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1.
J Chem Ecol ; 45(8): 693-707, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31367970

RESUMO

Crop domestication and selective breeding have altered plant defense mechanisms, influencing insect-plant interactions. A reduction in plant resistance/tolerance against herbivory is generally expected in domesticated species, however, limited efforts have been made to compare inducibility of plant defenses between wild and domesticated genotypes. In the present study, the inducibility of several plant defense mechanisms (e.g. defensive chemicals, trichomes, plant volatiles) were investigated, and the performance and preference of the herbivore Helicoverpa zea were measured in three different tomato genotypes; a) wild tomato, Solanum pimpinellifolium L. (accession LA 2093), b) cherry tomato, S. lycopersicum L. var. cerasiforme (accession Matts Wild Cherry), and c) cultivated tomato, S. lycopersicum L. var. Better Boy). Enhanced inducibility of defensive chemicals, trichomes, and plant volatiles in the cultivated tomato, and a higher level of constitutive plant resistance against herbivory in the wild genotype was observed. When comparing the responses of damaged vs. undamaged leaves, the percent reduction in larval growth was higher on damaged leaves from cultivated tomato, suggesting a higher induced resistance compared to other two genotypes. While all tomato genotypes exhibited increased volatile organic compound (VOCs) emissions in response to herbivory, the cultivated variety responded with generally higher levels of VOCs. Differences in VOC patterns may have influenced the ovipositional preferences, as H. zea female moths significantly preferred laying eggs on the cultivated versus the wild tomato genotypes. Selection of traits during domestication and selective breeding could alter allocation of resources, where plants selected for higher yield performance would allocate resources to defense only when attacked.


Assuntos
Lycopersicon esculentum/química , Mariposas/fisiologia , Solanum/química , Animais , Comportamento Animal/efeitos dos fármacos , Catecol Oxidase/metabolismo , Feminino , Genótipo , Herbivoria , Larva/fisiologia , Lycopersicon esculentum/genética , Lycopersicon esculentum/metabolismo , Oviposição/efeitos dos fármacos , Fenóis/análise , Folhas de Planta/química , Folhas de Planta/metabolismo , Folhas de Planta/parasitologia , Proteínas de Plantas/análise , Análise de Componente Principal , Inibidores de Proteases/química , Solanum/genética , Solanum/metabolismo , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/metabolismo , Compostos Orgânicos Voláteis/farmacologia
2.
J Chem Ecol ; 45(8): 673-683, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31407198

RESUMO

Animals modulate intraspecific signal shape and intensity, notably during reproductive periods. Signal variability typically follows a seasonal scheme, traceable through the expression of visual, acoustic, chemical and behavioral patterns. The chemical channel is particularly important in lizards, as demonstrated by well-developed epidermal glands in the cloacal region that secrete lipids and proteins recognized by conspecifics. In males, the seasonal pattern of gland activity is underpinned by variation of circulating androgens. Changes in the composition of lipid secretions convey information about the signaler's quality (e.g., size, immunity). Presumably, individual identity is associated with a protein signature present in the femoral secretions, but this has been poorly investigated. For the first time, we assessed the seasonal variability of the protein signal in relation to plasma testosterone level (T), glandular activity and the concentration of provitamin D3 in the lipid fraction. We sampled 174 male common wall lizards (Podarcis muralis) over the entire activity season. An elevation of T was observed one to two months before the secretion peak of lipids during the mating season; such expected delay between hormonal fluctuation and maximal physiological response fits well with the assumption that provitamin D3 indicates individual quality. One-dimensional electrophoretic analysis of proteins showed that gel bands were preserved over the season with an invariant region; a result in agreement with the hypothesis that proteins are stable identity signals. However, the relative intensity of bands varied markedly, synchronously with that of lipid secretion pattern. These variations of protein secretion suggest additional roles of proteins, an issue that requires further studies.


Assuntos
Glândulas Exócrinas/metabolismo , Lipídeos/análise , Lagartos/fisiologia , Proteínas de Répteis/análise , Animais , Desidrocolesteróis/análise , Eletroforese em Gel de Campo Pulsado , Cromatografia Gasosa-Espectrometria de Massas , Metabolismo dos Lipídeos , Lipídeos/química , Masculino , Análise de Componente Principal , Estações do Ano , Comportamento Sexual Animal , Testosterona/sangue
3.
Rev Bras Epidemiol ; 22: e190041, 2019 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-31365598

RESUMO

INTRODUCTION: Statistical methods such as Principal Component Analysis (PCA) and Factor Analysis (FA) are increasingly popular in Nutritional Epidemiology studies. However, misunderstandings regarding the choice and application of these methods have been observed. OBJECTIVES: This study aims to compare and present the main differences and similarities between FA and PCA, focusing on their applicability to nutritional studies. METHODS: PCA and FA were applied on a matrix of 34 variables expressing the mean food intake of 1,102 individuals from a population-based study. RESULTS: Two factors were extracted and, together, they explained 57.66% of the common variance of food group variables, while five components were extracted, explaining 26.25% of the total variance of food group variables. Among the main differences of these two methods are: normality assumption, matrices of variance-covariance/correlation and its explained variance, factorial scores, and associated error. The similarities are: both analyses are used for data reduction, the sample size usually needs to be big, correlated data, and they are based on matrices of variance-covariance. CONCLUSION: PCA and FA should not be treated as equal statistical methods, given that the theoretical rationale and assumptions for using these methods as well as the interpretation of results are different.


Assuntos
Registros de Dieta , Análise Fatorial , Preferências Alimentares , Inquéritos Nutricionais/métodos , Análise de Componente Principal , Humanos
4.
J Agric Food Chem ; 67(37): 10543-10551, 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31464438

RESUMO

Adulteration of meat and meat products causes concerns to consumers. It is necessary to develop novel robust and sensitive methods that can authenticate the origin of meat by qualitative and quantitative means to minimize the drawbacks of the existing methods. This study has shown that the protein N-glycosylation profiles of different meats are species specific and thus can be used for meat authentication. Based on the N-glycan pattern, the investigated five meat species (beef, chicken, pork, duck, and mutton) can be distinguished by principal component analysis, and partial least square regression was performed to build a calibration and validation model for the prediction of adulteration ratio. Using this method, beef samples adulterated with a lower-value duck meat could be detected down to the addition ratio as low as 2.2%. The most distinguishing N-glycans from beef and duck were elucidated for the detailed structures.


Assuntos
Análise de Alimentos/métodos , Contaminação de Alimentos/análise , Glicômica/métodos , Polissacarídeos/química , Animais , Bovinos , Galinhas , Análise Discriminante , Patos , Glicosilação , Carne , Análise de Componente Principal , Carne Vermelha , Suínos
5.
Rev Bras Epidemiol ; 22: e190048, 2019 Aug 19.
Artigo em Português, Inglês | MEDLINE | ID: mdl-31432988

RESUMO

INTRODUCTION: Dietary patterns are based on the concept that food consumed together or by itself is as important as food or nutrient intake. OBJECTIVES: To identify dietary patterns in a sample of nursing professionals and to explore the differences between the patterns found using two techniques: principal components (PC) and principal factorial axis (PAF). METHOD: The current report was based on data from 309 participants on a nursing team at a public hospital in Rio de Janeiro. A 24-hour dietary recall was used, resulting in 24 food groups. To identify the dietary patterns, we applied a multivariate analysis, specifically the PC and the PAF, followed by a Varimax orthogonal rotation. RESULTS: The Cattell graphic test indicated three factors to be extracted. The communality varied between 0.41 and 0.76. Higher loads than 0.30 were considered in the pattern composition. The two methods identified similar dietary patterns, called traditional patterns. The other two patterns were nominated as healthy and snacks, having inverted position of factors in the applied techniques. CONCLUSION: The observed differences refer to: the number of food groups that enter the composition of components and factors; the size of the smaller loads in the PAF and the order of the alimentary patterns, especially those derived from loads of a smaller magnitude. However, these differences do not seem to impact the interpretability of dietary patterns in this population.


Assuntos
Inquéritos sobre Dietas/métodos , Comportamento Alimentar , Enfermeiras e Enfermeiros/estatística & dados numéricos , Adulto , Brasil , Ingestão de Energia , Análise Fatorial , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Análise de Componente Principal , Valores de Referência , Inquéritos e Questionários
6.
Environ Monit Assess ; 191(9): 539, 2019 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-31377943

RESUMO

The externalities generated by disorderly urbanization and lack of proper planning becomes one of the main factors that must be considered in water resource management. To address the multiple uses of water and avoid conflicts among users, decision-making must integrate these factors into quality and quantity aspects. The water quality index (WQI), using the correlation matrix and the multivariate principal component analysis (PCA) and cluster analysis (CA) techniques were used to analyze the surface water quality, considering urban, rural, and industrial regions in an integrated way, even with data gaps. The results showed that the main parameters that impacted the water quality index were dissolved oxygen, elevation, and total phosphorus. The results of PCA analysis showed 86.25% of the variance in the data set, using physicochemical and topographic parameters. In the cluster analysis, the dissolved oxygen, elevation, total coliforms, E. coli, total phosphorus, total nitrogen, and temperature parameters showed a significant correlation between the data's dimensions. In the industrial region, the characteristic parameter was the organic load, in the rural region were nutrients (phosphorus and nitrogen), and in the urban region was E. coli (an indicator of the pathogenic organisms' presence). In the classification of the samples, there was a predominance of "Good" quality, however, samples classified as "Acceptable" and "Bad" occurred during the winter and spring months (dry season) in the rural and industrial regions. Water pollution is linked to inadequate land use and occupation and population density in certain regions without access to sanitation services.


Assuntos
Monitoramento Ambiental , Escherichia coli/crescimento & desenvolvimento , Poluição da Água/análise , Qualidade da Água/normas , Recursos Hídricos , Brasil , Análise por Conglomerados , Análise Multivariada , Nitrogênio/análise , Fósforo/análise , Análise de Componente Principal , Rios , Estações do Ano , Temperatura Ambiente , Urbanização
7.
Environ Monit Assess ; 191(9): 540, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31378832

RESUMO

In this work, we present the results of the investigation of trace elements (Fe, Mg, Ni, Zn, Cu, Cr, Co, Cd, Pb) accumulation potential of Noccaea kovatsii (Heuff.) F. K. Mey., from the Balkan Peninsula. The study included eight populations from ultramafic soils, six from Bosnia and Herzegovina, and two from Serbia. Principal component analysis (PCA) was used to reveal relationships of elements in soil, and Pearson's correlation coefficients for analysing associations of available quantities of elements in soil and those in roots and shoots of N. kovatsii. Uptake and translocation efficiency was assessed by using bioconcentration (BCF) and translocation factors (TF). All the analysed populations of N. kovatsii emerged as strong Ni accumulators, with the highest shoot concentrations of 12,505 mg kg-1. Even thought contents of Zn in plant tissues of N. kovatsii were under the hyperaccumulation level (602 mg kg-1 and 1120 mg kg-1 respectively), BCF was up to 667, indicating that certain surveyed populations have strong accumulative potential for this element.


Assuntos
Brassicaceae/metabolismo , Poluentes do Solo/análise , Solo/química , Oligoelementos/análise , Bósnia e Herzegóvina , Brassicaceae/química , Monitoramento Ambiental , Raízes de Plantas/química , Raízes de Plantas/metabolismo , Brotos de Planta/química , Brotos de Planta/metabolismo , Análise de Componente Principal , Sérvia , Poluentes do Solo/metabolismo , Oligoelementos/metabolismo
8.
BMC Bioinformatics ; 20(1): 410, 2019 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-31362714

RESUMO

BACKGROUND: Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. Predicting drug resistance to previously unobserved variants is therefore very important for an optimum medical treatment. In this paper, we propose the use of weighted categorical kernel functions to predict drug resistance from virus sequence data. These kernel functions are very simple to implement and are able to take into account HIV data particularities, such as allele mixtures, and to weigh the different importance of each protein residue, as it is known that not all positions contribute equally to the resistance. RESULTS: We analyzed 21 drugs of four classes: protease inhibitors (PI), integrase inhibitors (INI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI). We compared two categorical kernel functions, Overlap and Jaccard, against two well-known noncategorical kernel functions (Linear and RBF) and Random Forest (RF). Weighted versions of these kernels were also considered, where the weights were obtained from the RF decrease in node impurity. The Jaccard kernel was the best method, either in its weighted or unweighted form, for 20 out of the 21 drugs. CONCLUSIONS: Results show that kernels that take into account both the categorical nature of the data and the presence of mixtures consistently result in the best prediction model. The advantage of including weights depended on the protein targeted by the drug. In the case of reverse transcriptase, weights based in the relative importance of each position clearly increased the prediction performance, while the improvement in the protease was much smaller. This seems to be related to the distribution of weights, as measured by the Gini index. All methods described, together with documentation and examples, are freely available at https://bitbucket.org/elies_ramon/catkern.


Assuntos
Algoritmos , Biologia Computacional/métodos , Farmacorresistência Viral/genética , HIV-1/genética , Fármacos Anti-HIV/farmacologia , Farmacorresistência Viral/efeitos dos fármacos , Infecções por HIV/virologia , HIV-1/efeitos dos fármacos , HIV-1/isolamento & purificação , Humanos , Modelos Lineares , Análise de Componente Principal
9.
BMC Bioinformatics ; 20(1): 418, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409293

RESUMO

BACKGROUND: Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult. RESULTS: We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved. CONCLUSIONS: The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC . This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., "cases" and "controls") equally distributed in each library.


Assuntos
Biblioteca Gênica , Análise de Sequência de RNA/métodos , Transcriptoma , Linhagem Celular , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Componente Principal , RNA/química , RNA/metabolismo , Interface Usuário-Computador
10.
J Agric Food Chem ; 67(32): 9112-9120, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31314506

RESUMO

A reliable and robust tool for supporting the panel test in virgin olive oil classification is still required. We propose four chemometric approaches based on t test, principal component analysis (PCA) and linear discriminant analysis (LDA), applied for combining sensorial data, and chemical measurements. The former was from the panel test, and the latter was from headspace solid-phase microextraction-gas chromatography-mass spectrometry quantitation of 73 volatile organic compounds (VOCs) of 1223 typical commercial virgin olive oils, with most of them recognized as difficult to classify with accuracy by the panel test. The approaches were developed and validated, and the best results, with 83.5% correct classification, were using the PCA-LDA approach. Among the other methods, developed for proposing simplified procedures based on a smaller number of VOCs, the best method gave 80.1% correct classification only using 10 VOCs. All of the approaches suggested that octane, heptanal, pent-1-en-3-ol, Z-3-hexenal, nonanal, and 4-ethylphenol should be considered as a basis of volatiles for classification of olive oil samples.


Assuntos
Cromatografia Gasosa-Espectrometria de Massas/métodos , Azeite de Oliva/química , Microextração em Fase Sólida/métodos , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/isolamento & purificação , Análise Discriminante , Humanos , Olea/química , Azeite de Oliva/classificação , Análise de Componente Principal , Paladar
11.
BMC Bioinformatics ; 20(Suppl 13): 384, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31337332

RESUMO

BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, "Soybean-VCF2Genomes", http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. CONCLUSION: The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.


Assuntos
Genoma de Planta , Soja/genética , Interface Usuário-Computador , Análise por Conglomerados , Bases de Dados Factuais , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Aprendizado de Máquina , Fenótipo , Filogenia , Análise de Componente Principal , Sementes/genética , Soja/classificação , Soja/crescimento & desenvolvimento
12.
J Chem Ecol ; 45(7): 579-587, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31256322

RESUMO

Domestic cats (Felis silvestris catus) are solitary and territorial, and mark their territories by spraying urine, which emits a strong odor produced by volatile organic compounds (VOCs). Previous studies have focused on identifications of specific VOCs, such as 3-mercpto-3-methyl-1-butanol, a cat-specific VOCs. However, little is known about how whole volatile profiles of their sprayed urine change over time or how the profiles differ among individuals. This study investigated temporal changes and individual differences of volatile profiles produced by whole VOCs in cat urine, and the ability of cats to discriminate between these scent differences. Volatile profiles of fresh and aged cat urine were analyzed by using two-dimensional gas chromatography-mass spectrometry with a VOC preconcentrator comprehensively. Volatile profiles produced by hundreds of VOCs emitted from cat urine were influenced primarily by the age of the urine, and secondarily by individuality. During habituation-dishabituation tests, subjects discriminated between fresh and 24 h-old samples of same individuals, and between odor of different individuals from 0 h-, 3 h-old, and 24 h-old samples. These results strongly suggest that cats can recognize conspecific individuals via olfaction. Since most VOCs varied among individuals but were not stable over time, their urine may contain unknown VOCs that vary among individuals, are stable over time, and act as individual recognition signals.


Assuntos
Cromatografia Gasosa-Espectrometria de Massas/métodos , Compostos Orgânicos Voláteis/urina , Animais , Comportamento Animal , Gatos , Análise Discriminante , Masculino , Análise de Componente Principal , Fatores de Tempo , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/isolamento & purificação
13.
J Chem Ecol ; 45(7): 610-625, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31281942

RESUMO

Plants use volatile organic compounds (VOCs) to cue natural enemies to their herbivore prey on plants. Simultaneously, herbivores utilize volatile cues to identify appropriate hosts. Despite extensive efforts to understand sources of variation in plant communication by VOCs, we lack an understanding of how ubiquitous belowground mutualists, such as arbuscular mycorrhizal fungi (AMF), influence plant VOC emissions. In a full factorial experiment, we subjected plants of two milkweed (Asclepias) species under three levels of AMF availability to damage by aphids (Aphis nerii). We then measured plant headspace volatiles and chemical defenses (cardenolides) and compared these to VOCs emitted and cardenolides produced by plants without herbivores. We found that AMF have plant species-specific effects on constitutive and aphid-induced VOC emissions. High AMF availability increased emissions of total VOCs, two green leaf volatiles (3-hexenyl acetate and hexyl acetate), and methyl salicylate in A. curassavica, but did not affect emissions in A. incarnata. In contrast, aphids consistently increased emissions of 6-methyl-5-hepten-2-one and benzeneacetaldehyde in both species, independent of AMF availability. Both high AMF availability and aphids alone suppressed emissions of individual terpenes. However, aphid damage on plants under high AMF availability increased, or did not affect, emissions of those terpenes. Lastly, aphid feeding suppressed cardenolide concentrations only in A. curassavica, and AMF did not affect cardenolides in either plant species. Our findings suggest that by altering milkweed VOC profiles, AMF may affect both herbivore performance and natural enemy attraction.


Assuntos
Afídeos/fisiologia , Asclepias/química , Micorrizas/fisiologia , Compostos Orgânicos Voláteis/análise , Animais , Asclepias/metabolismo , Asclepias/parasitologia , Cardenolídeos/análise , Cromatografia Gasosa-Espectrometria de Massas , Herbivoria , Interações entre Hospedeiro e Microrganismos , Interações Hospedeiro-Parasita , Folhas de Planta/química , Folhas de Planta/metabolismo , Folhas de Planta/parasitologia , Análise de Componente Principal
14.
Ceska Slov Farm ; 68(2): 69-77, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31331176

RESUMO

Currently, the method of external ionic gelation for the preparation of alginate particles is successfully used not only in the field of pharmacy and medicine, but also especially in the field of biotechnology. Therefore, the preparation of alginate particles and their subsequent evaluation using principal component analysis was the key task of our experiment. To optimize this method, we focused on the evaluation of the effect of formulation (the polymer concentration, the hardening solution concentration) and process parameters (the outer diameter of the injection needle) on the properties of the resulting beads (yield, sphericity factor, equivalent diameter and swelling capacity at pH 6). Using multivariate data analysis, the major influence on the resulting properties of the prepared particles was confirmed only in sodium alginate concentration. Obtained results verified the reliable and safe potential of the external ionic gelation for preparation alginate-based particulate dosage forms.


Assuntos
Alginatos/química , Cobre/química , Polímeros , Análise de Componente Principal
15.
BMC Bioinformatics ; 20(1): 369, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262249

RESUMO

BACKGROUND: Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. Single cell RNA-seq has a far larger fraction of missing data reported as zeros (dropouts) than traditional bulk RNA-seq, and unsupervised clustering combined with Principal Component Analysis (PCA) can be used to overcome this limitation. After clustering, however, one has to interpret the average expression of markers on each cluster to identify the corresponding cell types, and this is normally done by hand by an expert curator. RESULTS: We present a computational tool for processing single cell RNA-seq data that uses a voting algorithm to automatically identify cells based on approval votes received by known molecular markers. Using a stochastic procedure that accounts for imbalances in the number of known molecular signatures for different cell types, the method computes the statistical significance of the final approval score and automatically assigns a cell type to clusters without an expert curator. We demonstrate the utility of the tool in the analysis of eight samples of bone marrow from the Human Cell Atlas. The tool provides a systematic identification of cell types in bone marrow based on a list of markers of immune cell types, and incorporates a suite of visualization tools that can be overlaid on a t-SNE representation. The software is freely available as a Python package at https://github.com/sdomanskyi/DigitalCellSorter . CONCLUSIONS: This methodology assures that extensive marker to cell type matching information is taken into account in a systematic way when assigning cell clusters to cell types. Moreover, the method allows for a high throughput processing of multiple scRNA-seq datasets, since it does not involve an expert curator, and it can be applied recursively to obtain cell sub-types. The software is designed to allow the user to substitute the marker to cell type matching information and apply the methodology to different cellular environments.


Assuntos
Células da Medula Óssea/citologia , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Software , Algoritmos , Células da Medula Óssea/metabolismo , Análise por Conglomerados , Humanos , Análise de Componente Principal , Análise de Célula Única
16.
J Chem Ecol ; 45(8): 708-714, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31313135

RESUMO

Plants are able to sense their environment and respond appropriately to different stimuli. Vibrational signals (VS) are one of the most widespread yet understudied ways of communication between organisms. Recent research into the perception of VS by plants showed that they are ecologically meaningful signals involved in different interactions of plants with biotic and abiotic agents. We studied changes in the concentration of alkaloids in tobacco plants induced by VS produced by Phthorimaea operculella (Lepidoptera: Gelechiidae), a generalist caterpillar that naturally feeds on the plant. We measured the concentration of nicotine, nornicotine, anabasine and anatabine in four treatments applied to 11-weeks old tobacco plant: a) Co = undamaged plants, b) Eq = Playback equipment attached to the plant without VS, c) Ca = Plants attacked by P. operculella herbivory and d) Pl = playback of VS of P. operculella feeding on tobacco. We found that nicotine, the most abundant alkaloid, increased more than 2.6 times in the Ca and Pl treatments as compared with the Co and Eq treatments, which were similar between them. Nornicotine, anabasine and anatabine were mutually correlated and showed similar concentration patterns, being higher in the Eq treatment. Results are discussed in terms of the adaptive significance of plant responses to ecologically important VS stimuli.


Assuntos
Alcaloides/análise , Lepidópteros/fisiologia , Tabaco/química , Alcaloides/metabolismo , Anabasina/análise , Animais , Cromatografia Gasosa-Espectrometria de Massas , Herbivoria , Interações Hospedeiro-Parasita , Larva/fisiologia , Modelos Lineares , Nicotina/análogos & derivados , Nicotina/análise , Análise de Componente Principal , Piridinas/análise , Tabaco/metabolismo , Tabaco/parasitologia , Vibração
17.
Food Chem ; 298: 125046, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31260981

RESUMO

We established a novel Dianhong black tea grades discriminant analytic technique based on a fluorescence image along with carbon quantum dots (CDs) as fluorescent probes. Different grades of Dianhong black tea contain different various amounts of tea polyphenols. Tea polyphenols can quench the fluorescent intensity of CDs, resulting in different fluorescent peaks; Dianhong black tea grades can then be discriminated through the use of principal component analysis and Bayesian analysis. Compared with the additional data processing required in other methods, the advantage of our method is that the fluorescence curve can be used directly, and it achieves satisfactory results. We firstly used CDs combined with chemometrics to identify eight grades of Dianhong black tea, and we also provide a new method that improves the identification rate using nanotechnology to avoid performing complex data processing.


Assuntos
Camellia sinensis/química , Corantes Fluorescentes/química , Teorema de Bayes , Camellia sinensis/metabolismo , Análise Discriminante , Polifenóis/análise , Análise de Componente Principal , Pontos Quânticos/química , Espectrometria de Fluorescência
18.
Food Chem ; 298: 125052, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31261003

RESUMO

Scotch Whisky has been analysed as a complex mixture in its raw form using high resolution Nuclear Magnetic Resonance (NMR) and previously developed water and ethanol suppression techniques. This has allowed for the positive identification of 25 compounds in Scotch Whisky by means of comparison to reference standards, spike-in experiments, and advanced 1D and 2D NMR experiments. Quantification of compounds was hindered by signal overlap, though peak alignment strategies were largely successful. Statistical total correlation spectroscopy (STOCSY) yielded information on signals arising from the same compound or compounds of similar origin. Statistical analysis of the spectra was performed using Independent and Principal Components Analysis (ICA, PCA) as well as Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Several whisky production parameters were successfully modelled, including blend or malt status, use of peated malt, alcohol strength, generic authentication and maturation wood type, whilst age and geographical origin could not be modelled.


Assuntos
Bebidas Alcoólicas/análise , Espectroscopia de Prótons por Ressonância Magnética/métodos , Bebidas Alcoólicas/normas , Análise Discriminante , Análise dos Mínimos Quadrados , Análise de Componente Principal , Espectroscopia de Prótons por Ressonância Magnética/normas , Padrões de Referência
19.
Food Chem ; 298: 125047, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31261012

RESUMO

Extra virgin olive oil (EVO) is among the most counterfeit foodstuffs in the present market. The Italian production is with no doubt one of the most valuable and therefore mostly counterfeit, due to the difficulty in checking the geographic provenance of olives. In order to provide a way for verifying the provenance of EVO, the role of microelements and, in particular, of lanthanides in the oil production chain has been studied. The distribution of lanthanides as determined by means of ICP-MS analysis appeared to provide a good tool for tracing the EVO production chain. Lanthanides and other microelements were then used for distinguishing a particularly prised EVO production from Liguria (northwestern Italy) made from Taggiasca olive variety, verifying that this production can be easily authenticated on the base of these chemical descriptors.


Assuntos
Elementos da Série dos Lantanídeos/análise , Olea/química , Azeite de Oliva/química , Itália , Espectrometria de Massas , Olea/metabolismo , Análise de Componente Principal
20.
Nature ; 571(7766): 500-504, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31292546

RESUMO

Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern. By contrast, Apidima 1 dates to more than 210 thousand years ago and presents a mixture of modern human and primitive features. These results suggest that two late Middle Pleistocene human groups were present at this site-an early Homo sapiens population, followed by a Neanderthal population. Our findings support multiple dispersals of early modern humans out of Africa, and highlight the complex demographic processes that characterized Pleistocene human evolution and modern human presence in southeast Europe.


Assuntos
Cavernas , Fósseis , Crânio/anatomia & histologia , Animais , Evolução Biológica , Grécia , Humanos , Homem de Neandertal/anatomia & histologia , Homem de Neandertal/classificação , Análise de Componente Principal , Datação Radiométrica , Fatores de Tempo
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