MA and the water molecules. Through Fourier analysis of the rotational dynamics on several MA · (H2O)n complexes, we conclude that the water molecules dampen the rotational motion of the MA as the intermolecular bonds formed between the water molecules and the MA act to hinder the rotation of the cation; these findings give explanatory support to earlier computational observations of humidity effects on perovskites (i.e., CH3NH3PbI3) materials. This work is a step toward understanding the water-MA cation interaction in bulk perovskites, thus providing greater understanding of in situ instability/degradation of perovskite bulk materials.
Towards a Fishing Pressure Prediction System for a Western Pacific EEZ
Authors: Cimino Megan A. , Anderson Mark , Schramek Travis , Merrifield Sophia , Terrill Eric J. 
Published: January 2019

AbstractFisheries management faces numerous monitoring and enforcement challenges that are becoming more complex as fish stocks are depleted; and illegal, unregulated, and unreported fishing becomes more sophisticated. For remote island nations, the challenges are compounded by a loosely understood association of pelagic stocks to the ocean environment, and the tyranny of distance in monitoring and surveilling large exclusive economic zones (EEZ). An approach to ocean conservation is establishing protected areas, with the Pacific island nation of Palau as a leader with the recently established National Marine Sanctuary, which closes 80% of their EEZ to commercial fishing in 2020. Here we present an EEZ-wide analysis of Palau commercial fishing over a 6-year period (2011–2016), and develop a system for predicting fishing activity accounting for oceanic variables, climate indices, and vessel flag. Linking pelagic habitat to fishing activity provides high-resolution decision aids for management, highlighting the need for EEZ-specific analyses in addressing fisheries.
Influence of surface ocean density on planktonic foraminifera calcification
Authors: Zarkogiannis Stergios D. , Antonarakou Assimina , Tripati Aradhna , Kontakiotis George , Mortyn P. Graham , Drinia Hara , Greaves Mervyn 
Published: January 2019

AbstractThis study provides evidence that ambient seawater density influences calcification and may account for the observed planktonic foraminifera shell mass increase during glacial times. Volumes of weighed fossil Globigerina bulloides shells were accurately determined using X-ray Computer Tomography and were combined with water density reconstructions from Mg/Ca and δ18O measurements to estimate the buoyancy force exerted on each shell. After assessment of dissolution effects, the resulting relationship between shell mass and buoyancy suggests that heavier shells would need to be precipitated in glacial climates in order for these organisms to remain at their optimum living depth, and counterbalance the increased buoyant force of a denser, glacial ocean. Furthermore, the reanalysis of bibliographic data allowed the determination of a relationship between G. bulloides shell mass and ocean density, which introduces implications of a negative feedback mechanism for the uptake of atmospheric CO2 by the oceans.
Prominent action of butyrate over β-hydroxybutyrate as histone deacetylase inhibitor, transcriptional modulator and anti-inflammatory molecule
Authors: Chriett Sabrina , Dąbek Arkadiusz , Wojtala Martyna , Vidal Hubert , Balcerczyk Aneta , Pirola Luciano 
Published: January 2019

AbstractButyrate and R-β-hydroxybutyrate are two related short chain fatty acids naturally found in mammals. Butyrate, produced by enteric butyric bacteria, is present at millimolar concentrations in the gastrointestinal tract and at lower levels in blood; R-β-hydroxybutyrate, the main ketone body, produced by the liver during fasting can reach millimolar concentrations in the circulation. Both molecules have been shown to be histone deacetylase (HDAC) inhibitors, and their administration has been associated to an improved metabolic profile and better cellular oxidative status, with butyrate inducing PGC1α and fatty acid oxidation and R-β-hydroxybutyrate upregulating oxidative stress resistance factors FOXO3A and MT2 in mouse kidney. Because of the chemical and functional similarity between the two molecules, we compared here their impact on multiple cell types, evaluating i) histone acetylation and hydroxybutyrylation levels by immunoblotting, ii) transcriptional regulation of metabolic and inflammatory genes by quantitative PCR and iii) cytokine secretion profiles using proteome profiling array analysis. We confirm that butyrate is a strong HDAC inhibitor, a characteristic we could not identify in R-β-hydroxybutyrate in vivo nor in vitro. Butyrate had an extensive impact on gene transcription in rat myotubes, upregulating PGC1α, CPT1b, mitochondrial sirtuins (SIRT3-5), and the mitochondrial anti-oxidative genes SOD2 and catalase. In endothelial cells, butyrate suppressed gene expression and LPS-induced secretion of several pro-inflammatory genes, while R-β-hydroxybutyrate acted as a slightly pro-inflammatory molecule. Our observations indicate that butyrate induces transcriptional changes to a higher extent than R-β-hydroxybutyrate in rat myotubes and endothelial cells, in keep with its HDAC inhibitory activity. Also, in contrast with previous reports, R-β-hydroxybutyrate, while inducing histone β-hydroxybutyrylation, did not display a readily detectable HDAC inhibitor activity and exerted a slight pro-inflammatory action on endothelial cells.
Nucleotide-level Convolutional Neural Networks for Pre-miRNA Classification
Authors: Zheng Xueming , Xu Shungao , Zhang Ying , Huang Xinxiang 
Published: January 2019

AbstractDue to the biogenesis difference, miRNAs can be divided into canonical microRNAs and mirtrons. Compared to canonical microRNAs, mirtrons are less conserved and hard to be identified. Except stringent annotations based on experiments, many in silico computational methods have be developed to classify miRNAs. Although several machine learning classifiers delivered high classification performance, all the predictors depended heavily on the selection of calculated features. Here, we introduced nucleotide-level convolutional neural networks (CNNs) for pre-miRNAs classification. By using “one-hot” encoding and padding, pre-miRNAs were converted into matrixes with the same shape. The convolution and max-pooling operations can automatically extract features from pre-miRNAs sequences. Evaluation on test dataset showed that our models had a satisfactory performance. Our investigation showed that it was feasible to apply CNNs to extract features from biological sequences. Since there are many hyperparameters can be tuned in CNNs, we believe that the performance of nucleotide-level convolutional neural networks can be greatly improved in the future.
Soluble urokinase plasminogen activation receptor and long-term outcomes in persons undergoing coronary angiography
Authors: Sommerer Claudia , Zeier Martin , Morath Christian , Reiser Jochen , Scharnagl Hubert , Stojakovic Tatjana , Delgado Graciela E. , März Winfried , Kleber Marcus E. 
Published: January 2019

AbstractSoluble urokinase plasminogen activation receptor (suPAR) is risk factor for kidney disease and biomarker for cardiovascular outcomes but long term longitudinal analyses in a large European cohort have not been perfomed. To hus, we studied suPAR in participants of the Ludwigshafen Risk and Cardiovascular Health study over a very long follow-up time of nearly 10 years. We estimated overall risk of all-cause and cardiovascular death by Cox proportional hazards regression according to quartiles of suPAR, including age, sex, use of lipid-lowering drugs, body mass index, diabetes mellitus, hypertension, smoking, lipids, as well as glomerular filtration rate (eGFR), NT-proBNP, interleukin-6 and high-sensitive CRP as covariates. A total of 2940 participants (age 62.7 ± 10.5years) having a median eGFR of 83.8 mL/min/1.73 m2 were included. The median suPAR concentration was 3010 pg/mL (interquartile range, 2250–3988 pg/mL). Using the lowest quartile of suPAR as the reference, crude hazard ratio for cardiovascular mortality were 1.58 (95% CI 1.16–2.16), 1.85 (95% CI 1.37–2.52) and 2.75 (95% CI 2.03–3.71) in the second, third and fourth quartile, respectively. Adjusting for NT-proBNPeGFR or inflammation (interleukin-6 and high-sensitive CRP) confirmed results. suPAR predicts all-cause and cardiovascular death over a period of ten years in persons undergoing coronary angiography, independent of the natriuretic peptide NT-proBNP, kidney function and of markers of systemic inflammation. Future investigation into a potential causal role of suPAR in cardiovascular disease is warranted.
Process calculi may reveal the equivalence lying at the heart of RNA and proteins
Authors: Maestri Stefano , Merelli Emanuela 
Published: January 2019

AbstractThe successful use of process calculi to specify behavioural models allows us to compare RNA and protein folding processes from a new perspective. We model the folding processes as behaviours resulting from the interactions that nucleotides and amino acids (the elementary units that compose RNAs and proteins respectively) perform on their linear sequences. This approach is intended to provide new knowledge about the studied systems without strictly relying on empirical data. By applying Milner’s CCS process algebra to highlight the distinguishing features of the two folding processes, we discovered an abstraction level at which they show behavioural equivalences. We believe that this result could be interpreted as a clue in favour of the highly-debated RNA World theory, according to which, in the early stages of cell evolution, RNA molecules played most of the functional and structural roles carried out today by proteins.
Exploring the substrate scope of ferulic acid decarboxylase (FDC1) from Saccharomyces cerevisiae
Authors: Nagy Emma Zsófia Aletta , Nagy Csaba Levente , Filip Alina , Nagy Katalin , Gál Emese , Tőtős Róbert , Poppe László , Paizs Csaba , Bencze László Csaba 
Published: January 2019

AbstractFerulic acid decarboxylase fromSaccharomyces cerevisiae(ScFDC1) was described to possess a novel, prenylated flavin mononucleotide cofactor (prFMN) providing the first enzymatic 1,3-dipolar cycloaddition mechanism. The high tolerance of the enzyme towards several non-natural substrates, combined with its high quality, atomic resolution structure nominates FDC1 an ideal candidate as flexible biocatalyst for decarboxylation reactions leading to synthetically valuable styrenes. Herein the substrate scope ofScFDC1 is explored on substituted cinnamic acids bearing different functional groups (–OCH3, –CF3or –Br) at all positions of the phenyl ring (o−,m−,p−),as well as on several biaryl and heteroaryl cinnamic acid analogues or derivatives with extended alkyl chain. It was found thatE. coliwhole cells expressing recombinantScFDC1 could transform a large variety of substrates with high conversion, including several bulky aryl and heteroaryl cinnamic acid analogues, that characterizeScFDC1 as versatile and highly efficient biocatalyst. Computational studies revealed energetically favoured inactive binding positions and limited active site accessibility for bulky and non-linear substrates, such as 2-phenylthiazol-4-yl-, phenothiazine-2-yl- and 5-(4-bromophenyl)furan-2-yl) acrylic acids. In accordance with the computational predictions, site-directed mutagenesis of residue I330 provided variants with catalytic activity towards phenothiazine-2-yl acrylic acid and provides a basis for altering the substrate specificity of ScFDC1 by structure based rational design.
Potential for high yield with increased seedling density and decreased N fertilizer application under seedling-throwing rice cultivation
Authors: Liu Yang , Li Chao , Fang Baohua , Fang Yong , Chen Kailin , Zhang Yuzhu , Zhang Haiqing 
Published: January 2019

AbstractFertilizer application for rice production has increased significantly in southern China to raise yields, but has led to problems with lodging, quality decline and environmental pollution. Therefore, research on fertilizer-saving cultivation technologies for high-yielding rice is necessary. A two-factor experiment was conducted to evaluate the effects of seedling-addition treatment (SAT) and nitrogen-saving treatment (NST) on yield formation and nitrogen absorption of individual plants and plant groups under the seedling-throwing cultivation system. Numbers of spikelets per panicle and filled grains per panicle of individual plants declined under decreased nitrogen application, but was compensated by substantially increased effective panicles number and total number of glumous flowers under SAT. Under the optimal SAT–NST treatments of 18% less N fertilizer and 32% additional seedlings, yield increased 1.79% and 4.29% compared with that of conventional practice (CK) in 2015 and 2016, respectively. The mature-stage individual-plant biomass under SAT–NST treatments decreased by 27.46% and 20.49% compared with CK in 2015 and 2016, but plant-group biomass did not differ significantly (all >16 t ha−1). Under SAT–NST treatments, effective number of panicles was positively correlated with maximum number of seedlings (r = 0.643) and N absorption amount in the tillering stage (r = 0.901).
Evaluation of selected polychlorinated biphenyls (PCBs) congeners and dichlorodiphenyltrichloroethane (DDT) in fresh root and leafy vegetables using GC-MS
Authors: Olatunji Olatunde S. 
Published: January 2019

AbstractPersistent organic pollutants (POPs) are dangerous and toxic pollutants that may cause adverse effects on human and animal health, including death. POPs such as polychlorinated biphenyls (PCBs) and pesticides are subtly released into the environment from industrial and agricultural use. Global circulation is due to their trans-boundary transport capacity, contingent on aerodynamic and hydrological properties. Plants have capacity to take-up POPs, and these bio-magnify along heterotrophic transfer pathways. In this study, levels of selected 6-PCB congeners and 3- DDTs in some leaf and root vegetables were investigated. Leaf and root vegetables were collected from different horticultural farms areas in Cape Town. The 6-PCBs and 3-DDTs were recovered from the samples using solid phase extraction(SPE), followed by GC-MS analysis. The ΣPCBs and ΣDDT (on-whole basis), were ranged: 90.9–234 ng/g and 38.9–66.1 ng/g respectively. The 3-PCBs and 6-DDTs levels were slightly higher in leaf vegetables compared to root vegetables. The detection of PCBs and DDTs in the vegetables suggest the probable use of PCBs containing pesticides. Although the observed concentrations were below the WHO maximum residue limits, consumption of such contaminated leaf and root vegetables portend a health risk.
Efficient coralline algal psbA mini barcoding and High Resolution Melt (HRM) analysis using a simple custom DNA preparation
Authors: Anglès d’Auriac Marc B. , Le Gall Line , Peña Viviana , Hall-Spencer Jason M. , Steneck Robert S. , Fredriksen Stein , Gitmark Janne , Christie Hartvig , Husa Vivian , Grefsrud Ellen Sofie , Rinde Eli 
Published: January 2019

AbstractCoralline algae form extensive maerl and rhodolith habitats that support a rich biodiversity. Calcium carbonate harvesting as well as trawling activities threatens this ecosystem. Eleven species were recorded so far as maerl-forming in NE Atlantic, but identification based on morphological characters is unreliable. As for most red algae, we now use molecular characters to resolve identification of these taxa. However, obtaining DNA sequences requires time and resource demanding methods. The purpose of our study was to improve methods for achieving simple DNA extraction, amplification, sequencing and sequence analysis to allow robust identification of maerl species and other coralline algae. Our novel and easy DNA preparation method for coralline algae was of sufficient quality for qPCR amplification and sequencing of all 47 tested samples. The new psbA qPCR assay successfully amplified a 350 bp fragment identifying six species and uncovering two new Operational Taxonomic Units. Molecular results were corroborated with anatomical examination using i.e. scanning electron microscopy. Finally, the qPCR assay was coupled with High Resolution Melt analysis that successfully differentiated the closely related species Lithothamnion erinaceum and L. cf. glaciale. This DNA preparation and qPCR technique should vitalize coralline research by reducing time and cost associated with molecular systematics.
Ni-Co bimetal decorated carbon nanotube aerogel as an efficient anode catalyst in urea fuel cells
Authors: Tesfaye Robel Mehari , Das Gautam , Park Bang Ju , Kim Jihyeon , Yoon Hyon Hee 
Published: January 2019

AbstractNi-based catalysts have been considered as an efficient anode material for urea fuel cells due to the low cost and high activity in alkaline media. Herein, we demonstrate that Ni-Co bimetallic nanoparticles decorated carbon nanotube aerogels as catalysts for urea oxidation reaction (UOR) can be synthesized by a polyol reduction and sol-gel method. The morphology, structure, and composition of the Ni-Co/MWCNT aerogels were characterized by scanning electron microscopy and X-Ray diffraction. The electro-catalytic activity of the Ni-Co/MWCNT aerogels towards UOR was investigated using cyclic voltammetry. It was found that the Co-doping at 25% (Co/Ni) significantly increased the oxidation peak current and reduced the overpotential of the UOR. Furthermore, the MWCNT aerogel support also remarkably enhanced electro-catalytic activity by providing a high surface area and fast mass transport for the UOR owing to the porous 3D network structures with uniform distribution of Ni-Co nanoparticles. Urea/O2 fuel cell with Ni-Co/MWCNT aerogel as anode material exhibited an excellent performance with maximum power density of 17.5 mWcm−2 with an open circuit voltage of 0.9 V. Thus, this work showed that the highly porous three-dimensional Ni-Co/MWCNT aerogel catalysts can be used for urea oxidation and as an efficient anode material for urea fuel cells.