147 research outputs found
Mir-150-5p transfection mimics GR like gene activation and repression response in MM1S and lack of response in MM1R cells.
No full text<p>(<b>A</b>) Realtime quantitative PCR (QPCR) validation of GILZ (TSC22D3) and FKBP5 mRNA induction in MM1S and in MM1R cells, following 72 h treatment with 1 nM or 1 µM Dex (left panel), or following 72 h transfection with synthetic mir-150-5p, 72 h treatment with 1 nM Dex, or a combination thereof (right panel). Data represent (mean ± SEM) values of three independent experiments normalized to 28S RNA housekeeping gene and relative to the respective untreated/solvent (UT) or MOCK control setups. Means with ***, **, * are significantly different (p<0.001, <0.01 or <0.05) from control setup as determined by two-way ANOVA (Bonferroni posttest). (<b>B</b>) Realtime quantitative PCR (QPCR) validation of MYB, IL23A, SKP2, BUB1, SREBF1 mRNA repression levels in MM1S or MM1R cells, following 72 h treatment with 1 nM or 1 µM Dex, or following 72 h transfection with synthetic mir-150-5p, 72 h treatment with 1 nM Dex, or a combination thereof. Data represent (mean ± SEM) values of three independent experiments normalized to 28S RNA housekeeping gene and relative to the respective untreated/solvent (UT) or MOCK control setups. Means with ***, **, * are significantly different (p<0.001, <0.01 or <0.05) from control setup as determined by two-way ANOVA (Bonferroni posttests) (<b>C</b>) Illumina BeadChip Gene Expression Array results of selected genes are presented as bargraphs, reflecting mean of gene expression fold change from three independent experiments of MM1S cells, treated for 72 h with 1 µM Dex, or else of MM1S cells transfected for 72 h with synthetic mir-150-5p versus mock transfection, treated for 72 h with 1 nM Dex or a combination thereof versus control samples.</p
Conformational Switching in Self-Assembling Mechanical Systems
No full textA study of 1D self-assembly of a type of mechanical conformational switches, minus devices is presented where assembly occurs via the sequential mating of a random pair of parts selected from a part bin, referred to as sequential random bin-picking. The minus devices facilitate the robust yield of a desired assembly against the variation in the initial fraction of the part types, by specifying a fixed assembly sequence during the self-assembling process. It is also found that while the minus devices can encode" some assembly sequences, encoding other assembly sequences requires the use of another type of conformational switches, plus devices. It is proved that the local rules corresponding to the minus and plus devices, and three conformations per each component, can encode any assembly sequences of a 1D assembly of distinct components with arbitrary lengthPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87253/4/Saitou44.pd
Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter
No full textInaccuracies
in ion detection and signal processing can undermine
confidence in the molecular formula assignment of high-resolution
mass spectrometry, which relies on precise matching of the mass-to-charge
ratio (m/z). This study proposes
a novel graph-based spectra calibration method, MSCMcalib, which implements
coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect
plot, facilitating the automatic calibration of detected lines, i.e.,
the calibration of uncalibrated peaks aligned with these lines. The
“propagation” method is subsequently employed to accurately
and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval
undergoing a process of “scaling” calibration. The utilization
of narrower partitions effectively mitigates divergence issues at
both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is
validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6
ppm, resulting in an additional assignment of 11%–30% more
molecular formulas compared to the quadratic fitting calibration
Quantitative Molecular Characterization of Petroleum Asphaltenes Derived Ruthenium Ion Catalyzed Oxidation Product by ESI FT-ICR MS
No full textMolecular
structure of heavy petroleum could be investigated by
the composition of its ruthenium ion catalyzed oxidation (RICO) products.
However, the interpretation of the results was not comprehensive due
to the limited compositional information obtained solely by gas chromatography
(GC) analysis. In this study, a semiquantitative method based on electrospray
ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry
(FT-ICR MS) was established and applied for the molecular characterization
of RICO products. Thousands of polar compounds were detected by negative-ion
ESI FT-ICR MS in the RICO products of the Canadian oil sands bitumen
derived asphaltenes. Besides alkyl carboxylic acids, naphthenic acids
with one to five naphtha rings, nitrogen- and sulfur-containing carboxylic
acids, and acidic compounds with multioxygen atoms were observed.
The upper carbon number limit of alkyl moieties connected to the aromatic
cores of the asphaltenes was found up to 60, which is much higher
than the results derived from GC analysis. Normal and isomer alkyl
carboxylic acids, as well as naphthenic acids, were quantitatively
analyzed separately. The quantitative results of alkyl carboxylic
acids from ESI FT-ICR MS agreed well with the GC results. The FT-ICR
MS results indicate that additional compositional information could
be obtained from RICO analysis. In addition, the method is instructive
for the development of quantitative analysis technology for petroleum
molecular characterization based on ESI FT-ICR MS
Viscosity Modeling of Heavy Crude Oil Using the Friction Theory Combined with PC-SAFT
No full textSmall changes in temperature or pressure can lead to
crude oil
phase separation and multiple orders of magnitude change in viscosity.
The one-parameter friction theory framework using the SARA-based method
with the perturbed-chain statistical association fluid theory (PC-SAFT)
EoS has proven to have high accuracy in viscosity predictions of light
oil. However, it failed for heavy crude oil. In this work, the above
model is modified in two aspects to enhance the accuracy of heavy
crude oil viscosity prediction: to include the effect of asphaltene
polydispersity and to include the temperature effect to the friction
theory parameter. The average absolute relative deviation of the four
studied heavy oils is reduced by 16.81, 24.26, 97.31, and 87.75% compared
to the one-parameter f-theory SARA-based PC-SAFT model. The f-theory
parameter Kc is modified as a function
of temperature fitted to the viscosity at normal temperature and pressure.
Following the simplicity of the expansion of the method, it is recommended
to use this methodology when dealing with heavy crude oils such as
those with viscosity more than 20,000 cP at 25 °C
Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter
No full textInaccuracies
in ion detection and signal processing can undermine
confidence in the molecular formula assignment of high-resolution
mass spectrometry, which relies on precise matching of the mass-to-charge
ratio (m/z). This study proposes
a novel graph-based spectra calibration method, MSCMcalib, which implements
coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect
plot, facilitating the automatic calibration of detected lines, i.e.,
the calibration of uncalibrated peaks aligned with these lines. The
“propagation” method is subsequently employed to accurately
and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval
undergoing a process of “scaling” calibration. The utilization
of narrower partitions effectively mitigates divergence issues at
both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is
validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6
ppm, resulting in an additional assignment of 11%–30% more
molecular formulas compared to the quadratic fitting calibration
Ionizing Aromatic Compounds in Petroleum by Electrospray with HCOONH<sub>4</sub> as Ionization Promoter
No full textElectrospray ionization (ESI) coupled
with Fourier ion cyclotron
resonance mass spectrometry (FTICR MS) has been successfully used
for molecular characterization of petroleum. However, ESI can not
ionize nonpolar components which generally are dominant in the petroleum
fraction. Here, we introduce a novel approach for aromatic compounds
molecular characterization. Aromatics in petroleum fractions were
ionized to [M + H]+ by positive-ion ESI with HCOONH4 as an ionization promoter, and when ESI is combined with
high resolution FTICR MS, aromatic hydrocarbons and heteroatoms in
petroleum fractions can be simultaneously analyzed. The method is easily available
and has potential for the characterization of aromatic compounds in
any other matrix
Acidic and Neutral Polar NSO Compounds in Heavily Biodegraded Oils Characterized by Negative-Ion ESI FT-ICR MS
No full textFive heavily biodegraded
tar sand bitumens from an oil column were
separated into maltene and asphaltene fractions for analysis by negative-ion
electrospray (ESI) Fourier transform ion cyclotron resonance mass
spectrometry (FT-ICR MS). These bitumens have an identical source,
which have experienced a natural sequence of biodegradation. The polar
NSO compounds in maltene fractions contain O<sub>1</sub>, S<sub>1</sub>O<sub>1</sub>, O<sub>2</sub>, S<sub>1</sub>O<sub>2</sub>, S<sub>2</sub>O<sub>2</sub>, O<sub>3</sub>, S<sub>1</sub>O<sub>3</sub>, O<sub>4</sub>, S<sub>1</sub>O<sub>4</sub>, N<sub>1</sub>, N<sub>1</sub>O<sub>1</sub>, N<sub>1</sub>O<sub>2</sub>, N<sub>1</sub>S<sub>1</sub>, and S<sub>1</sub> classes, while the polar NSO compounds in asphaltene fractions
contain O<sub>1</sub>, S<sub>1</sub>O<sub>1</sub>, S<sub>2</sub>O<sub>1</sub>, O<sub>2</sub>, S<sub>1</sub>O<sub>2</sub>, S<sub>2</sub>O<sub>2</sub>, O<sub>3</sub>, S<sub>1</sub>O<sub>3</sub>, S<sub>2</sub>O<sub>3</sub>, O<sub>4</sub>, S<sub>1</sub>O<sub>4</sub>, S<sub>2</sub>O<sub>4</sub>, O<sub>5</sub>, S<sub>1</sub>O<sub>5</sub>, S<sub>2</sub>O<sub>5</sub>, O<sub>6</sub>, N<sub>1</sub>, N<sub>1</sub>O<sub>1</sub>, N<sub>1</sub>O<sub>2</sub>, N<sub>1</sub>O<sub>3</sub>, N<sub>1</sub>S<sub>1</sub>, and N<sub>2</sub> classes. Polar NSO compounds with
stronger molecular polarity and larger molecular weight are readily
fractionated into asphaltene fractions. The O<sub>2</sub> class is
prevalent in polar NSO compounds of both maltene and asphaltene fractions
of all bitumen samples. The N<sub>1</sub> class in maltene fractions
is dominated by compounds with DBE values of 9, 10, 12 and 13, while
the N<sub>1</sub> class in asphaltene fractions is dominated by compounds
with a DBE of 15. Most of these N<sub>1</sub> compounds are likely
pyrrolic compounds with various numbers of aromatic rings. The biodegradation
pathways of nitrogen-containing compounds are also explored in this
study. N<sub>1</sub> species are likely converted to N<sub>1</sub>O<sub>1</sub> and N<sub>1</sub>O<sub>2</sub> species following biodegradation
pathways such as ring-opening reaction or carbazole dioxygenase (CARDO)
catalytic oxidation reaction. S<sub>1</sub>O<sub>2–5</sub> classes
are identified as the dominant sulfur-containing compound classes
under negative-ion ESI mode. These classes are considered to contain
acid functionalities with higher polarity because the sulfur-containing
compounds without oxygen are difficult to analyze by negative-ion
ESI in which acids can be ionized by deprotonation. Both progressive
oxidation and sulfuration may be involved in the anaerobic biodegradation
of sulfur-containing acidic compounds
Pattern Recognition Technology Application in Intelligent Processing of Heavy Oil
No full textReliable and efficient product yield estimation for unknown
oils after the fluid catalytic cracking (FCC) reaction is one of the
key components in heavy oil intelligent processing. This paper describes
the use of two chemometric pattern recognition methods, <i>k</i>-nearest neighbor (<i>k</i>-NN) classification and supervised
self-organizing maps (SSOMs), for building classification models to
determine the most similar oil sample to an unknown sample in a given
data set and to use the FCC yields record of the correspondent oil
as the product yield prediction for the unknown sample under the same
reaction conditions. Two-sided <i>t</i> test, correlation
analysis, and hierarchical cluster heat map analysis were performed
to assess the quality of the models. The work provides laboratory
evidence that <i>k</i>-NN or SSOMs techniques could all
be employed for FCC product yield estimation, while the <i>k</i>-NN model would be more suitable for industrial application in terms
of stability and efficiency
Potential of Using Coal Tar as a Quenching Agent for Coal Gasification
No full textTo
reduce water usage and wastewater treatment in coal gasification
processing, the use of non-aqueous quenching agents was proposed.
The purpose of this study is to assess the potential of using coal
tar as a quenching agent for the Luger coal gasification. A low-temperature
gasification-derived coal tar and an ethylene tar obtained from the
petroleum naphtha cracking process in ethylene production were subjected
to thermal aging tests to determine the effect of thermal severity
on their viscosity and chemical composition. The viscosities of coal
tar and ethylene tar as a function of the aging time were similar
and relatively constant at 200 °C. At 250 °C, the coal tar
was more unstable and had a shorter viscosity increase onset time
than the ethylene tar. The tar samples before and after thermal aging
tests were subjected to gas chromatography–mass spectrometry
(GC–MS) and Fourier transform ion cyclotron resonance mass
spectrometry (FT-ICR MS) to determine the molecular composition. The
results indicated that olefins, especially aromatic olefins in the
coal tar, were unstable, which likely caused polymerization of coal
tar species during thermal aging and resulted in a short viscosity
increase onset time. By adding a polymerization inhibitor, the viscosity
increase onset time of coal tar was prolonged. The coal tar is potential
for use as a quenching agent for coal gasification
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