A shortest-path based clustering algorithm for joint human-machine analysis of complex datasets

Clustering is a technique for the analysis of datasets obtained by empirical studies in several disciplines with a major application for biomedical research. Essentially, clustering algorithms are executed by machines aiming at finding groups of related points in a dataset. However, the result of grouping depends on both metrics for point-to-point similarity and rules for point-to-group association. Indeed, non-appropriate metrics and rules can lead to undesirable clustering artifacts. This is especially relevant for datasets, where groups with heterogeneous structures co-exist. In this work, we propose an algorithm that achieves clustering by exploring the paths between points. This allows both, to evaluate the properties of the path (such as gaps, density variations, etc.), and expressing the preference for certain paths. Moreover, our algorithm supports the integration of existing knowledge about admissible and non-admissible clusters by training a path classifier. We demonstrate the accuracy of the proposed method on challenging datasets including points from synthetic shapes in publicly available benchmarks and microscopy data

The human CD53 gene, coding for a four transmembrane domain protein, maps to chromosomal region 1p13

The rat OX44/CD53 protein is the prototypic member of a"novel" family of proteins. These proteins are characterizedby four highly hydrophobic transmembrane domains, twosmall extracellular domains, one of which is extensively N-glycosylated,and both the amino and the carboxy terminus intracytoplasmic.This work has been supported by grants from Fundación Ramón Areces and CICYT (SAL90-0209 and SAL91-0043) to P.A.L. and FIS(92-0889) to S.R.CS

Reducción de etilfenoles por formación de piranoantocianos vinilfenólicos

Los géneros Brettanomyces/Dekkera son responsables de la aparición de aromas fenólicos [Figura 1]. Dichos olores son resultado de la evolución de ácidos hidroxicinámicos hacia etilfenoles como consecuencia de las actividades hidroxicinamato descarboxilasa (HCDC) y vinilfenolreductasa (VphR) de estos géneros [Figura 2]. El objetivo del trabajo fue facilitar la formación de piranoantocianos vinilfenólicos usando cepas de Saccharomyces HCDC+ (pero VphR-) , con objeto de reducir el contenido inicial de ácidos hidroxicinámicos del vino durante la fermentación y prevenir de esta forma la formación de etilfenoles en caso de contaminación por Brettanomyces/Dekkera

CD44 Modulates Cell Migration and Invasion in Ewing Sarcoma Cells

The chimeric EWSR1::FLI1 transcription factor is the main oncogenic event in Ewing sarcoma. Recently, it has been proposed that EWSR1::FLI1 levels can fluctuate in Ewing sarcoma cells, giving rise to two cell populations. EWSR1::FLI1low cells present a migratory and invasive phenotype, while EWSR1::FLI1high cells are more proliferative. In this work, we described how the CD44 standard isoform (CD44s), a transmembrane protein involved in cell adhesion and migration, is overexpressed in the EWSR1::FLI1low phenotype. The functional characterization of CD44s (proliferation, clonogenicity, migration, and invasion ability) was performed in three doxycycline-inducible Ewing sarcoma cell models (A673, MHH-ES1, and CADO-ES1). As a result, CD44s expression reduced cell proliferation in all the cell lines tested without affecting clonogenicity. Additionally, CD44s increased cell migration in A673 and MHH-ES1, without effects in CADO-ES1. As hyaluronan is the main ligand of CD44s, its effect on migration ability was also assessed, showing that high molecular weight hyaluronic acid (HMW-HA) blocked cell migration while low molecular weight hyaluronic acid (LMW-HA) increased it. Invasion ability was correlated with CD44 expression in A673 and MHH-ES1 cell lines. CD44s, upregulated upon EWSR1::FLI1 knockdown, regulates cell migration and invasion in Ewing sarcoma cells.This project was funded by Instituto de Salud Carlos III, grant numbers PI20CIII/00020, DTS18CIII/00005, Asociación Pablo Ugarte, grant numbers TRPV205/18; Asociación Candela Riera, Asociación Todos Somos Iván & Fundación Sonrisa de Alex, grant numbers TVP333-19, TVP-1324/15; ASION, grant number TVP141/17. Enrique Fernández-Tabanera is supported by Asociación Candela Riera, Asociación Todos Somos Iván & Fundación Sonrisa de Alex, Saint T. Cervera is supported by Asociación Pablo Ugarte and Raquel M. Melero is supported by a CIBERER contract.S

Use of Schizosaccharomyces pombe to produce stable pigments during red winemaking

This work has studied the production of stable pyranoanthocyanin pigments during fermentation using S. pombe and Saccharomyces cerevisiae. Along the fermentation, anthocyanins were determined by HPLC-DAD/MS, acetaldehyde was measured using GC-FID and pyruvic acid was quantified by enzymatic tests. Results show that S. pombe strains produce higher amounts of pyruvic acid, and therefore also of vitisin A, than Saccharomyces controls

Epidemiological Characteristics and Underlying Risk Factors for Mortality during the Autumn 2009 Pandemic Wave in Mexico

Background: Elucidating the role of the underlying risk factors for severe outcomes of the 2009 A/H1N1 influenza pandemic could be crucial to define priority risk groups in resource-limited settings in future pandemics. Methods: We use individual-level clinical data on a large series of ARI (acute respiratory infection) hospitalizations from a prospective surveillance system of the Mexican Social Security medical system to analyze clinical features at presentation, admission delays, selected comorbidities and receipt of seasonal vaccine on the risk of A/H1N1-related death. We considered ARI hospitalizations and inpatient-deaths, and recorded demographic, geographic, and medical information on individual patients during August-December, 2009. Results: Seasonal influenza vaccination was associated with a reduced risk of death among A/H1N1 inpatients (OR = 0.43 (95% CI: 0.25, 0.74)) after adjustment for age, gender, geography, antiviral treatment, admission delays, comorbidities and medical conditions. However, this result should be interpreted with caution as it could have been affected by factors not directly measured in our study. Moreover, the effect of antiviral treatment against A/H1N1 inpatient death did not reach statistical significance (OR = 0.56 (95% CI: 0.29, 1.10)) probably because only 8.9% of A/H1N1 inpatients received antiviral treatment. Moreover, diabetes (OR = 1.6) and immune suppression (OR = 2.3) were statistically significant risk factors for death whereas asthmatic persons (OR = 0.3) or pregnant women (OR = 0.4) experienced a reduced fatality rate among A/ H1N1 inpatients. We also observed an increased risk of death among A/H1N1 inpatients with admission delays .2 days after symptom onset (OR = 2.7). Similar associations were also observed for A/H1N1-negative inpatients. Conclusions: Geographical variation in identified medical risk factors including prevalence of diabetes and immune suppression may in part explain between-country differences in pandemic mortality burden. Furthermore, access to care including hospitalization without delay and antiviral treatment and are also important factors, as well as vaccination coverage with the 2008–09 trivalent inactivated influenza vaccine

Processing of grapes by high hydrostatic pressure. Influence on wine quality

The aim of this work is to evaluate the influence of S. pombe and T. delbrueckii species on the sensory quality of red wine when used in sequential and mixed fermentations with S. cerevisiae

GPCRtm : An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors

Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. In this work, an amino acid substitution matrix (GPCRtm) is calculated for the membrane spanning segments of the G protein-coupled receptor (GPCR) rhodopsin family; one of the largest transmembrane protein family in humans with great importance in health and disease. The GPCRtm matrix reveals the amino acid compositional bias distinctive of the GPCR rhodopsin family and differs from other standard substitution matrices. These membrane receptors, as expected, are characterized by a high content of hydrophobic residues with regard to globular proteins. On the other hand, the presence of polar and charged residues is higher than in average membrane proteins, displaying high frequencies of replacement within themselves. Analysis of amino acid frequencies and values obtained from the GPCRtm matrix reveals patterns of residue replacements different from other standard substitution matrices. GPCRs prioritize the reactivity properties of the amino acids over their bulkiness in the transmembrane regions. A distinctive role is that charged and polar residues seem to evolve at different rates than other amino acids. This observation is related to the role of the transmembrane bundle in the binding of ligands, that in many cases involve electrostatic and hydrogen bond interactions. This new matrix can be useful in database search and for the construction of more accurate sequence alignments of GPCRs. The online version of this article (doi:10.1186/s12859-015-0639-4) contains supplementary material, which is available to authorized users

Iberian Neanderthals in forests and savannahs

This article aims to delve into the reality of glacial refuges of forests and tree species (including conifers, mesothermophilous angiosperms and xerothermic scrub) during the cold dry phases of the Iberian Pleistocene in which there is evidence of occupation of Middle Palaeolithic people. The research framework focuses on the eastern sector of the Iberian Peninsula due to the physiographic, palaeobotanical and archaeological peculiarities, substantiated by recent studies. We contend that some Neanderthal occupations developed in the context of high geobiological complexity, high biological diversity and highly structured forest ecosystems. We highlight the importance of glacial refuges as local anomalies that, however, would be contingent on vegetational development, and on the survival of Palaeolithic groups in areas with a broad diversity of natural resources.Peer reviewe