Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Astrocyte Ca²⁺ signalling: an unexpected complexity.

Astrocyte Ca(2+) signalling has been proposed to link neuronal information in different spatial-temporal dimensions to achieve a higher level of brain integration. However, some discrepancies in the results of recent studies challenge this view and highlight key insufficiencies in our current understanding. In parallel, new experimental approaches that enable the study of astrocyte physiology at higher spatial-temporal resolution in intact brain preparations are beginning to reveal an unexpected level of compartmentalization and sophistication in astrocytic Ca(2+) dynamics. This newly revealed complexity needs to be attentively considered in order to understand how astrocytes may contribute to brain information processing.

Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

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.

Information and risk management during the first trimester care for pregnant women: Some reflections about the ethical challenges and the legal framework in Switzerland. [L'information et la gestion des risques dans le suivi de la grossesse lors du 1er trimestre : quelques réflexions sur le défi éthique et le cadre légal en Suisse.]

The progress in prenatal medicine raises complex questions with respect to the physician-patient relationship. The physician needs to reconcile medical aspects, ethical principles as well as judicial norms. Already, during the first trimester, the physician has to put into practice the schedule combining for each individual pregnancy physical, laboratory and other appropriate exams. Physicians are under the obligation to inform in a clear and comprehensive way without creating unnecessary anxiety for their patients. Legal requirements include informed consent, the respect for the patient's right to self-determination, and compliance with the Swiss federal law on genetic testing, especially with its articles on prenatal screening and diagnosis. This article discusses the complexity of obstetrical practice when it comes to delivering adequate information within the scope of ethical and legal requirements in Switzerland. L'évolution de la médecine prénatale soulève des enjeux complexes dans la relation médecin-patient. Il s'agit de concilier à la fois les aspects médicaux, les principes éthiques et les normes juridiques. Dès le premier trimestre de la grossesse le médecin doit poser le cadre du suivi et des examens appropriés pour chaque grossesse. Son devoir est d'informer de manière claire et précise sans inquiéter inutilement, en respectant l'exigence légale d'un consentement éclairé et plus largement le droit de la patiente à l'autodétermination ainsi que le cadre de la loi fédérale suisse sur l'analyse génétique humaine dans le domaine du dépistage et du diagnostic prénatal. Cet article discute de la complexité de l'information et de l'application des principes éthiques et légaux dans la pratique obstétricale en Suisse.

A comparison of Bayesian and frequentist approaches to incorporating external information for the prediction of prostate cancer risk.

We present the most comprehensive comparison to date of the predictive benefit of genetics in addition to currently used clinical variables, using genotype data for 33 single-nucleotide polymorphisms (SNPs) in 1,547 Caucasian men from the placebo arm of the REduction by DUtasteride of prostate Cancer Events (REDUCE®) trial. Moreover, we conducted a detailed comparison of three techniques for incorporating genetics into clinical risk prediction. The first method was a standard logistic regression model, which included separate terms for the clinical covariates and for each of the genetic markers. This approach ignores a substantial amount of external information concerning effect sizes for these Genome Wide Association Study (GWAS)-replicated SNPs. The second and third methods investigated two possible approaches to incorporating meta-analysed external SNP effect estimates - one via a weighted PCa 'risk' score based solely on the meta analysis estimates, and the other incorporating both the current and prior data via informative priors in a Bayesian logistic regression model. All methods demonstrated a slight improvement in predictive performance upon incorporation of genetics. The two methods that incorporated external information showed the greatest receiver-operating-characteristic AUCs increase from 0.61 to 0.64. The value of our methods comparison is likely to lie in observations of performance similarities, rather than difference, between three approaches of very different resource requirements. The two methods that included external information performed best, but only marginally despite substantial differences in complexity.

Finding the Fit Between Engineering Design and Cost Information

This paper analyzes the possibilities of integrating cost information and engineering design. Special emphasis is put on finding the potential of using the activity-based costing (ABC) method. Today, the problem of cost estimation in engineering design is that there are two separate extremes of knowledge. On the one extreme, the engineers model the technical parametres behindcosts in great detail but do not get appropriate cost information to their elegant models. On the other extreme, the accounting professionals are stuck with traditional cost accounting methods driven by the procedures and cycles of financial accounting. Therefore, in many cases, the cost information needs of various decision making groups, for example design engineers, are not served satisfactorily. This paper studies if the activity-based costing (ABC) method could offer a compromise between the two extremes. Recognizing activities and activity chains as well as activity and cost drivers could be specially beneficial for design engineers. Also, recognizing the accurate and reliable product costs of existing products helps when doing variant design. However, ABC is not at its best if the cost system becomes too complicated. This is why a comprehensive ABC-cost information system with detailed cost information for the use of design engineers should be examined critically. ABC is at its best when considering such issues as which activities drive costs, the cost of product complexity, allocating indirect costs on the products, the relationships between processes and costs, and the cost of excess capacity.

Task complexity, the Cognition Hypothesis and second language learning and performance

In this paper we describe a taxonomy of task demands which distinguishes between Task Complexity, Task Condition and Task Difficulty. We then describe three theoretical claims and predictions of the Cognition Hypothesis (Robinson 2001, 2003b, 2005a) concerning the effects of task complexity on: (a) language production; (b) interaction and uptake of information available in the input to tasks; and (c) individual differences-task interactions. Finally we summarize the findings of the empirical studies in this special issue which all address one or more of these predictions and point to some directions for continuing, future research into the effects of task complexity on learning and performance.

Cross-border post-acquisition integration performed by a Nordic information & telecommunication technology company in the transition economy context of the Czech Republic

Diplomityön tarkoituksena oli arvioida akvisition jälkeistä integraatioprosessia. Integraation tarkoitus on mukauttaa ostettu yritys toimivaksi osaksi konsernia. Työn empiirisenä ongelmana oli yleisesti tunnustettu integraatiojohtamisen kompleksisuus. Samoin myöskin akateemisesta kirjallisuudesta puuttui koherentti malli, jolla arvioida integraatiota. Tutkimuskohteena oli akvisitio, jossa suomalainen tietotekniikkan suuryritys osti osake-enemmistön tsekkiläisestä keskisuuresta ohjelmistoyrityksestä. Tutkimuksessa generoitiin integraatiojohtamisen malli tietopohjaiseen organisaatioon. Mallin mukaan integraatio koostuu kolmesta eriävästä, mutta toisiaan tukevasta alueesta: organisaatiokulttuurin yhdentyminen, tietopääoman tasaaminen ja konsernin sisäisten prosessien yhdenmukaistaminen. Näistä kaksi kaksi jälkimmäistä ovat johdettavissa, mutta kulttuurin yhdentymiseen integraatiojohtamisella voidaan vaikuttaa vain katalysoivasti. Organisaatiokulttuuri levittäytyy vain osallisten vuorovaikuksien kautta. Lisäksi tutkimus osoitti, miten akvisitio on revolutionaarinen vaihe yrityksen kehityksessä. Integraation ensimmäinen ajanjakso on revolutionaarista. Tällöin suurimmat ja näkyvimmät johdettavat muutokset pyritään saamaan aikaan, jotta integraatiossa edettäisiin evolutionaariseen kehitykseen. Revolutionaarisen intergaation vetojuhtana toimii integraatiojohto, kun taas evolutionaarinen integraatio etenee osallisten (organisaation jäsenten) itsensä toiminnan ja vuorovaikutusten kautta.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Impact of model complexity on cross-temporal transferability in Maxent species distribution models: An assessment using paleobotanical data

Maximum entropy modeling (Maxent) is a widely used algorithm for predicting species distributions across space and time. Properly assessing the uncertainty in such predictions is non-trivial and requires validation with independent datasets. Notably, model complexity (number of model parameters) remains a major concern in relation to overfitting and, hence, transferability of Maxent models. An emerging approach is to validate the cross-temporal transferability of model predictions using paleoecological data. In this study, we assess the effect of model complexity on the performance of Maxent projections across time using two European plant species (Alnus giutinosa (L.) Gaertn. and Corylus avellana L) with an extensive late Quaternary fossil record in Spain as a study case. We fit 110 models with different levels of complexity under present time and tested model performance using AUC (area under the receiver operating characteristic curve) and AlCc (corrected Akaike Information Criterion) through the standard procedure of randomly partitioning current occurrence data. We then compared these results to an independent validation by projecting the models to mid-Holocene (6000 years before present) climatic conditions in Spain to assess their ability to predict fossil pollen presence-absence and abundance. We find that calibrating Maxent models with default settings result in the generation of overly complex models. While model performance increased with model complexity when predicting current distributions, it was higher with intermediate complexity when predicting mid-Holocene distributions. Hence, models of intermediate complexity resulted in the best trade-off to predict species distributions across time. Reliable temporal model transferability is especially relevant for forecasting species distributions under future climate change. Consequently, species-specific model tuning should be used to find the best modeling settings to control for complexity, notably with paleoecological data to independently validate model projections. For cross-temporal projections of species distributions for which paleoecological data is not available, models of intermediate complexity should be selected.

Situational awareness concept in a multinational collaboration environment : challenges in the information sharing framework

Technological capabilities are built to support different types of collaboration, and this gives the justification to widely observe, how activity environments are influenced by technology. Technology as an enabler can be addressed from different perspectives, other than merely technological. Dynamic, evolving environment is at the same time interesting but also challenging. As a multinational collaboration environment, the maritime surveillance is an good example of time critical and evolving environment, where technological solutions enable new ways of collaboration. Justification for the inspiration to use maritime environment as the baseline for understanding the challenges in creating and maintaining adequate level of situational awareness, derives from the complexity of the collaboration and information sharing environment elements, needed to be taken into account, when analyzing criticalities related to decision making. Situational awareness is an important element supporting decision making, and challenges related to it can also be observed in the maritime environment. This dissertation describes the structures and factors involved in this complex setting, found from the case studies that should be taken into account when trying to understand, how these elements affect the activities. This dissertation focuses on the gray area that is between a life threatening situation and normal everyday activities. From the multinational experimentation series case studies, MNE5 and MNE6 it was possible to observe situations that were not life threatening for the participants themselves, but not also basic every day activities. These case studies provided a unique possibility to see situations, where gaining of situational awareness and decision making are challenged with time critical crisis situations. Unfortunately organizations do not normally take the benefit from the everyday work to prepare themselves for possible emerging crisis situations. This dissertation focuses on creating a conceptual model and a concept that supports organizations – also outside the maritime community – to improve their ability to support gaining of situational awareness from the individual training level, all the way to changes in organizational structures in aiming for better support for decision making from the individual level to the highest decision making level. Quick changes and unpredictability are reality in organizations and organizations do not have the possibility to control all the factors that affect their functioning. Since we cannot be prepared for everything, and predict every crisis, individual activities inside teams and as a part of organizations, need to be supported with guidance, tools and training in order to support acting in challenging situations. In fact the ideology of the conceptual model created, lies especially in the aim of not controlling everything in beforehand, but supporting organizations with concrete procedures to help individuals to react in different, unpredictable situations, instead of focusing on traditional risk prevention and management. Technological capabilities are not automatically solutions for functional challenges; this is why it is justified to broaden the problem area observation from the technological perspective. This dissertation demonstrates that it is possible to support collaboration in a multinational environment with technological solutions, but it requires the recognition of technological limitations and accepting the possible restrictions related to technological innovations. Technology should not be considered value per se, the value of technology should be defined according to the support of activities, including strategic and operational environment evaluation, identification of organizational elements, and taking into account also the social factors and their challenges. Then we are one step closer to providing technological solutions that support the actual activities by taking into account the variables of the activity environment in question. The multidisciplinary view to approach the information sharing and collaboration framework, is derived especially from the complexity of decision making and building of situational awareness, since they are not build or created in vacuity, but in the organizational framework by the people doing it with the technological capabilities, enabled by the organizational structures. Introduced case studies were related to maritime environment, but according to the research results, it is valid to argue, that based on the lessons learned it is possible to create and further develop conceptual model and to create a general concept to support a wider range of organizations in their attempt to gain better level of situational awareness (SA) and to support decision making. To proof the versatile usage of the developed concept, I have introduced the case study findings to the health care environment and reflected the identified elements from the trauma center to the created concept. The main contribution to complete this adventure is the presented situational awareness concept created in the respect to NATO concept structure. This has been done to tackle the challenge of collaboration by focusing on situational awareness in the information sharing context by providing a theoretical ground and understanding, of how these issues should be approached, and how these elements can be generalized and used to support activities in other environments as well. This dissertation research has been a several year evolving process reflecting and affecting presented case studies and this learning experience from the case studies has also affected the goals and research questions of this dissertation. This venture has been written from a retro perspective according to ideology of process modeling and design rationale to present to the reader how this entire journey took place and what where the critical milestones that affected the end result, conceptual model. Support in a challenging information sharing framework can be provided with the right type of combination of tools, procedures and individual effort. This dissertation will provide insights to those with a new approach to war technology for the organizations to gain a better level of awareness and to improve the capabilities in decision making. This dissertation will present, from the war technology starting point, a new approach and possibility for the organizations to create a better level of awareness and support for decision making with the right combination of tools, procedures and individual effort.

Learning information technology business in a changing industry landscape. Introducing Team Entrepreneurship in Renewing Bachelor Education in Renewing Bachelor Education in Information

Speed, uncertainty and complexity are increasing in the business world all the time. When knowledge and skills become quickly irrelevant, new challenges are set for information technology (IT) education. Meta-learning skills – learning how to learn rapidly - and innovation skills have become more essential than single technologies or other specific issues. The drastic changes in the information and communications technology (ICT) sector have caused a need to reconsider how IT Bachelor education in Universities of Applied Sciences should be organized and employed to cope with the change. The objective of the study was to evaluate how a new approach to IT Bachelor education, the ICT entrepreneurship study path (ICT-ESP) fits IT Bachelor education in a Finnish University of Applied Sciences. This kind of educational arrangement has not been employed elsewhere in the context of IT Bachelor education. The study presents the results of a four-year period during which IT Bachelor education was renewed in a Finnish University of Applied Sciences. The learning environment was organized into an ICT-ESP based on Nonaka’s knowledge theory and Kolb’s experiental learning. The IT students who studied in the ICT-ESP established a cooperative and learned ICT by running their cooperative at the University of Applied Sciences. The students (called team entrepreneurs) studied by reading theory in books and other sources of explicit information, doing projects for their customers, and reflecting in training sessions on what was learnt by doing and by studying the literature. Action research was used as the research strategy in this study. Empirical data was collected via theme-based interviews, direct observation, and participative observation. Grounded theory method was utilized in the data analysis and the theoretical sampling was used to guide the data collection. The context of the University of Applied Sciences provided a good basis for fostering team entrepreneurship. However, the results showed that the employment of the ICT-ESP did not fit into the IT Bachelor education well enough. The ICT-ESP was cognitively too tough for the team entrepreneurs because they had two different set of rules to follow in their studies. The conventional courses engaged lot of energy which should have been spent for professional development in the ICT-ESP. The amount of competencies needed in the ICT-ESP for professional development was greater than those needed for any other ways of studying. The team entrepreneurs needed to develop skills in ICT, leadership and self-leadership, team development and entrepreneurship skills. The entrepreneurship skills included skills on marketing and sales, brand development, productization, and business administration. Considering the three-year time the team entrepreneurs spent in the ICT-ESP, the challenges were remarkable. Changes to the organization of IT Bachelor education are also suggested in the study. At first, it should be admitted that the ICT-ESP produces IT Bachelors with a different set of competencies compared to the conventional way of educating IT Bachelors. Secondly, the number of courses on general topics in mathematics, physics, and languages for team entrepreneurs studying in the ICTESP should be reconsidered and the conventional course-based teaching of the topics should be reorganized to support the team coaching process of the team entrepreneurs with their practiceoriented projects. Third, the upcoming team entrepreneurs should be equipped with relevant information about the ICT-ESP and what it would require in practice to study as a team entrepreneur. Finally, the upcoming team entrepreneurs should be carefully selected before they start in the ICT-ESP to have a possibility to eliminate solo players and those who have a too romantic view of being a team entrepreneur. The results gained in the study provided answers to the original research questions and the objectives of the study were met. Even though the IT degree programme was terminated during the research process, the amount of qualitative data gathered made it possible to justify the interpretations done.

Heart rate recovery after exercise: relations to heart rate variability and complexity

Physical exercise is associated with parasympathetic withdrawal and increased sympathetic activity resulting in heart rate increase. The rate of post-exercise cardiodeceleration is used as an index of cardiac vagal reactivation. Analysis of heart rate variability (HRV) and complexity can provide useful information about autonomic control of the cardiovascular system. The aim of the present study was to ascertain the association between heart rate decrease after exercise and HRV parameters. Heart rate was monitored in 17 healthy male subjects (mean age: 20 years) during the pre-exercise phase (25 min supine, 5 min standing), during exercise (8 min of the step test with an ascending frequency corresponding to 70% of individual maximal power output) and during the recovery phase (30 min supine). HRV analysis in the time and frequency domains and evaluation of a newly developed complexity measure - sample entropy - were performed on selected segments of heart rate time series. During recovery, heart rate decreased gradually but did not attain pre-exercise values within 30 min after exercise. On the other hand, HRV gradually increased, but did not regain rest values during the study period. Heart rate complexity was slightly reduced after exercise and attained rest values after 30-min recovery. The rate of cardiodeceleration did not correlate with pre-exercise HRV parameters, but positively correlated with HRV measures and sample entropy obtained from the early phases of recovery. In conclusion, the cardiodeceleration rate is independent of HRV measures during the rest period but it is related to early post-exercise recovery HRV measures, confirming a parasympathetic contribution to this phase.

Learning about brain physiology and complexity from the study of the epilepsies

The brain is a complex system, which produces emergent properties such as those associated with activity-dependent plasticity in processes of learning and memory. Therefore, understanding the integrated structures and functions of the brain is well beyond the scope of either superficial or extremely reductionistic approaches. Although a combination of zoom-in and zoom-out strategies is desirable when the brain is studied, constructing the appropriate interfaces to connect all levels of analysis is one of the most difficult challenges of contemporary neuroscience. Is it possible to build appropriate models of brain function and dysfunctions with computational tools? Among the best-known brain dysfunctions, epilepsies are neurological syndromes that reach a variety of networks, from widespread anatomical brain circuits to local molecular environments. One logical question would be: are those complex brain networks always producing maladaptive emergent properties compatible with epileptogenic substrates? The present review will deal with this question and will try to answer it by illustrating several points from the literature and from our laboratory data, with examples at the behavioral, electrophysiological, cellular and molecular levels. We conclude that, because the brain is a complex system compatible with the production of emergent properties, including plasticity, its functions should be approached using an integrated view. Concepts such as brain networks, graphics theory, neuroinformatics, and e-neuroscience are discussed as new transdisciplinary approaches dealing with the continuous growth of information about brain physiology and its dysfunctions. The epilepsies are discussed as neurobiological models of complex systems displaying maladaptive plasticity.