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https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#1
Andrey Smelter, Eric C Rouchka, Hunter N B Moseley
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values...
August 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28813537/metabolite-patterns-predicting-sex-and-age-in-participants-of-the-karlsruhe-metabolomics-and-nutrition-karmen-study
#2
Manuela J Rist, Alexander Roth, Lara Frommherz, Christoph H Weinert, Ralf Krüger, Benedikt Merz, Diana Bunzel, Carina Mack, Björn Egert, Achim Bub, Benjamin Görling, Pavleta Tzvetkova, Burkhard Luy, Ingrid Hoffmann, Sabine E Kulling, Bernhard Watzl
Physiological and functional parameters, such as body composition, or physical fitness are known to differ between men and women and to change with age. The goal of this study was to investigate how sex and age-related physiological conditions are reflected in the metabolome of healthy humans and whether sex and age can be predicted based on the plasma and urine metabolite profiles. In the cross-sectional KarMeN (Karlsruhe Metabolomics and Nutrition) study 301 healthy men and women aged 18-80 years were recruited...
2017: PloS One
https://www.readbyqxmd.com/read/28813483/muroid-rodent-phylogenetics-900-species-tree-reveals-increasing-diversification-rates
#3
Scott J Steppan, John J Schenk
We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids...
2017: PloS One
https://www.readbyqxmd.com/read/28811200/globular-adiponectin-reverses-osteo-sarcopenia-and-altered-body-composition-in-ovariectomized-rats
#4
Shyamsundar Pal China, Subhashis Pal, Sourav Chattopadhyay, Konica Porwal, Sapana Kushwaha, Sharmishtha Bhattacharyya, Monika Mittal, Anagha A Gurjar, Tarun Barbhuyan, Abhishek K Singh, Arun K Trivedi, Jiaur R Gayen, Sabyasachi Sanyal, Naibedya Chattopadhyay
Adiponectin regulates various metabolic processes including glucose flux, lipid breakdown and insulin response. We recently reported that adiponectin receptor1 (adipoR1) activation by a small molecule reverses osteopenia in leptin receptor deficient db/db (diabetic) mice. However, the role of adiponectin in bone metabolism under the setting of post-menopausal (estrogen-deficiency) osteopenia and associated metabolic derangements has not been studied. Here, we studied the therapeutic effect of the globular form of adiponectin (gAd), which is predominantly an adipoR1 agonist, in aged ovariectomized (OVX) rats and compared it with standard-of-care anti-osteoporosis drugs...
August 12, 2017: Bone
https://www.readbyqxmd.com/read/28806693/persistence-of-urban-organic-aerosols-composition-decoding-their-structural-complexity-and-seasonal-variability
#5
João T V Matos, Regina M B O Duarte, Sónia P Lopes, Artur M S Silva, Armando C Duarte
Organic Aerosols (OAs) are typically defined as highly complex matrices whose composition changes in time and space. Focusing on time vector, this work uses two-dimensional nuclear magnetic resonance (2D NMR) techniques to examine the structural features of water-soluble (WSOM) and alkaline-soluble organic matter (ASOM) sequentially extracted from fine atmospheric aerosols collected in an urban setting during cold and warm seasons. This study reveals molecular signatures not previously decoded in NMR-related studies of OAs as meaningful source markers...
August 11, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28801166/nuclear-factor-erythroid-derived-2-like-2-nrf2-drug-discovery-biochemical-toolbox-to-develop-nrf2-activators-by-reversible-binding-of-kelch-like-ech-associated-protein-1-keap1
#6
REVIEW
Alberto Bresciani, Antonino Missineo, Mariana Gallo, Mauro Cerretani, Paola Fezzardi, Licia Tomei, Daniel Oscar Cicero, Sergio Altamura, Alessia Santoprete, Raffaele Ingenito, Elisabetta Bianchi, Robert Pacifici, Celia Dominguez, Ignacio Munoz-Sanjuan, Steven Harper, Leticia Toledo-Sherman, Larry C Park
Mechanisms that activate innate antioxidant responses, as a way to mitigate oxidative stress at the site of action, hold much therapeutic potential in diseases, such as Parkinson's disease, Alzheimer's disease and Huntington's disease, where the use of antioxidants as monotherapy has not yielded positive results. The nuclear factor NRF2 is a transcription factor whose activity upregulates the expression of cell detoxifying enzymes in response to oxidative stress. NRF2 levels are modulated by KEAP1, a sensor of oxidative stress...
August 8, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28800760/perceptions-of-patients-and-providers-on-myocardial-perfusion-imaging-for-asymptomatic-patients-choosing-wisely-and-professional-liability
#7
Kristopher P Kline, Leslee Shaw, Rebecca J Beyth, Jared Plumb, Linda Nguyen, Tianyao Huo, David E Winchester
BACKGROUND: Despite efforts by professional societies to reduce low value care, many reports indicate that unnecessary tests, such as nuclear myocardial perfusion imaging (MPI), are commonly used in contemporary practice. The degree to which lack of awareness and professional liability concerns drive these behaviors warrants further study. We sought to investigate patient and provider perceptions about MPI in asymptomatic patients, the Choosing Wisely (CW) campaign, and professional liability concerns...
August 11, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28798228/technical-peer-review-methods-and-outcomes
#8
Andrew M Keenan, Toni Cranston, Kelsey Hill, Derek J Stocker
Peer review among physicians, nurses and pharmacy staff is routine, yet uncommon in the field of nuclear medicine technology. While not a requirement of regulatory agencies, nuclear medicine technical peer review can greatly enhance the quality of patient care in both hospital and outpatient settings. To date, detailed methods for accomplishing this task have not been previously published. Methods: 19,688 nuclear medicine studies performed at a single institution over a five-year period were critically reviewed...
August 10, 2017: Journal of Nuclear Medicine Technology
https://www.readbyqxmd.com/read/28797839/building-a-complex-complex-assembly-of-mitochondrial-respiratory-chain-complex-i
#9
REVIEW
Luke E Formosa, Marris G Dibley, David A Stroud, Michael T Ryan
Mitochondrial complex I is the primary entry point for electrons into the electron transport chain, required for the bulk of cellular ATP production via oxidative phosphorylation. Complex I consists of 45 subunits, which are encoded by both nuclear and mitochondrial DNA. Currently, at least 15 assembly factors are known to be required for the complete maturation of complex I. Mutations in the genes encoding subunits and assembly factors leads to complex I deficiency, which can manifest as mitochondrial disease...
August 7, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28797551/behavior-of-137-cs-in-ponds-in-the-vicinity-of-the-fukushima-dai-ichi-nuclear-power-plant
#10
Yoshifumi Wakiyama, Alexei Konoplev, Toshihiro Wada, Tsugiko Takase, Ian Byrnes, Matthew Carradine, Kenji Nanba
(137)Cs activity concentration in the water of four ponds, Suzuuchi (SU), Funasawa (FS), Inkyozaka (IZ), and Kashiramori (KM), that are within 10 km of the Fukushima Dai-ichi nuclear power plant were observed from April 2015 to August 2016. (137)Cs inventories in soils surrounding SU, FS, IZ, and KM were 6.4, 2.9, 2.1, and 0.9 MBq m(-2), respectively. (137)Cs inventories in the bottom sediments of SU, FS, IZ, and KM were 13, 8.9, 1.6, and 1.1 MBq m(-2), respectively. Higher (137)Cs inventories in bottom sediment than those of soil in SU and FS suggest that (137)Cs was delivered to and accumulated in these ponds...
August 8, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28797155/-clinical-significance-of-%C3%AF-1-receptor-over-expression-in-cervical-cancer-and-the-effect-of-its-synthetic-ligands-on-the-growth-of-cervical-cancer-cells
#11
Y Q Deng, X H Zhou, L L Jiang, X J Tang, Y X Zhang, J Q Cui
Objective: To explore the role of σ1 receptor (σ1R) in the clinical prognosis of cervical cancer,and provide a theoretical basis for σ1R targeted molecular therapy through observing the inhibition of synthetic σ1R-specific ligand compounds on the growth of cervical cancer cells. Methods: (1) Immunohistochemical or immunocytochemistry staining were respectively used to detect the expression and localization of σ1R protein. (2) The Cancer Genome Atlas (TCGA) data set was used to validate our results. (3) Two series of 4 novel σ1R ligand compounds were synthesized by altering the N-terminal substituents on the piperidine ring of the prezamicol analogue, named as 14a, 14e, 15c and 15f...
July 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28797013/effects-of-berberine-on-acute-necrotizing-pancreatitis-and-associated-lung-injury
#12
Sun-Bok Choi, Gi-Sang Bae, Il-Joo Jo, Ho-Joon Song, Sung-Joo Park
OBJECTIVES: We set out to examine whether berberine (BBR) might affect the severity of pancreatitis and pancreatitis-associated lung injury in choline-deficient ethionine-supplemented (CDE) diet-induced severe acute pancreatitis. METHODS: Severe acute pancreatitis was induced by feeding a CDE diet for 3 days. Berberine was administered intraperitoneally during CDE diet. Mice were killed on days 1, 2, and 3 after the onset of CDE diet. The severity of pancreatitis was assessed by evaluating changes to the pancreas and lung and survival rate...
September 2017: Pancreas
https://www.readbyqxmd.com/read/28793337/assessment-of-gold-nanoparticles-on-human-peripheral-blood-cells-by-metabolic-profiling-with-1h-nmr-spectroscopy-a-novel-translational-approach-on-a-patient-specific-basis
#13
Martina Palomino-Schätzlein, Hermenegildo García, Patricia Gutiérrez-Carcedo, Antonio Pineda-Lucena, José Raul Herance
Human peripheral blood cells are relevant ex vivo models for characterizing diseases and evaluating the pharmacological effects of therapeutic interventions, as they provide a close reflection of an individual pathophysiological state. In this work, a new approach to evaluate the impact of nanoparticles on the three main fractions of human peripheral blood cells by nuclear magnetic resonance spectroscopy is shown. Thus, a comprehensive protocol has been set-up including the separation of blood cells, their in vitro treatment with nanoparticles and the extraction and characterization of metabolites by nuclear magnetic resonance...
2017: PloS One
https://www.readbyqxmd.com/read/28791516/nlscore-a-novel-quantitative-algorithm-based-on-3-dimensional-structural-determinants-to-predict-the-probability-of-nuclear-localization-in-proteins-containing-classical-nuclear-localization-signals
#14
P S Hari, T S Sridhar, R Pravin Kumar
The presence of a nuclear localization signal (NLS) in proteins can be inferred by the presence of a stretch of basic amino acids (KRKK). These NLSs are termed classical NLS (cNLS). However, only a fraction of proteins containing the cNLS pattern are transported into the nucleus by binding to importin α. Hence, there must exist, additional structural determinants that guide the appropriate interaction between putative NLSs containing cargo and importin α. Using 52 protein structures containing cNLS obtained from RCSB PDB, we assembled a training set and a validation set such that both sets were comprised of a combination of proteins with proven nuclear localization and ones that were non-nuclear...
August 9, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28790982/isolation-and-characterization-of-terrein-an-antimicrobial-and-antitumor-compound-from-endophytic-fungus-aspergillus-terreus-jas-2-associated-from-achyranthus-aspera-varanasi-india
#15
Jyoti Goutam, Gunjan Sharma, Vinod K Tiwari, Amrita Mishra, Ravindra N Kharwar, Vijayakumar Ramaraj, Biplob Koch
The present study aimed at characterizing biological potentials of endophyte Aspergillus terreus JAS-2 isolated from Achyranthus aspera. Crude extracted from endophytic fungus JAS-2 was purified and chemically characterized by chromatographic and spectroscopic studies respectively. Spectral assignment of NMR (nuclear magnetic resonance) data, (1)H proton and (13)C carbon analysis along with FTIR data elucidated the structure of compound as 4,5-Dihydroxy-3-(1-propenyl)-2-cyclopenten-1-one. After purification and identification a set of experiment was conducted to explore efficacy of compound...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28790194/characterization-of-the-potent-selective-nrf2-activator-pstc-in-cellular-and-in-vivo-models-of-pulmonary-oxidative-stress
#16
John G Yonchuk, Joseph P Foley, Brian J Bolognese, Gregory A Logan, William E Wixted, Jen-Pyng Kou, Diana G Chalupowicz, Heidi G Feldser, Yolanda Sanchez, Hong Nie, James F Callahan, Jeffrey K Kerns, Patricia L Podolin
Nrf2 is a key regulator of oxidative stress and cellular repair, and can be activated through inhibition of its cytoplasmic repressor, Keap1. Several small molecule disrupters of the Nrf2-Keap1 complex have recently been tested and/or approved for human therapeutic use but lack either potency or selectivity. The main goal of our work was to develop a potent, selective activator of NRF2 as protection against oxidative stress. In human bronchial epithelial cells our Nrf2 activator, PSTC, induced Nrf2 nuclear translocation, Nrf2-regulated gene expression, and downstream signaling events including induction of NQO1 enzyme activity and HO-1 protein expression, in an Nrf2-dependent manner...
August 8, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28789534/excited-state-wavepacket-dynamics-in-no2-probed-by-strong-field-ionization
#17
Ruaridh Forbes, Andrey E Boguslavskiy, Iain Wilkinson, Jonathan G Underwood, Albert Stolow
We present an experimental femtosecond time-resolved study of the 399 nm excited state dynamics of nitrogen dioxide using channel-resolved above threshold ionization (CRATI) as the probe process. This method relies on photoelectron-photoion coincidence and covariance to correlate the strong-field photoelectron spectrum with ionic fragments, which label the channel. In all ionization channels observed, we report apparent oscillations in the ion and photoelectron yields as a function of pump-probe delay. Further, we observe the presence of a persistent, time-invariant above threshold ionization comb in the photoelectron spectra associated with most ionization channels at long time delays...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28783477/a-high-content-live-cell-viability-assay-and-its-validation-on-a-diverse-12k-compound-screen
#18
Jeanne Chiaravalli, J Fraser Glickman
We have developed a new high-content cytotoxicity assay using live cells, called "ImageTOX." We used a high-throughput fluorescence microscope system, image segmentation software, and the combination of Hoechst 33342 and SYTO 17 to simultaneously score the relative size and the intensity of the nuclei, the nuclear membrane permeability, and the cell number in a 384-well microplate format. We then performed a screen of 12,668 diverse compounds and compared the results to a standard cytotoxicity assay. The ImageTOX assay identified similar sets of compounds to the standard cytotoxicity assay, while identifying more compounds having adverse effects on cell structure, earlier in treatment time...
August 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28778066/inhibition-of-lsd1-epigenetically-attenuates-oral-cancer-growth-and-metastasis
#19
Saqer F Alsaqer, Mustafa M Tashkandi, Vinay K Kartha, Ya-Ting Yang, Yazeed Alkheriji, Andrew Salama, Xaralabos Varelas, Maria Kukuruzinska, Stefano Monti, Manish V Bais
Lysine-specific demethylase 1 (LSD1) is a nuclear histone demethylase and a member of the amine oxidase (AO) family. LSD1 is a flavin-containing AO that specifically catalyzes the demethylation of mono- and di-methylated histone H3 lysine 4 through an FAD-dependent oxidative reaction. LSD1 is inappropriately upregulated in lung, liver, brain and esophageal cancers, where it promotes cancer initiation, progression, and metastasis. However, unlike other lysine-specific demethylases, the role and specific targets of LSD1 in oral squamous cell carcinoma (OSCC) pathogenesis remain unknown...
July 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28776575/an-oral-cavity-squamous-cell-carcinoma-quantitative-histomorphometric-based-image-classifier-of-nuclear-morphology-can-risk-stratify-patients-for-disease-specific-survival
#20
Cheng Lu, James S Lewis, William D Dupont, W Dale Plummer, Andrew Janowczyk, Anant Madabhushi
Oral cavity squamous cell carcinoma is the most common type of head and neck carcinoma. Its incidence is increasing worldwide, and it is associated with major morbidity and mortality. It is often unclear which patients have aggressive, treatment refractory tumors vs those whose tumors will be more responsive to treatment. Better identification of patients with high- vs low-risk cancers could help provide more tailored treatment approaches and could improve survival rates while decreasing treatment-related morbidity...
August 4, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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