The multiplex relations between cities: a lexicon-based approach to detect urban systems

Cities relate to other cities in many ways, and much scholarly effort goes into uncovering those relationships. Building on the principle that strongly related cities will co-occur frequently in texts, we propose a novel method to classify those toponym co-occurrences using a lexicon-based text-mining method. Millions of webpages are analysed to retrieve how 293 Chinese cities are related in terms of six types: industry, information technology, finance, research, culture and government. Each class displays different network patterns, and this multiplexity is mapped and analysed. Further refinement of this lexicon-based approach can revolutionize the study of inter-urban relationships.</p

Additional file 4: of Nonlytic exocytosis of Cryptococcus neoformans from neutrophils in the brain vasculature

Movie S1. FITC-labeled C. neoformans H99 were incubated with anti-Gr-1 (pseudocolored red) and anti-F4/80 (pseudocolored blue) prestained neutrophils in a glass-bottomed dish with a precoated monolayer of mouse brain endothelial bEnd.3 cells in the presence of anti-capsule antibody E1. After 1 h of incubation, nonadherent cells were removed. Multichannel time-lapse fluorescence images (oil-immersion objective lens) were captured to record the dynamic process of nonlytic exocytosis of C. neoformans by the neutrophil (marked by an arrow), with one frame captured every 30 s for 3 h or until the occurrence of expulsion. The time-series images were exported as a video at 5 frames per second. Also refer to Fig. 1. (MOV 1612 kb

Insights into the Associations between Optical and Molecular Signatures of Dissolved Organic Matter from Urban Stormwater Runoff

Modern fluorescence techniques are widely employed to determine the dissolved organic matter (DOM) fluorescent components and quality in urban stormwater runoff. However, its molecular basis is still poorly defined, leading to unclear and unspecific interpretations of fluorescence characterization. This research focused on the correlation analysis between optical and molecular signatures of DOM. The optical parameters are effectively correlated with the individual molecules detected by mass spectrometry. Moreover, molecular characterization parameters are also associated with three-dimensional fluorescence spectroscopy in reverse. Through nonmetric multidimensional scaling (NMDS), the fluorescence indices tracing the source of DOM are effectively categorized and verified by molecular characteristics. Meanwhile, Spearman rank correlation analysis indicated that humic-like components derived from microbial- and tryptophan-like compositions are associated with aromaticity; however, terrestrial humic-like constituents are closely correlated with H/C, O/C, and N/C ratios. In addition, the molecular mechanism of four fluorescent components indicated that the nitrogen (N)-containing components, reduced constituents, and aliphatic compounds are resistant to degradation, while the oxidized and aromatic components are preferentially removed. Those signatures observed for individual molecules are consistent with the bulk characteristics of DOM, as reflected by optical properties

Cascade Signal Amplification Based on Copper Nanoparticle-Reported Rolling Circle Amplification for Ultrasensitive Electrochemical Detection of the Prostate Cancer Biomarker

An ultrasensitive and highly selective electrochemical assay was first attempted by combining the rolling circle amplification (RCA) reaction with poly­(thymine)-templated copper nanoparticles (CuNPs) for cascade signal amplification. As proof of concept, prostate specific antigen (PSA) was selected as a model target. Using a gold nanoparticle (AuNP) as a carrier, we synthesized the primer–AuNP–aptamer bioconjugate for signal amplification by increasing the primer/aptamer ratio. The specific construction of primer–AuNP–aptamer/PSA/anti-PSA sandwich structure triggered the effective RCA reaction, in which thousands of tandem poly­(thymine) repeats were generated and directly served as the specific templates for the subsequent CuNP formation. The signal readout was easily achieved by dissolving the RCA product-templated CuNPs and detecting the released copper ions with differential pulse stripping voltammetry. Because of the designed cascade signal amplification strategy, the newly developed method achieved a linear range of 0.05–500 fg/mL, with a remarkable detection limit of 0.020 ± 0.001 fg/mL PSA. Finally, the feasibility of the developed method for practical application was investigated by analyzing PSA in the real clinical human serum samples. The ultrasensitivity, specificity, convenience, and capability for analyzing the clinical samples demonstrate that this method has great potential for practical disease diagnosis applications

Additional file 3: of Nonlytic exocytosis of Cryptococcus neoformans from neutrophils in the brain vasculature

Figure S2. Chloroquine increased the fungicidal activity of neutrophils against C. neoformans. In a 96-well plate, C. neoformans (5 × 103 cells per well) were incubated alone or with neutrophils (1 × 105 cells per well) and chloroquine (10 μM, working concentration) for 4 h. After incubation, the live fungi were quantified on YPA agar. *, p < 0.05. (TIF 235 kb

Table_1_A Moss 2-Oxoglutarate/Fe(II)-Dependent Dioxygenases (2-ODD) Gene of Flavonoids Biosynthesis Positively Regulates Plants Abiotic Stress Tolerance.DOCX

Flavonoids, the largest group of polyphenolic secondary metabolites present in all land plants, play essential roles in many biological processes and defense against abiotic stresses. In the flavonoid biosynthesis pathway, flavones synthase I (FNSI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS) all belong to 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs) family, which catalyzes the critical oxidative reactions to form different flavonoid subgroups. Here, a novel 2-ODD gene was cloned from Antarctic moss Pohlia nutans (Pn2-ODD1) and its functions were investigated both in two model plants, Physcomitrella patens and Arabidopsis thaliana. Heterologous expression of Pn2-ODD1 increased the accumulation of anthocyanins and flavonol in Arabidopsis. Meanwhile, the transgenic P. patens and Arabidopsis with expressing Pn2-ODD1 exhibited enhanced tolerance to salinity and drought stresses, with larger gametophyte sizes, better seed germination, and longer root growth. Heterologous expression of Pn2-ODD1 in Arabidopsis also conferred the tolerance to UV-B radiation and oxidative stress by increasing antioxidant capacity. Therefore, we showed that Pn2-ODD1 participated in the accumulation of anthocyanins and flavonol in transgenic plants, and regulated the tolerance to abiotic stresses in plants, contributing to the adaptation of P. nutans to the polar environment.</p

Additional file 1: of Nonlytic exocytosis of Cryptococcus neoformans from neutrophils in the brain vasculature

Table S1. Antibodies in the study. (DOCX 14 kb

Additional file 6: of Nonlytic exocytosis of Cryptococcus neoformans from neutrophils in the brain vasculature

Movie S3. A 3D movie reconstructed from z-stack images of immunofluorescence stained cells showing the nonlytic exocytosis of C. neoformans from neutrophils in the brain vasculature. Also refer to Fig. 4. (MOV 2676 kb

Additional file 5: of Nonlytic exocytosis of Cryptococcus neoformans from neutrophils in the brain vasculature

Movie S2. A 3D reconstruction from z-stack images taken at the end of the image acquisition period (81 min after the microscopy observation began) showing the “empty” neutrophil (pseudocolored red) and the two expelled fungal cells (pseudocolored green) beside the neutrophil. Also refer to Fig. 1. (MOV 8570 kb

Image_1_A Moss 2-Oxoglutarate/Fe(II)-Dependent Dioxygenases (2-ODD) Gene of Flavonoids Biosynthesis Positively Regulates Plants Abiotic Stress Tolerance.tif

Flavonoids, the largest group of polyphenolic secondary metabolites present in all land plants, play essential roles in many biological processes and defense against abiotic stresses. In the flavonoid biosynthesis pathway, flavones synthase I (FNSI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS) all belong to 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs) family, which catalyzes the critical oxidative reactions to form different flavonoid subgroups. Here, a novel 2-ODD gene was cloned from Antarctic moss Pohlia nutans (Pn2-ODD1) and its functions were investigated both in two model plants, Physcomitrella patens and Arabidopsis thaliana. Heterologous expression of Pn2-ODD1 increased the accumulation of anthocyanins and flavonol in Arabidopsis. Meanwhile, the transgenic P. patens and Arabidopsis with expressing Pn2-ODD1 exhibited enhanced tolerance to salinity and drought stresses, with larger gametophyte sizes, better seed germination, and longer root growth. Heterologous expression of Pn2-ODD1 in Arabidopsis also conferred the tolerance to UV-B radiation and oxidative stress by increasing antioxidant capacity. Therefore, we showed that Pn2-ODD1 participated in the accumulation of anthocyanins and flavonol in transgenic plants, and regulated the tolerance to abiotic stresses in plants, contributing to the adaptation of P. nutans to the polar environment.</p