Developing methodologies to allow the robust prediction dynamic context dominated by perturbations

El principal objectiu del projecte era desenvolupar millores conceptuals i metodològiques que permetessin una millor predicció dels canvis en la distribució de les espècies (a una escala de paisatge) derivats de canvis ambientals en un context dominat per pertorbacions. En un primer estudi, vàrem comparar l'eficàcia de diferents models dinàmics per a predir la distribució de l'hortolà (Emberiza hortulana). Els nostres resultats indiquen que un model híbrid que combini canvis en la qualitat de l'hàbitat, derivats de canvis en el paisatge, amb un model poblacional espacialment explícit és una aproximació adequada per abordar canvis en la distribució d'espècies en contextos de dinàmica ambiental elevada i una capacitat de dispersió limitada de l'espècie objectiu. En un segon estudi abordarem la calibració mitjançant dades de seguiment de models de distribució dinàmics per a 12 espècies amb preferència per hàbitats oberts. Entre les conclusions extretes destaquem: (1) la necessitat de que les dades de seguiment abarquin aquelles àrees on es produeixen els canvis de qualitat; (2) el biaix que es produeix en la estimació dels paràmetres del model d'ocupació quan la hipòtesi de canvi de paisatge o el model de qualitat d'hàbitat són incorrectes. En el darrer treball estudiarem el possible impacte en 67 espècies d’ocells de diferents règims d’incendis, definits a partir de combinacions de nivells de canvi climàtic (portant a un augment esperat de la mida i freqüència d’incendis forestals), i eficiència d’extinció per part dels bombers. Segons els resultats dels nostres models, la combinació de factors antropogènics del regim d’incendis, tals com l’abandonament rural i l’extinció, poden ser més determinants per als canvis de distribució que els efectes derivats del canvi climàtic. Els productes generats inclouen tres publicacions científiques, una pàgina web amb resultats del projecte i una llibreria per a l'entorn estadístic R.

Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond.

Many assays to evaluate the nature, breadth, and quality of antigen-specific T cell responses are currently applied in human medicine. In most cases, assay-related protocols are developed on an individual laboratory basis, resulting in a large number of different protocols being applied worldwide. Together with the inherent complexity of cellular assays, this leads to unnecessary limitations in the ability to compare results generated across institutions. Over the past few years a number of critical assay parameters have been identified which influence test performance irrespective of protocol, material, and reagents used. Describing these critical factors as an integral part of any published report will both facilitate the comparison of data generated across institutions and lead to improvements in the assays themselves. To this end, the Minimal Information About T Cell Assays (MIATA) project was initiated. The objective of MIATA is to achieve a broad consensus on which T cell assay parameters should be reported in scientific publications and to propose a mechanism for reporting these in a systematic manner. To add maximum value for the scientific community, a step-wise, open, and field-spanning approach has been taken to achieve technical precision, user-friendliness, adequate incorporation of concerns, and high acceptance among peers. Here, we describe the past, present, and future perspectives of the MIATA project. We suggest that the approach taken can be generically applied to projects in which a broad consensus has to be reached among scientists working in fragmented fields, such as immunology. An additional objective of this undertaking is to engage the broader scientific community to comment on MIATA and to become an active participant in the project.

Clinical management and burden of bipolar disorder: a multinational longitudinal study (WAVE-bd Study)

BACKGROUND: Studies in bipolar disorder (BD) to date are limited in their ability to provide a whole-disease perspective--their scope has generally been confined to a single disease phase and/or a specific treatment. Moreover, most clinical trials have focused on the manic phase of disease, and not on depression, which is associated with the greatest disease burden. There are few longitudinal studies covering both types of patients with BD (I and II) and the whole course of the disease, regardless of patients' symptomatology. Therefore, the Wide AmbispectiVE study of the clinical management and burden of Bipolar Disorder (WAVE-bd) (NCT01062607) aims to provide reliable information on the management of patients with BD in daily clinical practice. It also seeks to determine factors influencing clinical outcomes and resource use in relation to the management of BD. METHODS: WAVE-bd is a multinational, multicentre, non-interventional, longitudinal study. Approximately 3000 patients diagnosed with BD type I or II with at least one mood event in the preceding 12 months were recruited at centres in Austria, Belgium, Brazil, France, Germany, Portugal, Romania, Turkey, Ukraine and Venezuela. Site selection methodology aimed to provide a balanced cross-section of patients cared for by different types of providers of medical aid (e.g. academic hospitals, private practices) in each country. Target recruitment percentages were derived either from scientific publications or from expert panels in each participating country. The minimum follow-up period will be 12 months, with a maximum of 27 months, taking into account the retrospective and the prospective parts of the study. Data on demographics, diagnosis, medical history, clinical management, clinical and functional outcomes (CGI-BP and FAST scales), adherence to treatment (DAI-10 scale and Medication Possession Ratio), quality of life (EQ-5D scale), healthcare resources, and caregiver burden (BAS scale) will be collected. Descriptive analysis with common statistics will be performed. DISCUSSION: This study will provide detailed descriptions of the management of BD in different countries, particularly in terms of clinical outcomes and resources used. Thus, it should provide psychiatrists with reliable and up-to-date information about those factors associated with different management patterns of BD. TRIAL REGISTRATION NO: ClinicalTrials.gov: NCT01062607.

Experimental insights into deformation dynamics and intermittency in rapid granular shear flows

This work concerns the experimental study of rapid granular shear flows in annular Couette geometry. The flow is induced by continuous driving of the horizontal plate at the top of the granular bed in an annulus. The compressive pressure, driving torque, instantaneous bed height and rotational speed of the shearing plate are measured. Moreover, local stress fluctuations are measured in a medium made of steel spheres 2 and 3 mm in diameter. Both monodisperse packing and bidisperse packing are investigated to reveal the influence of size diversity in intermittent features of granular materials. Experiments are conducted in an annulus that can contain up to 15 kg of spherical steel balls. The shearing granular medium takes place via the rotation of the upper plate which compresses the material loaded inside the annulus. Fluctuations of compressive force are locally measured at the bottom of the annulus using a piezoelectric sensor. Rapid shear flow experiments are pursued at different compressive forces and shear rates and the sensitivity of fluctuations are then investigated by different means through monodisperse and bidisperse packings. Another important feature of rapid granular shear flows is the formation of ordered structures upon shearing. It requires a certain range for the amount of granular material (uniform size distribution) loaded in the system in order to obtain stable flows. This is studied more deeply in this thesis. The results of the current work bring some new insights into deformation dynamics and intermittency in rapid granular shear flows. The experimental apparatus is modified in comparison to earlier investigations. The measurements produce data for various quantities continuously sampled from the start of shearing to the end. Static failure and dynamic shearing ofa granular medium is investigated. The results of this work revealed some important features of failure dynamics and structure formation in the system. Furthermore, some computer simulations are performed in a 2D annulus to examine the nature of kinetic energy dissipation. It is found that turbulent flow models can statistically represent rapid granular flows with high accuracy. In addition to academic outcomes and scientific publications our results have a number of technological applications associated with grinding, mining and massive grain storages.

Update on osteoporosis from the 2014 Santa Fe Bone symposium.

The 2014 Santa Fe Bone Symposium provided a setting for the presentation and discussion of the clinical relevance of recent advances in the fields of osteoporosis and metabolic bone disease. The format included oral presentations of abstracts by endocrinology fellows, plenary lectures, panel discussions and breakout sessions, with ample opportunities for informal discussions before and after scheduled events. Topics addressed in these proceedings included a review of the important scientific publications in the past year, fracture prevention in patients with dysmobility and immobility, fracture liaison services for secondary fracture prevention, management of pre-menopausal osteoporosis, the role of bone microarchitecture in determining bone strength, measurement of microarchitecture in clinical practice and methods to improve the quality of bone density testing. This is a report of the proceedings of the 2014 Santa Fe Bone Symposium.

Immateriaalioikeuksien merkitys ohjelmistotuotantoprosessissa

Työn tavoitteena on selvittää immateriaalioikeuksien merkitystä ja käytäntöä ohjelmistotuotantoprosessissa. Työn painopiste on ohjelmistojen tekijänoikeudellisten ja patenttioikeudellisten kysymysten tarkastelussa sekä niiden sitomisessa osaksi ohjelmistotuotantoprosessia. Tarkastelun lisäksi työn tarkoituksena on antaa käytännön ohjeita patentoinnin ja ohjelmistoprosessin yhteensovittamisesta. Tarkastelu on tehty suomalaisen tuotekehittelijän näkökulmasta. Pääpaino on Suomen käytännössä ja lainsäädännössä, mutta koska ohjelmistotuotteiden markkinat ovat maailmanlaajuiset, on tärkeää tietää miten tuote voidaan suojata kaikilla markkina-alueilla. Käytäntö eri markkina-alueilla vaihtelee merkittävästi. Tämän jälkeen immateriaalioikeuksia tarkastellaan itse ohjelmistoprosessin kannalta vaihe vaiheelta. Tarkastelua ei rajoiteta vain yhteen näkökulmaan, vaan ohjelmistoprosessia tarkastellaan immateriaalioikeuksien näkökulmasta ja immateriaalioikeuksia ohjelmistoprosessin näkökulmasta. Koska tarkastelu keskittyy itse prosessin teknisiin näkökohtiin, immateriaalioikeuksissa keskitytään patentointiin. Työ on tehty kirjallisuustyönä tarkastelemalla alan viimeisintä kirjallisuutta, tieteellisiä julkaisuja, lakien valmistelua sekä EU:n direktiivejä sekä ehdotuksia direktiiveiksi, Euroopan patenttiviraston valituslautakunnan päätöksiä ja oikeustapauksia. Työn tuloksena on kattava katsaus käytettävissä olevista tietokoneohjelmien suojamuodoista. Erityisesti työssä on keskitytty patentoinnin ja ohjelmistotuotantoprosessin vaiheisiin ja niiden yhteensovittamiseen. Tarkastelun tuloksena huomataan, että suurin osa vaiheista on yhteisiä, joten yhteensovittamisessa ei tarvitse tehdä merkittävää lisätyötä. Tämän ansiosta ohjelmistotuotantoprosessin ja patentoinnin yhteensovittaminen on edullista, vaikka omia patentteja ei olisi tarkoitus hankkiakaan. Tämä tiedostamalla ohjelmistoprosessia voidaan tehostaa. Vaikka omia patentteja ei olisikaan tarkoitus hankkia, patentoinnin huomioiminen kannattaa ottaa osaksi ohjelmistotuotantoprosessia kilpailijoiden patenttien havaitsemiseksi.

Clinical management and burden of bipolar disorder: a multinational longitudinal study (WAVE-bd Study)

BACKGROUND: Studies in bipolar disorder (BD) to date are limited in their ability to provide a whole-disease perspective--their scope has generally been confined to a single disease phase and/or a specific treatment. Moreover, most clinical trials have focused on the manic phase of disease, and not on depression, which is associated with the greatest disease burden. There are few longitudinal studies covering both types of patients with BD (I and II) and the whole course of the disease, regardless of patients' symptomatology. Therefore, the Wide AmbispectiVE study of the clinical management and burden of Bipolar Disorder (WAVE-bd) (NCT01062607) aims to provide reliable information on the management of patients with BD in daily clinical practice. It also seeks to determine factors influencing clinical outcomes and resource use in relation to the management of BD. METHODS: WAVE-bd is a multinational, multicentre, non-interventional, longitudinal study. Approximately 3000 patients diagnosed with BD type I or II with at least one mood event in the preceding 12 months were recruited at centres in Austria, Belgium, Brazil, France, Germany, Portugal, Romania, Turkey, Ukraine and Venezuela. Site selection methodology aimed to provide a balanced cross-section of patients cared for by different types of providers of medical aid (e.g. academic hospitals, private practices) in each country. Target recruitment percentages were derived either from scientific publications or from expert panels in each participating country. The minimum follow-up period will be 12 months, with a maximum of 27 months, taking into account the retrospective and the prospective parts of the study. Data on demographics, diagnosis, medical history, clinical management, clinical and functional outcomes (CGI-BP and FAST scales), adherence to treatment (DAI-10 scale and Medication Possession Ratio), quality of life (EQ-5D scale), healthcare resources, and caregiver burden (BAS scale) will be collected. Descriptive analysis with common statistics will be performed. DISCUSSION: This study will provide detailed descriptions of the management of BD in different countries, particularly in terms of clinical outcomes and resources used. Thus, it should provide psychiatrists with reliable and up-to-date information about those factors associated with different management patterns of BD. TRIAL REGISTRATION NO: ClinicalTrials.gov: NCT01062607.

INASP: la hora del protagonismo local en la cooperación al desarrollo científico y bibliotecario

La International Network for the Availability of Scientific Publications (INASP) es una ONG de cooperación al desarrollo, que persigue la mejora del acceso, producción y uso de la información científica, de forma que cada país cuente con recursos en este ámbito para afrontar sus propios retos de desarrollo. Surgió en 1992 por iniciativa del ICSU (International Council of Scientific Unions, actualmente International Council for Science) y contó con el apoyo de UNESCO, TWAS-The Academy of Sciences for the Developing World y AAAS (American Association for the Advancement of Science).

SAHAUSTEKNOLOGIA TEOLLISILLA SAHALAITOKSILLA NYT JA TULEVAISUUDESSA

Diplomityössä on selvitetty teollisen sahaustekniikan nykytilaa ja sahausprosessissa käytettävien sahakoneiden teknistä kehitystä Pohjois- ja Keski-Euroopassa. Sahakonevalmistajia on tutkittu niiden tuottamien laitteiden kautta sekä yleisen saatavilla olevan taloudellisen ja tieteellisten tutkimusten tarjoaman informaation avulla. Tutkimuksessa mukana oleviin sahakoneisiin tutustuminen suoritettiin sahalaitosvierailuilla suomalaisilla sahalaitoksilla kevään 2002 aikana. Tieteellisten julkaisujen tietoja verrattiin samalla vallitsevaan tilanteeseen sahoilla. Samalla tehtyjen haastatteluiden avulla selvitettiin sahakoneisiin liittyvien investointien vaikuttimia. Haastatteluiden kohteena olivat sahateollisuuden tuotannosta ja teknisestä suunnittelusta sekä johtamisesta vastaavia henkilöitä erikokoisista sahateollisuusyrityksistä. Myös muutamat sahakonevalmistajien edustajat antoivat haastattelun omia laitteitaan koskien. Sahaustuotannon raaka-ainetilannetta tutkittiin tutkimusalueella maakohtaisesti. Sahaustekniikkana nelisahaus on vallitseva työstömuoto. Siinä käytettävät sahakoneet ovat pelkkahakkuri, joka hakettaa tukin sivut sivutuotehakkeeksi, profilointiyksiköt, jotka työstävät tukin tai pelkan pintaan sivutavarakappaleiden leveyden ennen tai jälkeen pyörösahayksiköitä, jotka erottavat sahatavarakappaleet toisistaan. Merkittävimmät oheislaitteet ovat tukin ja pelkan mittauslaitteet sekä tukinsyöttölaitteet, joiden perusteella puun käytön optimointi sahausprosessissa ja suuntaus sahakoneisiin tapahtuu. Mittatarkimmat ja tuotantonopeudeltaan nopeimmat pyörösahayksiköt ovat kaksiakselisia, profiloivia sahakoneita. Näillä ominaisuuksilla on suurin painoarvo myös sahojen investointisuunnittelussa nopean käyntiinajon lisäksi. Sahakoneiden kehitykseen vaikuttavia seikkoja ovat tulevaisuudessa tukkien koon pieneneminen istutusmetsien jalostuksen lisääntyessä ja suurten aarniometsien vähetessä. Terätekniikan kehitys on tuottaa edelleen ohuempia teriä teräohjaimin, luomalla teriin sisäisiä jännityksiä tai kehittämällä uusia terägeometrioita.

Quality in services marketing in infocom sector in Finland

Tutkielman tavoitteena oli selvittää, mikä on palvelun laadun taso infocom sektorilla Suomessa, ja miten sitä voidaan parantaa. Teoriaosassa tavoitteeseen pyrittiin muodostamalla teoriakirjallisuuteen, tieteellisiin julkaisuihin sekä aikaisempaan aihealuetta sivuavaan tutkimukseen perustuva viitekehysmalli. Empiirisessä osassa tavoitetta lähestyttiin tutkimalla infocom sektorin kunkin toimialueen (telekommunikaatio, informaatio teknologia ja sisältötuotanto) palvelujen laatua case-kuvausten muodossa. Tutkielman empiirinen osuus toteutettiin kvalitatiivisena multiple case -tutkimuksena teemahaastattelu-menetelmää soveltaen. Case-analyysi suorittiin käyttäen ns. explanation- building -menetelmää. Teoreettiset ja empiiriset tutkimustulokset yhdistettiin erityisiksi infocom sektorille soveltuviksi toimenpidesuosituksiksi. Tutkielman empiirinen osuus antoi tukea teoreettisen osuuden pohjalta kehitetylle viitekehykselle. Tutkimuksen tavoitteena oli case-analyysi- menetelmän mukaisesti luoda perusta syvemmälle aihepiiriä käsittelevälle jatkotutkimukselle ja luoda kuva infocom sektorin tämän hetkisestä laadullisesta tilasta. Yhteenvetona voidaan sanoa, että laatu palvelujen markkinoinnissa infocom sektorilla on suhteellisen heikkoa, vaikka tutkimusaineiston mukaan laatu arvostetaan hyvin korkealle. Yritysten tämänhetkiset panostukset laatuun liittyvät lähinnä liiketoiminnan tukifunktioihin ja prosessien ohjausmenetelmiä koskeviin järjestelmiin. Tutkimuksen pohjalta tehtävät varsinaiset toimenpidesuositukset liittyvät laadun sisäistämiseen jo strategiaa luotaessa, asiakaslähtöisyyteen, laatujohtamiseen, laatukoulutukseen ja kokonaisvaltaisen laatukulttuurin luomiseen organisaatioissa. Turbulentissa, nopeasti kansainvälistyvässä ja erittäin voimakkaasti kilpaillussa liiketoimintaympäristössä nämä ovat elintärkeitä menestymisen kriteerejä.

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.

O impacto do PADCT na química brasileira: uma visão acadêmica

An appraisal has been conducted of the impact PADCT (Support Program for Scientific and Technological Development) has caused on brazilian Chemistry and Chemical Engineering over a ten years period (1985-1995). During this time PADCT invested US$ 87.5 million dollars to support both scientific and technolgical development of chemistry. The main results, from an academic point of view, has been the strengthening of support services for academic research, including libraries and analytical facilities, and a consequent increase of the number and quality of human resources trained at the graduate level as well as a significant increase in the number of scientific publications.

Patrones de publicación internacional, (ssci) de los autores afiliados a universidades españolas, en el ámbito económico-empresarial (1994-2004)

In this paper we analyse the status of scientific publications in Economics and Business in Spain (1994-2004). We focus our research in showing the preferred journals of the authors affiliated to Spanish universities, the quality of these journals and also the evolution along the decade. Throughout the paper we study deeply the areas of knowledge: which are more productive and also how the articles are distributed among Universities considering the areas of knowledge. The results show an important stability concerning the growth of published articles considering different levels of quality of journals. A second result is the important concentration in a few areas of knowledge: Fundamentals of Economic Analysis and Applied Economics. We observe a degree of specialization of several universities. Last, we display the relationship between journal publication and university’s publication pattern.

Identification of the Emerging Issues in Recycled Fiber Processing

The objectives of this research work “Identification of the Emerging Issues in Recycled Fiber processing” are discovering of emerging research issues and presenting of new approaches to identify promising research themes in recovered paper application and production. The projected approach consists of identifying technological problems often encountered in wastepaper preparation processes and also improving the quality of recovered paper and increasing its proportion in the composition of paper and board. The source of information for the problem retrieval is scientific publications in which waste paper application and production were discussed. The study has exploited several research methods to understand the changes related to utilization of recovered paper. The all assembled data was carefully studied and categorized by applying software called RefViz and CiteSpace. Suggestions were made on the various classes of these problems that need further investigation in order to propose an emerging research trends in recovered paper.

Turun yliopiston julkaisut 2008 - Publication of the University of Turku 2008

Bibliografia Turun yliopiston tieteellisestä julkaisutoiminnasta vuodelta 2008