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https://www.readbyqxmd.com/read/28425476/lncrnas2pathways-identifying-the-pathways-influenced-by-a-set-of-lncrnas-of-interest-based-on-a-global-network-propagation-method
#1
Junwei Han, Siyao Liu, Zeguo Sun, Yunpeng Zhang, Fan Zhang, Chunlong Zhang, Desi Shang, Haixiu Yang, Fei Su, Yanjun Xu, Chunquan Li, Huan Ren, Xia Li
Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, we have developed a novel computational method, LncRNAs2Pathways, to identify the functional pathways influenced by the combinatorial effects of a set of lncRNAs of interest based on a global network propagation algorithm...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28416487/metabolic-markers-and-statistical-prediction-of-serous-ovarian-cancer-aggressiveness-by-ambient-ionization-mass-spectrometry-imaging
#2
Marta Sans, Kshipra M Gharpure, Robert Tibshirani, Jialing Zhang, Li Liang, Jinsong Liu, Jonathan H Young, Robert Dood, Anil K Sood, Livia Eberlin
Ovarian high-grade serous carcinoma (HGSC) results in the highest mortality among gynecological cancers, developing rapidly and aggressively. Dissimilarly, serous borderline ovarian tumors (BOT) can progress into low-grade serous carcinomas and have relatively indolent clinical behavior. The underlying biological differences between HGSC and BOT call for accurate diagnostic methodologies and tailored treatment options, and identification of molecular markers of aggressiveness could provide valuable biochemical insights and improve disease management...
April 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28400509/oncogene-kras-activates-fatty-acid-synthase-resulting-in-specific-erk-and-lipid-signatures-associated-with-lung-adenocarcinoma
#3
Arvin M Gouw, Livia S Eberlin, Katherine Margulis, Delaney K Sullivan, Georgia G Toal, Ling Tong, Richard N Zare, Dean W Felsher
KRAS gene mutation causes lung adenocarcinoma. KRAS activation has been associated with altered glucose and glutamine metabolism. Here, we show that KRAS activates lipogenesis, and this activation results in distinct proteomic and lipid signatures. By gene expression analysis, KRAS is shown to be associated with a lipogenesis gene signature and specific induction of fatty acid synthase (FASN). Through desorption electrospray ionization MS imaging (DESI-MSI), specific changes in lipogenesis and specific lipids are identified...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28370721/detection-and-imaging-of-thermochromic-ink-compounds-in-erasable-pens-using-desorption-electrospray-ionization-mass-spectrometry-desi-ms
#4
Amin Khatami, Shamina S Prova, Aafreen Bagga, Michelle Ting, Gurnoor Brar, Demian R Ifa
RATIONALE: Thermochromic ink pens are widely accessible worldwide and have gained popularity among the general public. These pens are very useful to undo mistakes while writing important documents or exams. They are also, however, extensively misused in committing crimes such as counterfeiting checks or wills. Thus, the forensics community is in need of techniques that will allow these forgeries to be detected rapidly, reliably and conveniently. METHODS: Thermochromic ink compounds were investigated using Desorption Electrospray Ionization (DESI) coupled with an LTQ mass spectrometer and Thin Layer Chromatography (TLC)...
March 30, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28361233/rna-seq-analysis-for-transcriptome-profiling-in-response-to-classical-swine-fever-vaccination-in-indigenous-and-crossbred-pigs
#5
Shalu Kumari Pathak, Amit Kumar, G Bhuwana, Vaishali Sah, Vikramadiya Upmanyu, A K Tiwari, A P Sahoo, A R Sahoo, Sajjad A Wani, Manjit Panigrahi, N R Sahoo, Ravi Kumar
In present investigation, differential expression of transcriptome after classical swine fever (CSF) vaccination has been explored at the cellular level in crossbred and indigenous (desi) piglets. RNA Sequencing by Expectation-Maximization (RSEM) package was used to quantify gene expression from RNA Sequencing data, and differentially expressed genes (DEGs) were identified using EBSeq, DESeq2, and edgeR softwares. After analysis, 5222, 6037, and 6210 common DEGs were identified in indigenous post-vaccinated verses pre-vaccinated, crossbred post-vaccinated verses pre-vaccinated, and post-vaccinated crossbred verses indigenous pigs, respectively...
March 30, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28360165/complete-genome-sequence-of-lactobacillus-fermentum-mtcc-25067-formerly-tds030603-a-viscous-exopolysaccharide-producing-strain-isolated-from-indian-fermented-milk
#6
Ni Putu Desy Aryantini, Jashbhai B Prajapati, Tadasu Urashima, Kenji Fukuda
Lactobacillus fermentum MTCC 25067 (formerly TDS030603) is capable of producing a highly viscous slime exopolysaccharide. We report here the complete genome sequence of the strain, which was deciphered by using PacBio single-molecule real-time sequencing technology.
March 30, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28352134/diagnosis-making-desi-msi-desirable
#7
Clemens Thoma
No abstract text is available yet for this article.
March 29, 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/28352074/optimized-mass-spectrometry-analysis-workflow-with-polarimetric-guidance-for-ex-vivo-and-in-situ-sampling-of-biological-tissues
#8
Michael Woolman, Adam Gribble, Emma Bluemke, Jing Zou, Manuela Ventura, Nicholas Bernards, Megan Wu, Howard J Ginsberg, Sunit Das, Alex Vitkin, Arash Zarrine-Afsar
Spatially Targeted Mass Spectrometry (MS) analysis using survey scans with an imaging modality often requires consecutive tissue slices, because of the tissue damage during survey scan or due to incompatible sample preparation requirements between the survey modality and MS. We report two spatially targeted MS analysis workflows based on polarized light imaging guidance that use the same tissue sample for survey and targeted analysis. The first workflow is applicable for thin-slice analysis, and uses transmission-polarimetry-guided Desorption ElectroSpray Ionization Mass Spectrometry (DESI-MS), and confirmatory H&E histopathology analysis on the same slice; this is validated using quantitative digital pathology methods...
March 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337399/clinical-application-of-ambient-ionization-mass-spectrometry
#9
Li-Hua Li, Hua-Yi Hsieh, Cheng-Chih Hsu
Ambient ionization allows mass spectrometry analysis directly on the sample surface under atmospheric pressure with almost zero sample pretreatment. Since the development of desorption electrospray ionization (DESI) in 2004, many other ambient ionization techniques were developed. Due to their simplicity and low operation cost, rapid and on-site clinical mass spectrometry analysis becomes real. In this review, we will highlight some of the most widely used ambient ionization mass spectrometry approaches and their applications in clinical study...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28333282/anchorless-cell-surface-proteins-function-as-laminin-binding-adhesins-in-lactobacillus-rhamnosus-fsmm22
#10
Ni Putu Desy Aryantini, Daisuke Kondoh, Keita Nishiyama, Yuji Yamamoto, Takao Mukai, I Nengah Sujaya, Tadasu Urashima, Kenji Fukuda
Anchorless cell surface proteins (CSPs) were extracted with 1 M lithium chloride solution from Lactobacillus rhamnosus FSMM22. Loss of the anchorless CSPs resulted in a 2-fold decrease in FSMM22 cells bound to a constitutive extracellular matrix glycoprotein, laminin, in vitro. DNA-binding protein HU, glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase and 30S ribosomal protein S19 (RpsS) were identified by mass spectrometry in the extract as laminin-binding adhesins. Among the four proteins, RpsS was immunohistochemically confirmed to exist on the cell surface...
March 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28320493/the-nicu-environment-infusing-single-family-room-benefits-into-the-open-bay-setting
#11
Jenna L Meredith, Amy Jnah, Desi Newberry
Two distinct architectural designs are found in today's NICUs-the open-bay (OPBY) and the single-family room (SFR) designs. When neonatology was recognized as a medical subspecialty in the 1970s, the OPBY design was the only platform offered to neonates and families. The OPBY design facilitated communication between staff, collegiality, and interprofessional collaboration among members of the neonatal team. Over time, pitfalls to the design were recognized, including increased transmission of sound and light...
March 1, 2017: Neonatal Network: NN
https://www.readbyqxmd.com/read/28315234/ammonium-bicarbonate-addition-improves-the-detection-of-proteins-by-desorption-electrospray-ionization-mass-spectrometry
#12
Elahe Honarvar, Andre R Venter
The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents...
March 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28306315/hard-two-photon-contribution-to-elastic-lepton-proton-scattering-determined-by-the-olympus-experiment
#13
B S Henderson, L D Ice, D Khaneft, C O'Connor, R Russell, A Schmidt, J C Bernauer, M Kohl, N Akopov, R Alarcon, O Ates, A Avetisyan, R Beck, S Belostotski, J Bessuille, F Brinker, J R Calarco, V Carassiti, E Cisbani, G Ciullo, M Contalbrigo, R De Leo, J Diefenbach, T W Donnelly, K Dow, G Elbakian, P D Eversheim, S Frullani, Ch Funke, G Gavrilov, B Gläser, N Görrissen, D K Hasell, J Hauschildt, Ph Hoffmeister, Y Holler, E Ihloff, A Izotov, R Kaiser, G Karyan, J Kelsey, A Kiselev, P Klassen, A Krivshich, I Lehmann, P Lenisa, D Lenz, S Lumsden, Y Ma, F Maas, H Marukyan, O Miklukho, R G Milner, A Movsisyan, M Murray, Y Naryshkin, R Perez Benito, R Perrino, R P Redwine, D Rodríguez Piñeiro, G Rosner, U Schneekloth, B Seitz, M Statera, A Thiel, H Vardanyan, D Veretennikov, C Vidal, A Winnebeck, V Yeganov
The OLYMPUS Collaboration reports on a precision measurement of the positron-proton to electron-proton elastic cross section ratio, R_{2γ}, a direct measure of the contribution of hard two-photon exchange to the elastic cross section. In the OLYMPUS measurement, 2.01 GeV electron and positron beams were directed through a hydrogen gas target internal to the DORIS storage ring at DESY. A toroidal magnetic spectrometer instrumented with drift chambers and time-of-flight scintillators detected elastically scattered leptons in coincidence with recoiling protons over a scattering angle range of ≈20° to 80°...
March 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28304192/direct-analysis-of-samples-of-various-origin-and-composition-using-specific-types-of-mass-spectrometry
#14
Hubert Byliński, Jacek Gębicki, Tomasz Dymerski, Jacek Namieśnik
One of the major sources of error that occur during chemical analysis utilizing the more conventional and established analytical techniques is the possibility of losing part of the analytes during the sample preparation stage. Unfortunately, this sample preparation stage is required to improve analytical sensitivity and precision. Direct techniques have helped to shorten or even bypass the sample preparation stage; and in this review, we comment of some of the new direct techniques that are mass-spectrometry based...
March 17, 2017: Critical Reviews in Analytical Chemistry
https://www.readbyqxmd.com/read/28303051/near-isogenic-lines-of-desi-chickpea-cicer-arietinum-l-that-differ-in-milling-ease-differences-in-chemical-composition
#15
Jennifer A Wood, Edmund J Knights, Grant M Campbell, Mingan Choct
Milling performance is an important attribute for desi chickpea and other pulses, as varieties that are more difficult-to-mill lead to processing yield loss and damage to the resulting split cotyledons (dhal) such as chipping and abrasion which are unattractive to the consumer. Poor milling performance leads to poor dhal quality and therefore lower prices and profitability along the pulse value chain. The Pulse Breeding Australia Chickpea Program identified near-isogenic desi lines that differed in seed shape and milling yields, however it was unknown whether this was due simply to a difference in physical forces on the seed during milling, mediated by seed shape, or whether there were underlying differences in chemical composition that could explain these differences...
March 2017: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28299204/the-coadministration-of-unoxidized-and-oxidized-desi-ghee-ameliorates-the-toxic-effects-of-thermally-oxidized-ghee-in-rabbits
#16
Alam Zeb, Islam Uddin
Desi Ghee was thermally oxidized at 160°C for 9 h and characterized for peroxide value (PV), free fatty acid (FFA), thiobarbituric acid reactive substances (TBARS), radical scavenging activity (RSA), and fatty acid and cholesterol composition using GC-MS. Oxidized (OG) and normal ghee (NG) were fed to rabbits in different doses. Blood was collected for hematology and biochemical analyses after 7 and 14 days. The oxidation of desi ghee increased the PV, FFA, and TBARS values and showed a decline in the RSA values...
2017: Journal of Nutrition and Metabolism
https://www.readbyqxmd.com/read/28294642/cost-effectiveness-of-sequenced-treatment-of-rheumatoid-arthritis-with-targeted-immune-modulators
#17
Jeroen P Jansen, Devin Incerti, Alex Mutebi, Desi Peneva, Joanna P MacEwan, Bradley Stolshek, Primal Kaur, Mahdi Gharaibeh, Vibeke Strand
AIMS: To determine the cost-effectiveness of treatment sequences of biologic disease-modifying anti-rheumatic drugs or Janus kinase/STAT pathway inhibitors (collectively referred to as bDMARDs) vs conventional DMARDs (cDMARDs) from the US societal perspective for treatment of patients with moderately to severely active rheumatoid arthritis (RA) with inadequate responses to cDMARDs. MATERIALS AND METHODS: An individual patient simulation model was developed that assesses the impact of treatments on disease based on clinical trial data and real-world evidence...
April 5, 2017: Journal of Medical Economics
https://www.readbyqxmd.com/read/28294229/molecular-imaging-of-small-molecule-drugs-in-animal-tissues-using-laser-desorption-postionization-mass-spectrometry
#18
Jiaxin Chen, Yongjun Hu, Qiao Lu, Pengchao Wang, Huaqi Zhan
Localization and quantification of the target drug in tissues is a key indicator of efficacy in drug discovery. In contrast to established methods that require matrices and complex sample pretreatment steps, matrix-free and low cost in situ analysis of small molecule drugs by mass spectrometry (MS) remains challenging. Here, we present a novel approach, laser desorption postionization (LDPI), which is coupled to a linear time-of-flight (TOF) MS and used to image the distribution of acriflavine (ACF) directly from a histological section of mouse kidney without any matrix or sample pretreatment...
March 15, 2017: Analyst
https://www.readbyqxmd.com/read/28292895/diagnosis-of-prostate-cancer-by-desorption-electrospray-ionization-mass-spectrometric-imaging-of-small-metabolites-and-lipids
#19
Shibdas Banerjee, Richard N Zare, Robert J Tibshirani, Christian A Kunder, Rosalie Nolley, Richard Fan, James D Brooks, Geoffrey A Sonn
Accurate identification of prostate cancer in frozen sections at the time of surgery can be challenging, limiting the surgeon's ability to best determine resection margins during prostatectomy. We performed desorption electrospray ionization mass spectrometry imaging (DESI-MSI) on 54 banked human cancerous and normal prostate tissue specimens to investigate the spatial distribution of a wide variety of small metabolites, carbohydrates, and lipids. In contrast to several previous studies, our method included Krebs cycle intermediates (m/z <200), which we found to be highly informative in distinguishing cancer from benign tissue...
March 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28254286/synchrotron-based-xrd-from-rat-bone-of-different-age-groups
#20
D V Rao, G E Gigante, R Cesareo, A Brunetti, N Schiavon, T Akatsuka, T Yuasa, T Takeda
Synchrotron-based XRD spectra from rat bone of different age groups (w, 56 w and 78w), lumber vertebra at early stages of bone formation, Calcium hydroxyapatite (HAp) [Ca10(PO4)6(OH)2] bone fill with varying composition (60% and 70%) and bone cream (35-48%), has been acquired with 15keV synchrotron X-rays. Experiments were performed at Desy, Hamburg, Germany, utilizing the Resonant and Diffraction beamline (P9), with 15keV X-rays (λ=0.82666 A(0)). Diffraction data were quantitatively analyzed using the Rietveld refinement approach, which allowed us to characterize the structure of these samples in their early stages...
May 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
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