bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interfacial pH of acidic degradable polymeric biomaterials and its effects on osteoblast behavior
Authors: Ruan Changshun , Hu Nan , Ma Yufei , Li Yuxiao , Liu Juan , Zhang Xinzhou , Pan Haobo 
Published: July 2017

AbstractA weak alkaline environment is established to facilitate the growth of osteoblasts. Unfortunately, this is inconsistent with the application of biodegradable polymer in bone regeneration, as the degradation products are usually acidic. In this study, the variation of the interfacial pH of poly (D, L-lactide) and piperazine-based polyurethane ureas (P-PUUs), as the representations of acidic degradable materials, and the behavior of osteoblasts on these substrates with tunable interfacial pH were investigated in vitro. These results revealed that the release of degraded products caused a rapid decrease in the interfacial pH, and this could be relieved by the introduction of alkaline segments. On the contrary, when culturing with osteoblasts, the variation of the interfacial pH revealed an upward tendency, indicating that cell could construct the microenvironment by secreting cellular metabolites to satisfy its own survival. In addition, the behavior of osteoblasts on substrates exhibited that P-PUUs with the most PP units were better for cell growth and osteogenic differentiation of cells. This is due to the hydrophilic surface and the moderate N% in P-PUUs, key factors in the promotion of the early stages of cellular responses, and the interfacial pH contributing to the enhanced effect on osteogenic differentiation.
The Predictive Value of Genetic Analyses in the Diagnosis of Tetrahydrobiopterin (BH4)-Responsiveness in Chinese Phenylalanine Hydroxylase Deficiency Patients
Authors: Zhu Tianwen , Ye Jun , Han Lianshu , Qiu Wenjuan , Zhang Huiwen , Liang Lili , Gu Xuefan 
Published: July 2017

AbstractMolecular characterization of PAH deficiency has been proven essential in establishing treatment options. We examine the diagnostic accuracy of two genetic assays to predict BH4 responsiveness: to determine whether the AV sum test or mutation-status assessment test can obviate the need for BH4 loading in Chinese patients. The overall predicted response in 346 patients was 31.65% by the AV sum test and 25.43% by the other assay; both percentages were lower than 51.06% derived from loading results in 94 patients. Responders were compound heterozygotes with definite BH4 responsive mutations, while non-responders had null/null ones; some consistently with specific mutations and genotypes. The sensitivity and specificity of the assays were 81.1% and 92.5% for the AV sum, and 82.9%, 97.3% for the other. An AV sum cutoff >2 has a positive predictive value (PPV) of 90.9%, while the presence of at least one BH4 responsive mutation has a PPV of 97.1%. The two approaches showed good concordance. Our data confirmed that the mutation-status assessment has a higher diagnostic accuracy in predicting response for Chinese patients than the AV sum test. BH4-responsiveness may be predicted or excluded from patients’ molecular characteristics to some extent, thus some patients may avoid the initial loading.
Probing microtubules polarity in mitotic spindles in situ using Interferometric Second Harmonic Generation Microscopy
Authors: Bancelin S. , Couture C.-A. , Pinsard M. , Rivard M. , Drapeau P. , Légaré F. 
Published: July 2017

AbstractThe polarity of microtubules is thought to be involved in spindle assembly, cytokinesis or active molecular transport. However, its exact role remains poorly understood, mainly because of the challenge to measure microtubule polarity in intact cells. We report here the use of fast Interferometric Second Harmonic Generation microscopy to study the polarity of microtubules forming the mitotic spindles in a zebrafish embryo. This technique provides a powerful tool to study mitotic spindle formation and may be directly transferable for investigating the kinetics and function of microtubule polarity in other aspects of subcellular motility or in native tissues.
Mass spectrometry-based determination of Kallikrein-related peptidase 7 (KLK7) cleavage preferences and subsite dependency
Authors: Silva Lakmali Munasinghage , Stoll Thomas , Kryza Thomas , Stephens Carson Ryan , Hastie Marcus Lachlan , Irving-Rodgers Helen Frances , Dong Ying , Gorman Jeffrey John , Clements Judith Ann 
Published: July 2017

AbstractThe cleavage preferences of Kallikrein-related peptidase 7 (KLK7) have previously been delineated using synthetic peptide libraries of fixed length, or single protein chains and have suggested that KLK7 exerts a chymotryptic-like cleavage preference. Due to the short length of the peptides utilised, only a limited number of subsites have however been assessed. To determine the subsite preferences of KLK7 in a global setting, we used a mass spectrometry (MS)-based in-depth proteomics approach that utilises human proteome-derived peptide libraries of varying length, termed Proteomic Identification of protease Cleavage Sites (PICS). Consistent with previous findings, KLK7 was found to exert chymotryptic-like cleavage preferences. KLK7 subsite preferences were also characterised in the P2-P2′ region, demonstrating a preference for hydrophobic residues in the non-prime and hydrophilic residues in the prime subsites. Interestingly, single catalytic triad mutant KLK7 (mKLK7; S195A) also showed residual catalytic activity (kcat/KM = 7.93 × 102 s−1M−1). Catalytic inactivity of KLK7 was however achieved by additional mutation in this region (D102N). In addition to characterising the cleavage preferences of KLK7, our data thereby also suggests that the use of double catalytic triad mutants should be employed as more appropriate negative controls in future investigations of KLK7, especially when highly sensitive MS-based approaches are employed.
Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM
Authors: Liu Xiaoqing , Tian Jian , Liu Lihui , Zhu Tao , Yu Xiaoxia , Chu Xiaoyu , Yao Bin , Wu Ningfeng , Fan Yunliu 
Published: July 2017

AbstractFluorine is ubiquitous and the most active non-metal element in nature. While many microorganisms have developed fluoride resistance as a result of the widespread and prolonged application of oral hygiene products, the mechanisms used by these organisms to overcome fluoride toxicity are incompletely understood. In this study, a fluoride-resistant strain, Enterobacter cloacae FRM, was identified which could grow well at a fluoride concentration of 4,000 mg/L. According to comparative genomics, transcriptome under fluoride stress, and sequence analyses of two fluoride-resistant fosmid clones, the genomic island GI3 was found to be important for fluoride resistance. The result of quantitative RT-PCR indicated that six genes on GI3, ppaC, uspA, eno, gpmA, crcB, and orf5249, which encode a fluoride transporter, fluoride-inhibited enzymes, and a universal stress protein, reside in an operon and are transcribed into two mRNAs activated by fluoride with a fluoride riboswitch. The results of knockout and complementation experiments indicated that these genes work together to provide high fluoride resistance to E. cloacae FRM. This study clarified the resistance mechanism of this high fluoride-resistant organism and has expanded our understanding of the biological effects of fluoride.
ShadowY: a dark yellow fluorescent protein for FLIM-based FRET measurement
Authors: Murakoshi Hideji , Shibata Akihiro C. E. 
Published: July 2017

AbstractFluorescence lifetime imaging microscopy (FLIM)-based Förster resonance energy transfer (FRET) measurement (FLIM-FRET) is one of the powerful methods for imaging of intracellular protein activities such as protein–protein interactions and conformational changes. Here, using saturation mutagenesis, we developed a dark yellow fluorescent protein named ShadowY that can serve as an acceptor for FLIM-FRET. ShadowY is spectrally similar to the previously reported dark YFP but has a much smaller quantum yield, greater extinction coefficient, and superior folding property. When ShadowY was paired with mEGFP or a Clover mutant (CloverT153M/F223R) and applied to a single-molecule FRET sensor to monitor a light-dependent conformational change of the light-oxygen-voltage domain 2 (LOV2) in HeLa cells, we observed a large FRET signal change with low cell-to-cell variability, allowing for precise measurement of individual cell responses. In addition, an application of ShadowY to a separate-type Ras FRET sensor revealed an EGF-dependent large FRET signal increase. Thus, ShadowY in combination with mEGFP or CloverT153M/F223R is a promising FLIM-FRET acceptor.
Effect of Sodium Treatment on the Performance of Electrostatic Spray Assisted Vapour Deposited Copper-poor Cu(In,Ga)(S,Se)
2
Solar Cells
Authors: Wang Mingqing , Hossain Md. Anower , Choy Kwang-Leong 
Published: July 2017

AbstractIn our work, eco-friendly, non-vacuum and low cost Electrostatic Spray Assisted Vapour Deposition (ESAVD) method has been used to produce Cu(In,Ga)(S,Se)2 (CIGS) solar cells. Copper (Cu) deficient (Cu/In + Ga = 0.76) CIGS films were designed to avoid the rather dangerous KCN treatment step for the removal of conductive minor phases of Cu2S/Cu2Se. A simple sodium (Na) treatment method was used to modify the morphology and electronic properties of the absorber and it clearly improved the solar cell performance. The SEM and XRD results testified a slightly increase of the grain size and (112) crystal orientation in the Na-incorporated CIGS thin films. From the Mott-schottky results, it can be seen that the functions of the Na treatment in our non-vacuum deposited CIGS are mainly used for defect passivation and reduction of charge recombination. Photovoltaic characteristics and j-V curve demonstrated that the dipping of CIGS films in 0.2 M NaCl solution for 20 minutes followed by selenization at 550 °C under selenium vapor resulted in the optimum photovoltaic performance, with jsc, Voc, FF and η of the optimized solar cell of 29.30 mA cm−2, 0.564 V, 65.59% and 10.83%, respectively.
Two dopamine D2-like receptor genes from the silkworm (Bombyx mori) and their evolutionary history in metazoan
Authors: Chen Ping , Chen Peng , Li Tian , Shen Qi , Yan Deng-Feng , Zhang Liang , Chen Xi , Li Yan , Zhao Wei 
Published: July 2017

AbstractDopamine is widely distributed in metazoans and is implicated in many physiological functions. Dopaminergic signaling is mediated through two classes of dopamine receptors, D1-like and D2-like. Phylogeny analysis reveals that, the dopamine receptors probably appeared ahead of the cnidarian divergence, two distinct classes of dopamine receptors likely formed prior to the separation of deuterostomes and protostomes, and INDRs probably split from its ancestor before the emergence of nematodes. Two D2-like genes are closely linked on the same scaffold, and the chromosome region around D2-like gene loci show colinearity among different species within Lepidoptera. These indicate two D2-like and their adjunction genes are likely Lepidoptera-specific orthologs, and occur by gene duplication event taken place after Lepidoptera ancestor split from the common ancestor of Lepidoptera and Diptera. In silkworm, two D2-like genes were expressed in examined tissues, and encoded BmDop2R2 having all the features of D2-like receptors and BmDop2R1 being a truncated variant without the region of N-terminal to TM II. Only dopamine distinctly lowered cAMP levels in BmDop2R2-expressing cells, whereas all tested amines for BmDop2R1 had not markedly effect in pharmacological test. These suggest there is functional difference between the two genes, which are likely resulted from subfunctionalization of gene duplication.
Time trends of esophageal and gastric cancer mortality in China, 1991–2009: an age-period-cohort analysis
Authors: Li Mengmeng , Wan Xia , Wang Yanhong , Sun Yuanyuan , Yang Gonghuan , Wang Li 
Published: July 2017

AbstractEsophageal and gastric cancers share some risk factors. This study aimed to compare the long-term trends in mortality rates of esophageal and gastric cancers in China to provide evidence for cancer prevention and control. Mortality data were derived from 103 continuous points of the Disease Surveillance Points system during 1991–2009, stratified by gender and urban-rural locations. Age-period-cohort models were used to disentangle the time trends of esophageal and gastric cancer mortality. The downward slope of the period effect for esophageal cancer was steeper than that for gastric cancer in rural areas. Cohort effect patterns were similar between esophageal and gastric cancers, with an inverse U-shape peaking around the late 1920s and early 1930s. A second peak, appearing around the 1950s, was weaker than the first but apparent in males, especially for esophageal cancer. The more marked changes in period effect for esophageal cancer in rural areas suggest esophageal cancer screening practices are effective in reducing mortality, and similar programs targeting gastric cancer should be implemented. The similarities of the cohort effects in these two cancers support the implication of nutrition deficiency in early childhood in the development of upper gastrointestinal cancer.
Assessments of iodoindoles and abamectin as inducers of methuosis in pinewood nematode, Bursaphelenchus xylophilus
Authors: Rajasekharan Satish Kumar , Lee Jin-Hyung , Ravichandran Vinothkannan , Lee Jintae 
Published: July 2017

AbstractBursaphelenchus xylophilus is a quarantined migratory endoparasite known to cause severe economic losses in pine forest ecosystems. The study presents the nematicidal effects of halogenated indoles on B. xylophilus and their action mechanisms. 5-Iodoindole and abamectin (positive control) at low concentration (10 µg/mL) presented similar and high nematicidal activities against B. xylophilus. 5-Iodoindole diminished fecundity, reproductive activities, embryonic and juvenile lethality and locomotor behaviors. Molecular interactions of ligands with invertebrate-specific glutamate gated chloride channel receptor reinforced the notion that 5-iodoindole, like abamectin, rigidly binds to the active sites of the receptor. 5-Iodoindole also induced diverse phenotypic deformities in nematodes including abnormal organ disruption/shrinkage and increased vacuolization. These findings suggest the prospective role of vacuoles in nematode death by methuosis. Importantly, 5-iodoindole was nontoxic to two plants, Brassica oleracea and Raphanus raphanistrum. Henceforth, the study warrants the application of iodoindoles in ecological environments to control the devastating pine destruction by B. xylophilus.
A cell-based high-throughput screening assay system for inhibitor compounds of antigen presentation by HLA class II molecule
Authors: Watanabe Nobuo , Suzuki Yusuke , Yonezu Takahisa , Nakagawa Yuki , Shiina Takashi , Hirayama Noriaki , Inokuchi Sadaki , Inoue Shigeaki 
Published: July 2017

AbstractA number of autoimmune diseases are associated with the genotypes of human leukocyte antigen class II (HLA), some of which present peptides derived from self-proteins, resulting in clonal expansion of self-reactive T cells. Therefore, selective inhibition of self-peptide loading onto such disease-associated HLA could ameliorate the diseases. To effectively identify such compounds, in this study, we established, for the first time, a cell- and 96-well microplate-based high-throughput screening system for inhibitors of antigen presentation. A panel of DRB1 genes plus DRA*01:01 gene were expressed in HEK293T cells and in 3T3 cells, and their binding with biotinylated known self-antigen peptides was measured by flow cytometry. HLA-DR1 (DRB1*01:01) and DR15 (DRB1*15:01) showed a high affinity with myelin basic protein peptide (MBP83-98). Therefore, in 96-well plate wells, MBP83-99 was allowed to bind to DR1 or DR15 on 3T3 cells in competition with a test compound, and the HLA-bound peptide was detected by streptavidin-conjugated β-galactosidase, thereby identifying inhibitor compounds for rheumatoid arthritis or multiple sclerosis. Our assay system has a potential for broad applications, including designing peptide vaccines.
Integrated diagnostic network construction reveals a 4-gene panel and 5 cancer hallmarks driving breast cancer heterogeneity
Authors: Dai Xiaofeng , Hua Tongyan , Hong Tingting 
Published: July 2017

AbstractBreast cancer encompasses a group of heterogeneous diseases, each associated with distinct clinical implications. Dozens of molecular biomarkers capable of categorizing tumors into clinically relevant subgroups have been proposed which, though considerably contribute in precision medicine, complicate our understandings toward breast cancer subtyping and its clinical translation. To decipher the networking of markers with diagnostic roles on breast carcinomas, we constructed the diagnostic networks by incorporating 6 publically available gene expression datasets with protein interaction data retrieved from BioGRID on previously identified 1015 genes with breast cancer subtyping roles. The Greedy algorithm and mutual information were used to construct the integrated diagnostic network, resulting in 37 genes enclosing 43 interactions. Four genes, FAM134B, KIF2C, ALCAM, KIF1A, were identified having comparable subtyping efficacies with the initial 1015 genes evaluated by hierarchical clustering and cross validations that deploy support vector machine and k nearest neighbor algorithms. Pathway, Gene Ontology, and proliferation marker enrichment analyses collectively suggest 5 primary cancer hallmarks driving breast cancer differentiation, with those contributing to uncontrolled proliferation being the most prominent. Our results propose a 37-gene integrated diagnostic network implicating 5 cancer hallmarks that drives breast cancer heterogeneity and, in particular, a 4-gene panel with clinical diagnostic translation potential.
Forest understory trees can be segmented accurately within sufficiently dense airborne laser scanning point clouds
Authors: Hamraz Hamid , Contreras Marco A. , Zhang Jun 
Published: July 2017

AbstractAirborne laser scanning (LiDAR) point clouds over large forested areas can be processed to segment individual trees and subsequently extract tree-level information. Existing segmentation procedures typically detect more than 90% of overstory trees, yet they barely detect 60% of understory trees because of the occlusion effect of higher canopy layers. Although understory trees provide limited financial value, they are an essential component of ecosystem functioning by offering habitat for numerous wildlife species and influencing stand development. Here we model the occlusion effect in terms of point density. We estimate the fractions of points representing different canopy layers (one overstory and multiple understory) and also pinpoint the required density for reasonable tree segmentation (where accuracy plateaus). We show that at a density of ~170 pt/m² understory trees can likely be segmented as accurately as overstory trees. Given the advancements of LiDAR sensor technology, point clouds will affordably reach this required density. Using modern computational approaches for big data, the denser point clouds can efficiently be processed to ultimately allow accurate remote quantification of forest resources. The methodology can also be adopted for other similar remote sensing or advanced imaging applications such as geological subsurface modelling or biomedical tissue analysis.
Dual-Function Au@Y2O3:Eu3+ Smart Film for Enhanced Power Conversion Efficiency and Long-Term Stability of Perovskite Solar Cells
Authors: Kim Chang Woo , Eom Tae Young , Yang In Seok , Kim Byung Su , Lee Wan In , Kang Yong Soo , Kang Young Soo 
Published: July 2017

AbstractIn the present study, a dual-functional smart film combining the effects of wavelength conversion and amplification of the converted wave by the localized surface plasmon resonance has been investigated for a perovskite solar cell. This dual-functional film, composed of Au nanoparticles coated on the surface of Y2O3:Eu3+ phosphor (Au@Y2O3:Eu3+) nanoparticle monolayer, enhances the solar energy conversion efficiency to electrical energy and long-term stability of photovoltaic cells. Coupling between the Y2O3:Eu3+ phosphor monolayer and ultraviolet solar light induces the latter to be converted into visible light with a quantum yield above 80%. Concurrently, the Au nanoparticle monolayer on the phosphor nanoparticle monolayer amplifies the converted visible light by up to 170%. This synergy leads to an increased solar light energy conversion efficiency of perovskite solar cells. Simultaneously, the dual-function film suppresses the photodegradation of perovskite by UV light, resulting in long-term stability. Introducing the hybrid smart Au@Y2O3:Eu3+ film in perovskite solar cells increases their overall solar-to-electrical energy conversion efficiency to 16.1% and enhances long-term stability, as compared to the value of 15.2% for standard perovskite solar cells. The synergism between the wavelength conversion effect of the phosphor nanoparticle monolayer and the wave amplification by the localized surface plasmon resonance of the Au nanoparticle monolayer in a perovskite solar cell is comparatively investigated, providing a viable strategy of broadening the solar spectrum utilization.
Influence of aridity and salinity on plant nutrients scales up from species to community level in a desert ecosystem
Authors: Gong Yanming , Lv Guanghui , Guo Zhenjie , Chen Yue , Cao Jing 
Published: July 2017

AbstractSoil moisture and salt play key roles in regulating desert plant nutrient cycles on a local scale. However, information on the response of plant nutrient stoichiometric patterns to soil water and salt gradients is limited. Here, we assessed leaf N and P levels of 18 species of desert plants and measured the corresponding soil nutrient, water and salt concentrations, at four dry sites, five humid-saline sites and four humid-non-saline sites (reference sites) along a transect in a temperate desert in Xinjiang Province, northwest China. Our results indicated that the desert plants had lower N and P concentrations and higher N:P mass ratios in dry and humid-saline sites than in the humid-non-saline sites. Unlike the single-factor effect of salinity driving the plasticity of species N concentration, aridity and salinity interacted in their impact on the plasticity of plant P and the N:P ratio. Moreover, the plant community N and P concentrations and N:P ratio exhibited significant positive linear and nonlinear correlations with soil moisture in shallow and deep soil, respectively. Aridity reduced the N plasticity and increased P plasticity of the plant community. The results strongly supported the hypothesis that soil moisture and salt concentration were the dominant drivers of leaf N and P concentrations and their plasticity across species and community scales.