bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designed synthesis of a “One for Two” hydrophilic magnetic amino-functionalized metal-organic framework for highly efficient enrichment of glycopeptides and phosphopeptides
Authors: Xie Yiqin , Deng Chunhui 
Published: April 2017

AbstractHighly efficient enrichment of glycopeptides or phosphopeptides from complex biological samples is indispensable for high-throughput mass spectrometry analysis. In this study, for the first time, a “one for two” hydrophilic magnetic amino-functionalized metal-organic framework (MOF) was designed and synthesized for selective enrichment of both glycopeptides and phosphopeptides. A well-known solvo-thermal reaction was adopted to prepare a magnetic core Fe3O4, followed by self- polymerization of dopamine, creating a polydopamine (PDA) onto Fe3O4. Thanks to the hydroxyl and amino group of PDA, Zr3+ was easily adhered to the surface, inducing the following one-pot MOF reaction with amino ligand. After characterization of the as-prepared MOFs (denoted as Fe3O4@PDA@UiO-66-NH2), its ultrahigh surface area, excellent hydrophilicity and strong magnetic responsiveness were highly confirmed. Based on hydrophilic interaction, it was applied to glycopeptide enrichment, while based on strong binding between Zr and phosphopeptides, it was applied to phosphopeptide enrichment, both exhibiting excellent performance in standard proteins and human serum with high sensitivity and selectivity. These results showed the as-prepared MOFs had great potential in proteomics research.
The MAPKKK and MAPKK gene families in banana: identification, phylogeny and expression during development, ripening and abiotic stress
Authors: Wang Lianzhe , Hu Wei , Tie Weiwei , Ding Zehong , Ding Xupo , Liu Yang , Yan Yan , Wu Chunlai , Peng Ming , Xu Biyu , Jin Zhiqiang 
Published: April 2017

AbstractThe mitogen-activated protein kinase (MAPK) cascade, which is a major signal transduction pathway widely distributed in eukaryotes, has an important function in plant development and stress responses. However, less information is known regarding the MAPKKK and MAPKK gene families in the important fruit crop banana. In this study, 10 MAPKK and 77 MAPKKK genes were identified in the banana genome, and were classified into 4 and 3 subfamilies respectively based on phylogenetic analysis. Majority of MAPKKK and MAPKK genes in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis indicated that MAPKKK-MAPKK genes is involved in tissue development, fruit development and ripening, and response to abiotic stress of drought, cold and salt in two banana genotypes. Interaction networks and co-expression assays demonstrated that MAPK signaling cascade mediated network participates in multiple stress signaling, which was strongly activated in Fen Jiao (FJ). The findings of this study advance understanding of the intricately transcriptional control of MAPKKK-MAPKK genes and provide robust candidate genes for further genetic improvement of banana.
Surgical treatment in Paget’s disease with invasive ductal carcinoma: an observational study based on SEER
Authors: Wu Qi , Ding Xiaojun , Li Juanjuan , Sun Si , Zhu Shan , Wu Juan , Liu Qian , Yao Feng , Sun Shengrong 
Published: April 2017

AbstractThe aim is to analyse the clinical presentation, treatment and outcomes in patients with Paget’s disease with invasive ductal carcinoma (PD-IDC), with special emphasis on the role of surgical treatment. Using data obtained by the Surveillance, Epidemiology, and End Results (SEER) program from 2010–2013, we investigated the differences in characteristics, overall survival (OS), and breast cancer-specific mortality (BCSM) between patients with PD-IDC and those with invasive ductal carcinoma (IDC). Compared with IDC group, patients with PD-IDC had a better prognosis and lower mortality in adjusted analyses. In the multivariate analysis of cases with PD-IDC, history of ALND was significantly associated with OS while Her2 status were associated with BCSM. Further, subgroup analysis demonstrated no difference between surgical treatment subgroups for either OS or BCSM. The results demonstrated that PD-IDC appears to alter the association between prognosis and Her2 status. Meanwhile, breast-conserving surgery with radiotherapy may be a feasible treatment alternative and sentinel lymph node biopsy should be considered as an appropriate treatment for patients with PD-IDC.
Clustering by fast search and merge of local density peaks for gene expression microarray data
Authors: Mehmood Rashid , El-Ashram Saeed , Bie Rongfang , Dawood Hussain , Kos Anton 
Published: April 2017

AbstractClustering is an unsupervised approach to classify elements based on their similarity, and it is used to find the intrinsic patterns of data. There are enormous applications of clustering in bioinformatics, pattern recognition, and astronomy. This paper presents a clustering approach based on the idea that density wise single or multiple connected regions make a cluster, in which density maxima point represents the center of the corresponding density region. More precisely, our approach firstly finds the local density regions and subsequently merges the density connected regions to form the meaningful clusters. This idea empowers the clustering procedure, in which outliers are automatically detected, higher dense regions are intuitively determined and merged to form clusters of arbitrary shape, and clusters are identified regardless the dimensionality of space in which they are embedded. Extensive experiments are performed on several complex data sets to analyze and compare our approach with the state-of-the-art clustering methods. In addition, we benchmarked the algorithm on gene expression microarray data sets for cancer subtyping; to distinguish normal tissues from tumor; and to classify multiple tissue data sets.
The relationship between climate change and the endangered rainforest shrub Triunia robusta (Proteaceae) endemic to southeast Queensland, Australia
Authors: Shimizu-Kimura Yoko , Accad Arnon , Shapcott Alison 
Published: April 2017

AbstractThreatened species in rainforests may be vulnerable to climate change, because of their potentially narrow thermal tolerances, small population sizes and restricted distributions. This study modelled climate induced changes on the habitat distribution of the endangered rainforest plant Triunia robusta, endemic to southeast Queensland, Australia. Species distribution models were developed for eastern Australia at 250 m grids and southeast Queensland at 25 m grids using ground-truthed presence records and environmental predictor data. The species’ habitat distribution under the current climate was modelled, and the future potential habitat distributions were projected for the epochs 2030, 2050 and 2070. The eastern Australia model identified several spatially disjunct, broad habitat areas of coastal eastern Australia consistent with the current distribution of rainforests, and projected a southward and upslope contraction driven mainly by average temperatures exceeding current range limits. The southeast Queensland models suggest a dramatic upslope contraction toward locations where the majority of known populations are found. Populations located in the Sunshine Coast hinterland, consistent with past rainforest refugia, are likely to persist long-term. Upgrading the level of protection for less formal nature reserves containing viable populations is a high priority to better protect refugial T. robusta populations with respect to climate change.
Effective in vivo therapeutic IgG antibody against VP3 of enterovirus 71 with receptor-competing activity
Authors: Jia Qiang , Ng Qingyong , Chin Wenjie , Meng Tao , Chow Vincent Tak Kwong , Wang Cheng-I , Kwang Jimmy , He Fang 
Published: April 2017

AbstractPassive immunization is an effective option for treatment against hand, foot and mouth disease caused by EV71, especially with cross-neutralizing IgG monoclonal antibodies. In this study, an EV71-specific IgG2a antibody designated 5H7 was identified and characterized. 5H7 efficiently neutralizes the major EV71 genogroups (A, B4, C2, C4). The conformational epitope of 5H7 was mapped to the highly conserved amino acid position 74 on VP3 capsid protein using escape mutants. Neutralization with 5H7 is mediated by the inhibition of viral attachment, as revealed by virus-binding and post-attachment assays. In a competitive pull-down assay with SCARB2, 5H7 blocks the receptor-binding site on EV71 for virus neutralization. Passive immunization of chimeric 5H7 protected 100% of two-week-old AG129 mice from lethal challenge with an EV71 B4 strain for both prophylactic and therapeutic treatments. In contrast, 10D3, a previously reported neutralizing antibody that takes effect after virus attachment, could only confer prophylactic protection. These results indicate that efficient interruption of viral attachment is critical for effective therapeutic activity with 5H7. This report documents a novel universal neutralizing IgG antibody for EV71 therapeutics and reveals the underlying mechanism.
Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis
Authors: Ju Ming , Zhou Zijian , Mu Cong , Zhang Xuecai , Gao Jingyang , Liang Yakun , Chen Jiafa , Wu Yabin , Li Xiaopeng , Wang Shiwei , Wen Jingjing , Yang Luming , Wu Jianyu 
Published: April 2017

AbstractFusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.
Monitoring seasonal influenza epidemics by using internet search data with an ensemble penalized regression model
Authors: Guo Pi , Zhang Jianjun , Wang Li , Yang Shaoyi , Luo Ganfeng , Deng Changyu , Wen Ye , Zhang Qingying 
Published: April 2017

AbstractSeasonal influenza epidemics cause serious public health problems in China. Search queries-based surveillance was recently proposed to complement traditional monitoring approaches of influenza epidemics. However, developing robust techniques of search query selection and enhancing predictability for influenza epidemics remains a challenge. This study aimed to develop a novel ensemble framework to improve penalized regression models for detecting influenza epidemics by using Baidu search engine query data from China. The ensemble framework applied a combination of bootstrap aggregating (bagging) and rank aggregation method to optimize penalized regression models. Different algorithms including lasso, ridge, elastic net and the algorithms in the proposed ensemble framework were compared by using Baidu search engine queries. Most of the selected search terms captured the peaks and troughs of the time series curves of influenza cases. The predictability of the conventional penalized regression models were improved by the proposed ensemble framework. The elastic net regression model outperformed the compared models, with the minimum prediction errors. We established a Baidu search engine queries-based surveillance model for monitoring influenza epidemics, and the proposed model provides a useful tool to support the public health response to influenza and other infectious diseases.
Isothiocyanates induce UGT1A1 in humanized UGT1 mice in a CAR dependent fashion that is highly dependent upon oxidative stress
Authors: Yoda Emiko , Paszek Miles , Konopnicki Camille , Fujiwara Ryoichi , Chen Shujuan , Tukey Robert H. 
Published: April 2017

AbstractIsothiocyanates, such as phenethyl isothiocyanate (PEITC), are formed following the consumption of cruciferous vegetables and generate reactive oxygen species (ROS) that lead to the induction of cytoprotective genes such as the UDP-glucuronosyltransferases (UGTs). The induction of ROS activates the Nrf2-Keap 1 pathway leading to the induction of genes through antioxidant response elements (AREs). UGT1A1, the sole enzyme responsible for the metabolism of bilirubin, can be induced following activation of Nrf2. When neonatal humanized UGT1 (hUGT1) mice, which exhibit severe levels of total serum bilirubin (TSB) because of a developmental delay in expression of the UGT1A1 gene, were treated with PEITC, TSB levels were reduced. Liver and intestinal UGT1A1 were induced, along with murine CYP2B10, a consensus CAR target gene. In both neonatal and adult hUGT1/Car−/− mice, PEITC was unable to induce CYP2B10. A similar result was observed following analysis of UGT1A1 expression in liver. However, TSB levels were still reduced in hUGT1/Car−/− neonatal mice because of ROS induction of intestinal UGT1A1. When oxidative stress was blocked by exposing mice to N-acetylcysteine, induction of liver UGT1A1 and CYP2B10 by PEITC was prevented. Thus, new findings in this report link an important role in CAR activation that is dependent upon oxidative stress.
Antioxidant synergistic effects of Osmanthus fragrans flowers with green tea and their major contributed antioxidant compounds
Authors: Mao Shuqin , Wang Kaidi , Lei Yukun , Yao Shuting , Lu Baiyi , Huang Weisu 
Published: April 2017

AbstractThe antioxidant synergistic effects of Osmanthus fragrans flowers with green tea were evaluated, and their major antioxidant compounds contributed to the total amount of synergy were determined. The antioxidant compounds in O. fragrans flowers with green tea were identified by LC-MS and quantified by UPLC-PDA. The synergistic antioxidant interactions between O. fragrans flowers with green tea and their antioxidant compounds were tested using the Prieto’s model after the simulated digestion. The main antioxidant compounds in O. fragrans flowers were acteoside and salideroside, whereas the main antioxidant compounds in green tea were caffeine, gallic acid, and L-epicatechin. The significant synergistic effect between O. fragrans flowers and green tea was observed and among nearly all of the combinations of their antioxidant compounds. Among the combinations, acteoside and gallic acid contributed most to the antioxidant synergy between O. fragrans flowers and green tea. However, the simulated digestion decreased this antioxidant synergy because it reduced the contents and the antioxidant capacities of their compounds, as well as the antioxidant synergy among the compounds.
In vitro biocompatibility study of sub-5 nm silica-coated magnetic iron oxide fluorescent nanoparticles for potential biomedical application
Authors: Foglia Sabrina , Ledda Mario , Fioretti Daniela , Iucci Giovanna , Papi Massimiliano , Capellini Giovanni , Lolli Maria Grazia , Grimaldi Settimio , Rinaldi Monica , Lisi Antonella 
Published: April 2017

AbstractMagnetic iron oxide nanoparticles (IONPs), for their intriguing properties, have attracted a great interest as they can be employed in many different biomedical applications. In this multidisciplinary study, we synthetized and characterized ultrafine 3 nm superparamagnetic water-dispersible nanoparticles. By a facile and inexpensive one-pot approach, nanoparticles were coated with a shell of silica and contemporarily functionalized with fluorescein isothiocyanate (FITC) dye. The obtained sub-5 nm silica-coated magnetic iron oxide fluorescent (sub-5 SIO-Fl) nanoparticles were assayed for cellular uptake, biocompatibility and cytotoxicity in a human colon cancer cellular model. By confocal microscopy analysis we demonstrated that nanoparticles as-synthesized are internalized and do not interfere with the CaCo-2 cell cytoskeletal organization nor with their cellular adhesion. We assessed that they do not exhibit cytotoxicity, providing evidence that they do not affect shape, proliferation, cellular viability, cell cycle distribution and progression. We further demonstrated at molecular level that these nanoparticles do not interfere with the expression of key differentiation markers and do not affect pro-inflammatory cytokines response in Caco-2 cells. Overall, these results showed thein vitrobiocompatibility of the sub-5 SIO-Fl nanoparticles promising their safe employ for diagnostic and therapeutic biomedical applications.
Spastic paraplegia-linked phospholipase PAPLA1 is necessary for development, reproduction, and energy metabolism in Drosophila
Authors: Gáliková Martina , Klepsatel Peter , Münch Judith , Kühnlein Ronald P. 
Published: April 2017

AbstractThe human PAPLA1 phospholipase family is associated with hereditary spastic paraplegia (HSP), a neurodegenerative syndrome characterized by progressive spasticity and weakness of the lower limbs. Taking advantage of a new Drosophila PAPLA1 mutant, we describe here novel functions of this phospholipase family in fly development, reproduction, and energy metabolism. Loss of Drosophila PAPLA1 reduces egg hatchability, pre-adult viability, developmental speed, and impairs reproductive functions of both males and females. In addition, our work describes novel metabolic roles of PAPLA1, manifested as decreased food intake, lower energy expenditure, and reduced ATP levels of the mutants. Moreover, PAPLA1 has an important role in the glycogen metabolism, being required for expression of several regulators of carbohydrate metabolism and for glycogen storage. In contrast, global loss of PAPLA1 does not affect fat reserves in adult flies. Interestingly, several of the PAPLA1 phenotypes in fly are reminiscent of symptoms described in some HSP patients, suggesting evolutionary conserved functions of PAPLA1 family in the affected processes. Altogether, this work reveals novel physiological functions of PAPLA1, which are likely evolutionary conserved from flies to humans.
G protein-coupled KISS1 receptor is overexpressed in triple negative breast cancer and promotes drug resistance
Authors: Blake Alexandra , Dragan Magdalena , Tirona Rommel G. , Hardy Daniel B. , Brackstone Muriel , Tuck Alan B. , Babwah Andy V. , Bhattacharya Moshmi 
Published: April 2017

AbstractTriple-negative breast cancer (TNBC) lacks the expression of estrogen receptor α, progesterone receptor and human epidermal growth factor receptor 2 (HER2). TNBC patients lack targeted therapies, as they fail to respond to endocrine and anti-HER2 therapy. Prognosis for this aggressive cancer subtype is poor and survival is limited due to the development of resistance to available chemotherapies and resultant metastases. The mechanisms regulating tumor resistance are poorly understood. Here we demonstrate that the G protein-coupled kisspeptin receptor (KISS1R) promotes drug resistance in TNBC cells. KISS1R binds kisspeptins, peptide products of the KISS1 gene and in numerous cancers, this signaling pathway plays anti-metastatic roles. However, in TNBC, KISS1R promotes tumor invasion. We show that KISS1 and KISS1R mRNA and KISS1R protein are upregulated in TNBC tumors, compared to normal breast tissue. KISS1R signaling promotes drug resistance by increasing the expression of efflux drug transporter, breast cancer resistance protein (BCRP) and by inducing the activity and transcription of the receptor tyrosine kinase, AXL. BCRP and AXL transcripts are elevated in TNBC tumors, compared to normal breast, and TNBC tumors expressing KISS1R also express AXL and BCRP. Thus, KISS1R represents a potentially novel therapeutic target to restore drug sensitivity in TNBC patients.
A study of the effects of synthesis conditions on Li5FeO4/carbon nanotube composites
Authors: Lee Suk-Woo , Kim Hyun-Kyung , Kim Myeong-Seong , Roh Kwang Chul , Kim Kwang-Bum 
Published: April 2017

AbstractLi5FeO4/carbon nanotube (LFO/CNT) composites composed of sub-micron sized LFO and a nanocarbon with high electrical conductivity were successfully synthesized for the use as lithium ion predoping source in lithium ion cells. The phase of LFO in the composite was found to be very sensitive to the synthesis conditions, such as the heat treatment temperature, type of lithium salt, and physical state of the precursors (powder or pellet), due to the carbothermic reduction of Fe3O4 by CNTs during high temperature solid state reaction. Under optimized synthesis conditions, LFO/CNT composites could be synthesized without the formation of impurities. To the best of our knowledge, this is the first report on the synthesis and characterization of a sub-micron sized LFO/CNT composites.
High expression of matrix metalloproteinases 16 is associated with the aggressive malignant behavior and poor survival outcome in colorectal carcinoma
Authors: Wu Shengwen , Ma Congchao , Shan Shaoyin , Zhou Lei , Li Wenhui 
Published: April 2017

AbstractRecent evidence suggested an important role of matrix metalloproteinases 16 (MMP16) in the progression of several cancers. However, the contribution of MMP16 to colorectal cancer (CRC) remains elusive. In this study, we combined analyzed the MMP16 expression in The Cancer Genome Atlas (TCGA), GSE39582 database and in-house database. In TCGA and GSE39584 database, the log-rank test demonstrated that overall survival (OS) for patients with low MMP16 expression in tumor tissues was significantly higher than those with high expression (P < 0.05). In the validation cohort, high MMP16 expression was significantly correlated with N stage (P = 0.008) and lymphovascular invasion (P = 0.002). The 5-year OS and disease free survival (DFS) in high and low MMP16 expression groups were 66.0% and 80.6%, 54.3% and 72.8%, respectively. Univariate and multivariate analysis showed that high MMP16 expression was an independently prognosis factor for both OS and DFS (P < 0.05). Functional study found that silencing MMP16 expression could inhibit migration and invasion of colon cancer cells. In conclusion, high expression of MMP16 is associated with the aggressive malignant behavior and poor survival outcome of CRC patients. MMP16 can serve as an indicator of prognosis as well as a potential novel target for treatment of CRC patients.