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Huihui Han, Hengfeng Miao, Yajing Zhang, Minfeng Lu, Zhenxing Huang, Wenquan Ruan
Disinfection byproduct (DBP) precursors in wastewater during the reversed anaerobic-anoxic-oxic (A2 /O) process, as well as their molecular weight (MW) and polarity-based fractions, were characterized with UV scanning, fluorescence excitation emission matrix, Fourier transform infrared and nuclear magnetic resonance spectroscopy. Their DBP formation potentials (DBPFPs) after chlorination were further tested. Results indicated that the reversed A2 /O process could not only effectively remove the dissolved organic carbon (DOC) and dissolved total nitrogen in the wastewater, but also affect the MW distribution and hydrophilic-hydrophobic properties of dissolved organic matter (DOM)...
March 2018: Journal of Environmental Sciences (China)
Quang Viet Ly, Jin Hur
This study assessed the relative contributions of different constitutes in dissolved organic matter (DOM) with two different sources (i.e., urban river and effluent) to membrane fouling on three types of ultrafiltration (UF) membranes via excitation emission matrix - parallel factor analysis (EEM-PARAFAC), size exclusion chromatography (SEC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Two polyethersulfone membranes with different pore sizes and one regenerated cellulose membrane were used as representative hydrophobic (HPO) and hydrophilic (HPI) UF membranes, respectively...
March 1, 2018: Chemosphere
Johanna C Herkert, Kristin M Abbott, Erwin Birnie, Martine T Meems-Veldhuis, Ludolf G Boven, Marloes Benjamins, Gideon J du Marchie Sarvaas, Daniela Q C M Barge-Schaapveld, J Peter van Tintelen, Paul A van der Zwaag, Yvonne J Vos, Richard J Sinke, Maarten P van den Berg, Irene M van Langen, Jan D H Jongbloed
PurposeWe evaluated the diagnostic yield in pediatric dilated cardiomyopathy (DCM) of combining exome sequencing (ES)-based targeted analysis and genome-wide copy-number variation (CNV) analysis. Based on our findings, we retrospectively designed an effective approach for genetic testing in pediatric DCM.MethodsWe identified 95 patients (in 85 families) with pediatric onset of DCM. We initially excluded 13 of these families because they already had a genetic diagnosis, leaving a total of 31 probands for single-nucleotide polymorphism (SNP) array and trio-ES...
March 8, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Yu-Chiuan Chang, Jhen-Wei Wu, Yi-Chi Hsieh, Tzu-Han Huang, Zih-Min Liao, Yi-Shan Huang, James A Mondo, Denise Montell, Anna C-C Jang
In collective cell migration, directional protrusions orient cells in response to external cues, which requires coordinated polarity among the migrating cohort. However, the molecular mechanism has not been well defined. Drosophila border cells (BCs) migrate collectively and invade via the confined space between nurse cells, offering an in vivo model to examine how group polarity is organized. Here, we show that the front/back polarity of BCs requires Rap1, hyperactivation of which disrupts cluster polarity and induces misoriented protrusions and loss of asymmetry in the actin network...
February 20, 2018: Cell Reports
Ju-Won Jang, Min-Kyu Kim, Suk-Chul Bae
Yes-associated protein 1 (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) (YAP/TAZ) are transcriptional coactivators that regulate genes involved in proliferation and transformation by interacting with DNA-binding transcription factors. Remarkably, YAP/TAZ are essential for cancer initiation or growth of most solid tumors. Their activation induces cancer stem cell attributes, proliferation, and metastasis. The oncogenic activity of YAP/TAZ is inhibited by the Hippo cascade, an evolutionarily conserved pathway that is governed by two kinases, mammalian Ste20-like kinases 1/2 (MST1/2) and Large tumor suppressor kinase 1/2 (LATS1/2), corresponding to Drosophila's Hippo (Hpo) and Warts (Wts), respectively...
February 18, 2018: Small GTPases
Ajay Anand Kumar, Lut Van Laer, Maaike Alaerts, Amin Ardeshirdavani, Yves Moreau, Kris Laukens, Bart Loeys, Geert Vandeweyer, Inanc Birol
Motivation: Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model.We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations...
February 14, 2018: Bioinformatics
Tae Il Kim, Dong Hyun Lim, Kwang Soo Baek, Sun Sik Jang, Beom Young Park, Vijayakumar Mayakrishnan
The important platform polysaccharide N-acetylglucosamine (GlcNAc) has great potential to be used in the fields of food, cosmetics, agricultural, pharmaceutical, medicine and biotechnology. This GlcNAc is being produced by traditional methods of environment-unfriendly chemical digestion with strong acids. Therefore, researchers have been paying more attention to enzymatic hydrolysis process for the production of GlcNAc. Hence, in this study, we isolated novel chitinase (Escherichia fergusonii) and chitosanase (Chryseobacterium indologenes, Comamonas koreensis) producing strains from Korean native calves feces, and developed the potential of an eco-friendly microbial progression for GlcNAc production from swollen chitin and chitosan by enzymatic degradation...
February 13, 2018: International Journal of Biological Macromolecules
Jae-Myung Jang, Tae-Eon Park, Seung-Dai Kim, Han-Cheol Choe
The modified surface during implantation is considered to be an effective strategy to improve high adhesion of bone cell and osseointegration activity. In this paper, the TiO2 barrier oxide Layer has been fabricated by using the ion characteristic of an electrolytic solution, the surface characteristics have been investigated by EDS, XPS, and FE-SEM. From the analysis of the chemical states, phosphorus and calcium were observed in the TiO2 barrier layer, which were penetrated from the electrolyte into the oxide layer during deposit process...
March 1, 2018: Journal of Nanoscience and Nanotechnology
Sylvie Maiella, Annie Olry, Marc Hanauer, Valérie Lanneau, Halima Lourghi, Bruno Donadille, Charlotte Rodwell, Sebastian Köhler, Dominik Seelow, Simon Jupp, Helen Parkinson, Tudor Groza, Michael Brudno, Peter N Robinson, Ana Rath
HIPBI-RD (Harmonising phenomics information for a better interoperability in the rare disease field) is a three-year project which started in 2016 funded via the E-Rare 3 ERA-NET program. This project builds on three resources largely adopted by the rare disease (RD) community: Orphanet, its ontology ORDO (the Orphanet Rare Disease Ontology), HPO (the Human Phenotype Ontology) as well as PhenoTips software for the capture and sharing of structured phenotypic data for RD patients. Our project is further supported by resources developed by the European Bioinformatics Institute and the Garvan Institute...
February 6, 2018: European Journal of Medical Genetics
Sadegh Kaviani, Mohammad Izadyar, Mohammad Reza Housaindokht
The chelating agents for Al3+ and Fe3+ metal cations with therapeutic applications have been considered in the recent years. In designing of the hydroxypyridinones (HPOs) as the therapeutic chelating agents for iron and aluminium overload pathologies, quantum mechanical (QM) calculations are necessary for predicting the binding energies and thermodynamic parameters of the metal-HPO complexes. Three derivatives of the HPOs called 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (DFP), 3-hydroxy-4(1H)-pyridinone (HOPO) and 5-hydroxy-2-(hydroxymethyl)pyridin-4(1H)-one (P1) were investigated for complexation with Fe3+ and Al3+ metal ions...
January 29, 2018: Journal of Molecular Graphics & Modelling
Wei-Ming Xu, Kuo Yang, Li-Jie Jiang, Jing-Qing Hu, Xue-Zhong Zhou
Background: Ischemic heart disease (IHD) has been the leading cause of death for several decades globally, IHD patients usually hold the symptoms of phlegm-stasis cementation syndrome (PSCS) as significant complications. However, the underlying molecular mechanisms of PSCS complicated with IHD have not yet been fully elucidated. Materials and Methods: Network medicine methods were utilized to elucidate the underlying molecular mechanisms of IHD phenotypes. Firstly, high-quality IHD-associated genes from both human curated disease-gene association database and biomedical literatures were integrated...
2018: Frontiers in Physiology
Angela Adler, Pia Kirchmeier, Julian Reinhard, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, H-Werner Mewes, Matthias Arnold, Andreas Ruepp
BACKGROUND: Thoroughly annotated data resources are a key requirement in phenotype dependent analysis and diagnosis of diseases in the area of precision medicine. Recent work has shown that curation and systematic annotation of human phenome data can significantly improve the quality and selectivity for the interpretation of inherited diseases. We have therefore developed PhenoDis, a comprehensive, manually annotated database providing symptomatic, genetic and imprinting information about rare cardiac diseases...
January 25, 2018: Orphanet Journal of Rare Diseases
Liang Cheng, Yue Jiang, Hong Ju, Jie Sun, Jiajie Peng, Meng Zhou, Yang Hu
BACKGROUND: Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area. Though similarities between terms within each ontology have been studied with in silico methods, term similarities across different ontologies were not investigated as deeply...
January 19, 2018: BMC Genomics
Amit Kumar Verma, Bhakti Laha, Monika Pandey, Uttariya Pal, Monidipa Ghosh
Leishmania establishes a successful parasitism by evading both oxidative and non-oxidative killing pathways, and its drug resistance against the currently available therapeutics demands for a safe and cheap drug. Since the parasite synthesizes ergosterol instead of cholesterol, using the same biochemical pathway and enzymes, an inhibitor of HMG-CoA-Reductase, Lovastatin, has been tried for its anti-Leishmanial effect. Lovastatin, being an inhibitor of HMG-CoA-Reductase, inhibits infection by cholesterol depletion, while chromium chloride complexes, at their higher concentrations, are reported to exhibit cytotoxicity...
September 2017: Journal of Biosciences
Jiajie Peng, Qianqian Li, Xuequn Shang
BACKGROUND: Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically...
September 20, 2017: Journal of Biomedical Semantics
Yonggang Zheng, Bo Liu, Li Wang, Huiyan Lei, Katiuska Daniela Pulgar Prieto, Duojia Pan
The Hippo pathway controls organ size and tissue homeostasis through a kinase cascade leading from the Ste20-like kinase Hpo (MST1/2 in mammals) to the transcriptional coactivator Yki (YAP/TAZ in mammals). Whereas previous studies have uncovered positive and negative regulators of Hpo/MST, how they are integrated to maintain signaling homeostasis remains poorly understood. Here, we identify a self-restricting mechanism whereby autophosphorylation of an unstructured linker in Hpo/MST creates docking sites for the STRIPAK PP2A phosphatase complex to inactivate Hpo/MST...
December 19, 2017: Cell Reports
Manuel Lobo, Andre Lamurias, Francisco M Couto
Named-Entity Recognition is commonly used to identify biological entities such as proteins, genes, and chemical compounds found in scientific articles. The Human Phenotype Ontology (HPO) is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases. This article presents the Identifying Human Phenotypes (IHP) system, tuned to recognize HPO entities in unstructured text. IHP uses Stanford CoreNLP for text processing and applies Conditional Random Fields trained with a rich feature set, which includes linguistic, orthographic, morphologic, lexical, and context features created for the machine learning-based classifier...
2017: BioMed Research International
Ademola C Famurewa, Onyebuchi E Nwankwo, Abiola M Folawiyo, Emeka C Igwe, Michael A Epete, Odomero G Ufebe
BACKGROUND: The literature reports that the health benefits of vegetable oil can be deteriorated by repeated heating, which leads to lipid oxidation and the formation of free radicals. Virgin coconut oil (VCO) is emerging as a functional food oil and its health benefits are attributed to its potent polyphenolic compounds. We investigated the beneficial effect of VCO supplementation on lipid profile, liver and kidney markers in rats fed repeatedly heated palm kernel oil (HPO). METHODS: Rats were divided into four groups (n = 5)...
October 2017: Acta Scientiarum Polonorum. Technologia Alimentaria
Raffaella Demichelis, Natalya A Garcia, Paolo Raiteri, Riccardo Innocenti Malini, Colin L Freeman, John H Harding, Julian D Gale
A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO4 3- , HPO4 2- , and H2 PO4 - ) with water were calibrated through comparison with the results obtained from ab initio molecular dynamics using both GGA and hybrid density functional theory with dispersion corrections. In the solid state, the force field has been evaluated by benchmarking against experiment and other existing models and is shown to reproduce the structural and mechanical properties well, despite the primary focus being on thermodynamics...
February 1, 2018: Journal of Physical Chemistry. B
Mitra Ashayeri-Panah, Fereshteh Eftekhar, Bahram Kazemi, Joan Joseph
Background and Objectives: Rv1733c is a latency antigen from Mycobacterium tuberculosis , a probable integral-membrane protein with promiscuous T-cell and B-cell epitopes, making it a potential vaccine candidate against tuberculosis. This study aimed to clone and optimize the expression of recombinant Rv1733c in Escherichia coli for purification. Materials and Methods: Chemically synthesized rv1733c coding sequence was cloned in pET-23a(+) followed by transforming E...
April 2017: Iranian Journal of Microbiology
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