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2.
Biomed Pharmacother ; 143: 112217, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34560544

RESUMO

Hepatitis C virus (HCV) infection induces a long-term inflammatory response and oxidative-stress in the liver microenvironment, leading to hepatic fibrosis and metabolic alterations. Direct-acting-antiviral-agents (DAAs) induce HCV-clearance, even though liver damage is only partially restored. In this context, understanding the impact of viral-eradication on liver metabolic activities could allow optimizing the metabolic care of the patient. The present prospective longitudinal study aims at characterizing the urinary metabolic profile of HCV-induced severe liver fibrosis and the metabolic changes induced by DAAs and HCV-clearance by nuclear magnetic resonance-based metabolomics. The urinary metabolic profile of 23 HCV males with severe liver fibrosis and 20 age-matched healthy-controls was analyzed by NMR-based-metabolomics before starting DAAs, at the end-of-therapy, after one and three months of follow-up. The urinary metabolic profile of patients with severe liver fibrosis was associated to pseudouridine, hypoxanthine, methylguanidine and dimethylamine, highlighting a profile related to oxidative damage, and to tyrosine and glutamine, related to a decreased breakdown of aromatic aminoacids and ammonia detoxification, respectively. 1-methylnicotinamide, a catabolic intermediate of nicotinamide-adenine-dinucleotide, was significantly increased in HCV-patients and restored after HCV-clearance, probably due to the reduced hepatic inflammation. 3-hydroxy-3-methylbutyrate, an intermediate of leucine-catabolism which was permanently restored after HCV-clearance, suggested an improvement of skeletal muscle protein synthesis. Finally, 3-hydroxyisobutyrate and 2,3-dihydroxy-2-methylbutyrate, intermediates of valine-catabolism, glycine and choline increased temporarily during therapy, resulting as potential biomarkers of DAAs systemic effects.

3.
Int J Mol Sci ; 22(15)2021 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-34360816

RESUMO

Hypothalamic dysfunction is an initial event following diet-induced obesity, primarily involving areas regulating energy balance such as arcuate nucleus (Arc) and median eminence (ME). To gain insights into the early hypothalamic diet-induced alterations, adult CD1 mice fed a high-fat diet (HFD) for 6 weeks were studied and compared with normo-fed controls. Transmission and scanning electron microscopy and histological staining were employed for morphological studies of the ME, while Raman spectroscopy was applied for the biochemical analysis of the Arc-ME complex. In HFD mice, ME ß2-tanycytes, glial cells dedicated to blood-liquor crosstalk, exhibited remarkable ultrastructural anomalies, including altered alignment, reduced junctions, degenerating organelles, and higher content of lipid droplets, lysosomes, and autophagosomes. Degenerating tanycytes also displayed an electron transparent cytoplasm filled with numerous vesicles, and they were surrounded by dilated extracellular spaces extending up to the subependymal layer. Consistently, Raman spectroscopy analysis of the Arc-ME complex revealed higher glycogen, collagen, and lipid bands in HFD mice compared with controls, and there was also a higher band corresponding to the cyanide group in the former compared to the last. Collectively, these data show that ME ß2-tanycytes exhibit early structural and chemical alterations due to HFD and reveal for the first-time hypothalamic cyanide presence following high dietary lipids consumption, which is a novel aspect with potential implications in the field of obesity.


Assuntos
Núcleo Arqueado do Hipotálamo/efeitos dos fármacos , Dieta Hiperlipídica/efeitos adversos , Eminência Mediana/efeitos dos fármacos , Animais , Núcleo Arqueado do Hipotálamo/patologia , Metabolismo Energético , Masculino , Eminência Mediana/patologia , Camundongos , Obesidade/patologia
4.
Sci Rep ; 11(1): 16591, 2021 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-34400712

RESUMO

Lipidomics is advantageous in the study of sebum perturbations occurring in acne. An extended evaluation of the sebum lipid profiles in acne-prone sebaceous areas is lacking in dark skin. Yet, there is a void space in understanding how the building blocks of sebum lipids, i.e. individual fatty acids (FAs), are intertwined with acne-prone skin. We aimed to determine the sebum lipidome in facial areas of adolescents with and without acne in Nigeria. A cross-sectional analytical study was conducted in 60 adolescents/young adults divided in 30 acne patients (15F, 15M) and 30 age and sex-matched controls. Sebum samples obtained from foreheads and cheeks were analysed separately by gas chromatography-mass spectrometry (GCMS) and thin layer chromatography (HPTLC). Distributions of sebum components were investigated with multivariate ANOVA-simultaneous component analysis (ASCA). Sebum incretion in acne was paralleled by significantly higher abundance of triglycerides, wax esters, and squalene together with monounsaturated FAs (MUFAs), and straight chain saturated FAs (SFAs), especially those with odd-carbon chain, i.e. C13:0, C15:0, and C17:0. Profiling weight/weight percentage of individual components revealed that, in acne, the free FAs (FFAs) array was shifted towards higher relative abundance of the SFAs C15:0, C16:0, and C17:0 and lower percentage of the anteiso-branched FFAs with 12, 14, 16, and 18 carbons. In acne patients, MUFAs and PUFAs were quantitatively increased and decreased on foreheads and cheeks, respectively. Relative abundance of fatty alcohols was decreased in acne independent on the site. The results indicated that acne associates with site-specific derangement of the pathways regulating the balance among odd straight-chain and branched-chain SFAs, MUFAs, which included sapienate (C16:1n-10), PUFAs, and squalene.

5.
Sci Immunol ; 6(62)2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376481

RESUMO

To understand how a protective immune response against SARS-CoV-2 develops over time, we integrated phenotypic, transcriptional and repertoire analyses on PBMCs from mild and severe COVID-19 patients during and after infection, and compared them to healthy donors (HD). A type I IFN-response signature marked all the immune populations from severe patients during the infection. Humoral immunity was dominated by IgG production primarily against the RBD and N proteins, with neutralizing antibody titers increasing post infection and with disease severity. Memory B cells, including an atypical FCRL5+ T-BET+ memory subset, increased during the infection, especially in patients with mild disease. A significant reduction of effector memory, CD8+ T cells frequency characterized patients with severe disease. Despite such impairment, we observed robust clonal expansion of CD8+ T lymphocytes, while CD4+ T cells were less expanded and skewed toward TCM and TH2-like phenotypes. MAIT cells were also expanded, but only in patients with mild disease. Terminally differentiated CD8+ GZMB+ effector cells were clonally expanded both during the infection and post-infection, while CD8+ GZMK+ lymphocytes were more expanded post-infection and represented bona fide memory precursor effector cells. TCR repertoire analysis revealed that only highly proliferating T cell clonotypes, which included SARS-CoV-2-specific cells, were maintained post-infection and shared between the CD8+ GZMB+ and GZMK+ subsets. Overall, this study describes the development of immunity against SARS-CoV-2 and identifies an effector CD8+ T cell population with memory precursor-like features.


Assuntos
COVID-19/genética , COVID-19/imunologia , Interações Hospedeiro-Patógeno/imunologia , Imunofenotipagem , SARS-CoV-2/imunologia , Transcriptoma , Adulto , Idoso , Anticorpos Antivirais/imunologia , Linfócitos B/imunologia , Linfócitos B/metabolismo , Biomarcadores , COVID-19/virologia , Plasticidade Celular/genética , Plasticidade Celular/imunologia , Evolução Clonal/imunologia , Feminino , Perfilação da Expressão Gênica , Humanos , Isotipos de Imunoglobulinas/imunologia , Memória Imunológica , Leucócitos Mononucleares/imunologia , Leucócitos Mononucleares/metabolismo , Contagem de Linfócitos , Masculino , Pessoa de Meia-Idade , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo
6.
Molecules ; 26(16)2021 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-34443532

RESUMO

The aim of the present work was to develop a green multi-platform methodology for the quantification of l-DOPA in solid-state mixtures by means of MIR and NIR spectroscopy. In order to achieve this goal, 33 mixtures of racemic and pure l-DOPA were prepared and analyzed. Once spectra were collected, partial least squares (PLS) was exploited to individually model the two different data blocks. Additionally, three different multi-block approaches (mid-level data fusion, sequential and orthogonalized partial least squares, and sequential and orthogonalized covariance selection) were used in order to simultaneously handle data from the different platforms. The outcome of the chemometric analysis highlighted the quantification of the enantiomeric excess of l-DOPA in enantiomeric mixtures in the solid state, which was possible by coupling NIR and PLS, and, to a lesser extent, by using MIR. The multi-platform approach provided a higher accuracy than the individual block analysis, indicating that the association of MIR and NIR spectral data, especially by means of SO-PLS, represents a valid solution for the quantification of the l-DOPA excess in enantiomeric mixtures.


Assuntos
Composição de Medicamentos , Levodopa/química , Soluções/química , Estereoisomerismo , Química Verde , Espectroscopia de Luz Próxima ao Infravermelho
7.
Talanta ; 230: 122313, 2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-33934778

RESUMO

Cannabis sativa is traditionally classified according to five chemotypes based on the concentration of the main phytocannabinoids tetrahydrocannabinol (THC), cannabidiol (CBD), and cannabigerol (CBG). However, cannabis chemovars and varieties very often present similar concentrations of such phytocannabinoids but different chemical profiles, which is unavoidably translated into different pharmacological effects when used for therapeutic purposes. For this reason, a more refined approach is needed for chemovar distinction, which is described in this study and named phytocannabinomics. The classification was achieved by a comprehensive characterization of the phytocannabinoid composition, by liquid chromatography coupled to high-resolution mass spectrometry untargeted metabolomics for the detection of over a hundred phytocannabinoids, and data analysis by chemometrics for chemovars differentiation. The method was developed on fifty cannabis varieties, grown under the same conditions, and was validated to discriminate between the standard chemotypes by partial least squares discriminant analysis. Then, the method was extended to consider the entire chemical variety of the cannabis accessions, by an unsupervised approach based on the principal component analysis. The latter approach clearly indicated several new subgroups within the traditional classifications, which arise from a unique composition of the minor phytocannabinoids. The existence of these subgroups, which were never described before, is of critical importance for evaluating the pharmacological effects of cannabis chemovars.


Assuntos
Canabidiol , Cannabis , Alucinógenos , Dronabinol , Metabolômica
8.
Spectrochim Acta A Mol Biomol Spectrosc ; 253: 119546, 2021 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-33677373

RESUMO

NIR spectroscopy combined with chemometric analysis has proven to be a rapid and cost-effective screening tool for the detection of syrup-adulterated honey. Processing and storage conditions which alter the chemical and physical state of honey may affect the spectra. The effects of age, storage temperature, syrup adulteration (10 and 20% w/w) and irradiation treatment on the NIR spectra of honey were investigated as a function of time with ANOVA-simultaneous component analysis (ASCA), an experimental design-focused exploratory data analysis method. The factors 'time', 'temperature' and 'adulteration' were found to have significant effects (p < 0.05), but no significant effect was observed for irradiation treatment. A significant interaction effect was found between factors 'time' and 'adulteration', with the greatest disparity between authentic and adulterated class signals found immediately after adulteration and decreasing within three months thereafter.


Assuntos
Mel , Análise de Variância , Contaminação de Alimentos/análise , Mel/análise , Espectroscopia de Luz Próxima ao Infravermelho , Temperatura
9.
Talanta ; 227: 122173, 2021 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-33714468

RESUMO

Predictive models have been developed for the early identification of novel anabolic androgenic steroids and to obtain information on their molecular structure. To this purpose, gas-chromatographic and mass spectrometric characteristic parameters of 136 anabolic androgenic steroids have been specifically considered. Starting from Principal Component Analysis, different chemometric methods were applied, such as classification and clustering techniques, outlining a spectral and structural characterization for each steroid subclass, and considering the contribution of more than 30 variables. Mass spectrometric data on the TMS-derivatives of the target steroids were obtained by gas chromatography coupled to quadrupole-time of flight mass spectrometry using electron ionization. Steroids included in the training set were grouped in 5 subclasses according to their structural similarity, and the experimental data, processed by the chemometric models, allowed the identification of class-specific common fragments and spectral trends. The results of this study, validated on a test set of 21 steroids, have confirmed that the proposed approach allows tracing novel "designer anabolic steroids", including those previously unknown new structures that may have been designed and illicitly synthesized to be invisible to the current anti-doping tests.


Assuntos
Anabolizantes , Doping nos Esportes , Cromatografia Gasosa-Espectrometria de Massas , Espectrometria de Massas , Esteroides , Congêneres da Testosterona
10.
Talanta ; 225: 121955, 2021 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-33592710

RESUMO

Pasta is a key element of the Mediterranean Diet and it has been declared by Unesco intangible cultural heritage of humanity. Despite seems a simple food, only made of semolina and water, pasta is produced following a multi-step process that strongly affect the final product. Drying stage is the one that has the greater influence on its organoleptic/nutritional characteristics. This study aimed to analyse the flavour of pasta to test whether the different drying treatments (High Temperature-Short time or Low Temperature-Long time) have a direct impact on its composition and consequently whether they could influence the end-product quality. The headspace solid-phase microextraction was optimized using an experimental design and 52 samples were analysed by HS-SPME/GC-MS and classified by PLS-DA. The resulting classification model (validated by repeated double cross-validation and permutation tests) allowed correctly predicting more than 80% of samples, confirming that drying may have a significant impact on pasta flavour.


Assuntos
Farinha , Triticum , Dessecação , Farinha/análise , Manipulação de Alimentos , Temperatura
11.
Free Radic Biol Med ; 165: 152-170, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33516914

RESUMO

Dysregulation of brain insulin signaling with reduced downstream neuronal survival and plasticity mechanisms are fundamental abnormalities observed in Alzheimer disease (AD). This phenomenon, known as brain insulin resistance, is associated with poor cognitive performance and is driven by the inhibition of IRS1. Since Down syndrome (DS) and AD neuropathology share many common features, we investigated metabolic aspects of neurodegeneration in DS and whether they contribute to early onset AD in DS. We evaluated levels and activation of proteins belonging to the insulin signaling pathway (IR, IRS1, BVR-A, MAPK, PTEN, Akt, GSK3ß, PKCζ, AS160, GLUT4) in the frontal cortex of Ts65dn (DS model) (n = 5-6/group) and euploid mice (n = 6/group) at different ages (1, 3, 9 and 18 months). Furthermore, we analyzed whether changes of brain insulin signaling were associated with alterations of: (i) proteins regulating brain energy metabolism (mitochondrial complexes, hexokinase-II, Sirt1); (ii) oxidative stress (OS) markers (iii) APP cleavage; and (iv) proteins mediating synaptic plasticity mechanisms (PSD95, syntaxin-1 and BDNF). Ts65dn mice showed an overall impairment of the above-mentioned pathways, mainly characterized by defects of proteins activation state. Such alterations start early in life (at 1 month, during brain maturation). In particular, accumulation of inhibited IRS1, together with the uncoupling among the proteins downstream from IRS1 (brain insulin resistance), characterize Ts65dn mice. Furthermore, reduced levels of mitochondrial complexes and Sirt1, as well as increased indices of OS also were observed. These alterations precede the accumulation of APP-C99 in Ts65dn mice. Tellingly, oxidative stress levels were negatively associated with IR, IRS1 and AS160 activation as well as mitochondrial complexes levels in Ts65dn mice, suggesting a role for oxidative stress in the observed alterations. We propose that a close link exists among brain insulin resistance, mitochondrial defects and OS that contributes to brain dysfunctions observed in DS, likely favoring the development of AD in DS.


Assuntos
Síndrome de Down , Resistência à Insulina , Animais , Encéfalo , Modelos Animais de Doenças , Síndrome de Down/genética , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Estresse Oxidativo
12.
Nucleic Acids Res ; 49(D1): D243-D253, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-32976578

RESUMO

Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3' end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3' end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3' end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.


Assuntos
Regiões 3' não Traduzidas , Fator de Especificidade de Clivagem e Poliadenilação/genética , Bases de Dados Genéticas , Poliadenilação , Transcriptoma , Fator de Especificidade de Clivagem e Poliadenilação/metabolismo , Regulação da Expressão Gênica , Humanos , Internet , Transcrição Genética , Interface Usuário-Computador
13.
Geroscience ; 43(2): 727-740, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-32488674

RESUMO

Physical frailty and sarcopenia (PF&S) is a prototypical geriatric condition characterized by reduced physical function and low muscle mass. The aim of the present study was to provide an initial selection of biomarkers for PF&S using a novel multivariate analytic strategy. Two-hundred community-dwellers, 100 with PF&S and 100 non-physically frail, non-sarcopenic (nonPF&S) controls aged 70 and older were enrolled as part of the BIOmarkers associated with Sarcopenia and Physical frailty in EldeRly pErsons (BIOSPHERE) study. A panel of 74 serum analytes involved in inflammation, muscle growth and remodeling, neuromuscular junction damage, and amino acid metabolism was assayed. Biomarker selection was accomplished through sequential and orthogonalized covariance selection (SO-CovSel) analysis. Separate SO-CovSel models were constructed for the whole study population and for the two genders. The model with the best prediction ability obtained with the smallest number of variables was built using seven biomolecules. This model allowed correct classification of 80.6 ± 5.3% PF&S participants and 79.9 ± 5.1% nonPF&S controls. The PF&S biomarker profile was characterized by higher serum levels of asparagine, aspartic acid, and citrulline. Higher serum concentrations of platelet-derived growth factor BB, heat shock protein 72 (Hsp72), myeloperoxidase, and α-aminobutyric acid defined the profile of nonPF&S participants. Gender-specific SO-CovSel models identified a "core" biomarker profile of PF&S, characterized by higher serum levels of aspartic acid and Hsp72 and lower concentrations of macrophage inflammatory protein 1ß, with peculiar signatures in men and women.SO-CovSel analysis allowed identifying a set of potential biomarkers for PF&S. The adoption of such an innovative multivariate approach could help address the complex pathophysiology of PF&S, translate biomarker discovery from bench to bedside, and unveil novel targets for interventions.


Assuntos
Fragilidade , Sarcopenia , Idoso , Idoso de 80 Anos ou mais , Biomarcadores , Feminino , Idoso Fragilizado , Fragilidade/diagnóstico , Humanos , Inflamação , Masculino , Sarcopenia/diagnóstico
14.
Minerva Urol Nephrol ; 73(1): 98-106, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31833333

RESUMO

BACKGROUND: The serum prostate-specific antigen is the most widespread biomarker for prostate disease. Its low specificity for prostatic malignancies is a matter of concern and the reason why new biomarkers for screening purposes are needed. The correlation between altered production of the main steroids and prostate carcinoma (PCa) occurrence is historically known. The purpose of this study is to evaluate the modifications of a comprehensive urinary endogenous steroidal profile (USP) induced by PCa, by multivariate statistical methods. METHODS: A total of 283 Italian subjects were included in the study, 139 controls and 144 PCa-affected patients. The USP, including 17 steroids and five urinary steroidal ratios, was quantitatively evaluated using gas chromatography coupled with single quadrupole mass spectrometry (GC-MS). The data were interpreted using a chemometric, multivariate approach (intrinsically more sensible to alterations with respect to traditional statistics) and a model for the discrimination of cancer-affected profiles was built. RESULTS: Two multivariate classification models were calculated, the former including three steroids with the highest statistical significance (e.g. testosterone, etiocholanolone and 7ß-OH-DHEA) and PSA values, the latter considering the three steroids' levels only. Both models yielded high sensitivity and specificity scores near to 70%, resulting significantly higher than PSA alone. CONCLUSIONS: Three USP steroids resulted significantly altered in our PCa population. These preliminary results, combined with the simplicity and low-cost of the analysis, open to further investigation of the potential role of this restricted USP in PCa diagnosis.

16.
Cancer Gene Ther ; 28(5): 359-374, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33070159

RESUMO

KRAS is one of the most frequently mutated oncogenes, especially in lung cancers. Targeting of KRAS directly or the downstream effector signaling machinery is of prime interest in treating lung cancers. Here, we uncover that ERK3, a ubiquitously expressed atypical MAPK, is required for KRAS-mediated NSCLC tumors. ERK3 is highly expressed in lung cancers, and oncogenic KRAS led to the activation and stabilization of the ERK3 protein. In particular, phosphorylation of serine 189 in the activation motif of ERK3 is significantly increased in lung adenocarcinomas in comparison to adjacent normal controls in patients. Loss of ERK3 prevents the anchorage-independent growth of KRAS G12C-transformed human bronchial epithelial cells. We further find that loss of ERK3 reduces the oncogenic growth of KRAS G12C-driven NSCLC tumors in vivo and that the kinase activity of ERK3 is required for KRAS-driven oncogenesis in vitro. Our results demonstrate an obligatory role for ERK3 in NSCLC tumor progression and suggest that ERK3 kinase inhibitors can be pursued for treating KRAS G12C-driven tumors.

17.
Appl Spectrosc ; 75(5): 545-555, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33052052

RESUMO

Heroin is one of the most frequently seized drugs in Southeastern Europe. Due to the position in the Balkan route, the Republic of Serbia keeps important role in suppression of the trafficking of heroin for domestic and foreign illegal market. This research is aimed to provide a good scientific approach in the field of seized heroin analysis. Two different forms of heroin are present in the illegal market, mostly in mixtures with typical "cutting" agents: caffeine, paracetamol, and sugars. It was observed that the quantity of pure heroin in seized samples slightly increases from year to year. The aim of this study was to produce a reliable and fast procedure for classification of illicit heroin samples and determination of the concentration range of heroin in the samples. For that purpose, the attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) technique was used and combined with such chemometric methods as principal component analysis, cluster analysis, and partial least squares. Principal component analysis (PCA) as an unsupervised model was used for exploratory purposes to identify trends, similarities, and differences between samples by reducing the dimensionality of the data. The cluster classification of examined samples turned out to be extremely useful to evaluate the possibilities of the ATR FT-IR technique to classify the samples appropriately into the patterns, the constituted clusters. Additionally, partial least square was the suitable method for the purpose of determination of the heroin hydrochloride concentration range in examined samples. It is proved that the joined application of spectroscopy and chemometrics can be extremely convenient and useful for forensic and drugs control laboratories.

18.
Talanta ; 223(Pt 1): 121693, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33303145

RESUMO

Near-infrared (NIR) spectroscopy of fuels can suffer from scattering effects which may mask the signals corresponding to key analytes in the spectra. Therefore, scatter correction techniques are often used prior to any modelling so to remove scattering and improve predictive performances. However, different scatter correction techniques may carry complementary information so that, if jointly used, both model stability and performances could be improved. A solution to that is the fusion of complementary information from differently scatter corrected data. In the present work, the use of a preprocessing fusion approach called sequential preprocessing through orthogonalization (SPORT) is demonstrated for predicting key quality parameters in diesel fuels. In particular, the possibility of predicting four different key properties, i.e., boiling point (°C), density (g/mL), aromatic mass (%) and viscosity (cSt), was considered. As a comparison, standard partial least-squares (PLS) regression modelling was performed on data pretreated by SNV and 2nd derivative (which is a widely used preprocessing combination). The results showed that the SPORT models, based on the fusion of scatter correction techniques, outperformed the standard PLS models in the prediction of all the four properties, suggesting that selection and use of a single scatter correction technique is often not sufficient. Up to complete bias removal with 50% reduction in prediction error was obtained. The R2P was increased by up to 8%. The sequential scatter fusion approach (SPORT) is not limited to NIR data but can be applied to any other spectral data where a preprocessing optimization step is required.

19.
Talanta ; 223(Pt 2): 121733, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33298261

RESUMO

Near infrared (NIR) spectroscopy allows rapid estimation of quality traits in fresh fruit. Several portable spectrometers are available in the market as a low-cost solution to perform NIR spectroscopy. However, portable spectrometers, being lower in cost than a benchtop counterpart, do not cover the complete near infrared (NIR) spectral range. Often portable sensors either use silicon-based visible and NIR detector to cover 400-1000 nm, or InGaAs-based short wave infrared (SWIR) detector covering the 900-1700 nm. However, these two spectral regions carry complementary information, since the 400-1000 nm interval captures the color and 3rd overtones of most functional group vibrations, while the 1st and the 2nd overtones of the same transitions fall in the 1000-1700 nm range. To exploit such complementarity, sequential data fusion strategies were used to fuse the data from two portable spectrometers, i.e., Felix F750 (~400-1000 nm) and the DLP NIR Scan Nano (~900-1700 nm). In particular, two different sequential fusion approaches were used, namely sequential orthogonalized partial-least squares (SO-PLS) regression and sequential orthogonalized covariate selection (SO-CovSel). SO-PLS improved the prediction of moisture content (MC) and soluble solids content (SSC) in pear fruit, leading to an accuracy which was not obtainable with models built on any of the two spectral data set individually. Instead, SO-CovSel was used to select the key wavelengths from both the spectral ranges mostly correlated to quality parameters of pear fruit. Sequential fusion of the data from the two portable spectrometers led to an improved model prediction (higher R2 and lower RMSEP) of MC and SSC in pear fruit: compared to the models built with the DLP NIR Scan Nano (the worst individual block) where SO-PLS showed an increase in R2p up to 56% and a corresponding 47% decrease in RMSEP. Differences were less pronounced to the use of Felix data alone, but still the R2p was increased by 2.5% and the RMSEP was reduced by 6.5%. Sequential data fusion is not limited to NIR data but it can be considered as a general tool for integrating information from multiple sensors.


Assuntos
Pyrus , Frutas , Análise dos Mínimos Quadrados , Espectroscopia de Luz Próxima ao Infravermelho
20.
BMC Bioinformatics ; 21(1): 565, 2020 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-33297942

RESUMO

BACKGROUND: RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking. RESULTS: We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility. CONCLUSION: ideal is distributed as an R package in the Bioconductor project ( http://bioconductor.org/packages/ideal/ ), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.


Assuntos
Perfilação da Expressão Gênica , Software , Sequência de Bases , Interpretação Estatística de Dados , Regulação da Expressão Gênica , Humanos , Reprodutibilidade dos Testes
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