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Abstract Within search-on-speech, Spoken Term Detection (STD) aims to retrieve data from a speech repository given a textual representation of a search term. This paper presents an international open evaluation for search-on-speech based on STD in Spanish and an analysis of the results. The evaluation has been designed carefully so that several analyses of the main results can be carried out. The evaluation consists in retrieving the speech files that contain the search terms, providing their start and end times, and a score value that reflects the confidence given to the detection. Two different Spanish speech databases have been employed in the evaluation: MAVIR database, which comprises a set of talks from workshops, and EPIC database, which comprises a set of European Parliament sessions in Spanish. We present the evaluation itself, both databases, the evaluation metric, the systems submitted to the evaluation, the results, and a detailed discussion. Five different research groups took part in the evaluation, and ten different systems were submitted in total. We compare the systems submitted to the evaluation and make a deep analysis based on some search term properties (term length, within-vocabulary/out-of-vocabulary terms, single-word/multi-word terms, and native (Spanish)/foreign terms).

Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5’-UTR regions.

The understanding of interaction dynamics in signaling pathways can shed light on pathway architecture and provide insights into targets for intervention. Here, we explored the relevance of kinetic rate constants of a key upstream osmosensor in the yeast high-osmolarity glycerol-mitogen-activated protein kinase (HOG-MAPK) pathway to signaling output responses. We created mutant pairs of the Sln1-Ypd1 complex interface that caused major compensating changes in the association (kon) and dissociation (koff) rate constants (kinetic perturbations) but only moderate changes in the overall complex affinity (Kd). Yeast cells carrying a Sln1-Ypd1 mutant pair with moderate increases in kon and koff displayed a lower threshold of HOG pathway activation than wild-type cells. Mutants with higher kon and koff rates gave rise to higher basal signaling and gene expression but impaired osmoadaptation. Thus, the kon and koff rates of the components in the Sln1 osmosensor determine proper signaling dynamics and osmoadaptation.

Abstract Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool (RanSEPs) with “‐omics” approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in Mycoplasma pneumoniae proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16 ± 9% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non‐coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide‐binding categories. Additionally, 9.7% of the SEPs included a N‐terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.

The construction of large renewable energy projects is characterized by the great uncertainties associated with their administrative complexity and their constructive characteristics. For proper management, it is necessary to undertake a thorough project risk assessment prior to construction. The work presented in this paper is based on a hierarchical risk structure identified by a group of experts, from which a Probabilistic Fuzzy Sets with Analysis Hierarchy Process (PFSAHP) was applied. This probabilistic analysis approach used expert opinion based on the Monte Carlo Method that allows for extracting more information from the original data. In addition, the coherence of the experts' opinions is assessed using a novel parameter known as Confidence Level, which allows for adjusting the opinions of experts and weighting their judgments regarding impact and probability according to their coherence. This model has the advantage of offering a risk analysis in the early stages of the management of renewable energy projects in which there is no detailed information. This model is also more accurate than the classic fuzzy methodology when working with complete distribution functions, whilst it avoids the loss of information that results from the traditional mathematical operations with Fuzzy numbers. To test the model, it was applied to a 250 MW photovoltaic solar plant construction project located in southeast of Spain (Region of Murcia). As a result of the application of the proposed method, risk rankings are obtained with respect to the cost, the time, the scope and from a general point of view of the project.

Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. Despite the existence of several bioinformatic algorithms and servers that predict if a SAS is pathogenic or not, they give little or no information at all on the reasons for pathogenicity prediction and on the actual predicted effect of the SAS on the protein function. Moreover, few actual methods take into account structural information when available for automated analysis. Moreover, many of these algorithms are able to predict an effect that no necessarily translates directly into pathogenicity. VarQ is a bioinformatic pipeline that incorporates structural information for the detailed analysis and prediction of SAS effect on protein function. It is an online tool which uses UniProt id and automatically analyzes known and user provided SAS for their effect on protein activity, folding, aggregation and protein interactions, among others. We show that structural information, when available, can improve the SAS pathogenicity diagnosis and more important explain its causes. We show that VarQ is able to correctly reproduce previous analysis of RASopathies related mutations, saving extensive and time consuming manual curation. VarQ assessment was performed over a set of previously manually curated RASopathies (diseases that affects the RAS/MAPK signaling pathway) related variants, showing its ability to correctly predict the phenotypic outcome and its underlying cause. This resource is available online at http://varq.qb.fcen.uba.ar/. Supporting Information & Tutorials may be found in the webpage of the tool.

In the present work, an abundant and unused residue (wheat straw) has been employed to synthesize a polyol as a substituent of castor oil in polyurethane foams. The liquefied product showed excellent properties for the proposed application. Castor oil was substituted with up to 50% wheat straw polyol in the formulation of polyurethane foams, which were prepared using two different isocyanates (methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI)). The evaluation of physical, mechanical, and thermal properties of the foams revealed that these materials can successfully be formed with up to 40% wheat straw polyols since all the results were improved. Moreover, at this polyol concentration, the morphology of the foams was presented as a compact and ordered structure. Following this trend, the foams showed excellent biodegradability at 30 days (5.60 and 7.31% for TDI and MDI foams, respectively) and 60 days (8.49 and 9.88% for TDI and MDI foams, respectively) in the soil media tests carried out. Thus, the materials prepared in this work can be proposed for agricultural applications such as use in plant nurseries.

Copy number alterations (CNAs) in cancer patients show a large variability in their number, length and position, but the sources of this variability are not known. CNA number and length are linked to patient survival, suggesting clinical relevance. We have identified genes that tend to be mutated in samples that have few or many CNAs, which we term CONIM genes (COpy Number Instability Modulators). CONIM proteins cluster into a densely connected subnetwork of physical interactions and many of them are epigenetic modifiers. Therefore, we investigated how the epigenome of the tissue-of-origin influences the position of CNA breakpoints and the properties of the resulting CNAs. We found that the presence of heterochromatin in the tissue-of-origin contributes to the recurrence and length of CNAs in the respective cancer type.

Communication is a huge challenge for oesophageal speakers, be it for interactions with fellow humans or with digital voice assistants. We aim to quantify these communication challenges (both human−human and human−machine interactions) by measuring intelligibility and Listening Effort (LE) of Oesophageal Speech (OS) in comparison to Healthy Laryngeal Speech (HS). We conducted two listening tests (one web-based, the other in laboratory settings) to collect these measurements. Participants performed a sentence recognition and LE rating task in each test. Intelligibility, calculated as Word Error Rate, showed significant correlation with self-reported LE ratings. Speaker type (healthy or oesophageal) had a major effect on intelligibility and effort. More LE was reported for OS compared to HS even when OS intelligibility was close to HS. Listeners familiar with OS reported less effort when listening to OS compared to nonfamiliar listeners. However, such advantage of familiarity was not observed for intelligibility. Automatic speech recognition scores were higher for OS compared to HS.

Speech and singing voice discrimination is an important task in the speech processing area given that each type of voice requires different information retrieval and signal processing techniques. This discrimination task is hard even for humans depending on the length of voice segments. In this article, we present an automatic speech and singing voice classification method using pitch parameters derived from musical note information and f 0 stability analysis. We applied our method to a database containing speech and a capella singing and compared the results with other discrimination techniques based on information derived from pitch and spectral envelope. Our method obtains good results discriminating both voice types, is efficient, has good generalisation capabilities and is computationally fast. In the process, we have also created a note detection algorithm with parametric control of the characteristics of the notes it detects. We compared the agreement of this algorithm with a state-of-the-art note detection algorithm and performed an experiment that proves that speech and singing discrimination parameters can represent generic information about the music style of the singing voice.

Films containing bay leaves essential oils (BEOs) were prepared and evaluated for edible packaging applications. The BEOs were extracted by the Soxhlet method, using ethanol or methanol as organic solvent. Then, films were prepared by “solvent casting” technique using carboxymethyl cellulose (CMC), with different concentrations for the as-obtained BEOs (from 1% to 30% wt.). The resulting films were characterized to evaluate their physical (thickness, moisture content, water solubility and water vapor permeability), optical (transparency and UV-light barrier), mechanical (tensile strength and elongation at break), antioxidant and antimicrobiological properties Attractive films were obtained for food active packaging applications, as they presented a high antioxidant activity (up to 99%) and total phenolic content, and good barrier properties against water vapor (50% improved of CMC) in the case of CMC-film containing 15% wt. ethanolic extract. Related to optical properties, UV-light barrier effect was increased (almost 100% of protection) avoiding typical lipids oxidation in food systems. High water solubility (93%) was also found, ensuring also their biodegradability. Moreover, it was demonstrated that developed films inhibit microorganisms’ growth (Escherichia coli and Candida glabrata), this avoiding an early food oxidation.

In-vehicle applications that are based on Vehicle-to-Everything (V2X) communication technologies need to be evaluated under lab-controlled conditions before performing field tests. The need for a tailored platform to perform specific research on the cooperative Advanced Driving Assistance System (ADAS) to assess the effect on driver behavior and driving performance motivated the development of a driver-centric traffic simulator that is built over a 3D graphics engine. The engine creates a driving situation as it communicates with a traffic simulator as a means to simulate real-life traffic scenarios. The TraCI as a Service (TraaS) library was implemented to perform the interaction between the driver-controlled vehicle and the Simulation of Urban MObility (SUMO). An extension of a previous version, this work improves simulation performance and realism by reducing computational demand and integrating a tailored scenario with the ADAS to be tested. The usability of the implemented simulation platform was evaluated by means of an experiment related to the efficiency of a Traffic Light Assistant (TLA), showing the analysis of the answer that 80% of the participants were satisfied with the simulator and the TLA system implemented.

In this work, a novel ambulatory ECG monitoring device developed in-house called HOLTIN is analyzed when operating in complex indoor scenarios. The HOLTIN system is described, from the technological platform level to its functional model. In addition, by using in-house 3D ray launching simulation code, the wireless channel behavior, which enables ubiquitous operation, is performed. The effect of human body presence is taken into account by a novel simplified model embedded within the 3D Ray Launching code. Simulation as well as measurement results are presented, showing good agreement. These results may aid in the adequate deployment of this novel device to automate conventional medical processes, increasing the coverage radius and optimizing energy consumption.

Many driver mutations in cancer are specific in that they occur at significantly higher rates than – presumably – functionally alternative mutations. For example, V600E in the BRAF hydrophobic activation segment (AS) pocket accounts for >95% of all kinase mutations. While many hypotheses tried to explain such significant mutation patterns, conclusive explanations are lacking. Here, we use experimental and in silico structure-energy statistical analyses, to elucidate why the V600E mutation, but no other mutation at this, or any other positions in BRAF’s hydrophobic pocket, is predominant. We find that BRAF mutation frequencies depend on the equilibrium between the destabilization of the hydrophobic pocket, the overall folding energy, the activation of the kinase and the number of bases required to change the corresponding amino acid. Using a random forest classifier, we quantitatively dissected the parameters contributing to BRAF AS cancer frequencies. These findings can be applied to genome-wide association studies and prediction models.

Bleached kraft semichemical eucalyptus pulp was used as raw material to adsorb an organic compound, toluene, from aqueous solution. The pulp was sonicated with different powers and different times to obtain smaller cellulose fibers. The adsorption capacity for toluene of sonicated fibers and bleached eucalyptus pulp was measured by ultraviolet spectroscopy. The absorption capacity for toluene was increased considerably when cellulose nanofibres were obtained. The adsorption capacity of bleached eucalyptus pulp was 36 μmol/g, while sonicated fibres at 30 W and 20 hours increased the adsorption by 47% and at 50 W and 20 h increased it by 67% compared with untreated fibres. Visual examination and optical microscopy were used to observe the reduction of fibers width and the dispersion increase. Contact angle measurements were used to analyze the variation of hydrophilic character of cellulose. Fourier transform infrared spectroscopy was used to study variations introduced by the ultrasound treatments on the chemical structure of the samples. The adsorption capacity studies showed that the treatment with ultrasound improved the retention capacity of the fibres, increasing considerably the adsorption capacity when the fiber width approached the nanoscale.

The most outstanding feature of scanning force microscopy (SFM) is its capability to detect various different short and long range interactions. In particular, magnetic force microscopy (MFM) is used to characterize the domain configuration in ferromagnetic materials such as thin films grown by physical techniques or ferromagnetic nanostructures. It is a usual procedure to separate the topography and the magnetic signal by scanning at a lift distance of 25–50 nm such that the long range tip–sample interactions dominate. Nowadays, MFM is becoming a valuable technique to detect weak magnetic fields arising from low dimensional complex systems such as organic nanomagnets, superparamagnetic nanoparticles, carbon-based materials, etc. In all these cases, the magnetic nanocomponents and the substrate supporting them present quite different electronic behavior, i.e., they exhibit large surface potential differences causing heterogeneous electrostatic interaction between the tip and the sample that could be interpreted as a magnetic interaction. To distinguish clearly the origin of the tip–sample forces we propose to use a combination of Kelvin probe force microscopy (KPFM) and MFM. The KPFM technique allows us to compensate in real time the electrostatic forces between the tip and the sample by minimizing the electrostatic contribution to the frequency shift signal. This is a great challenge in samples with low magnetic moment. In this work we studied an array of Co nanostructures that exhibit high electrostatic interaction with the MFM tip. Thanks to the use of the KPFM/MFM system we were able to separate the electric and magnetic interactions between the tip and the sample.

Hesperaloe funifera was characterized in terms of its contents of holocellulose, α-cellulose, and lignin (74.1, 52.3, and 7.9%, respectively). Also, an experimental factor design was used to examine the influence of operational variables in the diethanolamine pulping of this material (viz. diethanolamine concentration (50-80%), cooking temperature (155-185 ºC), and time (30-90 minutes)) on the contents of holocellulose, α-cellulose, and lignin, as well as the yield, kappa number, and viscosity of the resulting pulps, and also on the brightness, tensile index, stretch, burst index, and tear index of paper sheets made from it. The predictions for these dependent variables departed by less than 1, 7, 6, 2, 2, 4, 15, 11, 12, 10, and 37% from their respective experimental values. Black liquors obtained from the pulping runs were characterized by determining pH, density, TDS, (total dissolved solids), MI (inorganic matter), MO (organic matter), and lignin content; lignin samples were characterized by different techniques (FTIR and TGA). Finally, the black liquors were acidified to separate solid fractions that were subjected to pyrolysis and gasification in order to obtain synthesis and fuel gases.

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In the context of hospital management and operation, Intensive Care Units (ICU) are one of the most challenging in terms of time responsiveness and criticality, in which adequate resource management and signal processing play a key role in overall system performance. In this work, a context aware Intensive Care Unit is implemented and analyzed to provide scalable signal acquisition capabilities, as well as to provide tracking and access control. Wireless channel analysis is performed by means of hybrid optimized 3D Ray Launching deterministic simulation to assess potential interference impact as well as to provide required coverage/capacity thresholds for employed transceivers. Wireless system operation within the ICU scenario, considering conventional transceiver operation, is feasible in terms of quality of service for the complete scenario. Extensive measurements of overall interference levels have also been carried out, enabling subsequent adequate coverage/capacity estimations, for a set of Zigbee based nodes. Real system operation has been tested, with ad-hoc designed Zigbee wireless motes, employing lightweight communication protocols to minimize energy and bandwidth usage. An ICU information gathering application and software architecture for Visitor Access Control has been implemented, providing monitoring of the Boxes external doors and the identification of visitors via a RFID system. The results enable a solution to provide ICU access control and tracking capabilities previously not exploited, providing a step forward in the implementation of a Smart Health framework.

Los libros de texto constituyen un recurso didáctico fundamental en todos los niveles educativos. Las investigaciones recientes sobre el aprendizaje de la probabilidad conceden un papel esencial a la simulación. En este trabajo presentamos un análisis del uso de este recurso en nueve libros de texto y deducimos algunos criterios a tener en cuenta en la elaboración de libros de texto para la enseñanza de la probabilidad en la educación secundaria.

En este trabajo realizamos un análisis teórico de los pasos necesarios en el cálculo de probabilidades inversas por medio del teorema de Bayes y presentamos un estudio empírico de errores en una muestra de 414 estudiantes de Psicología, después de la enseñanza del tema. Presentamos también los resultados de una experiencia de enseñanza del teorema de Bayes y sus aplicaciones a 78 alumnos de Psicología, apoyada en Excel, dirigida a superar las dificultades descritas. Los resultados indicaron la consecución de los objetivos didácticos en la mayoría de los alumnos participantes.

The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products ('di-chromatic'), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation.

To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida albicans, and Schizosaccharomyces pombe, encompassing 400 million years of evolution. We first aligned and catalogued the families of SH3-containing proteins in these four species to determine the relationships between homologous domains. Then, we tagged and purified all soluble SH3 domains (82 in total) to perform a quantitative peptide assay (SPOT) for each SH3 domain. All SPOT readouts were hierarchically clustered and we observed that the organization of the SH3 specificity landscape in three distinct profile classes remains conserved across these four yeast species. We also produced a specificity profile for each SH3 domain from manually aligned top SPOT hits and compared the within-family binding motif consensus. This analysis revealed a striking example of binding motif divergence in a C. albicans Rvs167 paralog, which cannot be explained by overall SH3 sequence or interface residue divergence, and we validated this specificity change with a yeast two-hybrid (Y2H) assay. In addition, we show that position-weighted matrices (PWM) compiled from SPOT assays can be used for binding motif screening in potential binding partners and present cases where motifs are either conserved or lost among homologous SH3 interacting proteins. Finally, by comparing pairwise SH3 sequence identity to binding profile correlation we show that for ~75% of all analyzed families the SH3 specificity profile was remarkably conserved over a large evolutionary distance. Thus, a high sequence identity within an SH3 domain family predicts conserved binding specificity, whereas divergence in sequence identity often coincided with a change in binding specificity within this family. As such, our results are important for future studies aimed at unraveling complex specificity networks of peptide recognition domains in higher eukaryotes, including mammals.

The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the sequence of the P1 adhesin gene. Here, we have sequenced the genomes of 23 clinical isolates of M. pneumoniae. Studying SNPs, non-synonymous mutations, indels and genome rearrangements of these 23 strains and 4 previously sequenced ones, has revealed new subclasses in the two main groups, some of them being associated with the country of isolation. Integrative analysis of in vitro gene essentiality and mutation rates enabled the identification of several putative virulence factors and antigenic proteins; revealing recombination machinery, glycerol metabolism and peroxide production as possible factors in the genetics and physiology of these pathogenic strains. Additionally, the transcriptomes and proteomes of two representative strains, one from each of the two main groups, have been characterized to evaluate the impact of mutations on RNA and proteins levels. This study has revealed that type 2 strains show higher expression levels of CARDS toxin, a protein recently shown to be one of the major factors of inflammation. Thus, we propose that type 2 strains could be more toxigenic than type 1 strains of M. pneumoniae.

En este trabajo comparamos las características de las secuencias de resultados aleatorios y distribuciones aleatorias de puntos generadas por tres grupos de alumnos de Educación Primaria y Secundaria con las propiedades matemáticas de las mismas. La finalidad es describir el significado personal que dichos estudiantes asignan a la aleatoriedad.

Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors) and the output (transcription factors) layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

We introduce a new basis of the non-commutative symmetric functions whose elements have Schur functions as their commutative images. Dually, we build a basis of the quasi-symmetric functions which expand positively in the fundamental quasi-symmetric functions and decompose Schur functions according to a signed combinatorial formula.

We introduce explicit combinatorial interpretations for the coefficients in some of the transition matrices relating to skew Hall-Littlewood polynomials $P_{\lambda / \mu}(x;t)$ and Hivert's quasisymmetric Hall-Littlewood polynomials $G_{\gamma}(x;t)$. More specifically, we provide the following: 1. $G_{\gamma}$-expansions of the $P_{\lambda}$, the monomial quasisymmetric functions, and Gessel's fundamental quasisymmetric functions $F_{\alpha}$, and 2. an expansion of the $P_{\lambda / \mu}$ in terms of the $F_{\alpha}$. The $F_{\alpha}$ expansion of the $P_{\lambda / \mu}$ is facilitated by introducing the set of $\textit{starred tableaux}$. In the full version of the article we also provide $G_{\gamma}$-expansions of the quasisymmetric Schur functions and the peak quasisymmetric functions of Stembridge.

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint‐based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time‐dependent changes, albeit using a static model. By performing an in silico knock‐out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.

In the bacterial world, methylation is most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, it is known that methylation plays functionally important roles, including timing of DNA replication, chromosome partitioning, DNA repair, and regulation of gene expression. However, full DNA methylome analyses are scarce due to a lack of a simple methodology for rapid and sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule Real-Time (SMRT) sequencing to determine the methylomes of two related human pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with single-base resolution. Our analysis identified two new methylation motifs not previously described in bacteria: a widespread 6 mA methylation motif common to both bacteria (5'-CTAT-3'), as well as a more complex Type I m6A sequence motif in M. pneumoniae (5'-GAN(7)TAY-3'/3'-CTN(7)ATR-5'). We identify the methyltransferase responsible for the common motif and suggest the one involved in M. pneumoniae only. Analysis of the distribution of methylation sites across the genome of M. pneumoniae suggests a potential role for methylation in regulating the cell cycle, as well as in regulation of gene expression. To our knowledge, this is one of the first direct methylome profiling studies with single-base resolution from a bacterial organism.

Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

Current curricular guidelines for probability at Primary school level imply the need for a specific training of prospective teachers, which should be based on the previous assessment of their training needs. In order to contribute to this need, in this paper we present the analysis of responses by 157 Spanish prospective teachers to an open question, taken from previous research on subjective perception of randomness. The results show a mixture of correct and wrong conceptions, some of which parallel some historical conceptions of randomness. Teachers’ educators could start from these intuitions to help prospective teachers advance to a broader meaning of the concept, adequate for their future teaching responsibility.

We prove that the Lam-Shimozono ``down operator'' on the affine Weyl group induces a derivation of the affine Fomin-Stanley subalgebra of the affine nilCoxeter algebra. We use this to verify a conjecture of Berg, Bergeron, Pon and Zabrocki describing the expansion of k-Schur functions of ``near rectangles'' in the affine nilCoxeter algebra. Consequently, we obtain a combinatorial interpretation of the corresponding k-Littlewood–Richardson coefficients.

E-cadherin is critical for the maintenance of tissue architecture due to its role in cell-cell adhesion. E-cadherin mutations are the genetic cause of Hereditary Diffuse Gastric Cancer (HDGC) and missense mutations represent a clinical burden, due to the uncertainty of their pathogenic role. In vitro and in vivo, most mutations lead to loss-of-function, although the causal factor is unknown for the majority. We hypothesized that destabilization could account for the pathogenicity of E-cadherin missense mutations in HDGC, and tested our hypothesis using in silico and in vitro tools. FoldX algorithm was used to calculate the impact of each mutation in E-cadherin native-state stability, and the analysis was complemented with evolutionary conservation, by SIFT. Interestingly, HDGC patients harbouring germline E-cadherin destabilizing mutants present a younger age at diagnosis or death, suggesting that the loss of native-state stability of E-cadherin accounts for the disease phenotype. To elucidate the biological relevance of E-cadherin destabilization in HDGC, we investigated a group of newly identified HDGC-associated mutations (E185V, S232C and L583R), of which L583R is predicted to be destabilizing. We show that this mutation is not functional in vitro, exhibits shorter half-life and is unable to mature, due to premature proteasome-dependent degradation, a phenotype reverted by stabilization with the artificial mutation L583I (structurally tolerated). Herein we report E-cadherin structural models suitable to predict the impact of the majority of cancer-associated missense mutations and we show that E-cadherin destabilization leads to loss-of-function in vitro and increased pathogenicity in vivo.

We exhibit a canonical connection between maximal $(0,1)$-fillings of a moon polyomino avoiding north-east chains of a given length and reduced pipe dreams of a certain permutation. Following this approach we show that the simplicial complex of such maximal fillings is a vertex-decomposable and thus a shellable sphere. In particular, this implies a positivity result for Schubert polynomials. For Ferrers shapes, we moreover construct a bijection to maximal fillings avoiding south-east chains of the same length which specializes to a bijection between $k$-triangulations of the $n$-gon and $k$-fans of Dyck paths. Using this, we translate a conjectured cyclic sieving phenomenon for $k$-triangulations with rotation to $k$-flagged tableaux with promotion.

San Felices de los Gallegos es un pueblo alejado, confín geográfico de la provincia, e injustamente olvidado de cualquier promoción institucional, dado el interés geográfico de la comarca y el valor arquitectónico de su núcleo urbano. Más conocido que por su interesantísima arquitectura popular1, San Felices lo es por su castillo, palimpsesto de defensas ha sido llamado, y como tal domina y abarcaba a todo el caserío. La población de San Felices de los Gallegos ha sido considerada históricamente como defensa avanzada, junto con la plaza de Ciudad Rodrigo, de la diócesis Mirobrigense frente al Reino de Portugal. Su nombre dícese fue impuesto por el obispo de Oporto, D. Félix XI, se supone que a una población ya existente, corriendo el año 690. De historia tan disputada frente al vecino reino da fe su conquista por el rey portugués don Dionís en 12962, monarca al que se atribuye también la erección de la fortaleza.

La historiografía española adolece de un tipo de estudios puntuales sobre una serie de manifestaciones económicas; manifestaciones aparentemente desligadas del mundo rural, marginales en determinadas épocas, pero siempre testimoniales y premonitorias de períodos en que el proceso manufacturero y mercantil adquirirá, un peso específico propio, en el mundo feudal. La manufactura textil representa la base de despegue para la industria medieval, la palanca que permite a un grupo social disperso constituirse en clase, el trabajo urbano que desarraigará a sectores del campesinado para convertirlos en plebe urbana. Nuestra historia textil no puede compararse a la de nuestros vecinos europeos, que supieron basar sus sociedades mercantiles en el proceso manufacturero de los paños. Las razones que nos impidieron conseguirlo son múltiples y quedan todas ellas fuera de nuestro limitado foco de atención, que no de nuestro interés.

Entre los siglos IX y XII, y en el norte peninsular, es frecuentre encontrarnos con varios tipos de documentos que nos revelan toda una variedad de objetos manufacturados de procedencia y utilidad diversa. En las apretadas riberas del Narcea el diácono Taielus dona, apenas comenzado el año 889, varios libros de su biblioteca para uso del monasterio de Elaba. En el año 922, es Ordoño II quien en el contexto de un privilegio al monasterio de Samos, quizá movido por su piedad, otorga muchos objetos útiles y otros de índole litúrgica, donde abunda la plata, y no menos de veinticinco libros entre los cuales se hallan las Etimologías. Ocho años después, es el monasterio de Piasca, en las cercanías de Potes, el beneficiado por una donación de libros, ganado y objetos sagrados que Theoda y Argonti tienen a bien ofrece

We introduce a shifted analog of the plactic monoid of Lascoux and Schützenberger, the \emphshifted plactic monoid. It can be defined in two different ways: via the \emphshifted Knuth relations, or using Haiman's mixed insertion. Applications include: a new combinatorial derivation (and a new version of) the shifted Littlewood-Richardson Rule; similar results for the coefficients in the Schur expansion of a Schur P-function; a shifted counterpart of the Lascoux-Schützenberger theory of noncommutative Schur functions in plactic variables; a characterization of shifted tableau words; and more.

Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of polycarborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photoenergy processes.

Evolutionary conservation of protein interaction properties has been shown to be a valuable indication for functional importance. Here we use homology interface modeling of 10 Ras-effector complexes by selecting ortholog proteins from 12 organisms representing the major eukaryotic branches, except plants. We find that with increasing divergence time the sequence similarity decreases with respect to the human protein, but the affinities and association rate constants are conserved as predicted by the protein design algorithm, FoldX. In parallel we have done computer simulations on a minimal network based on Ras-effector interactions, and our results indicate that in the absence of negative feedback, changes in kinetics that result in similar binding constants have strong consequences on network behavior. This, together with the previous results, suggests an important biological role, not only for equilibrium binding constants but also for kinetics in signaling processes involving Ras-effector interactions. Our findings are important to take into consideration in system biology approaches and simulations of biological networks.

As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed from smaller recurrent elements, between 4 and 8 residues long. Finally, we observed that a significant amount of short sequences tend to display strong structural ambiguity between alpha helix and extended conformations. When the sequence length increases, this so-called sequence plasticity is no longer observed, illustrating the context dependency of polypeptide structures.

Current experiments likely cover only a fraction of all protein-protein interactions. Here, we developed a method to predict SH2-mediated protein-protein interactions using the structure of SH2-phosphopeptide complexes and the FoldX algorithm. We show that our approach performs similarly to experimentally derived consensus sequences and substitution matrices at predicting known in vitro and in vivo targets of SH2 domains. We use our method to provide a set of high-confidence interactions for human SH2 domains with known structure filtered on secondary structure and phosphorylation state. We validated the predictions using literature-derived SH2 interactions and a probabilistic score obtained from a naive Bayes integration of information on coexpression, conservation of the interaction in other species, shared interaction partners, and functions. We show how our predictions lead to a new hypothesis for the role of SH2 domains in signaling.

Numerous studies have noted that the evolution of new enzymatic specificities is accompanied by loss of the protein's thermodynamic stability (DeltaDeltaG), thus suggesting a tradeoff between the acquisition of new enzymatic functions and stability. However, since most mutations are destabilizing (DeltaDeltaG>0), one should ask how destabilizing mutations that confer new or altered enzymatic functions relative to all other mutations are. We applied DeltaDeltaG computations by FoldX to analyze the effects of 548 mutations that arose from the directed evolution of 22 different enzymes. The stability effects, location, and type of function-altering mutations were compared to DeltaDeltaG changes arising from all possible point mutations in the same enzymes. We found that mutations that modulate enzymatic functions are mostly destabilizing (average DeltaDeltaG = +0.9 kcal/mol), and are almost as destabilizing as the "average" mutation in these enzymes (+1.3 kcal/mol). Although their stability effects are not as dramatic as in key catalytic residues, mutations that modify the substrate binding pockets, and thus mediate new enzymatic specificities, place a larger stability burden than surface mutations that underline neutral, non-adaptive evolutionary changes. How are the destabilizing effects of functional mutations balanced to enable adaptation? Our analysis also indicated that many mutations that appear in directed evolution variants with no obvious role in the new function exert stabilizing effects that may compensate for the destabilizing effects of the crucial function-altering mutations. Thus, the evolution of new enzymatic activities, both in nature and in the laboratory, is dependent on the compensatory, stabilizing effect of apparently "silent" mutations in regions of the protein that are irrelevant to its function.

p53 mediates cell cycle arrest or apoptosis in response to DNA damage. Its activity is subject to a tight regulation involving a multitude of post-translational modifications. The plethora of functional protein interactions of p53 at present precludes a clear understanding of regulatory principles in the p53 signaling network. To circumvent this complexity, we studied here the minimal requirements for functionally relevant p53 post-translational modifications by expressing human p53 together with its best characterized modifier Mdm2 in budding yeast. We find that expression of the human p53-Mdm2 module in yeast is sufficient to faithfully recapitulate key aspects of p53 regulation in higher eukaryotes, such as Mdm2-dependent targeting of p53 for degradation, sumoylation at lysine 386 and further regulation of this process by p14(ARF). Interestingly, sumoylation is necessary for the recruitment of p53-Mdm2 complexes to yeast nuclear bodies morphologically akin to human PML bodies. These results suggest a novel role for Mdm2 as well as for p53 sumoylation in the recruitment of p53 to nuclear bodies. The reductionist yeast model that was established and validated in this study will now allow to incrementally study simplified parts of the intricate p53 network, thus helping elucidate the core mechanisms of p53 regulation as well as test novel strategies to counteract p53 malfunctions.

Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10(-5) interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 10(3) interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show significantly different link dynamics. In particular, human proteins involved in immune response, transport, and establishment of localization show signs of positive selection for change of interactions. Our analysis suggests that a small degree of molecular divergence can give rise to important changes at the network level. We propose that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.