bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving satellite-based PM2.5 estimates in China using Gaussian processes modeling in a Bayesian hierarchical setting
Authors: Yu Wenxi , Liu Yang , Ma Zongwei , Bi Jun 
Published: July 2017

AbstractUsing satellite-based aerosol optical depth (AOD) measurements and statistical models to estimate ground-level PM2.5 is a promising way to fill the areas that are not covered by ground PM2.5 monitors. The statistical models used in previous studies are primarily Linear Mixed Effects (LME) and Geographically Weighted Regression (GWR) models. In this study, we developed a new regression model between PM2.5 and AOD using Gaussian processes in a Bayesian hierarchical setting. Gaussian processes model the stochastic nature of the spatial random effects, where the mean surface and the covariance function is specified. The spatial stochastic process is incorporated under the Bayesian hierarchical framework to explain the variation of PM2.5 concentrations together with other factors, such as AOD, spatial and non-spatial random effects. We evaluate the results of our model and compare them with those of other, conventional statistical models (GWR and LME) by within-sample model fitting and out-of-sample validation (cross validation, CV). The results show that our model possesses a CV result (R2 = 0.81) that reflects higher accuracy than that of GWR and LME (0.74 and 0.48, respectively). Our results indicate that Gaussian process models have the potential to improve the accuracy of satellite-based PM2.5 estimates.
Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks
Authors: Ghanat Bari Mehrab , Ung Choong Yong , Zhang Cheng , Zhu Shizhen , Li Hu 
Published: July 2017

AbstractEmerging evidence indicates the existence of a new class of cancer genes that act as “signal linkers” coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 108 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.
HPV prevalence in the foreskins of asymptomatic healthy infants and children: Systematic review and meta-analysis
Authors: Lee Bora , Lee Sang Wook , Kim Dae In , Kim Jae Heon 
Published: July 2017

AbstractThe true HPV prevalence in the foreskins of infants and children has been little documented, but reporting on this prevalence is of great importance given its impact on the rationale for treating asymptomatic boys. We searched multiple databases from 1960 to 2016 for observational or prospective studies that reported on HPV prevalence in foreskins. We conducted a meta-analysis using a random-effects model to pool for HPV prevalence in the foreskins of infants and children. Eight studies, with a total of 556 infants and children with phimosis, were eligible for the meta-analysis. The pooled overall prevalence of general HPV, high-risk HPV, low-risk HPV, HPV 16/18, HPV 16, and HPV 18 were 17.3 (95%CI: 0.8–46.3), 12.1 (95% CI: 0.9–31.5), 2.4 (95% CI: 0.0–11.2), 4.8 (95% CI: 0.0–16.8), 1.7 (95% CI: 0.0–5.1), and 0 (95% CI: 0–0.5), respectively. The estimated HPV prevalence in foreskins was not zero among infants and children, which implies HPV transmission other than by sexual contact. Considering that high-risk HPV is detected in asymptomatic infants and children, future studies are warranted to determine whether preventive treatments in asymptomatic infants and children could be effective in preventing persistence or transmission of high-risk HPV.
Removal of Copper (II) by Biochar Mediated by Dissolved Organic Matter
Authors: He Pinjing , Yu Qinfang , Zhang Hua , Shao Liming , Lü Fan 
Published: July 2017

AbstractThe effects of humic acid (HA) and fulvic acid (FA) on Cu2+ adsorption on biochar were investigated, with mechanisms confirmed by excitation-emission matrix spectroscopy, Fourier transform infrared spectroscopy, and scanning electron microscopy. HA loading enhanced Cu2+ adsorption on biochar, with the maximum enhancement of 55.0% occurring at an HA loading of 100 mg-C/L. The adsorbed HA introduced many additional functional groups to biochar, thus enhancing Cu2+ adsorption, which decreased at HA concentrations >100 mg-C/L due to self-association of HA at high loading concentrations. In contrast, FA loading caused no enhancement on Cu2+ adsorption on biochar. FA was adsorbed through H-bonding with the functional groups of biochar, which set up a competition with Cu2+ for adsorption on biochar. The functional groups occupied by adsorbed FA were offset by the newly introduced functional groups of FA, thus there was no net increase in the amount of Cu2+ adsorption upon FA loading. These findings imply that, because of the enhanced adsorption of HA-loaded biochar, the amount of Cu2+ immobilized would increase by 28.2% for mature compost and 31.9% for fresh compost if there exist interaction between biochar and HA compared with the amounts immobilized by non-interactive HA and biochar.
Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
Authors: Chuang Trees-Juen , Tseng Yu-Hsiang , Chen Chia-Ying , Wang Yi-Da 
Published: July 2017

AbstractGenomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and the removal of ASE events arising from non-imprinting factors. Here, we describe a pipeline with the pattern of reciprocal allele descendants (RADs) through genotyping and transcriptome sequencing data across independent parent-offspring trios to discriminate between varied types of ASE (e.g., imprinting, genetic variation-dependent ASE, and random monoallelic expression (RME)). We show that the vast majority of ASE events are due to sequence-dependent genetic variant, which are evolutionarily conserved and may themselves play a cis-regulatory role. Particularly, 74% of non-RAD ASE events, even though they exhibit ASE biases toward the same parentally-inherited allele across different individuals, are derived from genetic variation but not imprinting. We further show that the RME effect may affect the effectiveness of the population-based method for detecting imprinting events and our pipeline can help to distinguish between these two ASE types. Taken together, this study provides a good indicator for categorization of different types of ASE, opening up this widespread and complex mechanism for comprehensive characterization.
Polymeric hydrophilic ionic liquids used to modify magnetic nanoparticles for the highly selective enrichment of N-linked glycopeptides
Authors: Jiao Fenglong , Gao Fangyuan , Wang Heping , Deng Yulin , Zhang Yangjun , Qian Xiaohong , Zhang Yukui 
Published: July 2017

AbstractThe low abundance of glycopeptides in biological samples makes it necessary to enrich them before further analysis. In this study, the polymeric hydrophilic ionic liquid-modified magnetic (Fe3O4@MPS@PMAC) nanoparticles were synthesized via a one-step reflux-precipitation polymerization. Owing to the excellent hydrophilicity and strong electrostatic interaction toward glycopeptides of the polymerized hydrophilic ionic liquid, [2-(methacryloyloxy) ethyl] trimethylammonium chloride (MAC), the synthesized Fe3O4@MPS@PMAC nanoparticles exhibited outstanding performance in glycopeptide enrichment with high detection sensitivity (10 fmol), large binding capacity (100 μg mg−1) and satisfied enrichment recovery (approximately 82%). Furthermore, the newly developed Fe3O4@MPS@PMAC nanoparticles were applied for the glycopeptide enrichment of HeLa exosome proteins. A total of 1274 glycopeptides from 536 glycoproteins were identified in three replicate analyses of 50 μg of HeLa exosome proteins. These results demonstrate the potential of Fe3O4@MPS@PMAC nanoparticles for both glycoproteomic analysis and exosome research.
A facile method of transforming FGD gypsum to α-CaSO4·0.5H2O whiskers with cetyltrimethylammonium bromide (CTAB) and KCl in glycerol-water solution
Authors: Guan Qingjun , Sun Wei , Hu Yuehua , Yin Zhigang , Guan Changping 
Published: July 2017

AbstractA facile method to transform flue gas desulfurization gypsum (FGD gypsum) to α- calcium sulfate hemihydrate (α-HH) whiskers with high aspect ratios mediated by cetyltrimethylammonium bromide (CTAB) and KCl in glycerol-water solutions was studied. Addition of KCl facilitated the dissolution of calcium sulfate dihydrate (DH) and created a much higher supersaturation, which could come into being a larger driving force for the phase transformation from DH to α-HH. CTAB as the crystal modifier can significantly promoted 1-D growth of α-HH whiskers along the c axis and the presence of 0.25% CTAB (by weight of FGD gypsum) resulted in the increase of the average aspect ratio of α-HH whiskers from 28.9 to 188.4, which might be attributed to the preferential adsorption of C16H33(CH3)3N+ on the negative side facets of α-HH crystal.
Pediatric Sarcoma Data Forms a Unique Cluster Measured via the Earth Mover’s Distance
Authors: Chen Yongxin , Cruz Filemon Dela , Sandhu Romeil , Kung Andrew L. , Mundi Prabhjot , Deasy Joseph O. , Tannenbaum Allen 
Published: July 2017

AbstractIn this note, we combined pediatric sarcoma data from Columbia University with adult sarcoma data collected from TCGA, in order to see if one can automatically discern a unique pediatric cluster in the combined data set. Using a novel clustering pipeline based on optimal transport theory, this turned out to be the case. The overall methodology may find uses for the classification of data from other biological networking problems.
Fabrication of a protein microarray by fluorous-fluorous interactions
Authors: Li Ben-Yuan , Juang Duane S. , Adak Avijit K. , Hwang Kuo-Chu , Lin Chun-Cheng 
Published: July 2017

AbstractFluorous-modified surfaces have emerged as a powerful tool for the immobilization of fluorous-tagged biomolecules based on their specificity and the strength of fluorous-fluorous interactions. To fabricate a fluorous-based protein microarray, we designed two strategies for site-specific modification of proteins with a fluorous tag: attaching the fluorous tag to the C-termini of expressed proteins by native chemical ligation (NCL) or to the Fc domain of antibodies through boronic acid (BA)-diol interactions. The perfluoro-tagged proteins could be easily purified by fluorous-functionalized magnetic nanoparticles (MNPs) and immobilized on a fluorous chip with minimal non-specific adsorption. Importantly, proteins immobilized on the solid support through non-covalent fluorous-fluorous interactions were sufficiently stable to withstand continuous washing. We believe that this fluorous-fluorous immobilization strategy will be a highly valuable tool in protein microarray fabrication.
Hyperbolic-polaritons-enabled dark-field lens for sensitive detection
Authors: Shen Lian , Wang Huaping , Li Rujiang , Xu Zhiwei , Chen Hongsheng 
Published: July 2017

AbstractSensitive detection of features in a nanostructure may sometimes be puzzled in the presence of significant background noise. In this regard, background suppression and super-resolution are substantively important for detecting weakly scattering nanoscale features. Here, we present a lens design, termed hyperbolic-polaritons-enabled dark-field lens (HPEDL), which has the ability to accomplish straightforward sensitive detection. This HPEDL structure consists of type I and type II hyperbolic media that support high-k field waves via hyperbolic polaritons (HPs). We show that the cone-like characteristics of the HPs could be manipulated while the influence of the low-k field waves would be removed. Numerical simulations demonstrate that this proposed structure can successfully realize straightforward sensitive detection by modifying its thickness under the phase compensation condition. Besides, the minimum resolvable length and angular-dependent performance for sensitive detection are also demonstrated by simulations. Remarkably, these findings are very promising for propelling nanophotonics technologies and constitute a further important step towards practical applications of optical microscopy.
All-laser-micromachining of ridge waveguides in LiNbO3 crystal for mid-infrared band applications
Authors: Li Lingqi , Nie Weijie , Li Ziqi , Lu Qingming , Romero Carolina , Vázquez de Aldana Javier R. , Chen Feng 
Published: July 2017

AbstractThe femtosecond laser micromachining of transparent optical materials offers a powerful and feasible solution to fabricate versatile photonic components towards diverse applications. In this work, we report on a new design and fabrication of ridge waveguides in LiNbO3 crystal operating at the mid-infrared (MIR) band by all-femtosecond-laser microfabrication. The ridges consist of laser-ablated sidewalls and laser-written bottom low-index cladding tracks, which are constructed for horizontal and longitudinal light confinement, respectively. The ridge waveguides are found to support good guidance at wavelength of 4 μm. By applying this configuration, Y-branch waveguiding structures (1 × 2 beam splitters) have been produced, which reach splitting ratios of ∼1:1 at 4 μm. This work paves a simple and feasible way to construct novel ridge waveguide devices in dielectrics through all-femtosecond-laser micro-processing.
Structural and functional identification of vasculogenic mimicry in vitro
Authors: Racordon Dusan , Valdivia Andrés , Mingo Gabriel , Erices Rafaela , Aravena Raúl , Santoro Felice , Bravo Maria Loreto , Ramirez Carolina , Gonzalez Pamela , Sandoval Alejandra , González Alfonso , Retamal Claudio , Kogan Marcelo J. , Kato Sumie , Cuello Mauricio A. , Osorio German , Nualart Francisco , Alvares Pedro , Gago-Arias Araceli , Fabri Daniella , Espinoza Ignacio , Sanchez Beatriz , Corvalán Alejandro H. , Pinto Mauricio P. , Owen Gareth I. 
Published: July 2017

AbstractVasculogenic mimicry (VM) describes a process by which cancer cells establish an alternative perfusion pathway in an endothelial cell-free manner. Despite its strong correlation with reduced patient survival, controversy still surrounds the existence of an in vitro model of VM. Furthermore, many studies that claim to demonstrate VM fail to provide solid evidence of true hollow channels, raising concerns as to whether actual VM is actually being examined. Herein, we provide a standardized in vitro assay that recreates the formation of functional hollow channels using ovarian cancer cell lines, cancer spheres and primary cultures derived from ovarian cancer ascites. X-ray microtomography 3D-reconstruction, fluorescence confocal microscopy and dye microinjection conclusively confirm the existence of functional glycoprotein-rich lined tubular structures in vitro and demonstrate that many of structures reported in the literature may not represent VM. This assay may be useful to design and test future VM-blocking anticancer therapies.
The phenotypic variability of HK1-associated retinal dystrophy
Authors: Yuan Zhisheng , Li Baiyu , Xu Mingchu , Chang Emmanuel Y. , Li Huajin , Yang Lizhu , Wu Shijing , Soens Zachry T. , Li Yumei , Wong Lee-Jun C. , Lewis Richard A. , Sui Ruifang , Chen Rui 
Published: July 2017

AbstractInherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of Mendelian disorders primarily affecting photoreceptor cells. The same IRD-causing variant may lead to different retinal symptoms, demonstrating pleiotropic phenotype traits influenced by both underlying genetic and environmental factors. In the present study, we identified four unrelated IRD families with the HK1 p.E851K variant, which was previously reported to cause autosomal dominant retinitis pigmentosa (RP), and described their detailed clinical phenotypes. Interestingly, we found that in addition to RP, this particular variant can also cause dominant macular dystrophy and cone-rod dystrophy, which primarily affect cone photoreceptors instead of rods. Our results identified pleiotropic effects for an IRD-causing variant and provide more insights into the involvement of a hexokinase in retinal pathogenesis.
CVD graphene as an electrochemical sensing platform for simultaneous detection of biomolecules
Authors: Wang Xiaodan , Gao Delan , Li Mingji , Li Hongji , Li Cuiping , Wu Xiaoguo , Yang Baohe 
Published: July 2017

AbstractThe development of electrochemical biosensors for the simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA), tryptophan (Trp), and nitrite ($${{\rm{NO}}}_{2}^{-}$$NO2−) in human serum is reported in this work. Free-standing graphene nanosheets were fabricated on Ta wire using the chemical vapor deposition (CVD) method. CVD graphene, which here served as a sensing platform, provided a highly sensitive and selective option, with detection limits of AA, DA, UA, Trp, and$${{\rm{NO}}}_{2}^{-}$$NO2−of 1.58, 0.06, 0.09, 0.10, and 6.45 μM (S/N = 3), respectively. The high selectivity of the electrode is here explained by a relationship between the bandgap energy of analyte and the Fermi level of graphene. The high sensitivity in the oxidation current was determined by analyzing the influence of the high surface area and chemical structure of free-standing graphene nanosheets on analyte adsorption capacity. This finding strongly indicates that the CVD graphene electrode can be used as a biosensor to detect five analytes in human serum.
Performance measurement of intraoperative systolic arterial pressure to predict in-hospital mortality in adult liver transplantation
Authors: Lee Hyung-Chul , Ryu Ho-Geol , Jung Chul-Woo 
Published: July 2017

AbstractProfound hypotension during liver transplantation is aggressively treated with vasopressors thus frequently unrevealed in a retrospective study. The relationship between concealed intraoperative hypotension and in-hospital mortality after liver transplantation was evaluated using performance measurement (PM) of systolic arterial pressure (SAP). Median performance error (MDPE), median absolute performance error (MDAPE), and wobble of SAP were calculated using preoperative SAP as the reference value, and prereperfusion and postreperfusion SAPs as measured values. Univariable and multivariable logistic regression analyses were performed using 6 PM parameters and 36 traditional SAP-derived parameters to predict in-hospital mortality. In-hospital mortality was 3.9% (22/569 cases). Prereperfusion MDAPE and postreperfusion wobble were the only significant SAP-derived predictors of in-hospital mortality. The area under receiver operating characteristic curve of prediction model was 0.769 (95% confidence interval 0.732–0.803, P < 0.001; sensitivity = 55%, specificity = 94%). Severe hypotension during liver transplantation is concealed by proactive vasopressor treatment thus traditional measures of hypotension generally fail to detect the masked hypotension in retrospective analysis. PM analysis of intraoperative SAP including prereperfusion MDAPE and postreperfusion wobble is most likely to detect treated and therefore concealed hypotension, and was able to independently and quantitatively predict in-hospital mortality after liver transplantation with high diagnostic specificity.
Selection of reference genes for expression analysis using RT-qPCR in the dissemination system of Heliothis virescens ascovirus 3 h (HvAV-3h)
Authors: Chen Zi-Shu , Han Ning-Ning , Li Jian-Hong , Huang Guo-Hua , Wan Hu 
Published: July 2017

AbstractAscoviruses are double-stranded DNA viruses that mainly infect noctuid larvae, and are transmitted by the parasitoid wasp Microplitis similis Lyle. Ascovirus-parasitoids wasp-noctuid insects constitute the dissemination system. Selection of suitable reference genes for the dissemination system could play an important role in elucidating the pathogenic molecular mechanisms of ascovirus. Unfortunately, such studies on potential reference genes in the dissemination system of ascoviruses are lacking. In the present study, we evaluated 11 candidate reference genes: β-actin1 (ACT1), β-actin2 (ACT2), elongation factor 1 (EF1), elongation factor 2 (EF2), ribosomal protein L10 (L10), ribosomal protein L17A (L17A), superoxide dismutase (SOD), 28S ribosome (28S), Tubulin (TUB) and 18S ribosome (18S). The samples were originally from various virus concentrations and points-in-time of experimental treatments using RefFinder and four algorithms. The results showed that EF1 was the most stable internal gene in S. exigua and M. similis and that EF2 was the most stable in the IOZCAS-Spex-II-A cell line, and the stability of reference genes were confirmed via the expression levels of two inhibitor of apoptosis-like (iap-like) genes from Heliothis virescens ascovirus 3 h (HvAV-3h). This study provides a crucial basis for future research that explores the molecular mechanisms of the pathogenesis of ascoviruses.
Quantifying Crustal Thickness in Continental Collisional Belts: Global Perspective and a Geologic Application
Authors: Hu Fangyang , Ducea Mihai N. , Liu Shuwen , Chapman James B. 
Published: July 2017

AbstractWe present compiled geochemical data of young (mostly Pliocene-present) intermediate magmatic rocks from continental collisional belts and correlations between their whole-rock Sr/Y and La/Yb ratios and modern crustal thickness. These correlations, which are similar to those obtained from subduction-related magmatic arcs, confirm that geochemistry can be used to track changes of crustal thickness changes in ancient collisional belts. Using these results, we investigate temporal variations of crustal thickness in the Qinling Orogenic Belt in mainland China. Our results suggest that crustal thickness remained constant in the North Qinling Belt (~45–55 km) during the Triassic to Jurassic but fluctuates in the South Qinling Belt, corresponding to independently determined tectonic changes. In the South Qinling Belt, crustal thickening began at ~240 Ma and culminated with 60–70-km-thick crust at ~215 Ma. Then crustal thickness decreased to ~45 km at ~200 Ma and remained the same to the present. We propose that coupled use of Sr/Y and La/Yb is a feasible method for reconstructing crustal thickness through time in continental collisional belts. The combination of the empirical relationship in this study with that from subduction-related arcs can provide the crustal thickness evolution of an orogen from oceanic subduction to continental collision.