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https://www.readbyqxmd.com/read/28225587/compms2miner-an-automatable-metabolite-identification-visualization-and-data-sharing-r-package-for-high-resolution-lc-ms-datasets
#1
William Matthew Bell Edmands, Lauren M Petrick, Dinesh Kumar Barupal, Augustin Scalbert, Mark Wilson, Jeffrey Wickliffe, Stephen M Rappaport
A long-standing challenge of untargeted metabolomic profiling by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation, therefore a degree of software workflow autonomy is required for broad-scale metabolite annotation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28223486/serum-borne-bioactivity-caused-by-pulmonary-multiwalled-carbon-nanotubes-induces-neuroinflammation-via-blood-brain-barrier-impairment
#2
Mario J Aragon, Lauren Topper, Christina R Tyler, Bethany Sanchez, Katherine Zychowski, Tamara Young, Guy Herbert, Pamela Hall, Aaron Erdely, Tracy Eye, Lindsey Bishop, Samantha A Saunders, Pretal P Muldoon, Andrew K Ottens, Matthew J Campen
Pulmonary exposure to multiwalled carbon nanotubes (MWCNTs) causes indirect systemic inflammation through unknown pathways. MWCNTs translocate only minimally from the lungs into the systemic circulation, suggesting that extrapulmonary toxicity may be caused indirectly by lung-derived factors entering the circulation. To assess a role for MWCNT-induced circulating factors in driving neuroinflammatory outcomes, mice were acutely exposed to MWCNTs (10 or 40 µg/mouse) via oropharyngeal aspiration. At 4 h after MWCNT exposure, broad disruption of the blood-brain barrier (BBB) was observed across the capillary bed with the small molecule fluorescein, concomitant with reactive astrocytosis...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28222896/comparison-of-the-prognostic-value-of-chronic-liver-failure-consortium-scores-and-traditional-models-for-predicting-mortality-in-patients-with-cirrhosis
#3
Artur Gião Antunes, Cristina Teixeira, Ana Margarida Vaz, Cláudio Martins, Patrícia Queirós, Ana Alves, Francisco Velasco, Bruno Peixe, Ana Paula Oliveira, Horácio Guerreiro
BACKGROUND AND AIM: Recently, the European Association for the Study of the Liver - Chronic Liver Failure (CLIF) Consortium defined two new prognostic scores, according to the presence or absence of acute-on-chronic liver failure (ACLF): the CLIF Consortium ACLF score (CLIF-C ACLFs) and the CLIF-C Acute Decompensation score (CLIF-C ADs). We sought to compare their accuracy in predicting 30- and 90-day mortality with some of the existing models: Child-Turcotte-Pugh (CTP), Model for End-Stage Liver Disease (MELD), MELD-Na, integrated MELD (iMELD), MELD to serum sodium ratio index (MESO), Refit MELD and Refit MELD-Na...
February 17, 2017: Gastroenterología y Hepatología
https://www.readbyqxmd.com/read/28221953/comparative-evaluation-of-genomic-and-laboratory-approaches-for-determination-of-shiga-toxin-subtypes-in-escherichia-coli
#4
Catherine D Carrillo, Adam G Koziol, Amit Mathews, Noriko Goji, Dominic Lambert, George Huszczynski, Martine Gauthier, Kingsley Amoako, Burton W Blais
The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221766/proteoform-profile-mapping-of-the-human-serum-complement-component-c9-reveals-unexpected-new-features-of-n-o-and-c-glycosylation
#5
Vojtech Franc, Yang Yang, Albert J R Heck
The human complement C9 protein (~65 kDa) is a member of the complement pathway. It plays an essential role in the membrane attack complex (MAC), which forms a lethal pore on the cellular surface of pathogenic bacteria. Here, we charted in detail the structural micro-heterogeneity of C9 purified from human blood serum, using an integrative workflow combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The proteoform profile of C9 was acquired by high-resolution native mass spectrometry, which revealed the co-occurrence of ~50 distinct MS signals...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28220036/proposal-for-a-new-predictive-model-of-short-term-mortality-after-living-donor-liver-transplantation-due-to-acute-liver-failure
#6
Hyun Sik Chung, Yu Jung Lee, Yun Sung Jo
BACKGROUND Acute liver failure (ALF) is known to be a rapidly progressive and fatal disease. Various models which could help to estimate the post-transplant outcome for ALF have been developed; however, none of them have been proved to be the definitive predictive model of accuracy. We suggest a new predictive model, and investigated which model has the highest predictive accuracy for the short-term outcome in patients who underwent living donor liver transplantation (LDLT) due to ALF. MATERIAL AND METHODS Data from a total 88 patients were collected retrospectively...
February 21, 2017: Annals of Transplantation: Quarterly of the Polish Transplantation Society
https://www.readbyqxmd.com/read/28218403/unveiling-gene-trait-relationship-by-cross-platform-meta-analysis-on-chinese-hamster-ovary-cell-transcriptome
#7
Liang Zhao, Hsu-Yuan Fu, Ravali Raju, Nandita Vishwanathan, Wei-Shou Hu
In the past few years, transcriptome analysis has been increasingly employed to better understand the physiology of Chinese hamster ovary (CHO) cells at a global level. As more transcriptome data accumulated, meta-analysis on data sets collected from various sources can potentially provide better insights on common properties of those cells. Here, we performed meta-analysis on transcriptome data of different CHO cell lines obtained using NimbleGen or Affymetrix microarray platforms. Hierarchical clustering, non-negative matrix factorization (NMF) analysis, and principal component analysis (PCA) accordantly showed the samples were clustered into two groups: one consists of adherent cells in serum-containing medium, and the other suspension cells in serum-free medium...
February 20, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28215546/analysis-of-human-serum-metabolome-for-potential-biomarkers-identification-of-erosive-oral-lichen-planus
#8
Xu-Yan YangG, Shuai-Nan Zhang, Xu-Zhao Li, Yu Wang, Xiao-Dong Yin
BACKGROUND: Oral lichen planus (OLP) is a chronic auto-inflammatory mucositis and potentially oral premalignant lesion. Erosive OLP patients display the higher canceration rate as compared to the patients with non-erosive OLP. Identification of the potential biomarkers associated with erosive OLP may help to investigate the disease pathogenesis and to improve clinical treatment. METHODS: Ultra-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UPLC-QTOF-MS) combined with pattern recognition approaches were integrated to acquire differentially expressed metabolites for the pathways analysis and elucidate mechanisms of disease...
February 16, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28213328/an-integrated-dual-functional-recognition-amplification-bio-label-for-the-one-step-impedimetric-detection-of-micro-rna-21
#9
Sawsen Azzouzi, Wing Cheung Mak, Kamalodin Kor, Anthony P F Turner, Mounir Ben Ali, Valerio Beni
Alteration in expression of miRNAs has been correlated with different cancer types, tumour stage and response to treatments. In this context, a structurally responsive oligonucleotide-based electrochemical impedimetric biosensor has been developed for the simple and sensitive detection of miRNA-21. A highly specific biotinylated DNA/LNA molecular beacon (MB) probe was conjugated with gold nanoparticles (AuNPs) to create an integrated, dual function bio-label (biotin-MB-AuNPs) for both biorecognition and signal generation...
February 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28213275/a-single-microfluidic-chip-with-dual-surface-properties-for-protein-drug-delivery
#10
Mehrdad Bokharaei, Katayoun Saatchi, Urs O Häfeli
Principles of double emulsion generation were incorporated in a glass microfluidic chip fabricated with two different surface properties in order to produce protein loaded polymer microspheres. The microspheres were produced by integrating two microfluidic flow focusing systems and a multi-step droplet splitting and mixing system into one chip. The chip consists a hydrophobic and a hydrophilic section with two different heights, 12μm and 45μm, respectively. As a result, the protein is homogenously distributed throughout the polymer microsphere matrix, not just in its center (which has been studied before)...
February 14, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28213235/preparation-and-characterization-of-a-packed-bead-immobilized-trypsin-reactor-integrated-into-a-pdms-microfluidic-chip-for-rapid-protein-digestion
#11
Adam Kecskemeti, Attila Gaspar
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213228/smartphone-based-immunosensor-for-ca125-detection
#12
Oana Hosu, Andrea Ravalli, Giuseppe Mattia Lo Piccolo, Cecilia Cristea, Robert Sandulescu, Giovanna Marrazza
In this work, we report the design, the development and the characterization of the analytical performances of a colorimetric smartphone-based immunosensor for the detection of cancer antigen 125 (CA125). The immunosensor was based on a sandwich strategy in which the primary antibody was immobilized by spotting onto the 3D nitrocellulose membrane. The immunospots were subsequently incubated with CA125 solutions, followed by the affinity reaction with a secondary antibody labeled with gold nanoparticles (AuNPs)...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213091/convergence-of-hepcidin-deficiency-systemic-iron-overloading-heme-accumulation-and-rev-erb%C3%AE-%C3%AE-activation-in-aryl-hydrocarbon-receptor-elicited-hepatotoxicity
#13
Kelly A Fader, Rance Nault, Mathew P Kirby, Gena Markous, Jason Matthews, Timothy R Zacharewski
Persistent aryl hydrocarbon receptor (AhR) agonists elicit dose-dependent hepatic lipid accumulation, oxidative stress, inflammation, and fibrosis in mice. Iron (Fe) promotes AhR-mediated oxidative stress by catalyzing reactive oxygen species (ROS) production. To further characterize the role of Fe in AhR-mediated hepatotoxicity, male C57BL/6 mice were orally gavaged with sesame oil vehicle or 0.01-30μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) every 4days for 28days. Duodenal epithelial and hepatic RNA-Seq data were integrated with hepatic AhR ChIP-Seq, capillary electrophoresis protein measurements, and clinical chemistry analyses...
February 14, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28213045/identification-of-the-causes-for-chronic-hypokalemia-importance-of-urinary-sodium-and-chloride-excretion
#14
Kun-Lin Wu, Chih-Jen Cheng, Chih-Chen Sung, Ming-Hua Tseng, Yu-Juei Hsu, Sung-Sen Yang, Tom Chau, Shih-Hua Lin
BACKGROUND: Uncovering the correct diagnosis of chronic hypokalemia with potassium (K(+)) wasting from the kidneys or gut can be fraught with challenges. We identified clinical and laboratory parameters helpful for differentiating the causes of chronic hypokalemia. METHODS: Normotensive patients referred to our tertiary academic medical center for the evaluation of chronic hypokalemia were prospectively enrolled over five years. Clinical features, laboratory examinations-including blood and spot urine electrolytes, acid-base status, biochemistries and hormones-as well as genetic analysis were determined...
February 14, 2017: American Journal of Medicine
https://www.readbyqxmd.com/read/28212624/understanding-the-response-to-endurance-exercise-using-a-systems-biology-approach-combining-blood-metabolomics-transcriptomics-and-mirnomics-in-horses
#15
Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López, Laurence Le Moyec
BACKGROUND: Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of the relationships between blood metabolome, transcriptome, and miRNome during endurance exercise in horses could provide significant insights into the molecular response to endurance exercise. For this reason, the serum metabolome and whole-blood transcriptome and miRNome data were obtained from ten horses before and after a 160 km endurance competition...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212282/collagen-gold-nanoparticle-conjugates-for-versatile-biosensing
#16
Sarah Unser, Samuel Holcomb, ReJeana Cary, Laura Sagle
Integration of noble metal nanoparticles with proteins offers promising potential to create a wide variety of biosensors that possess both improved selectivity and versatility. The multitude of functionalities that proteins offer coupled with the unique optical properties of noble metal nanoparticles can allow for the realization of simple, colorimetric sensors for a significantly larger range of targets. Herein, we integrate the structural protein collagen with 10 nm gold nanoparticles to develop a protein-nanoparticle conjugate which possess the functionality of the protein with the desired colorimetric properties of the nanoparticles...
February 15, 2017: Sensors
https://www.readbyqxmd.com/read/28211533/integration-of-microrna-and-mrna-expression-profiles-in-the-skin-of-systemic-sclerosis-patients
#17
Bin Zhou, Xiao Xia Zuo, Yi Sha Li, Si Ming Gao, Xiao Dan Dai, Hong Lin Zhu, Hui Luo
MicroRNAs (miRNAs) play important roles in the fibrosis of systemic sclerosis (SSc). However, the underlying miRNA-mRNA regulatory network is not fully understood. A systemic investigation of the role of miRNAs would be very valuable for increasing our knowledge of the pathogenesis of SSc. Here, we combined miRNA and mRNA expression profiles and bioinformatics analyses and then performed validation experiments. we identified 21 miRNAs and 2698 mRNAs that were differentially expressed in SSc. Among these, 17 miRNAs and their 33 target mRNAs (55 miRNA-mRNA pairs) were involved in Toll-like receptor, transforming growth factor β and Wnt signalling pathways...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211028/short-term-supra-physiological-rhgh-administration-induces-transient-dna-damage-in-peripheral-lymphocytes-of-healthy-women
#18
C Fantini, P Sgrò, M Pittaluga, A de Perini, I Dimauro, A Sartorio, D Caporossi, L Di Luigi
PURPOSE: While a good safety for recombinant human growth hormone (rhGH) therapy at replacement doses is recognized, a possible link between high concentration of the GH-IGF-I axis hormones and side negative effect has been reported. The aim of this pilot study was to assess whether a short-term exposure to supra-physiological doses of rhGH may affect DNA integrity in human lymphocytes (PBL). METHODS: Eighteen healthy Caucasian female (24.2 ± 3.5 years) were randomly included in a Control (n = 9) and rhGH administration group (n = 9, 3-week treatment)...
February 16, 2017: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/28210754/targeted-lipidomics-profiling-of-acute-arsenic-exposure-in-mice-serum-by-on-line-solid-phase-extraction-stable-isotope-dilution-liquid-chromatography-tandem-mass-spectrometry
#19
Chao-Yu Chen, Pinpin Lin, Ming-Hsien Tsai, Hui-Ling Lee
Lipidomics is the area of study dedicated to the comprehensive analysis and characterization of the functions and metabolism of lipids in biological samples. One of the most comprehensively studied classes of lipids is polyunsaturated fatty acids (PUFAs). Eicosanoids are a series of bioactive lipid mediators that are metabolized from PUFAs and generated majorly from the precursor arachidonic acid. This study identified the profiles of target eicosanoids after acute exposure to arsenic. The principle objective was to determine and validate 10 eicosanoids in mouse serum using on-line solid-phase extraction integrated with liquid chromatography-electrospray tandem mass spectrometry...
February 16, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28206723/clinical-study-on-amplitude-integrated-electroencephalogram-in-cerebral-injury-caused-by-severe-neonatal-hyperbilirubinemia
#20
Hongwei Wu, Zhenguang Li, Jinfeng Liu, Gang Liu, Xia Yang
BACKGROUND: This study was designed in order to assess the validity of the use of amplitude-integrated electroencephalogram (aEEG) in cerebral injury caused by severe neonatal hyperbilirubinemia. METHODS: A total of 56 full-term neonates diagnosed with severe neonatal hyperbilirubinemia and admitted to the NICU of our hospital from July 2013 to December 2014 were continuously selected for the study. The total serum bilirubin (TSB) was higher than 342 μmo/l, and was dominated by a higher amount of unconjugated bilirubin...
February 15, 2017: Minerva Pediatrica
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