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wendy-clark-blog · 7 years ago

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JCM, Vol. 8, Pages 87: Altered Adipose Tissue DNA Methylation Status in Metabolic Syndrome: Relationships Between Global DNA Methylation and Specific Methylation at Adipogenic, Lipid Metabolism and Inflammatory Candidate Genes and Metabolic Variables

Journal of Clinical Medicine doi: 10.3390/jcm8010087

Authors: Daniel Castellano-Castillo Isabel Moreno-Indias Lidia Sanchez-Alcoholado Bruno Ramos-Molina Juan Alcaide-Torres Sonsoles Morcillo Luis Ocaña-Wilhelmi Francisco Tinahones María Isabel Queipo-Ortuño Fernando Cardona

Metabolic syndrome (MetS) has been postulated to increase the risk for type 2 diabetes, cardiovascular disease and cancer. Adipose tissue (AT) plays an important role in metabolic homeostasis, and AT dysfunction has an active role in metabolic diseases. MetS is closely related to lifestyle and environmental factors. Epigenetics has emerged as an interesting landscape to evaluate the possible interconnection between AT and metabolic disease, since it can be modulated by environmental factors and metabolic status. The aim of this study was to determine whether MetS has an impact on the global DNA methylation pattern and the DNA methylation of several genes related to adipogenesis (PPARG, PPARA), lipid metabolism (RXRA, SREBF2, SREBF1, SCD, LPL, LXRb), and inflammation (LRP1 C3, LEP and TNF) in visceral adipose tissue. LPL and TNF DNA methylation values were significantly different in the control-case comparisons, with higher and lower methylation respectively in the MetS group. Negative correlations were found between global DNA methylation (measured by LINE-1 methylation levels) and the metabolic deterioration and glucose levels. There were associations among variables of MetS, BMI, and HOMA-IR with DNA methylation at several CpG positions for the studied genes. In particular, there was a strong positive association between serum triglyceride levels (TG) with PPARA and LPL methylation levels. TNF methylation was negatively associated with the metabolic worsening and could be an important factor in preventing MetS occurrence according to logistic regression analysis. Therefore, global DNA methylation and methylation at specific genes related to adipogenesis, lipid metabolism and inflammation are related to the etiology of MetS and might explain in part some of the features associated to metabolic disorders.

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wendy-clark-blog · 7 years ago

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Materials, Vol. 12, Pages 248: The Effects of Silica on the Properties of Vitreous Enamels

Materials doi: 10.3390/ma12020248

Authors: Signo T. Reis Mike Koenigstein Liang Fan Genda Chen Luka Pavić Andrea Moguš-Milanković

Ground coat enamels for low carbon steel that contain silica as a mill addition have been developed to study the changes of their properties. Acid-resistant commercial enamel where silica addition was varied from 0 to 10.0 wt % was used for this investigation. The effects of the addition on the corrosion resistance, thermal properties, electrical properties, and mechanical adherence of the enamel to low carbon steel were studied. The corrosion resistance of the steel enameled coupons was tested using a salt spray (fog) apparatus for time periods reaching 168 h at room temperature. It was found that, although the density was not affected, the adherence decreased with an increase in silica content. As expected, the silica addition decreased the coefficient of thermal expansion, which is directly related to the increasing stress between the glass and steel in accordance with the adherence results. A mill addition of 7.5 wt% of silica to the samples was sufficient to obtain adequate enamel adherence and good corrosion resistance. Furthermore, the addition of silica influenced the electrical conductivity and dielectric permittivity measurements at room temperature and the conductivity measured in a wide frequency range (1 Hz–1 MHz). The dielectric permittivity measured at 1 MHz showed decrease after the addition of up to 7.5 wt% of silica.

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wendy-clark-blog · 7 years ago

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Personalized Medicine Agg

This feed was created by mixing existing feeds from various sources.

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wendy-clark-blog · 7 years ago

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IJMS, Vol. 20, Pages 264: Effects of Quercetin Metabolites on Triglyceride Metabolism of 3T3-L1 Preadipocytes and Mature Adipocytes

International Journal of Molecular Sciences doi: 10.3390/ijms20020264

Authors: Itziar Eseberri Jonatan Miranda Arrate Lasa Andrea Mosqueda-Solís Susana González-Manzano Celestino Santos-Buelga Maria P. Portillo

Quercetin (Q) has rapid metabolism, which may make it worthwhile to focus on the potential activity of its metabolites. Our aim was to evaluate the triglyceride-lowering effects of Q metabolites in mature and pre-adipocytes, and to compare them to those induced by Q. 3T3-L1 mature and pre-adipocytes were treated with 0.1, 1 and 10 µM of Q, tamarixetin (TAM), isorhamnetin (ISO), quercetin-3-O-glucuronide (3G), quercetin-3-O-sulfate (3S), as well as with 3S and quercetin-4-O-sulfate (4S) mixture (3S+4S). Triglyceride (TG) content in both cell types, as well as free fatty acid (FFA) and glycerol in the incubation medium of mature adipocytes were measured spectrophotometrically. Gene expression was assessed by RT-PCR. In mature adipocytes, Q decreased TG at 1 and 10 µM, 3S metabolite at 1 and 10 µM, and 3S+4S mixture at 10 µM. 3S treatment modified the glucose uptake, and TG assembling, but not lipolysis or apoptosis. During differentiation, only 10 µM of ISO reduced TG content, as did Q at physiological doses. In conclusion, 3S metabolite but not ISO, 3G, 4S and TAM metabolites can contribute to the in vivo delipidating effect of Q.

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wendy-clark-blog · 7 years ago

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IJMS, Vol. 20, Pages 249: Efficacy of Azatyrosine-Phenylbutyric Hydroxamides, a Histone Deacetylase Inhibitor, on Chemotherapy-Induced Gastrointestinal Mucositis

International Journal of Molecular Sciences doi: 10.3390/ijms20020249

Authors: Po-Lin Liao Shih-Hsuan Huang Chien-Hung Hung Wei-Kuang Huang Chi-Hao Tsai Jaw-Jou Kang Hui-Po Wang Yu-Wen Cheng

Gastrointestinal mucositis is a serious side effect of chemotherapy. Currently, no effective treatment exists for chemotherapy-induced mucositis, prompting the need to develop an anti-mucositis agent for use in clinics. The present study investigated whether azatyrosine-PBHA (AzP), a histone deacetylase inhibitor, has a therapeutic effect on intestinal mucosa. The results indicated that AzP did not affect the proliferation and viability of cancer cells, outcomes that are achieved by suberoylanilide hydroxamic acid (SAHA). However, AzP could decrease production of the inflammatory mediators interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), and tumor-necrosis factor-α (TNF-α). In vivo histopathological assessment showed that AzP reduced cisplatin-induced injury to the jejunum villi and triggered weight loss in the C57BL/6 mice. Immunohistochemistry (IHC) results demonstrated that mice treated with AzP also recovered from cisplatin-induced injury to the intestinal mucosa. Mechanistic in vitro study using DAVID/KEGG enrichment analysis of microarray data and confirmation by a Western blot indicated the influence of AzP on the MEK/ERK and AKT-dependent pathway. In conclusion, the study demonstrated that AzP might regulate the MEK/ERK MAPK signaling pathway to attenuate MCP-1, TNF-α, and IL-6 production and provide opportunities for the development of new anti-inflammatory drugs targeting mucositis.

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wendy-clark-blog · 7 years ago

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IJMS, Vol. 20, Pages 242: Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 (ROD1) Transcription Start Site

International Journal of Molecular Sciences doi: 10.3390/ijms20020242

Authors: Marta Kubiak Anna Jurek Katarzyna Kamińska Janusz Kowalewski Sui Huang Marzena Anna Lewandowska

The long-range control of gene expression is facilitated by chromatin looping and can be detected using chromosome conformation capture—3C. Here we focus on the chromatin architecture of the PTBP3 (Polypyrimidine tract binding protein 3) locus to evaluate its potential role in regulating expression of the gene. PTBP3 expression in prostate cancer cell lines is found significantly higher compared to skin fibroblasts using real-time PCR (p < 0.05) and digital droplet PCR (p < 0.01). Exploration of the chromatin spatial architecture of a nearly 200-kb fragment of chromosome 9 encompassing the PTBP3 gene identified two elements located 63 kb upstream and 48 kb downstream of PTBP3, which looped specifically to the PTBP3 promoter. These elements contain histone acetylation patterns characteristic of open chromatin regions with active enhancers. Our results reveal for the first time that long-range chromatin interactions between the −63 kb and +48 kb loci and the PTBP3 promoter regulate the expression of this gene in prostate cancer cells. These interactions support an open chromatin form for the PTBP3 locus in cancer cells and the three-dimensional structural model proposed in this paper.

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wendy-clark-blog · 7 years ago

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Applied Sciences, Vol. 9, Pages 154: Monitoring the Activated Sludge Activities Affected by Industrial Toxins via an Early-Warning System Based on the Relative Oxygen Uptake Rate (ROUR) Index

Applied Sciences doi: 10.3390/app9010154

Authors: Yu Du Yasong Chen Lina Zou Songqiang Deng Guanghe Li Dayi Zhang

Shock load from industrial wastewater is known to harm the microbial activities of the activated sludge in wastewater treatment plants (WWTPs) and disturb their performance. This study developed a system monitoring the activated sludge activities based on the relative oxygen uptake rate (ROUR) and explored the influential factors with wastewater and the activated sludge samples collected from a typical WWTP in the Taihu Lake of southern Jiangsu province, China. The ROUR was affected by the concentration of toxic substances, mixed liquid suspended solids (MLSS), hydraulic retention time (HRT) and pH. Higher toxin contents significantly decreased the ROUR and the EC50 value of Zn2+, Ni2+, Cr(VI), Cu2+, and Cd2+ was 13.40, 15.54, 97.56, 12.01, and 14.65 mg/L, respectively. The ROUR declined with the increasing HRT and MLSS above 2000 mg/L had buffering capacities for the impacts of toxic substances to some extent. The ROUR remained stable within a broad range pH (6–10), covering most of the operational pH in WWTPs and behaving as an appropriate indicator for monitoring the shock load. A toxicity model assessing and predicting the ROUR was developed and fitted well with experimental data. Coupling the ROUR monitoring system and toxicity model, an online early-warning system was assembled and successfully used for predicting the toxicity of different potential toxic metals. This study provides a new universal toxicity model and an online early-warning system for monitoring the shock load from industrial wastewater, which is useful for improving the performance of WWTPs.

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wendy-clark-blog · 7 years ago

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Seagrass saves beaches and money

Seagrass beds are so effective in protecting tropical beaches from erosion, that they can reduce the need for regular, expensive beach nourishments that are used now. Biologists and engineers from the Netherlands and Mexico describe experiments and field observations around the Caribbean Sea.

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wendy-clark-blog · 7 years ago

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Dentistry Journal, Vol. 7, Pages 2: Evaluation of Two Shaping Systems and Two Ultrasonic Irrigation Devices in Removing Root Canal Filling Material from Mesial Roots of Mandibular Molars: A Micro CT Study

Dentistry Journal doi: 10.3390/dj7010002

Authors: Marc Krikor Kaloustian Walid Nehme Claire El Hachem Carla Zogheib Nabil Ghosn Jérôme Michetti Alfred Naaman Franck Diemer

We assessed the efficiency of two shaping file systems and two passive ultrasonic irrigation (PUI) devices for removing filling material during retreatment. The mesial canals from 44 extracted mandibular molars were prepared and obturated. The teeth were randomly divided into two groups, and then one group was retreated with Reciproc R25 (VDW, Munich, Germany) (n = 44) and the other group was retreated with 2Shape (TS, Micro Mega, Besançon, France) (n = 44). A micro-computed tomography (CT) scan was taken before and after the retreatment to assess the volume of the filling material remnants. The teeth were then randomly divided into four groups to test two different PUI devices: Irrisafe (Satelec Acteon Group, Merignac, France) and Endo Ultra (Vista Dental Products, Racine, WI, USA). The teeth in Group A were retreated with 2Shape to test the Endo Ultra (n = 22) device, the teeth in Group B were retreated with 2Shape in order to test the Irrisafe (n = 22) device, the teeth in Group C were retreated with Reciproc to test the Endo Ultra (n = 22) device, and Group D was retreated with Reciproc to test the Irrisafe (n = 22) device. A third micro-CT scan was taken after the retreatment to test the PUIs. The percentage of Gutta-Percha (GP) and sealer removed was 94.75% for TS2 (p < 0.001) and 89.3% for R25 (p < 0.001). The PUI significantly enhanced the removal of the filling material by 0.76% for Group A (p < 0.001), 1.47% for Group B (p < 0.001), 2.61% for Group C (p < 0.001), and by 1.66% for Group D (p < 0.001). 2Shape was more effective at removing the GP and sealer during retreatment (p = 0.018). The supplementary approach with PUI significantly improved filling material removal, with no statistical difference between the four groups (p = 0.106).

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wendy-clark-blog · 7 years ago

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IJGI, Vol. 8, Pages 15: Geo-Tagged Social Media Data-Based Analytical Approach for Perceiving Impacts of Social Events

ISPRS International Journal of Geo-Information doi: 10.3390/ijgi8010015

Authors: Ruoxin Zhu Diao Lin Michael Jendryke Chenyu Zuo Linfang Ding Liqiu Meng

Studying the impact of social events is important for the sustainable development of society. Given the growing popularity of social media applications, social sensing networks with users acting as smart social sensors provide a unique channel for understanding social events. Current research on social events through geo-tagged social media is mainly focused on the extraction of information about when, where, and what happened, i.e., event detection. There is a trend towards the machine learning of more complex events from even larger input data. This research work will undoubtedly lead to a better understanding of big geo-data. In this study, however, we start from known or detected events, raising further questions on how they happened, how they affect people’s lives, and for how long. By combining machine learning, natural language processing, and visualization methods in a generic analytical framework, we attempt to interpret the impact of known social events from the dimensions of time, space, and semantics based on geo-tagged social media data. The whole analysis process consists of four parts: (1) preprocessing; (2) extraction of event-related information; (3) analysis of event impact; and (4) visualization. We conducted a case study on the “2014 Shanghai Stampede” event on the basis of Chinese Sina Weibo data. The results are visualized in various ways, thus ensuring the feasibility and effectiveness of our proposed framework. Both the methods and the case study can serve as decision references for situational awareness and city management.

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wendy-clark-blog · 7 years ago

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IJGI, Vol. 8, Pages 15: Geo-Tagged Social Media Data-Based Analytical Approach for Perceiving Impacts of Social Events

ISPRS International Journal of Geo-Information doi: 10.3390/ijgi8010015

Authors: Ruoxin Zhu Diao Lin Michael Jendryke Chenyu Zuo Linfang Ding Liqiu Meng

Studying the impact of social events is important for the sustainable development of society. Given the growing popularity of social media applications, social sensing networks with users acting as smart social sensors provide a unique channel for understanding social events. Current research on social events through geo-tagged social media is mainly focused on the extraction of information about when, where, and what happened, i.e., event detection. There is a trend towards the machine learning of more complex events from even larger input data. This research work will undoubtedly lead to a better understanding of big geo-data. In this study, however, we start from known or detected events, raising further questions on how they happened, how they affect people’s lives, and for how long. By combining machine learning, natural language processing, and visualization methods in a generic analytical framework, we attempt to interpret the impact of known social events from the dimensions of time, space, and semantics based on geo-tagged social media data. The whole analysis process consists of four parts: (1) preprocessing; (2) extraction of event-related information; (3) analysis of event impact; and (4) visualization. We conducted a case study on the “2014 Shanghai Stampede” event on the basis of Chinese Sina Weibo data. The results are visualized in various ways, thus ensuring the feasibility and effectiveness of our proposed framework. Both the methods and the case study can serve as decision references for situational awareness and city management.

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wendy-clark-blog · 7 years ago

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Sensors, Vol. 18, Pages 4005: A High-Sensitivity Microfluidic Sensor Based on a Substrate Integrated Waveguide Re-Entrant Cavity for Complex Permittivity Measurement of Liquids

Sensors doi: 10.3390/s18114005

Authors: Zhihua Wei Jie Huang Jing Li Guoqing Xu Zongde Ju Xuyang Liu Xingsheng Ni

In this study, a novel non-invasive and contactless microwave sensor using a square substrate integrated waveguide (SIW) re-entrant cavity is proposed for complex permittivity measurement of chemical solutions. The working principle of this sensor is based on cavity perturbation technique, in which the resonant properties of cavity are utilized as signatures to extract the dielectric information of liquid under test (LUT). A winding microfluidic channel is designed and embedded in the gap region of the cavity to obtain a strong interaction between the induced electric field and LUT, thus achieving a high sensitivity. Also, a mathematical predictive model which quantitatively associates the resonant properties of the sensor with the dielectric constant of LUT is developed through numerical analysis. Using this predictive model, quick and accurate extraction of the complex permittivity of LUT can be easily realized. The performance of this sensor is then experimentally validated by four pure chemicals (hexane, ethyl acetate, DMSO and water) together with a set of acetone/water mixtures in various concentrations. Experimental results demonstrate that the designed sensor is capable of characterizing the complex permittivities of various liquids with an accuracy of higher than 96.76% (compared with the theoretical values obtained by Debye relaxation equations), and it is also available for quantifying the concentration ratio of a given binary mixture.

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wendy-clark-blog · 7 years ago

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Water, Vol. 10, Pages 1676: Assessment of Machine Learning Techniques for Monthly Flow Prediction

Water doi: 10.3390/w10111676

Authors: Zahra Alizadeh Jafar Yazdi Joong Hoon Kim Abobakr Khalil Al-Shamiri

Monthly flow predictions provide an essential basis for efficient decision-making regarding water resource allocation. In this paper, the performance of different popular data-driven models for monthly flow prediction is assessed to detect the appropriate model. The considered methods include feedforward neural networks (FFNNs), time delay neural networks (TDNNs), radial basis neural networks (RBFNNs), recurrent neural network (RNN), a grasshopper optimization algorithm (GOA)-based support vector machine (SVM) and K-nearest neighbors (KNN) model. For this purpose, the performance of each model is evaluated in terms of several residual metrics using a monthly flow time series for two real case studies with different flow regimes. The results show that the KNN outperforms the different neural network configurations for the first case study, whereas RBFNN model has better performance for the second case study in terms of the correlation coefficient. According to the accuracy of the results, in the first case study with more input features, the KNN model is recommended for short-term predictions and for the second case with a smaller number of input features, but more training observations, the RBFNN model is suitable.

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wendy-clark-blog · 7 years ago

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TropicalMed, Vol. 3, Pages 119: Baseline Mapping of Schistosomiasis and Soil Transmitted Helminthiasis in the Northern and Eastern Health Regions of Gabon, Central Africa: Recommendations for Preventive Chemotherapy

Tropical Medicine and Infectious Disease doi: 10.3390/tropicalmed3040119

Authors: Mintsa Nguema Mavoungou Mengue Me Ngou-Milama Mabicka Mamfoumbi Koumba Sani Lamine Diarra Nkone Asseko Mourou Bouyou Akotet Moné Mouahid Atsame

In order to follow the Preventive Chemotherapy (PC) for the transmission control as recommended by WHO, Gabon initiated in 2014 the mapping of Schistosomiasis and Soil Transmitted Helminthiasis (STH). Here, we report the results of the Northern and Eastern health regions, representing a third of the land area and 12% of its total population. All nine departments of the two regions were surveyed and from each, five schools were examined with 50 schoolchildren per school. The parasitological examinations were realized using the filtration method for urine and the Kato-Katz technique for stool samples. Overall 2245 schoolchildren (1116 girls and 1129 boys), mean aged 11.28 ± 0.04 years, were examined. Combined schistosomiasis and STH affected 1270 (56.6%) with variation between regions, departments, and schools. For schistosomiasis, prevalence were 1.7% across the two regions, with no significant difference (p > 0.05) between the Northern (1.5%) and the Eastern (1.9%). Schistosomiasis is mainly caused by Schistosoma haematobium with the exception of one respective case of S. mansoni and S. guineensis. STH are more common than schistosomiasis, with an overall prevalence of 56.1% significantly different between the Northern (58.1%) and Eastern (53.6%) regions (p = 0.034). Trichuris trichiura is the most abundant infection with a prevalence of 43.7% followed by Ascaris lumbricoides 35.6% and hookworms 1.4%. According to these results, an appropriate PC strategy is given. In particular, because of the low efficacy of a single recommended drug on T. trichiura and hookworms, it is important to include two drugs for the treatment of STH in Gabon, due to the high prevalence and intensities of Trichuris infections.

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wendy-clark-blog · 7 years ago

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Molecules, Vol. 23, Pages 2910: In Silico Analysis of Bioactive Peptides Released from Giant Grouper (Epinephelus lanceolatus) Roe Proteins Identified by Proteomics Approach

Molecules doi: 10.3390/molecules23112910

Authors: Fenny Crista A. Panjaitan Honey Lyn R. Gomez Yu-Wei Chang

Major proteins contained in dried giant grouper roe (GR) such as vitellogenin (from Epinephelus coioides; NCBI accession number: AAW29031.1), apolipoprotein A-1 precursor (from Epinephelus coioides; NCBI accession number: ACI01807.1) and apolipoprotein E (from Epinephelus bruneus; NCBI accession number: AEB31283.1) were characterized through compiled proteomics techniques (SDS-PAGE, in-gel digestion, mass spectrometry and on-line Mascot database analysis). These proteins were subjected to in silico analysis using BLAST and BIOPEP-UWM database. Sequence similarity search by BLAST revealed that the aligned vitellogenin sequences from Epinephelus coioides and Epinephelus lanceolatus share 70% identity, which indicates that the sequence sample has significant similarity with proteins in sequence databases. Moreover, prediction of potential bioactivities through BIOPEP-UWM database resulted in high numbers of peptides predominantly with dipeptidyl peptidase-IV (DPP-IV) and angiotensin-I-converting enzyme (ACE-I) inhibitory activities. Pepsin (pH > 2) was predicted to be the most promising enzyme for the production of bioactive peptides from GR protein, which theoretically released 82 DPP-IV inhibitory peptides and 47 ACE-I inhibitory peptides. Overall, this work highlighted the potentiality of giant grouper roe as raw material for the generation of pharmaceutical products. Furthermore, the application of proteomics and in silico techniques provided rapid identification of proteins and useful prediction of its potential bioactivities.

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wendy-clark-blog · 7 years ago

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Appendix identified as a potential starting point for Parkinson's disease

Removing the appendix early in life reduces the risk of developing Parkinson's disease by 19 to 25 percent, according to the largest and most comprehensive study of its kind. The findings solidify the role of the gut and immune system in the genesis of the disease, and reveal that the appendix acts as a major reservoir for abnormally folded alpha-synuclein proteins, which are closely linked to Parkinson's onset and progression.

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wendy-clark-blog · 7 years ago

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Viruses, Vol. 10, Pages 578: Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394

Viruses doi: 10.3390/v10110578

Authors: Jeesun Chun Han-Eul Yang Dae-Hyuk Kim

An increasing number of novel mycoviruses have been described in fungi. Here, we report the molecular characteristics of a novel bisegmented double-stranded RNA (dsRNA) virus from the fungus Trichoderma atroviride NFCF394. We designated this mycovirus as Trichoderma atroviride partitivirus 1 (TaPV1). Electron micrographs of negatively stained, purified viral particles showed an isometric structure approximately of 30 nm in diameter. The larger segment (dsRNA1) of the TaPV1 genome comprised 2023 bp and contained a single open reading frame (ORF) encoding 614 amino acid (AA) residues of RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2012 bp with a single ORF encoding 577 AA residues of capsid protein (CP). The phylogenetic analysis, based on deduced amino acid sequences of RdRp and CP, indicated that TaPV1 is a new member of the genus Alphapartitivirus in the family Partitiviridae. Virus-cured isogenic strains did not show significant changes in colony morphology. In addition, no changes in the enzymatic activities of β-1,3-glucanase and chitinase were observed in virus-cured strains. To the best of our knowledge, this is the first report of an Alphapartitivirus in T. atroviride.

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