527 research outputs found
An open platform for Aerosol InfraRed Spectroscopy analysis – AIRSpec
AIRSpec is a platform consisting of several chemometric packages developed
for analysis of Fourier transform infrared (FTIR) spectra of atmospheric
aerosols. The packages are accessible through a browser-based interface,
which also generates the necessary input files based on user interactions for
provenance management and subsequent use with a command-line interface. The
current implementation includes the task of baseline correction, organic
functional group (FG) analysis, and multivariate calibration for any analyte
with absorption in the mid-infrared. The baseline correction package uses
smoothing splines to correct the drift of the baseline of ambient aerosol
spectra given the variability in both environmental mixture composition and
substrates. The FG analysis is performed by fitting individual Gaussian line
shapes for alcohol (aCOH), carboxylic acid (COOH), alkane (aCH), carbonyl (CO),
primary amine (aNH2), and ammonium (ammNH) for each spectrum.
The multivariate calibration model uses the
spectra to estimate the concentration of relevant target variables (e.g.,
organic or elemental carbon) measured with different reference instruments.
In each of these analyses, AIRSpec receives spectra and user choices on
parameters for model computation; input files with parameters that can later
be used with a command-line interface for batch computation are returned
together with diagnostic figures and tables in text format. AIRSpec is built
using the open-source software consisting of R and Shiny and is released
under the GNU Public License v3. Users can download, modify, and extend the
package, or access its functionality through the web application
(http://airspec.epfl.ch, last access: 3 April 2019) hosted at the École polytechnique
fédérale de Lausanne (EPFL). AIRSpec provides a unified framework by
which different chemometric techniques can be shared and accessed, and its
underlying suite of packages provides the basic functionality for extending
the platform with new types of analyses. For example, basic functionality
includes operations for populating and accessing spectra residing in
in-memory arrays or relational databases, input and output of spectra and
results of computation, and user interface development. Moreover, AIRSpec
facilitates the exploratory work, can be used by FTIR spectra acquired with
different methods, and can be extended easily with new chemometric packages
when they become available. Therefore AIRSpec provides a framework for
centralizing and disseminating such algorithms. This paper describes the
modular architecture and provides examples of the implemented packages using
the spectra of aerosol samples collected on PM2.5 polytetrafluoroethylene (Teflon) filters.</p
MiCASA is a new method for quantifying cellular organization
While many tools exist for identifying and quantifying individual cell types, few methods are available to assess the relationships between cell types in organs and tissues and how these relationships change during aging or disease states. We present a quantitative method for evaluating cellular organization, using the mouse thymus as a test organ. The thymus is the primary lymphoid organ responsible for generating T cells in vertebrates, and its proper structure and organization is essential for optimal function. Our method, Multitaper Circularly Averaged Spectral Analysis (MiCASA), identifies differences in the tissue-level organization with high sensitivity, including defining a novel type of phenotype by measuring variability as a specific parameter. MiCASA provides a novel and easily implemented quantitative tool for assessing cellular organization
The RhoA transcriptional program in pre-T cells
The GTPase RhoA is essential for the development of pre-T cells in the thymus. To investigate the mechanisms used by RhoA to control thymocyte development we have used Affymetrix gene profiling to identify RhoA regulated genes in T cell progenitors. The data show that RhoA plays a specific and essential role in pre-T cells because it is required for the expression of transcription factors of the Egr-1 and AP-1 families that have critical functions in thymocyte development. Loss of RhoA function in T cell progenitors causes a developmental block that pheno-copies the consequence of losing pre-TCR expression in Recombinase gene 2 (Rag2) null mice. Transcriptional profiling reveals both common and unique gene targets for RhoA and the pre-TCR indicating that RhoA participates in the pre-TCR induced transcriptional program but also mediates pre-TCR independent gene transcription
Influence of crustal dust and sea spray supermicron particle concentrations and acidity on inorganic NO_3^- aerosol during the 2013 Southern Oxidant and Aerosol Study
Inorganic aerosol composition was measured in the southeastern United States, a region that exhibits high aerosol mass loading during the summer, as part of the 2013 Southern Oxidant and Aerosol Study (SOAS) campaign. Measurements using a Monitor for AeRosols and GAses (MARGA) revealed two periods of high aerosol nitrate (NO_^3−) concentrations during the campaign. These periods of high nitrate were correlated with increased concentrations of supermicron crustal and sea spray aerosol species, particularly Na^+ and Ca^(2+), and with a shift towards aerosol with larger (1 to 2.5 μm) diameters. We suggest this nitrate aerosol forms by multiphase reactions of HNO_3 and particles, reactions that are facilitated by transport of crustal dust and sea spray aerosol from a source within the United States. The observed high aerosol acidity prevents the formation of NH_4NO_3, the inorganic nitrogen species often dominant in fine-mode aerosol at higher pH. Calculation of the rate of the heterogeneous uptake of HNO_3 on mineral aerosol supports the conclusion that aerosol NO_3^− is produced primarily by this process, and is likely limited by the availability of mineral cation-containing aerosol surface area. Modeling of NO_3^− and HNO_3 by thermodynamic equilibrium models (ISORROPIA II and E-AIM) reveals the importance of including mineral cations in the southeastern United States to accurately balance ion species and predict gas–aerosol phase partitioning
Widefield fluorescence imaging as an auxiliary tool to select the biopsy site for actinic cheilitis diagnosis
Actinic cheilitis (AC) is considered a potentially malignant disorder that mainly affects the lower lip, and it is caused by prolonged sun exposure. Clinical diagnosis relies on visual inspection by a trained clinician, when suspected of dysplasia changes, a biopsy is required. The heteregenous characteristics of the AC, makes the choice of the biopsy site a difficult task. Fluorescence detection has been presented as a useful tool to to detect biochemical and morphological tissue features related to cancer diagnosis, but still its effectiveness to discriminate premalignant lesion is not completely defined. In this clinical study, 57 AC patients were investigated using widefield fluorescence imaging (WFI) to evaluate the efficacy of this technique as an auxiliary tool to biopsy site location. A handheld fluorescence system based on 400-450 nm LED illumination Distinct trained clinicians evaluate the patient either with the conventional examination or the WFI, and were blinded to the other evaluation. A biopsy site was chosen based on the clinical examination, and another site was chosen using the fluorescence visualization. A total of 114 punch biopsies were performed, and 93% of the tissue samples presented epithelial dysplasia. The majority of the sites that presented moderate or severe dysplasia were sites chosen by WFI, showing its efficiency to improve the diagnosis of AC.CNPq (475322/2011-8)CEPID-CePOF/FAPESP (98/14270-8
Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. phaseolicola and Botrytis cinerea infection
Phaseolus vulgaris cv. Korona plants were
inoculated with the bacteria Pseudomonas syringae pv.
phaseolicola (Psp), necrotrophic fungus Botrytis cinerea
(Bc) or with both pathogens sequentially. The aim of the
experiment was to determine how plants cope with multiple
infection with pathogens having different attack strategy.
Possible suppression of the non-specific infection with
the necrotrophic fungus Bc by earlier Psp inoculation was
examined. Concentration of reactive oxygen species
(ROS), such as superoxide anion (O2
-) and H2O2 and
activities of antioxidant enzymes such as superoxide dismutase
(SOD), catalase (CAT) and peroxidase (POD) were
determined 6, 12, 24 and 48 h after inoculation. The
measurements were done for ROS cytosolic fraction and
enzymatic cytosolic or apoplastic fraction. Infection with
Psp caused significant increase in ROS levels since the
beginning of experiment. Activity of the apoplastic
enzymes also increased remarkably at the beginning of
experiment in contrast to the cytosolic ones. Cytosolic
SOD and guaiacol peroxidase (GPOD) activities achieved
the maximum values 48 h after treatment. Additional forms
of the examined enzymes after specific Psp infection were
identified; however, they were not present after single Bc
inoculation. Subsequent Bc infection resulted only in
changes of H2O2 and SOD that occurred to be especially
important during plant–pathogen interaction. Cultivar Korona
of common bean is considered to be resistant to Psp and mobilises its system upon infection with these bacteria.
We put forward a hypothesis that the extent of defence
reaction was so great that subsequent infection did not
trigger significant additional response
Biogenic and biomass burning organic aerosol in a boreal forest at Hyytiälä, Finland, during HUMPPA-COPEC 2010
Submicron aerosol particles were collected during July and August 2010 in Hyytiälä, Finland, to determine the composition and sources of aerosol at that boreal forest site. Submicron particles were collected on Teflon filters and analyzed by Fourier transform infrared (FTIR) spectroscopy for organic functional groups (OFGs). Positive matrix factorization (PMF) was applied to aerosol mass spectrometry (AMS) measurements and FTIR spectra to identify summertime sources of submicron aerosol mass at the sampling site. The two largest sources of organic mass (OM) in particles identified at Hyytiälä were (1) biogenic aerosol from surrounding local forest and (2) biomass burning aerosol, transported 4–5 days from large wildfires burning near Moscow, Russia, and northern Ukraine. The robustness of this apportionment is supported by the agreement of two independent analytical methods for organic measurements with three statistical techniques. FTIR factor analysis was more sensitive to the chemical differences between biogenic and biomass burning organic components, while AMS factor analysis had a higher time resolution that more clearly linked the temporal behavior of separate OM factors to that of different source tracers even though their fragment mass spectrum were similar. The greater chemical sensitivity of the FTIR is attributed to the nondestructive preparation and the functional group specificity of spectroscopy. The FTIR spectra show strong similarities among biogenic and biomass burning factors from different regions as well as with reference OM (namely olive tree burning organic aerosol and α-pinene chamber secondary organic aerosol (SOA)). The biogenic factor correlated strongly with temperature and oxidation products of biogenic volatile organic compounds (BVOCs), included more than half of the oxygenated OFGs (carbonyl groups at 29% and carboxylic acid groups at 22%), and represented 35% of the submicron OM. Compared to previous studies at Hyytiälä, the summertime biogenic OM is 1.5 to 3 times larger than springtime biogenic OM (0.64 μg m^−3 and 0.4 μg m^−3, measured in 2005 and 2007, respectively), even though it contributed only 35% of OM. The biomass burning factor contributed 25% of OM on average and up to 62% of OM during three periods of transported biomass burning emissions: 26–28 July, 29–30 July, and 8–9 August, with OFG consisting mostly of carbonyl (41%) and alcohol (25%) groups. The high summertime terrestrial biogenic OM (1.7 μg m^−3) and the high biomass burning contributions (1.2 μg m^−3) were likely due to the abnormally high temperatures that resulted in both stressed boreal forest conditions with high regional BVOC emissions and numerous wildfires in upwind regions
Aire-dependent production of XCL1 mediates medullary accumulation of thymic dendritic cells and contributes to regulatory T cell development
Aire regulates medullary epithelial cell production of XCL1, a chemoattractant for XCR1-expressing thymic DCs whose presence in the medulla contributes to the generation of T reg cells
Schwannoma-like pleomorphic adenoma of the parotid
Pleomorphic adenoma is the most common benign salivary gland tumour. It can occur in any salivary gland, but is most frequently found in the parotid gland. Chondroid metaplasia is a frequent finding in pleomorphic adenoma. Other forms of metaplasia have been described, but are encountered less frequently. We report a rare case of unusual pleomorphic adenoma of the parotid gland with schwannoma-like feature
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