A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

Uncertainties in 4pi-gamma coincidence counting

The 4πβ-γ coincidence counting method and its close relatives are widely used for the primary standardization of radioactivity. Both the general formalism and specific implementation of these methods have been well-documented. In particular, previous papers contain the extrapolation equations used for various decay schemes, methods for determining model parameters and, in some cases, tabulated uncertainty budgets. Two things often lacking from experimental reports are both the rationale for estimating uncertainties in a specific way and the details of exactly how a specific component of uncertainty was estimated. Furthermore, correlations among the components of uncertainty are rarely mentioned. To fill in these gaps, the present article shares the best-practices from a few practitioners of this craft. We explain and demonstrate with examples of how these approaches can be used to estimate the uncertainty of the reported massic activity. We describe uncertainties due to measurement variability, extrapolation functions, dead-time and resolving-time effects, gravimetric links, and nuclear and atomic data. Most importantly, a thorough understanding of the measurement system and its response to the decay under study can be used to derive a robust estimate of the measurement uncertainty.

Is Transnational Private Regulation Potentially an Effective Means of Promoting Collective Industrial Relations?

This paper asks whether collective industrial relations can be promoted by means other than seeking change in public policy. Recent research points to the increasing significance of transnational private regulation (TPR) in developing economies. There is an emerging consensus that market incentives to improve wages and conditions of work can have a modest positive effect on measurable outcomes like hours of work, and health and safety. However, it appears that TPR has little impact on the capacity of workers to pursue such improvements for themselves via collective action. The paper takes a closer look at the potential of TPR to enhance worker voice and participation. It argues that this potential cannot be properly evaluated without understanding how local actors mobilise the social and political resources that TPR provides. The case studies presented show how different TPR schemes have been used by unions in Africa as a means to pursue the interests of members. The authors found that the scale of the impact of TPR in all of the contexts studied depended almost entirely on the existing capacities and resources of the unions involved. TPR led to the creation of collective industrial relations processes, or helped unions to ensure that certain enterprises participated in existing industrial relations processes, but did virtually nothing to enhance the political and organisational capacity of the unions to influence the outcomes of those processes in terms of wages and conditions of employment. The paper concludes that the potential of TPR to promote the emergence of collective industrial relations systems is very low.

Paleontological research on late Triassic radiolarians from Oman and Sicily

Les radiolaires sont des unicellulaires planctoniques qui peuplent nos océans depuis plus de 500 millions d'années. Ces microorganismes développent un squelette en silice ayant des géométries extrêmement diversifiées et sophistiqués qui varient rapidement à l'échelle géologique et permettent de construire des échelles biochronologiques basées sur les différents assemblages qui se succèdent dans le temps. On retrouve ces organismes à l'état fossile dans les roches ma¬rines siliceuse desquelles on peut les extraire avec de l'acide. Des échantillons provenant du sultanat d'Oman et de Sicile ont été étudiés afin de mieux com¬prendre les relations de parenté entre les groupes et de comparer les faunes avec celles du même âge venant de Colombie britannique, du Japon et de Turquie, qui sont représentatives de divers domaines océaniques de l'époque. Certains radiolaires possèdent un anneau autour de leur coque centrale sphérique et ont ainsi été baptisés Saturnalides. Il y a 215 millions d'années, au Norien moyen, ce groupe se diversifie soudainement et donne naissance à une multitude d'espèces qui évoluent rapidement ce qui a permis d'établir des subdivisions temporelles supplémentaires et d'affiner les zonations exis¬tantes. L'étude détaillée de formes intermédiaires entre les espèces a permis d'établir de nouveaux liens de parenté et de considérer le genre Praehexasaturnalis comme l'ancêtre probable de nom¬breuses formes dans le Norien moyen et supérieur. Grâce à l'étude comparative des espèces de Saturnalidae allant du Mésozoïque au Cénozoïque, un certain type d'asymétrie de l'anneau a pu être identifiée comme étant propre à cette famille et plus précisément liée à la disposition de la coque la plus interne (microsphère). Deux nouveaux genres, Blechschmidtia et Tjerkium, s'inscrivent dans une lignée parallèle au Saturnalidae. Cette lignée met en évidence la formation au cours du temps d'un anneau à partir de la fusion de deux épines opposées. -- Late Triassic marine deposits of the Tethyan realm have been investigated in the Sultanate of Oman and in Sicily in order to contribute to the knowledge of radiolarian taxonomy and bio- stratigraphy of this key period preceding the Triassic-Jurassic boundary. In the middle Norian, the saturnalid radiolarians display intense diversification. This blooming of fast evolving spe¬cies has been used to establish a new zonation based on evolutionary successions that refine the existing zonal schemes. One new genus and 16 new species are described. The chronologic distribution of 172 species belonging to 72 genera is established from five sections in the Umar and Al Aridh units of the Hawasina Basin. Many Late Triassic saturnalid species are interpreted to originate from the genus Praehexasaturnalis Kozur & Mostler, which shows strong morpho¬logical diversification patterns. Detailed comparative studies of different types of asymmetric ring morphologies of Mesozoic to Cainozoic saturnalid species permitted to relate the origin of the asymmetry to the disposition of the initial skeletal structure and to gain new insight on the internal and external geometrical transformations of this group trough time and how the emergence of new families is induced by environmental stress. RÉSUMÉ Les formations marines du Trias supérieur du domaine téthysien ont été étudiées dans le Sultanat d'Oman et en Sicile afin de contribuer à la connaissance et au développement de la taxonomie et de la biostratigraphie des radiolaires de cette période clé qui précède la crise de la limite Trias-Jurassique. Au Norien moyen, les radiolaires Saturnalides montrent une intense diversi¬fication. Ce véritable "bloom" d'espèces qui évoluent rapidement a été utilisé pour l'établisse¬ment d'une nouvelle zonation basée sur les successions évolutives de ce groupe qui permettent d'affiner les subdivisions biochronologiques existantes. Un nouveau genre et seize nouvelles espèces sont décrits. La distribution stratigraphique de 172 espèces appartenant à 72 genres est établie pour 5 sections dans les unités d'Umar et d'Al Aridh du bassin de Hawasina. Un essai d'établissement d'une phylogénèse des Saturnalidae du Trias supérieur mène à proposer que le genre Praehexasaturnalis Kozur & Mostler est l'ancêtre de beaucoup d'espèces de Saturnalidae du Trias supérieur. L'étude comparative détaillée des différents types d'asymétrie de l'anneau chez les Saturnali¬dae du Mésozoïque au Cénozoïque a permis de lier l'origine de ce phénomène à la disposition de la structure initiale de leur squelette et par ce fait d'avoir une meilleure compréhension des transformations géométriques internes et externes subies par ce groupe au cours du temps et de concevoir comment l'émergence de nouvelles familles est induite lors de périodes de stress environnemental.

Convergent Approaches for the Synthesis of the Anti-tumoral Peptide, Kahalalide F. Study of Orthogonal Protecting Groups

Kahalalide compounds are peptides that are isolated from a Hawaiian herbivorous marine species of mollusc, Elysia rufescens, and its diet, the green alga Bryopsis sp. Kahalalide F and its synthetic analogues are the most promising compounds of the Kahalalide family because they show anti-tumoral activity. Linear solid-phase syntheses of Kahalalide F have been reported. Here we describe several new improved synthetic routes based on convergent approaches with distinct orthogonal protection schemes for the preparation of Kahaladide analogues. These strategies allow a better control and characterization of the intermediates because more reactions are performed in solution. Five derivatives of Kahalalide F were synthesized using several convergent approaches.

Assessment of Coastal Bird Populations and Habitats on the Finnish Coast of the Baltic Sea: Implications for Monitoring and Management

Coastal birds are an integral part of coastal ecosystems, which nowadays are subject to severe environmental pressures. Effective measures for the management and conservation of seabirds and their habitats call for insight into their population processes and the factors affecting their distribution and abundance. Central to national and international management and conservation measures is the availability of accurate data and information on bird populations, as well as on environmental trends and on measures taken to solve environmental problems. In this thesis I address different aspects of the occurrence, abundance, population trends and breeding success of waterbirds breeding on the Finnish coast of the Baltic Sea, and discuss the implications of the results for seabird monitoring, management and conservation. In addition, I assess the position and prospects of coastal bird monitoring data, in the processing and dissemination of biodiversity data and information in accordance with the Convention on Biological Diversity (CBD) and other national and international commitments. I show that important factors for seabird habitat selection are island area and elevation, water depth, shore openness, and the composition of island cover habitats. Habitat preferences are species-specific, with certain similarities within species groups. The occurrence of the colonial Arctic Tern (Sterna paradisaea) is partly affected by different habitat characteristics than its abundance. Using long-term bird monitoring data, I show that eutrophication and winter severity have reduced the populations of several Finnish seabird species. A major demographic factor through which environmental changes influence bird populations is breeding success. Breeding success can function as a more rapid indicator of sublethal environmental impacts than population trends, particularly for long-lived and slowbreeding species, and should therefore be included in coastal bird monitoring schemes. Among my target species, local breeding success can be shown to affect the populations of the Mallard (Anas platyrhynchos), the Eider (Somateria mollissima) and the Goosander (Mergus merganser) after a time lag corresponding to their species-specific recruitment age. For some of the target species, the number of individuals in late summer can be used as an easier and more cost-effective indicator of breeding success than brood counts. My results highlight that the interpretation and application of habitat and population studies require solid background knowledge of the ecology of the target species. In addition, the special characteristics of coastal birds, their habitats, and coastal bird monitoring data have to be considered in the assessment of their distribution and population trends. According to the results, the relationships between the occurrence, abundance and population trends of coastal birds and environmental factors can be quantitatively assessed using multivariate modelling and model selection. Spatial data sets widely available in Finland can be utilised in the calculation of several variables that are relevant to the habitat selection of Finnish coastal species. Concerning some habitat characteristics field work is still required, due to a lack of remotely sensed data or the low resolution of readily available data in relation to the fine scale of the habitat patches in the archipelago. While long-term data sets exist for water quality and weather, the lack of data concerning for instance the food resources of birds hampers more detailed studies of environmental effects on bird populations. Intensive studies of coastal bird species in different archipelago areas should be encouraged. The provision and free delivery of high-quality coastal data concerning bird populations and their habitats would greatly increase the capability of ecological modelling, as well as the management and conservation of coastal environments and communities. International initiatives that promote open spatial data infrastructures and sharing are therefore highly regarded. To function effectively, international information networks, such as the biodiversity Clearing House Mechanism (CHM) under the CBD, need to be rooted at regional and local levels. Attention should also be paid to the processing of data for higher levels of the information hierarchy, so that data are synthesized and developed into high-quality knowledge applicable to management and conservation.

Detection of severe obstructive sleep apnea through voice analysis

tThis paper deals with the potential and limitations of using voice and speech processing to detect Obstruc-tive Sleep Apnea (OSA). An extensive body of voice features has been extracted from patients whopresent various degrees of OSA as well as healthy controls. We analyse the utility of a reduced set offeatures for detecting OSA. We apply various feature selection and reduction schemes (statistical rank-ing, Genetic Algorithms, PCA, LDA) and compare various classifiers (Bayesian Classifiers, kNN, SupportVector Machines, neural networks, Adaboost). S-fold crossvalidation performed on 248 subjects showsthat in the extreme cases (that is, 127 controls and 121 patients with severe OSA) voice alone is able todiscriminate quite well between the presence and absence of OSA. However, this is not the case withmild OSA and healthy snoring patients where voice seems to play a secondary role. We found that thebest classification schemes are achieved using a Genetic Algorithm for feature selection/reduction.

Use of the Optical Cantilever Microphone in Photoacoustic Spectroscopy

A novel cantilever pressure sensor was developed in the Department of Physics at the University of Turku in order to solve the sensitivity problems which are encountered when condenser microphones are used in photoacoustic spectroscopy. The cantilever pressure sensor, combined with a laser interferometer for the measurement of the cantilever movements, proved to be highly sensitive. The original aim of this work was to integrate the sensor in a photoacoustic gas detector working in a differential measurement scheme. The integration was made successfully into three prototypes. In addition, the cantilever was also integrated in the photoacoustic FTIR measurement schemes of gas-, liquid-, and solid-phase samples. A theoretical model for the signal generation in each measurement scheme was created and the optimal celldesign discussed. The sensitivity and selectivity of the differential method were evaluated when a blackbody radiator and a mechanical chopper were used with CO₂, CH4, CO, and C2H4 gases. The detection limits were in the sub-ppm level for all four gases with only a 1.3 second integration time and the cross interference was well below one percent for all gas combinations other than those between hydrocarbons. Sensitivity with other infrared sources was compared using ethylene as an example gas. In the comparison of sensitivity with different infrared sources the electrically modulated blackbody radiator gave a 35 times higher and the CO2-laser a 100 times lower detection limit than the blackbody radiator with a mechanical chopper. As a conclusion, the differential system is well suited to rapid single gas measurements. Gas-phase photoacoustic FTIR spectroscopy gives the best performance, when several components have to be analyzed simultaneously from multicomponent samples. Multicomponent measurements were demonstrated with a sample that contained different concentrations of CO₂, H₂O, CO, and four different hydrocarbons. It required an approximately 10 times longer measurement time to achieve the same detection limit for a single gas as with the differential system. The properties of the photoacoustic FTIR spectroscopy were also compared to conventional transmission FTIR spectroscopy by simulations. Solid- and liquid-phase photoacoustic FTIR spectroscopy has several advantages compared to other techniques and therefore it also has a great variety of applications. A comparison of the signal-to-noise ratio between photoacoustic cells with a cantilever microphone and a condenser microphone was done with standard carbon black, polyethene, and sunflower oil samples. The cell with the cantilever microphone proved to have a 5-10 times higher signal-to-noise ratio than the reference detector, depending on the sample. Cantilever enhanced photoacoustics will be an effective tool for gas detection and analysis of solid- and liquid-phase samples. The preliminary prototypes gave good results in all three measurement schemes that were studied. According to simulations, there are possibilities for further enhancement of the sensitivity, as well as other properties, of each system.

The permanence of the client under uncertain estimations

Marketing has studied the permanence of a client within an enterprise because it is a key element in the study of the value (economic) of the client (CLV). The research that they have developed is based in deterministic or random models, which allowed estimating the permanence of the client, and the CLV. However, when it is not possible to apply these schemes for not having the panel data that this model requires, the period of time of a client with the enterprise is uncertain data. We consider that the value of the current work is to have an alternative way to estimate the period of time with subjective information proper of the theory of uncertainty.

Knapsack sets for cryptography

The basic goal of this study is to extend old and propose new ways to generate knapsack sets suitable for use in public key cryptography. The knapsack problem and its cryptographic use are reviewed in the introductory chapter. Terminology is based on common cryptographic vocabulary. For example, solving the knapsack problem (which is here a subset sum problem) is termed decipherment. Chapter 1 also reviews the most famous knapsack cryptosystem, the Merkle Hellman system. It is based on a superincreasing knapsack and uses modular multiplication as a trapdoor transformation. The insecurity caused by these two properties exemplifies the two general categories of attacks against knapsack systems. These categories provide the motivation for Chapters 2 and 4. Chapter 2 discusses the density of a knapsack and the dangers of having a low density. Chapter 3 interrupts for a while the more abstract treatment by showing examples of small injective knapsacks and extrapolating conjectures on some characteristics of knapsacks of larger size, especially their density and number. The most common trapdoor technique, modular multiplication, is likely to cause insecurity, but as argued in Chapter 4, it is difficult to find any other simple trapdoor techniques. This discussion also provides a basis for the introduction of various categories of non injectivity in Chapter 5. Besides general ideas of non injectivity of knapsack systems, Chapter 5 introduces and evaluates several ways to construct such systems, most notably the "exceptional blocks" in superincreasing knapsacks and the usage of "too small" a modulus in the modular multiplication as a trapdoor technique. The author believes that non injectivity is the most promising direction for development of knapsack cryptosystema. Chapter 6 modifies two well known knapsack schemes, the Merkle Hellman multiplicative trapdoor knapsack and the Graham Shamir knapsack. The main interest is in aspects other than non injectivity, although that is also exploited. In the end of the chapter, constructions proposed by Desmedt et. al. are presented to serve as a comparison for the developments of the subsequent three chapters. Chapter 7 provides a general framework for the iterative construction of injective knapsacks from smaller knapsacks, together with a simple example, the "three elements" system. In Chapters 8 and 9 the general framework is put into practice in two different ways. Modularly injective small knapsacks are used in Chapter 9 to construct a large knapsack, which is called the congruential knapsack. The addends of a subset sum can be found by decrementing the sum iteratively by using each of the small knapsacks and their moduli in turn. The construction is also generalized to the non injective case, which can lead to especially good results in the density, without complicating the deciphering process too much. Chapter 9 presents three related ways to realize the general framework of Chapter 7. The main idea is to join iteratively small knapsacks, each element of which would satisfy the superincreasing condition. As a whole, none of these systems need become superincreasing, though the development of density is not better than that. The new knapsack systems are injective but they can be deciphered with the same searching method as the non injective knapsacks with the "exceptional blocks" in Chapter 5. The final Chapter 10 first reviews the Chor Rivest knapsack system, which has withstood all cryptanalytic attacks. A couple of modifications to the use of this system are presented in order to further increase the security or make the construction easier. The latter goal is attempted by reducing the size of the Chor Rivest knapsack embedded in the modified system. '

Improving Label Space Usage for Ethernet Label Switched Paths

Ethernet is becoming the dominant aggregation technology for carrier transport networks; however, as it is a LAN technology, native bridged ethernet does not fulfill all the carrier requirements. One of the schemes proposed by the research community to make ethernet fulfill carrier requirements is ethernet VLAN-label switching (ELS). ELS allows the creation of label switched data paths using a 12-bit label encoded in the VLAN TAG control information field. Previous label switching technologies such as MPLS use more bits for encoding the label. Hence, they do not suffer from label sparsity issues as ELS might. This paper studies the sparsity issues resulting from the reduced ELS VLAN-label space and proposes the use of the label merging technique to improve label space usage. Experimental results show that label merging considerably improves label space usage

Finite-temperature T matrix in a real-time formalism

A generalized off-shell unitarity relation for the two-body scattering T matrix in a many-body medium at finite temperature is derived, through a consistent real-time perturbation expansion by means of Feynman diagrams. We comment on perturbation schemes at finite temperature in connection with an erroneous formulation of the Dyson equation in a paper recently published.

Automatització d'una planta de processos químics

Resum L’any 1969 es van començar a comercialitzar els sistemes digitals programables coneguts com autòmats programables o PLC’s, utilitzats per controlar qualsevol tipus de procés industrial. Al llarg de tots aquests anys, aquests sistemes i tota la tecnologia en general han evolucionat molt, i només és qüestió de temps que la tecnologia que utilitzem avui en dia quedi obsoleta i substituïda per una de millors característiques i amb més avantatges. Aquest és el motiu de l’elaboració d’aquest treball, que com a objectiu pretén modernitzar un procés de fabricació d’una industria química que ha quedat molt limitat a causa de l’antiguitat de la instal•lació. Per dur a terme aquesta modernització, s’introdueixen sistemes de control amb majors prestacions, s’utilitzen xarxes de comunicacions per facilitar el muntatge elèctric de la instal•lació i un sistema de supervisió i adquisició de dades per poder obtenir un control més estricte del procés de fabricació i de tots els factors que intervenen. El funcionament del procés de fabricació és que a partir d’unes matèries primeres líquides emmagatzemades en dipòsits, es dosifiquin aquestes matèries en l’ordre i la quantitat desitjada dins un o diversos recipients per barrejar-les i aplicar els tractaments que siguin necessaris. Tot aquest procés està controlat per un autòmat programable, i disposa de diferents terminals operadors per poder interactuar amb el sistema. També té implementat un sistema SCADA en diversos ordinadors per aportar una visió general de la planta en temps real, un registre de dades dels paràmetres que es controlen i alhora serveix per enllaçar amb la xarxa d’ordinadors existent. Com annex d’aquest treball, es presenten els esquemes elèctrics i el programa de l’autòmat programable per veure totes les característiques elèctriques dels dispositius i el mètode de funcionament del procés. S’ha aconseguit donar un salt tecnològic i poder gaudir de tots els avantatges que ofereixen les noves tecnologies, que com a resultat s’ha optimitzat i millorat el procés de fabricació. De totes les conclusions, la més destacada és la d’haver dissenyat un sistema de control basat en una estructura descentralitzada molt flexible, que es pot expandir i adaptar fàcilment als possibles canvis.

Interferência do acido ascórbico na determinação de açúcares redutores pelo método de Lane e Eynon

Two studies, both set up as completely randomized design, in a 5x5 and 7x5 factorial schemes, evaluated the interference of 5 and 7 ascorbic acid concentrations and 5 glucose or 5 sucrose concentrations, respectively, on the determination of total and reducing sugars by Lane and Eynon method. The ascorbic acid reducing power (AARP) over the Fehling liquor interfered in the results of total and reducing sugars. On average the AARP was equivalent to 74.83 and 69.71% of the reducing power of glucose and of hydrolyzed sucrose, respectively. The ascorbic acid was stable in all study conditions.

comparação entre processos em SHF e em SSF de bagaço de cana-de-açúcar para a produção de etanol por Saccharomyces cerevisiae

In this work, four different process configurations, including three simultaneous saccharification and fermentation (SSF) schemes and one separate hydrolysis and fermentation (SHF) scheme, were compared, at 8% water-insoluble solids, regarding ethanol production from steam-pretreated and alkali-delignified sugar cane bagasse. Two configurations included a 16 h lasting enzymatic presaccharification prior to SSF, and the third one was a classical SSF without presaccharification. Cellulose conversion was higher for the delignified bagasse, and higher in SSF experiments than in SHF. The highest cellulose-to-ethanol conversion (around 60% in 24 h) and maximum ethanol volumetric productivities (0.29-0.30 g/L.h) were achieved in the presaccharification-assisted SSF.