Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Hematological responses of tambaqui Colossoma macropomum (Serrassalmidae) fed with diets supplemented with essential oil from Mentha piperita (Lamiaceae) and challenged with Aeromonas hydrophila

ABSTRACTIn fish farmings, diseases can be reduced by using immunostimulants. The aim of this study was to evaluate the immunostimulant potential of Mentha piperita in tambaqui fed with 0, 0.5, 1.0 and 1.5% of oil per kg of commercial fish feed. The fish were inoculated with Aeromonas hydrophila to challenge them. Hematological and biochemical parameters were determined after 30 days of feeding and seven days after the challenge. There was no mortality and M. piperita oil did not influence fish production parameters. However, blood hemoglobin concentration (Hb) increased in the fish fed with 0.5 and 1.5% of oil per kg of diet; albumin increased in those fed with 1.0%; cholesterol increased in all groups with oil; and triglycerides increased in those fed with 0.5%. After the bacterial challenge, the fish showed decreases in Hb when fed with diet enriched with 1.5% oil per kg of diet, in mean corpuscular volume with 1.0% and in mean corpuscular hemoglobin concentration with 0 and 1.5%. Protein levels increased in groups with 0 and 1.5% of oil and albumin when fed with 0 and 1.0%; cholesterol levels increased in the control group; and high levels of triglycerides were observed in the groups with 0, 0.5 and 1.5%. Thus, M. piperita essential oil promoted hematological alterations in tambaqui and can be recommended in diets containing up to 1.0% per kg, because of the minimal physiological modifications caused. However, additional studies are necessary to obtain more information regarding to the physiological effects of this immunostimulant.

Implementação de um sistema de customer relationship management na broaden information solutions

Dissertação de mestrado em Sistemas de Informação

Essential Bacillus subtilis genes.

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximately 4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

Informatics competencies essential to decision making in nursing management

Abstract OBJECTIVE To identify informatics abilities essential to decision making in nursing management. METHOD Survey study with specialist nurses in health informatics and management. An electronic questionnaire was built based on the competencies Information Literacy (five categories; 40 abilities) and Information Management (nine categories; 69 abilities) of the TIGER - Technology Informatics Guiding Education Reform - initiative, with the guiding question: Which informatics abilities are essential to decision making in management? Answers were sorted in a Likert scale, ranging from 1 to 5. Rasch analysis was conducted with the software WINSTEPS ®. Results were presented in logits, with cutoff value zero. RESULTS Thirty-two specialists participated, coming from all regions of Brazil. In the information literacy competency, 18 abilities were considered essential and in Information Management, 38; these were sorted according to their degree of essentiality. CONCLUSION It is believed that the incorporation of these abilities in teaching can support the education of nurse managers and contribute to evidence-based practice, incorporation of information and communication technologies in health and information management.

Positional information by differential endocytosis splits auxin response to drive Arabidopsis root meristem growth.

In the Arabidopsis root meristem, polar auxin transport creates a transcriptional auxin response gradient that peaks at the stem cell niche and gradually decreases as stem cell daughters divide and differentiate [1-3]. The amplitude and extent of this gradient are essential for both stem cell maintenance and root meristem growth [4, 5]. To investigate why expression of some auxin-responsive genes, such as the essential root meristem growth regulator BREVIS RADIX (BRX) [6], deviates from this gradient, we combined experimental and computational approaches. We created cellular-level root meristem models that accurately reproduce distribution of nuclear auxin activity and allow dynamic modeling of regulatory processes to guide experimentation. Expression profiles deviating from the auxin gradient could only be modeled after intersection of auxin activity with the observed differential endocytosis pattern and positive autoregulatory feedback through plasma-membrane-to-nucleus transfer of BRX. Because BRX is required for expression of certain auxin response factor targets, our data suggest a cell-type-specific endocytosis-dependent input into transcriptional auxin perception. This input sustains expression of a subset of auxin-responsive genes across the root meristem's division and transition zones and is essential for meristem growth. Thus, the endocytosis pattern provides specific positional information to modulate auxin response.

Information retention during competitive interactions : siblings need to constantly repeat vocal displays

Memory is essential to adjust behaviour according to past experience. In societies where animals interact on numerous occasions, memory of previous social interactions may help optimise investment in competition. How long information about the resource holding potential and motivation to compete of conspecifics is retained depends on how fast the value of this information fades, but also on the cost and benefit of retaining information. Information retention has never been investigated in the context of interactions prevailing within the family and more specifically sibling competition. In the absence of parents, barn owl (Tyto alba) nestlings vocally compete for priority of access to the next indivisible food item brought by a parent. The finding that owlets eavesdrop on vocal interactions between siblings to adjust investment in vocalization once competing with them suggests that they memorize siblings' vocal interactions. Playback experiments showed that owlets take into account the past siblings' vocal performance that signals hunger for at least 15 min, but only if the performance was witnessed during a sufficiently long period of time (30 min). Moreover, using natural vocal exchanges in another set of individuals, we showed that sibling signalling was no more taken into account after a few minutes. This suggests that young barn owls need to continuously display their motivation to trigger siblings' withdrawal from the current competition. Repeating a vocal display may ensure its honesty. Studying the extent to which individuals retain past information is important to understand how individuals adjust their competitive investment over resources.

Database Rights in Safe European Home: The Path to More Rigorous Protection of Information

1. Introduction "The one that has compiled ... a database, the collection, securing the validity or presentation of which has required an essential investment, has the sole right to control the content over the whole work or over either a qualitatively or quantitatively substantial part of the work both by means of reproduction and by making them available to the public", Finnish Copyright Act, section 49.1 These are the laconic words that implemented the much-awaited and hotly debated European Community Directive on the legal protection of databases,2 the EDD, into Finnish Copyright legislation in 1998. Now in the year 2005, after more than half a decade of the domestic implementation it is yet uncertain as to the proper meaning and construction of the convoluted qualitative criteria the current legislation employs as a prerequisite for the database protection both in Finland and within the European Union. Further, this opaque Pan-European instrument has the potential of bringing about a number of far-reaching economic and cultural ramifications, which have remained largely uncharted or unobserved. Thus the task of understanding this particular and currently peculiarly European new intellectual property regime is twofold: first, to understand the mechanics and functioning of the EDD and second, to realise the potential and risks inherent in the new legislation in economic, cultural and societal dimensions. 2. Subject-matter of the study: basic issues The first part of the task mentioned above is straightforward: questions such as what is meant by the key concepts triggering the functioning of the EDD such as presentation of independent information, what constitutes an essential investment in acquiring data and when the reproduction of a given database reaches either qualitatively or quantitatively the threshold of substantiality before the right-holder of a database can avail himself of the remedies provided by the statutory framework remain unclear and call for a careful analysis. As for second task, it is already obvious that the practical importance of the legal protection providedby the database right is in the rapid increase. The accelerating transformationof information into digital form is an existing fact, not merely a reflection of a shape of things to come in the future. To take a simple example, the digitisation of a map, traditionally in paper format and protected by copyright, can provide the consumer a markedly easier and faster access to the wanted material and the price can be, depending on the current state of the marketplace, cheaper than that of the traditional form or even free by means of public lending libraries providing access to the information online. This also renders it possible for authors and publishers to make available and sell their products to markedly larger, international markets while the production and distribution costs can be kept at minimum due to the new electronic production, marketing and distributionmechanisms to mention a few. The troublesome side is for authors and publishers the vastly enhanced potential for illegal copying by electronic means, producing numerous virtually identical copies at speed. The fear of illegal copying canlead to stark technical protection that in turn can dampen down the demand for information goods and services and furthermore, efficiently hamper the right of access to the materials available lawfully in electronic form and thus weaken the possibility of access to information, education and the cultural heritage of anation or nations, a condition precedent for a functioning democracy. 3. Particular issues in Digital Economy and Information Networks All what is said above applies a fortiori to the databases. As a result of the ubiquity of the Internet and the pending breakthrough of Mobile Internet, peer-to-peer Networks, Localand Wide Local Area Networks, a rapidly increasing amount of information not protected by traditional copyright, such as various lists, catalogues and tables,3previously protected partially by the old section 49 of the Finnish Copyright act are available free or for consideration in the Internet, and by the same token importantly, numerous databases are collected in order to enable the marketing, tendering and selling products and services in above mentioned networks. Databases and the information embedded therein constitutes a pivotal element in virtually any commercial operation including product and service development, scientific research and education. A poignant but not instantaneously an obvious example of this is a database consisting of physical coordinates of a certain selected group of customers for marketing purposes through cellular phones, laptops and several handheld or vehicle-based devices connected online. These practical needs call for answer to a plethora of questions already outlined above: Has thecollection and securing the validity of this information required an essential input? What qualifies as a quantitatively or qualitatively significant investment? According to the Directive, the database comprises works, information and other independent materials, which are arranged in systematic or methodical way andare individually accessible by electronic or other means. Under what circumstances then, are the materials regarded as arranged in systematic or methodical way? Only when the protected elements of a database are established, the question concerning the scope of protection becomes acute. In digital context, the traditional notions of reproduction and making available to the public of digital materials seem to fit ill or lead into interpretations that are at variance with analogous domain as regards the lawful and illegal uses of information. This may well interfere with or rework the way in which the commercial and other operators have to establish themselves and function in the existing value networks of information products and services. 4. International sphere After the expiry of the implementation period for the European Community Directive on legal protection of databases, the goals of the Directive must have been consolidated into the domestic legislations of the current twenty-five Member States within the European Union. On one hand, these fundamental questions readily imply that the problemsrelated to correct construction of the Directive underlying the domestic legislation transpire the national boundaries. On the other hand, the disputes arisingon account of the implementation and interpretation of the Directive on the European level attract significance domestically. Consequently, the guidelines on correct interpretation of the Directive importing the practical, business-oriented solutions may well have application on European level. This underlines the exigency for a thorough analysis on the implications of the meaning and potential scope of Database protection in Finland and the European Union. This position hasto be contrasted with the larger, international sphere, which in early 2005 does differ markedly from European Union stance, directly having a negative effect on international trade particularly in digital content. A particular case in point is the USA, a database producer primus inter pares, not at least yet having aSui Generis database regime or its kin, while both the political and academic discourse on the matter abounds. 5. The objectives of the study The above mentioned background with its several open issues calls for the detailed study of thefollowing questions: -What is a database-at-law and when is a database protected by intellectual property rights, particularly by the European database regime?What is the international situation? -How is a database protected and what is its relation with other intellectual property regimes, particularly in the Digital context? -The opportunities and threats provided by current protection to creators, users and the society as a whole, including the commercial and cultural implications? -The difficult question on relation of the Database protection and protection of factual information as such. 6. Dsiposition The Study, in purporting to analyse and cast light on the questions above, is divided into three mainparts. The first part has the purpose of introducing the political and rationalbackground and subsequent legislative evolution path of the European database protection, reflected against the international backdrop on the issue. An introduction to databases, originally a vehicle of modern computing and information andcommunication technology, is also incorporated. The second part sets out the chosen and existing two-tier model of the database protection, reviewing both itscopyright and Sui Generis right facets in detail together with the emergent application of the machinery in real-life societal and particularly commercial context. Furthermore, a general outline of copyright, relevant in context of copyright databases is provided. For purposes of further comparison, a chapter on the precursor of Sui Generi, database right, the Nordic catalogue rule also ensues. The third and final part analyses the positive and negative impact of the database protection system and attempts to scrutinize the implications further in the future with some caveats and tentative recommendations, in particular as regards the convoluted issue concerning the IPR protection of information per se, a new tenet in the domain of copyright and related rights.

Controlling Access to Personal Information

Tässä diplomityössä käsitellään henkilökohtaisen tiedon saannin kontrollointia ja tiedon kuvaamista. Työn käytännön osuudessa suunniteltiin XML –malli henkilökohtaisen tiedon kuvaamiseen. Henkilökohtaisten tietojen käyttäminen mahdollistaa henkilökohtaisen palvelun tarjoamisen ja myös palvelun automatisoinnin käyttäjälle. Henkilökohtaisen tiedon kuvaaminen on hyvin oleellista, jotta palvelut voivat kysellä ja ymmärtää tietoja. Henkilökohtaiseen tietoon vaikuttaa erilaisia tekijöitä, jotka on myös otettava huomioon tietoa kuvattaessa. Henkilökohtaisen tiedon leviäminen eri palveluiden tarjoajille tuo mukanaan myös riskejä. Henkilökohtaisen tiedon joutuminen väärän henkilön käsiin saattaa aiheuttaa vakaviakin ongelmia tiedon omistajalle. Henkilökohtaisen tiedon turvallisen ja luotettavan käytettävyyden kannalta onkin hyvin oleellista, että käyttäjällä on mahdollisuus kontrolloida kenelle hän haluaa luovuttaa mitäkin tietoa.

Information Sharing in Drives Alliance Partner Concept

Työssä oli selkeästi kaksi tavoitetta. Ensimmäisenä tavoitteena oli tutkia, millaisesta kumppanuudesta Drives Alliance Partner -konsepti (DAP) muodostuu. Työn toisena tavoitteena oli selvittää ja analysoida DAP-konseptin informaation jakamiseen liittyvät tietotyypit, ja tehdä esitys siitä, mitä tietoa ABB:nja kumppaneiden välillä tulisi vaihtaa. Jotta kumppanuuden tila saatiin selville, tehtiin ABB:n sisäisiä haastatteluja sekä käytettiin hyväksi DAP-konseptista tehtyä dokumentaatiota. Informaation jakamiseen liittyvä tietotarpeiden kartoitus toteutettiin web-pohjaisen kyselyn avulla. Kysely toimitettiin osalle ABB:n nykyisistä kumppaneista sekä sellaisille ABB:n työntekijöille, jotka liittyvät DAP- konseptiin. Työssä luotiin malli kuvaamaan informaation vaihtoa partnereiden j a ABB :n välillä. Malliin otettiin mukaan ne tietotarpeet, jotka tehdyn kyselyn mukaan osoittautuivat tarpeellisiksi. Kumppanuuksiin syventymisen myötä tiedonvaihdon merkitys tulee entisestään korostumaan, mikä asettaa uusia haasteita ABB:lle.

Integration and Implementation of Accounting Information Systems in Global Companies Case: The UPM-Kymmene Group

Tämän tutkielman tavoitteena on perehtyä globaalin yrityksen laskentatoimen tietojärjestelmien yhtenäistämiseen ja käyttöönottoon esimerkkinä UPM-Kymmene konsernin projekti. Tutkielmassa sovelletaan hermeneuttista tutkimusotetta. Teoreettisesti aihetta tarkastellaan globalisoitumisen ja laskentatoimen tietojärjestelmille asetettavien vaatimusten pohjalta, sekä järjestelmän muutosprosessin eri vaiheissa huomioon otettavien muuttujien perusteella. Yhtenäisen laskentatoimen tietojärjestelmän tuomat edut globaalille yritykselle ovat ilmeisiä. Ennen yhtenäisen projektin kehittelyä on olennaista tutkia lähtökohdat projektin onnistumiselle ja suunnitella projektin eri vaiheet huolella. Tutkielmassa havaitaan myös, että globaalissa yrityksessä tulee huomioida eri yrityskulttuurit sekä tulosyksiköiden erilaiset toimintatavat. Johtopäätöksenä todetaan, että sekä yritysjohdon että tulosyksiköiden sitoutuneisuus projektiin ja yhtenäiset tavoitteet ovat oleellisia projektin onnistumisen kannalta.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines the propagation of knowledge across resources, as well as the credibility of results from high-throughput analyses. Seeded at a workshop during the Biocuration 2012 conference, a working group has been created to address this problem. We present here the elements that were identified as essential for assessing confidence in annotations, as well as a draft ontology--the Confidence Information Ontology--to illustrate how the problems identified could be addressed. We hope that this effort will provide a home for discussing this major issue among the biocuration community. Tracker URL: https://github.com/BgeeDB/confidence-information-ontology Ontology URL: https://raw.githubusercontent.com/BgeeDB/confidence-information-ontology/master/src/ontology/cio-simple.obo

High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex.

Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In contrast, the number of markers on each autosome is similar between the two maps. We also find strongly conserved synteny between H. arborea and Xenopus tropicalis across 200 million years of evolution, suggesting that the rate of chromosomal rearrangement in anurans is low. Finally, we show that recombination in males is greatly reduced at the centers of large chromosomes, consistent with previous cytogenetic findings. Our research shows the importance of high-density linkage maps for studies of recombination, chromosomal rearrangement and the genetic architecture of ecologically or economically important traits.

Development of tender information process by business intelligence in a global company unit

The purpose of this Thesis was to study what is the present situation of Business Intelligence of the company unit. This means how efficiently unit uses possibilities of modern information management systems. The aim was to resolve how operative informa-tion management of unit’s tender process could be improved by modern information technology applications. This makes it possible that tender processes could be faster and more efficiency. At the beginning it was essential to acquaint oneself with written literature of Business Intelligence. Based on Business Intelligence theory is was relatively easy but challenging to search and discern how tender business could be improved by methods of Busi-ness Intelligence. The empirical phase of this study was executed as qualitative research method. This phase includes theme and natural interviews on the company. Problems and challenges of tender process were clarified in a part an empirical phase. Group of challenges were founded when studying information management of company unit. Based on theory and interviews, group of improvements were listed which company could possible do in the future when developing its operative processes.

Expectations and Experiences of International Students in Information Technology Department

Education in Finland plays a significant role. International students are becoming an essential part of Finnish Educational system. The study was meant to examine their expectations and experiences in a Finnish University. As a case, Lappeenranta University of Technology (LUT) was chosen and, in particular, Information Technology (IT) Department. The main objectives of the study were to examine students’ satisfaction of their study experiences, their evaluation of the teaching quality of courses and last but not least the cultural impact on those. Data for the study were mainly collected with the help of three Internet surveys from a sample of 50 students – currently studying at LUT or already graduated. Response rate from questionnaire to questionnaire varied, however, still close to average and was considered as good and relevant enough. The study was initially meant as qualitative, however, a number of quantitative data analysis methods were used as well. Most of students’ expectations appear to become true, majority of students are satisfied with their experiences. Results show that teaching quality in LUT is evaluated as ‘good’. Nevertheless, students prefer particular courses to the other ones. In conclusion, it can be said that culture does affect students’ expectations, experiences, perception of the world, however, cultural differences do not cause any serious problems.