ICGE: an R package for detecting relevant clusters and atypical units in gene expression

Background: Gene expression technologies have opened up new ways to diagnose and treat cancer and other diseases. Clustering algorithms are a useful approach with which to analyze genome expression data. They attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. An important problem associated with gene classification is to discern whether the clustering process can find a relevant partition as well as the identification of new genes classes. There are two key aspects to classification: the estimation of the number of clusters, and the decision as to whether a new unit (gene, tumor sample ... ) belongs to one of these previously identified clusters or to a new group. Results: ICGE is a user-friendly R package which provides many functions related to this problem: identify the number of clusters using mixed variables, usually found by applied biomedical researchers; detect whether the data have a cluster structure; identify whether a new unit belongs to one of the pre-identified clusters or to a novel group, and classify new units into the corresponding cluster. The functions in the ICGE package are accompanied by help files and easy examples to facilitate its use. Conclusions: We demonstrate the utility of ICGE by analyzing simulated and real data sets. The results show that ICGE could be very useful to a broad research community.

Elementu anaforikoak eskolako testuetan

[EU]Artikulu honetan, eskolan eukeraz erabiltzen diren azalpenezko testu idatziaetan agetzen diren elementu anaforikoak aztertzen ditu egileak. Natur Zientzietako hiru testuliburetako unitate didaktiko batean erabilitako azalpenak aztertu ondoren, multzo bakoitzean ikusitako ezaugarri nagusienak eta bien artean dauden zenbait ezberdintasuni buruzko hausnarketak bildu dira lan honetan

An R package for permutations, Mallows and Generalized Mallows models

[EN]Probability models on permutations associate a probability value to each of the permutations on n items. This paper considers two popular probability models, the Mallows model and the Generalized Mallows model. We describe methods for making inference, sampling and learning such distributions, some of which are novel in the literature. This paper also describes operations for permutations, with special attention in those related with the Kendall and Cayley distances and the random generation of permutations. These operations are of key importance for the efficient computation of the operations on distributions. These algorithms are implemented in the associated R package. Moreover, the internal code is written in C++.

Group size and decision rules in legislative bargaining

We conduct experiments to investigate the effects of different majority requirements on bargaining outcomes in small and large groups. In particular, we use a Baron-Ferejohn protocol and investigate the effects of decision rules on delay (number of bargaining rounds needed to reach agreement) and measures of "fairness" (inclusiveness of coalitions, equality of the distribution within a coalition). We find that larger groups and unanimity rule are associated with significantly larger decision making costs in the sense that first round proposals more often fail, leading to more costly delay. The higher rate of failure under unanimity rule and in large groups is a combination of three facts: (1) in these conditions, a larger number of individuals must agree, (2) an important fraction of individuals reject offers below the equal share, and (3) proposers demand more (relative to the equal share) in large groups.

Altered expression of Alzheimer's disease-related genes in the cerebellum of autistic patients: a model for disrupted brain connectome and therapy

Autism and Alzheimer's disease (AD) are, respectively, neurodevelopmental and degenerative diseases with an increasing epidemiological burden. The AD-associated amyloid-beta precursor protein-alpha has been shown to be elevated in severe autism, leading to the 'anabolic hypothesis' of its etiology. Here we performed a focused microarray analysis of genes belonging to NOTCH and WNT signaling cascades, as well as genes related to AD and apoptosis pathways in cerebellar samples from autistic individuals, to provide further evidence for pathological relevance of these cascades for autism. By using the limma package from R and false discovery rate, we demonstrated that 31% (116 out of 374) of the genes belonging to these pathways displayed significant changes in expression (corrected P-values <0.05), with mitochondria- related genes being the most downregulated. We also found upregulation of GRIN1, the channel-forming subunit of NMDA glutamate receptors, and MAP3K1, known activator of the JNK and ERK pathways with anti-apoptotic effect. Expression of PSEN2 (presinilin 2) and APBB1 (or F65) were significantly lower when compared with control samples. Based on these results, we propose a model of NMDA glutamate receptor-mediated ERK activation of alpha-secretase activity and mitochondrial adaptation to apoptosis that may explain the early brain overgrowth and disruption of synaptic plasticity and connectome in autism. Finally, systems pharmacology analyses of the model that integrates all these genes together (NOWADA) highlighted magnesium (Mg2+) and rapamycin as most efficient drugs to target this network model in silico. Their potential therapeutic application, in the context of autism, is therefore discussed.

Financial and Economic Report of a Specific Business Group

As a result of the natural evolution of the economy, ever-changing, unpredictable and cyclical, companies must adapt as far as possible to the changes that have taken place in order to continue with their normal operating activities. Likewise, they should also try to maintain a structure for long-term growth, trying at all times to generate the maximum value. The main objective of this project is to provide financial advisory services to a business group, trying to forward solutions and measures that according to the author can be effective. For this end, the situation of the group in question is analysed from early 2008 to the present day, examining its evolution, what steps have been taken together with their corresponding results and the economic-financial situation of the company at the end of last year. Contact with the company was kept throughout the process of analysis and assessment trying to take advantage of the feedback generated so that the appropriate measures can be adopted if the management considers it to be adequate.

Análisis de las estrategias del sector de la máquina-herramienta y de la empresa Danobat Group

Analisis del sector de maquina herramienta y sus principales estrategias y analisis de una empresa importante del sector (DANOBAT GROUP).

Nuevo estilo de relaciones (ner). Análisis de las percepciones de los rasgos culturales del ner en las organizaciones de ner group

505 p.