The SwissLipids knowledgebase for lipid biology.

MOTIVATION: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it. RESULTS: To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology-SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge. AVAILABILITY: SwissLipids is freely available at http://www.swisslipids.org/. CONTACT: alan.bridge@isb-sib.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The political ecology of weeds : a scalar approach to landscape transformations

How do plants that move and spread across landscapes become branded as weeds and thereby objects of contention and control? We outline a political ecology approach that builds on a Lefebvrian understanding of the production of space, identifying three scalar moments that make plants into 'weeds' in different spatial contexts and landscapes. The three moments are: the operational scale, which relates to empirical phenomena in nature and society; the observational scale, which defines formal concepts of these phenomena and their implicit or explicit 'biopower' across institutional and spatial categories; and the interpretive scale, which is communicated through stories and actions expressing human feelings or concerns regarding the phenomena and processes of socio-spatial change. Together, these three scalar moments interact to produce a political ecology of landscape transformation, where biophysical and socio-cultural processes of daily life encounter formal categories and modes of control as well as emotive and normative expectations in shaping landscapes. Using three exemplar 'weeds' - acacia, lantana and ambrosia - our political ecology approach to landscape transformations shows that weeds do not act alone and that invasives are not inherently bad organisms. Humans and weeds go together; plants take advantage of spaces and opportunities that we create. Human desires for preserving certain social values in landscapes in contradiction to actual transformations is often at the heart of definitions of and conflicts over weeds or invasives.

Prediction of Complications After Pancreaticoduodenectomy: Validation of a Postoperative Complication Score.

OBJECTIVES: Pancreatic surgery remains associated with important morbidity. Efforts are most commonly concentrated on decreasing postoperative morbidity, but early detection of patients at risk could be another valuable strategy. A simple prognostic score has recently been published. This study aimed to validate this score and discuss possible clinical implications. METHODS: From 2000 to 2012, 245 patients underwent a pancreaticoduodenectomy. Complications were graded according to the Dindo-Clavien Classification. The Braga score is based on American Society of Anesthesiologists score, pancreatic texture, Wirsung duct diameter, and blood loss. An overall risk score (0-15) can be calculated for each patient. Score discriminant power was calculated using a receiver operating characteristic curve. RESULTS: Major complications occurred in 31% of patients compared with 17% in Braga's data. Pancreatic texture and blood loss were independently statistically significant for increased morbidity. Areas under the curve were 0.95 and 0.99 for 4-risk categories and for individual scores, respectively. CONCLUSIONS: The Braga score discriminates well between minor and major complications. Our validation suggests that it can be used as a prognostic tool for major complications after pancreaticoduodenectomy. The clinical implications, that is, whether postoperative treatment strategies should be adapted according to the patient's individual risk, remain to be elucidated.

A measurement framework for quality health care for adolescents in hospital.

PURPOSE: Despite growing interest in measurement of health care quality and patient experience, the current evidence base largely derives from adult health settings, at least in part because of the absence of appropriately developed measurement tools for adolescents. To rectify this, we set out to develop a conceptual framework and a set of indicators to measure the quality of health care delivered to adolescents in hospital. METHODS: A conceptual framework was developed from the following four elements: (1) a review of the evidence around what young people perceive as "adolescent-friendly" health care; (2) an exploration with adolescent patients of the principles of patient-centered care; (3) a scoping review to identify core clinical practices around working with adolescents; and (4) a scoping review of existing conceptual frameworks. Using criteria for indicator development, we then developed a set of indicators that mapped to this framework. RESULTS: Embedded within the notion of patient- and family-centered care, the conceptual framework for adolescent-friendly health care (quality health care for adolescents) was based on the constructs of experience of care (positive engagement with health care) and evidence-informed care. A set of 14 indicators was developed, half of which related to adolescents' and parents' experience of care and half of which related to aspects of evidence-informed care. CONCLUSIONS: The conceptual framework and indicators of quality health care for adolescents set the stage to develop measures to populate these indicators, the next step in the agenda of improving the quality of health care delivered to adolescents in hospital settings.

Unsupervised visual object categorization

The number of digital images has been increasing exponentially in the last few years. People have problems managing their image collections and finding a specific image. An automatic image categorization system could help them to manage images and find specific images. In this thesis, an unsupervised visual object categorization system was implemented to categorize a set of unknown images. The system is unsupervised, and hence, it does not need known images to train the system which needs to be manually obtained. Therefore, the number of possible categories and images can be huge. The system implemented in the thesis extracts local features from the images. These local features are used to build a codebook. The local features and the codebook are then used to generate a feature vector for an image. Images are categorized based on the feature vectors. The system is able to categorize any given set of images based on the visual appearance of the images. Images that have similar image regions are grouped together in the same category. Thus, for example, images which contain cars are assigned to the same cluster. The unsupervised visual object categorization system can be used in many situations, e.g., in an Internet search engine. The system can categorize images for a user, and the user can then easily find a specific type of image.

Clasificación automática de textos y explotación BI

El presente proyecto tiene como objetivo desarrollar una tecnología que permita codificar grandes cantidades de texto de manera automática para posteriormente ser visualizada y analizada mediante una aplicación diseñada en Qlikview. El motor de la investigación e implementación de este proyecto se ha encontrado en la incipiente presencia de tecnologías informáticas en los procesos de codificación para ciencias políticas. De esta manera, el programa creado tiene como objetivo automatizar un proceso que se desarrolla comúnmente de manera manual y, por ende, las ventajas de introducir técnicas informáticas son notablemente valiosas. Estas automatizaciones permiten ahorrar tanto en tiempo de codificación, como en recursos económicos o humanos. Se ha elaborado una revisión teórica y metodológica que han servido como instrumentos de estudio y mejora, con el firme propósito de reducir al máximo el margen de error y ofrecer un instrumento de calidad con salida de mercado real. El método de clasificación utilizado ha sido Bayes, y se ha implementado utilizando Matlab. Los resultados de la clasificación han llegado a índices del 99.2%. En la visualización y análisis mediante Qlikview se pueden modificar los parámetros referentes a partido político, año, categoría o región, con lo que se permite analizar numerosos aspectos relacionados con la distribución de las palabras repartidas entre las diferentes categorías y en el tiempo.

A Cartan-Eilenberg approach to Homotopical Algebra

In this paper we propose an approach to homotopical algebra where the basic ingredient is a category with two classes of distinguished morphisms: strong and weak equivalences. These data determine the cofibrant objects by an extension property analogous to the classical lifting property of projective modules. We define a Cartan-Eilenberg category as a category with strong and weak equivalences such that there is an equivalence of categories between its localisation with respect to weak equivalences and the relative localisation of the subcategory of cofibrant objects with respect to strong equivalences. This equivalence of categories allows us to extend the classical theory of derived additive functors to this non additive setting. The main examples include Quillen model categories and categories of functors defined on a category endowed with a cotriple (comonad) and taking values on a category of complexes of an abelian category. In the latter case there are examples in which the class of strong equivalences is not determined by a homotopy relation. Among other applications of our theory, we establish a very general acyclic models theorem.

The process of basic training, applied training, maintaining the performance of an observer

In the field of observational methodology the observer is obviously a central figure, and close attention should be paid to the process through which he or she acquires, applies, and maintains the skills required. Basic training in how to apply the operational definitions of categories and the rules for coding, coupled with the opportunity to use the observation instrument in real-life situations, can have a positive effect in terms of the degree of agreement achieved when one evaluates intra- and inter-observer reliability. Several authors, including Arias, Argudo, & Alonso (2009) and Medina and Delgado (1999), have put forward proposals for the process of basic and applied training in this context. Reid y De Master (1982) focuses on the observer's performance and how to maintain the acquired skills, it being argued that periodic checks are needed after initial training because an observer may, over time, become less reliable due to the inherent complexity of category systems. The purpose of this subsequent training is to maintain acceptable levels of observer reliability. Various strategies can be used to this end, including providing feedback about those categories associated with a good reliability index, or offering re-training in how to apply those that yield lower indices. The aim of this study is to develop a performance-based index that is capable of assessing an observer's ability to produce reliable observations in conjunction with other observers.

Evaluating Firm-Hosted Online Communities

This thesis centers to three firm-hosted online communities which operate in the field of software development. The communities were analyzed by using a particular design framework. This thesis investigates how companies can benefit from firm-hosted online communities and how well the design principles are present in analyzed communities. The framework also gives perspective and indicators which enables the possibility to analyze and compare communities with each other. This thesis also discuss how well a design framework designed for measuring social software fits to measuring online communities of software development.

Financier’s credit risk: A Performance-Based Classification Model

The purpose of this study is to view credit risk from the financier’s point of view in a theoretical framework. Results and aspects of the previous studies regarding measuring credit risk with accounting based scoring models are also examined. The theoretical framework and previous studies are then used to support the empirical analysis which aims to develop a credit risk measure for a bank’s internal use or a risk management tool for a company to indicate its credit risk to the financier. The study covers a sample of Finnish companies from 12 different industries and four different company categories and employs their accounting information from 2004 to 2008. The empirical analysis consists of six stage methodology process which uses measures of profitability, liquidity, capital structure and cash flow to determine financier’s credit risk, define five significant risk classes and produce risk classification model. The study is confidential until 15.10.2012.

Kunnossapitomittariston määrittäminen ja kunnossapidon kehittäminen

Diplomityössä pyritään määrittämään Kaukaan sahan kunnossapidon vallitsevaan tilanteeseen sopiva mittaristo. Tavoitteena on kunnossapitoprosessien tehostaminen sekä sahan kokonaistehokkuuden nostaminen. Diplomityön kirjallisessa osassa tutkimusongelmaa käsitellään kunnossapidon sekä mittaristojen ja tunnuslukujen näkökulmasta. Teoriaosa on rakennettu tukemaan työn tutkimusosaa. Tutkimuksen empiirisessä osassa tehdään nykytila-analyysi Kaukaan sahan kunnossapidosta. Nykytila-analyysi koostuu kyselytutkimuksesta, mitattavista tunnusluvuista sekä top-analyysista. Kyselytutkimus tehtiin lisäksi kaikilla UPM-Kymmene Oyj:n sahoilla. Kyselytutkimuksen pohjalta tehdään benchmarking-analyysia Kaukaan sahan ja suomen teollisuuden sekä UPM:n sahojen välillä. Lopuksi eroanalyysilla analysoidaan kyselytutkimuksessa syntynyttä eroa Kaukaan sahan ja UPM:n sahateollisuuden parhaan kunnossapidon välillä. Tutkimustulokset paljastivat useita kehityskohteita. Työssä annetaan suositus kyseisten kehityskohteiden mittaamisesta. Mittareiden ohella annetaan suosituksia uusista toimintamalleista.

Liiketoimintaprosessien mittaaminen ja mallintaminen

Tutkimuksessa tutkitaan mallintamista ja mittaamista osana liiketoimintaproses-sien parantamista, sekä näiden asioiden kuvaamista soveltuvalla työkalulla. Ensin esitetään teoreettinen viitekehys siihen, kuinka prosesseja voidaan mitata ja mal-lintaa. Sitten raportoidaan käytännössä suoritettu kehitystyö, jolle on määritetty lähtö- ja tavoitetila. Työn onnistumista mitataan johtajahaastatteluin ja saatuja tuloksia verrataan teoriaan. Tutkimuksessa yhdistettiin analyyttinen mallinrakennus, tieteellinen ongelman-ratkaisutoiminta sekä konsultointi tarkoituksena saada aikaan kohde organisaati-olle sopiva konstruktio esitettyyn ongelmaan. Johtajahaastattelut analysoitiin ja suoritettiin kvalitatiivinen tarveanalyysi. Haastatteluja täydennettiin muulla kerä-tyllä aineistolla ja analyysin tarkkuutta pyritään kasvattamaan eri lähdeaineistojen ristivertailuilla. Yrityksissä on niin liiketoiminnalle elintärkeitä ydinprosesseja kuin niitä tukevia tukiprosessejakin. Niiden toiminta perustuu ennalta suunniteltuihin ja uudelleen-käytettäviin menetelmiin. Prosessit tulee sopeuttaa yrityksen arkkitehtuuriin ja niitä on jatkuvasti kehitettävä. Kehittäminen voidaan toteuttaa suurilla kertamuu-toksilla, jatkuvalla laadun parantamisella tai niiden yhdistelmänä. Mallintamisella ja mittaamisella on tärkeä tehtävä liiketoimintaprosessien kehit-tämisessä. Niiden avulla voidaan helpottaa erityisesti prosessien suunnittelua luomalla konkreettisia malleja ja mittareita prosesseista. Toteutuksessa käytettiin prototyyppilähestymistapaa ja työn onnistumista arvioivat yhtiön johtajat. Tutki-muksen tuloksia ovat eri tason prosessimallit, joiden luomisessa käytettiin eri mallintamistekniikoita, sekä mittaristot mittaamaan yrityksen tuottavuutta ja te-hokkuutta.

Metsäsääntely Suomessa ja Venäjällä. Näkökulmia kestävään metsätalouteen

Sustainability is the aim of forest management and forest regulation in many countries. Accordingly, forest management has been steered towards more environmentally friendly methods and new regulatory instruments have been introduced. At the same time, wood trade and forest industry have become a global business. Even if the importance of national forest legislation has not decreased, it has been widely acknowledged that national regulation of forest management is no longer sufficient. The movement of goods does not acknowledge boundaries, even though most negative environmental and social consequences stay in the country of origin of wood and other raw materials. As a partial solution to this dilemma, different kinds of regulations have been developed. Various forest certification schemes and wood trade regulation in the EU (995/2010) are examples of efforts to prevent illegal logging and unsustainable forestry. The Finland-based forest industry is to a varying extent dependent on wood trade from Russia. Especially in the 1990‟s, ethical questions concerning import of wood from Russian old growth forests near the Finnish border were widely discussed. Consequently, forest industry enterprises have developed systems to trace the origin of wood and to buy certified wood from Russia. The aim of the research has been to evaluate Finnish and Russian forest regulations in order to investigate what kind of forest management these regulations enhance, and to what extent ecologically sustainable forest management has been integrated into different forms of regulation. I have examined Finnish and Russian forest regulation in four separate articles based on the topics of the Russian Forest Code, forest certification and other voluntary forest protection measures in Russia, Finnish forest certification and Finnish forest legislation. One objective has been to analyse the roles voluntary forest certification plays in promoting sustainable forest management in different countries. In my research, I have mainly concentrated on ecological sustainability and protection of biodiversity, although other aspects of sustainable forest management have been touched upon in different articles. In the following I shall conclude the findings of my research. When the current Russian Forest Code (2006) was being adopted, the main emphasis was not on ecological issues, but on reorganizing forest governance. The role of ecological requirements was even slightly diminished during the legislative reform. There are, nevertheless, still stipulations aiming at ecological sustainability, such as the division of forests into different forest management categories and various protection zones. In 2000, FSC forest certification arrived in Russia, at present covering already 28 million hectares of forests. The PEFC scheme is now in use as well, but to a much lesser extent. If properly implemented, Russian forest certification schemes clearly improve the level of ecological and social sustainability of forestry in Russia. Certification criteria, however, are partly in conflict with the Russian forest legislation and certified enterprises have been forced to pay fines or to negotiate with forest authorities. This clearly indicates that even if Russian forest legislation has otherwise been liberalized to a certain extent, some significant paternalism still exists. Voluntary, hands-on biodiversity protection measures are not valued, and they are not part of the official protection policies as in many other countries. However, there have been some regional solutions to this dilemma. In the Republic of Karelia forest authorities have approved a set of forest biodiversity protection rules created by a local NGO and a forest industry enterprise. By following these local rules, an enterprise can avoid fines for protection measures. The current Finnish Forest Act was adopted in 1996. It brought forest legislation into a new era as some ecological aspects were integrated into forest legislation. The various soft-law forest management recommendations further increased the level of biodiversity protection. My evaluation of the overall legitimacy of the Finnish forest legislation and forest management paradigm revealed, however, several problematic issues. As part of this study I analysed the history of the current forest management paradigm. This analysis revealed the path dependency which still hinders the protection of biodiversity and clearly decreases the general legitimacy of forest management. Due to several historical reasons only even-structured forest management based on clear cuts has for decades been officially approved in Finland. Due to increasing demands of forest owners the legislation is finally being revised. Yet, the official approval of uneven-structured forest management would not be enough to fully improve ecological, social and cultural legitimacy. The latest ecological theories and knowledge of endangered species should be taken into account in the on-going reform of forest legislation as well as the modernisation. Forest legislation is one of the very few spheres of Finnish environmental legislation where openness and participation are still considered a threat. The first Finnish forest certification scheme, PEFC, was established in 2000. It now covers more than 20 million hectares, about 95% of the forests in Finland. PEFC Finland does not require a higher level of biodiversity protection than the recommendations by Tapio (the Development Centre for Forestry), but certification has unified forest management practices and requires more protection measures than mere forest legislation. The study suggests that in Finland PEFC has not functioned as an instrument which would substantially improve the level of forest management. Rather it has supported the status quo of the forest sector. While the ecological and social responsibility of Finland-based forest corporations was one impetus for this research, I want to conclude that there are problems related to forest legislation and non-state regulation in both Finland and Russia. If an enterprise buying wood from Russia buys only certified wood, and carefully avoids wood coming from high conservation value forests that are either ecologically or socially valuable, it can be claimed to be as sustainably produced as in Finland. However, there must be continuous scrutiny of the circumstances. In Russia, the level of the compliance of certification criteria varies considerably, and there are vast unprotected invaluable forest areas. The utilisation of these areas should not be based on short-sighted decisions or lack of consensus among stakeholders.

Ratapihatyön turvallisuus rautatielogistiikassa

Diplomityön keskeisenä tavoitteena on ratapihahenkilöstön koulutuksessa käytettävien turvallisuusohjeiden uusiminen. Turvallisuusmateriaalia ei julkaista opinnäytetyön yhteydessä. Raportissa on käsitelty tapaturmien syntyyn liittyviä organisatorisia, inhimillisiä ja teknisiä syytekijöitä. Työhön sisältyy turvallisuuskulttuuria kartoittava mielipidekysely. Tapaturmien syntyyn on vaikea nimetä yksittäistä tekijää tai syytä. Osittain vaara menettää näkyvyytensä tapaturmattomana ajanjaksona, virheet ovat luonnollinen osa ihmisen toimintaa ja päätöksiä tehdään vajavaisen tiedon varassa. Toisaalta on vaikea luoda selkeitä mittareita ja indikaattoreita, jotka kertoisivat yrityksen todellisesta turvallisuustasosta.

Päivystyshoitotyön osaaminen valmistuvien sairaanhoitajaopiskelijoiden arvioimana

Potilaan hoitamisessa korostuvat mm. triagen tekeminen, potilaan voinnin seuranta ja hoitoa koskevien päätösten tekeminen nopeasti potilaan voinnin mukaan sekä potilaan jatkohoidon turvaaminen. Tämä kaksivaiheinen koulutustutkimus kohdistui päivystyshoitotyön osaamiseen. Tutkimuksen ensimmäisessä vaiheessa määriteltiin päivystyshoitotyön osaaminen ja toisessa vaiheessa arvioitiin valmistuvien sairaanhoitajaopiskelijoiden päivystyshoitotyön osaamista ja osaamiseen yhteydessä olevia tekijöitä. Osaamisen arvioinnin suorittivat opiskelijat itse ja vertailuperustana opiskelijoiden päivystyshoitotyön osaamiselle käytettiin ammatissa toimivien sairaanhoitajien päivystyshoitotyön osaamista. Tutkimuksen tavoitteena oli arvioinnin perusteella määrittää päivystyshoitotyön osaamisen nykytaso ja tehdä tarvittavat ehdotukset päivystyshoitotyön osaamisen kehittämiseen. Tutkimuksen ensimmäisessä vaiheessa (2006–2012) tiedonkeruumenetelminä oli kirjallisuuskatsaus ja asiantuntija-arviointi hyödyntäen delphi-menetelmää. Kirjallisuuskatsauksen perusteella muodostettiin päivystyshoitotyön osaamista kuvaavat pääkategoriat, yläkategoriat ja alakategoriat.Alakategoriat (n=61) annettiin asiantuntijoille (sairaanhoitajat, opettajat, ylihoitajat) arvioitavaksi.Kaksivaiheisen asiantuntija-arvioinnin perusteella muodostui 92 päivystyshoitotyön osaamista kuvaavaa alakategoriaa. Tutkimuksen toisessa vaiheessa (2007–2012) valmistuvien suomalaisten sairaanhoitaja-opiskelijoiden (N=382, n=208, vastausprosentti 55 %) päivystyshoitotyön osaamista arvioitiin tätä tutkimusta varten kehitetyllä mittarilla (Päivystyshoitotyön osaaminen -mittari). Mittari perustui tutkimuksen ensimmäisessä vaiheessa muodostettuun määrittelyyn päivystyshoitotyön osaamisesta. Osaamista mitattiin VAS-janalla (asteikko 0–100) arvon 100 ollessa optimaalinen taso, johon pyrittiin. Sairaanhoitajaopiskelijoiden tavoiteltavaksi osaamisen tasoksi asetettiin 80 olettaen opiskelijoiden osaamisen vielä kehittyvän työkokemuksen myötä. Ammatissa toimivien sairaanhoitajien (N=586, n=280, vastausprosentti 48 %) itsearvioitua osaamista käytettiin vertailuperustana opiskelijoiden osaamiselle. Aineisto analysoitiin tilastollisin menetelmin. Valmistuvien sairaanhoitajaopiskelijoiden itsearvioitu päivystyshoitotyön osaaminen oli alle tavoiteltavan osaamisen tason. Opiskelijoilla oli mielestään eniten eettistä osaamista sekä vuorovaikutus- ja yhteistyöosaamista ja vähiten päätöksenteko-osaamista ja kliinistä osaamista. Myös ammatissa toimivilla sairaanhoitajilla oli mielestään eniten vuorovaikutus- ja yhteistyöosaamista. Vähiten heillä oli ohjausosaamista ja päätöksenteko-osaamista. Sairaanhoitajilla oli tilastollisesti merkitsevästi enemmän päivystyshoitotyön osaamista kuin opiskelijoilla. Opiskelijoiden päivystyshoitotyön osaamista selitti eniten aikaisempi terveysalan tutkinto. Päivystyshoitotyön osaamisen kehittämisehdotukset kohdistuvat ammatillisen peruskoulutuksen ja täydennyskoulutuksen opetuksen sisältöihin ja määrään, opetus- ja opiskelumenetelmiin, osaamisen arviointiin sekä urasuunnitteluun. Jatkotutkimusehdotukset kohdistuvat päivystyshoitotyön osaamisen määrittelyn ja osaamista arvioivan mittarin edelleen kehittämiseen, erilaisten arviointimenetelmien kehittämiseen sekä osaamiseen yhteydessä olevien tekijöiden edelleen tutkimiseen.