Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

Global response sensitivity analysis of uncertain structures

The problem of characterizing global sensitivity indices of structural response when system uncertainties are represented using probabilistic and (or) non-probabilistic modeling frameworks (which include intervals, convex functions, and fuzzy variables) is considered. These indices are characterized in terms of distance measures between a fiducial model in which uncertainties in all the pertinent variables are taken into account and a family of hypothetical models in which uncertainty in one or more selected variables are suppressed. The distance measures considered include various probability distance measures (Hellinger,l(2), and the Kantorovich metrics, and the Kullback-Leibler divergence) and Hausdorff distance measure as applied to intervals and fuzzy variables. Illustrations include studies on an uncertainly parametered building frame carrying uncertain loads. (C) 2015 Elsevier Ltd. All rights reserved.

Capacity approaching codes for non-coherent orthogonal modulation

This paper describes a curve-fitting approach for the design of capacity approaching coded modulation for orthogonal signal sets with non-coherent detection. In particular, bit-interleaved coded modulation with iterative decoding is considered. Decoder metrics are developed that do not require knowledge of the signal-to-noise ratio, yet still offer very good performance. © 2007 IEEE.

Discriminative language model adaptation for Mandarin broadcast speech transcription and translation

This paper investigates unsupervised test-time adaptation of language models (LM) using discriminative methods for a Mandarin broadcast speech transcription and translation task. A standard approach to adapt interpolated language models to is to optimize the component weights by minimizing the perplexity on supervision data. This is a widely made approximation for language modeling in automatic speech recognition (ASR) systems. For speech translation tasks, it is unclear whether a strong correlation still exists between perplexity and various forms of error cost functions in recognition and translation stages. The proposed minimum Bayes risk (MBR) based approach provides a flexible framework for unsupervised LM adaptation. It generalizes to a variety of forms of recognition and translation error metrics. LM adaptation is performed at the audio document level using either the character error rate (CER), or translation edit rate (TER) as the cost function. An efficient parameter estimation scheme using the extended Baum-Welch (EBW) algorithm is proposed. Experimental results on a state-of-the-art speech recognition and translation system are presented. The MBR adapted language models gave the best recognition and translation performance and reduced the TER score by up to 0.54% absolute. © 2007 IEEE.

Improving speech transcription for Mandarin-english translation

This paper describes the development of the CU-HTK Mandarin Speech-To-Text (STT) system and assesses its performance as part of a transcription-translation pipeline which converts broadcast Mandarin audio into English text. Recent improvements to the STT system are described and these give Character Error Rate (CER) gains of 14.3% absolute for a Broadcast Conversation (BC) task and 5.1% absolute for a Broadcast News (BN) task. The output of these STT systems is then post-processed, so that it consists of sentence-like segments, and translated into English text using a Statistical Machine Translation (SMT) system. The performance of the transcription-translation pipeline is evaluated using the Translation Edit Rate (TER) and BLEU metrics. It is shown that improving both the STT system and the post-STT segmentations can lower the TER scores by up to 5.3% absolute and increase the BLEU scores by up to 2.7% absolute. © 2007 IEEE.

La oda latina a Venus de Garcilaso de la Vega: adopción de la tradición clásica y su traducción española como relación de transitividad

Resumen: Garcilaso de la Vega, siguiendo el canon pedagógico humanista, se constituyó en un poeta que no solo adoptó la tradición de la lírica clásica en la absorción de temas y motivos, sino que también ensayó la composición de odas, a la manera horaciana, en lengua latina. Estas composiciones, regidas por las reglas métricas que se enseñaban en las escuelas de gramática y retórica, conservan la estructura estrófica y la rigurosa alternancia de sílabas breves y largas. El interés filológico en torno de estos poemas, por los cuales Garcilaso fue elogiado por los intelectuales de su época, es tardío ya que en las primeras ediciones de la obra del toledano no aparecen; será a finales del siglo XIX cuando se ponga la mirada sobre ellos y se comprenderá cuál es la importancia del contexto italiano de composición y el compromiso del poeta con lo clásico. Este cruce de imaginarios, que tiene como límite último la producción poética de Garcilaso, puede entenderse como un ejercicio de traducibilidad entre el sentido de un sistema semiótico adoptado, como es en este caso la utilización de la lengua latina, y la posibilidad de decir algo de ello, lo que implica producir significación; asimismo este juego de traspasos enunciativos se completa con la traducción a la lengua española de las odas latinas de Garcilaso. En consecuencia, los objetivos de la presente comunicación están orientados a analizar los dos pasos de la actividad semántica que se opera en toda relación de traducción: en este caso entre la oda a Venus creada por el poeta hispano y la versión de Nemesia Matarrodona Vizcaíno, quien transpone al español el texto garcilasiano en la edición de Sotelo Salas, del año 1976.

Geometria et Geometriae : e mathematica ad philosopiam

Resumen: Luego de exponer las posibilidades filosóficas que las geometrías abren a las orientaciones de nuevos espacios, el artículo considera los procedimientos euclidianos y la conexión con las geometrías no-euclidianas. Hay muchas posiciones acerca de las bases filosóficas de las distintas geometrías. Hay además formulaciones muy importantes, desde la gnoseología a la ontología, respecto de las extensiones métricas de la alta geometría.

Consumer Expertise or Credit Risk? An empirical analysis of mortgage pricing

Loan mortgage interest rates are usually the result of a bank-customer negotiation process. Credit risk, consumer cross-buying potential, bundling, financial market competition and other features affecting the bargaining power of the parties could affect price. We argue that, since mortgage loan is a complex product, consumer expertise could be a relevant factor for mortgage pricing. Using data on mortgage loan prices for a sample of 1055 households for the year 2005 (Bank of Spain Survey of Household Finances, EFF-2005), and including credit risk, costs, potential capacity of the consumer to generate future business and bank competition variables, the regression results indicate that consumer expertise-related metrics are highly significant as predictors of mortgage loan prices. Other factors such as credit risk and consumer cross-buying potential do not have such a significant impact on mortgage prices. Our empirical results are affected by the credit conditions prior to the financial crisis and could shed some light on this issue.

Characterization of the benthos, marine debris and bottom fish at Gray’s Reef National Marine Sanctuary

Executive Summary: Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary. The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect. GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces. The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS. Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions). GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items. Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown. Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata. Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

The Value of Research Data

Scientific research revolves around the production, analysis, storage, management, and re-use of data. Data sharing offers important benefits for scientific progress and advancement of knowledge. However, several limitations and barriers in the general adoption of data sharing are still in place. Probably the most important challenge is that data sharing is not yet very common among scholars and is not yet seen as a regular activity among scientists, although important efforts are being invested in promoting data sharing. In addition, there is a relatively low commitment of scholars to cite data. The most important problems and challenges regarding data metrics are closely tied to the more general problems related to data sharing. The development of data metrics is dependent on the growth of data sharing practices, after all it is nothing more than the registration of researchers’ behaviour. At the same time, the availability of proper metrics can help researchers to make their data work more visible. This may subsequently act as an incentive for more data sharing and in this way a virtuous circle may be set in motion. This report seeks to further explore the possibilities of metrics for datasets (i.e. the creation of reliable data metrics) and an effective reward system that aligns the main interests of the main stakeholders involved in the process. The report reviews the current literature on data sharing and data metrics. It presents interviews with the main stakeholders on data sharing and data metrics. It also analyses the existing repositories and tools in the field of data sharing that have special relevance for the promotion and development of data metrics. On the basis of these three pillars, the report presents a number of solutions and necessary developments, as well as a set of recommendations regarding data metrics. The most important recommendations include the general adoption of data sharing and data publication among scholars; the development of a reward system for scientists that includes data metrics; reducing the costs of data publication; reducing existing negative cultural perceptions of researchers regarding data publication; developing standards for preservation, publication, identification and citation of datasets; more coordination of data repository initiatives; and further development of interoperability protocols across different actors.

KE Workshop report: Report Knowledge Exchange workshop Making data count - Research Data and Research Assessment

The possibilities of digital research have altered the production, publication and use of research results. Academic research practice and culture are changing or have already been transformed, but to a large degree the system of academic recognition has not yet adapted to the practices and possibilities of digital research. This applies especially to research data, which are increasingly produced, managed, published and archived, but play hardly a role yet in practices of research assessment. The aim of the workshop was to bring experts and stakeholders from research institutions, universities, scholarly societies and funding agencies together in order to review, discuss and build on possibilities to implement the culture of sharing and to integrate publication of data into research assessment procedures. The report 'The Value of Research Data - Metrics for datasets from a cultural and technical point of view' was presented and discussed. Some of the key finding were that data sharing should be considered normal research practice, in fact not sharing should be considered malpractice. Research funders and universities should support and encourage data sharing. There are a number of important aspects to consider when making data count in research and evaluation procedures. Metrics are a necessary tool in monitoring the sharing of data sets. However, data metrics are at present not very well developed and there is not yet enough experience in what these metrics actually mean. It is important to implement the culture of sharing through codes of conducts in the scientific communities. For further key findings please read the report.

BertsoBot: lehen urratsak

[EU]Hizkuntzaren prozesamenduko teknikak erabilita, poesia-sorkuntza automatikoan lehen urratsak eman dira. Hau erdiesteko, corpusen prozesamenduan oinarritutako bilaketak erabili dira, bai bilaketa arruntak eta baita bilaketa semantiko aurreratuak ere, horretarako IXA taldean garatutako tresna ezberdinak erabiliaz. Hizkuntza poetikoko testuek, gramatikaltasun eta metrika hertsitik haratago, semantika eta pragmatika barneratuta dituzte. Lan honetan semantikaren auziari heldu zaio nagusiki.

Black Holes, Cosmological Solutions, Future Singularities, and Their Thermodynamical Properties in Modified Gravity Theorie

54 p.

Extending Distance-based Ranking Models In Estimation of Distribution Algorithms

Recently, probability models on rankings have been proposed in the field of estimation of distribution algorithms in order to solve permutation-based combinatorial optimisation problems. Particularly, distance-based ranking models, such as Mallows and Generalized Mallows under the Kendall’s-t distance, have demonstrated their validity when solving this type of problems. Nevertheless, there are still many trends that deserve further study. In this paper, we extend the use of distance-based ranking models in the framework of EDAs by introducing new distance metrics such as Cayley and Ulam. In order to analyse the performance of the Mallows and Generalized Mallows EDAs under the Kendall, Cayley and Ulam distances, we run them on a benchmark of 120 instances from four well known permutation problems. The conducted experiments showed that there is not just one metric that performs the best in all the problems. However, the statistical test pointed out that Mallows-Ulam EDA is the most stable algorithm among the studied proposals.

Limited resources? Let the habitat priority planner help!

In this time of scarce resources, coastal resource managers must find ways to prioritize conservation, land use, and restoration efforts. The Habitat Priority Planner (HPP) is a free geospatial tool created by the National Oceanic and Atmospheric Administration’s Coastal Services Center that has received wide praise for its ease of use and broad applicability to conservation strategic planning, restoration, climate change scenarios, and other natural resource management actions. Not a geographic information system (GIS) user? Don’t worry―this tool was designed to be used in a team setting. One intermediate-level GIS user can push the buttons to show quick results while a roomful of resource managers and stakeholders provide input criteria that determine the results. The Habitat Priority Planner is a toolbar for ESRI’s ArcGIS platform that is composed of three modules: Habitat Classification, Habitat Analysis, and Data Explorer. The tool calculates basic ecological statistics that are used to examine how habitats function within a landscape. The tool pre‐packages several common landscape metrics into a user‐friendly interface for intermediate GIS users. In addition, HPP allows the user to build queries interactively using a graphical interface for demonstrating criteria selections quickly in a visual manner that is useful in stakeholder interactions. Tool advocates and users include land trusts, conservation alliances, nonprofit organizations, and select National Estuarine Research Reserves and refuges of the U.S. Fish and Wildlife Service. Participants in this session will learn the basic requirements for HPP use and the multiple ways the HPP has been applied to geographies nationwide. (PDF contains 5 pages)