Merged consensus clustering to assess and improve class discovery with microarray data

<p>Abstract</p> <p>Background</p> <p>One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups. There are a large number of methods available to perform clustering, but it is often unclear which method is best suited to the data and how to quantify the quality of the classifications produced.</p> <p>Results</p> <p>Here we describe an R package containing methods to analyse the consistency of clustering results from any number of different clustering methods using resampling statistics. These methods allow the identification of the the best supported clusters and additionally rank cluster members by their fidelity within the cluster. These metrics allow us to compare the performance of different clustering algorithms under different experimental conditions and to select those that produce the most reliable clustering structures. We show the application of this method to simulated data, canonical gene expression experiments and our own novel analysis of genes involved in the specification of the peripheral nervous system in the fruitfly, <it>Drosophila melanogaster</it>.</p> <p>Conclusions</p> <p>Our package enables users to apply the merged consensus clustering methodology conveniently within the R programming environment, providing both analysis and graphical display functions for exploring clustering approaches. It extends the basic principle of consensus clustering by allowing the merging of results between different methods to provide an averaged clustering robustness. We show that this extension is useful in correcting for the tendency of clustering algorithms to treat outliers differently within datasets. The R package, <it>clusterCons</it>, is freely available at CRAN and sourceforge under the GNU public licence.</p

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Using microalgae scenedesmus obliquus in the removal of chromium present in plating wastewaters

8 páginas, 5 figuras, 5 tablas.[ES] El vertido de aguas residuales con alto contenido de cromo, procedentes de las industrias galvanoplásticas, es un peligro potencial que se le presenta a la población y al medio ambiente. Se conoce que algunos metales, incluyendo los pesados, a concentraciones bajas participan en diferentes rutas metabólicas, pero en altas concentraciones pueden ser tóxicos para muchos organismos vivos. Algunos microorganismos toman los metales pesados del medio ambiente, siendo capaces de concentrar y acumular grandes cantidades de los mismos en diferentes estructuras citoplasmáticas, sin que lleguen a ocasionar efectos tóxicos en los mismos. Las microalgas son un ejemplo de este comportamiento, ya que tienen afinidad por los metales polivalentes, de ahí la posibilidad de su aplicación como agentes descontaminantes en aguas que contengan iones metálicos disueltos como método alternativo cuando no se pueda utilizar otro método de recuperación. En este trabajo se realizó un estudio de eliminación de cromo presente en las aguas residuales galvánicas, empleando un cultivo de scenedesmus obliquus. Se obtuvo una eficiencia de eliminación de Cr (VI) del 12 % y del 27 % para el Cr (III), y en condiciones de inmovilización del alga fue del 95 % para el Cr (III).[EN] Dumping wastewaters from plating industry with a high content in chromium is a potential hazard for people and environment. It is known that some metals, including the heavy metals, at low concentrations participate in different metabolic routes, but at high concentration are toxic for many living organisms. Some microorganism taking the heavy metals from the environment are capable of concentrating and accumulating large quantities of them in different citoplasmatic structures with no-toxic effects. Microalgae have affinity by the polyvalent metals making possible their use as depollutant agent in waters that contains dissolved metallic ions as alternative methods when others methods of recycle are unusable. In this report a chromium removal study from a plating wastewater, using scenedesmus obliquus culture was made. The removal efficiency of Cr (VI) was 12 % and Cr (III) was 27 % and for condition of algae's immobilization removal of Cr (III) was 95 %.Peer reviewe

Influence of the nature and amount of the second component of binary-palladium alloys on their catalytic activity with respect to the dehydrogenation of cyclohexane

1. The catalytic activity of palladium and binary alloys of it with nickel, silver, platinum, and boron with respect to the dehydrogenation of cyclohexane was studied. 2. Increasing the platinum content in the alloys to 1.5% increases their catalytic activity, while increasing the silver content in the range from 20 to 50% reduces their catalytic activity. The alloy of palladium with 5% nickel is more active, while the alloy with 10% nickel is less active than palladium. The apparent activation energy of the dehydrogenation of cyclohexane on all the indicated alloys, with the exception of alloys of palladium with platinum, are close to the value for palladium. 3. The catalytic activity of the alloys of palladium with boron studied is low and unstable. © 1971 Consultants Bureau

Influence of the nature and amount of the second component of binary-palladium alloys on their catalytic activity with respect to the dehydrogenation of cyclohexane

1. The catalytic activity of palladium and binary alloys of it with nickel, silver, platinum, and boron with respect to the dehydrogenation of cyclohexane was studied. 2. Increasing the platinum content in the alloys to 1.5% increases their catalytic activity, while increasing the silver content in the range from 20 to 50% reduces their catalytic activity. The alloy of palladium with 5% nickel is more active, while the alloy with 10% nickel is less active than palladium. The apparent activation energy of the dehydrogenation of cyclohexane on all the indicated alloys, with the exception of alloys of palladium with platinum, are close to the value for palladium. 3. The catalytic activity of the alloys of palladium with boron studied is low and unstable. © 1971 Consultants Bureau