Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Gestión de la actividad no presencial y autoevaluación de competencias = Management of Student Learning Outside the Classroom and the Self-evaluation of Competences

Psychological Assessment is a core subject of Psychology studies, and of the university degree Human development, at the University of Girona and according to the University regulations, had 12 credits. Until the 2005-06 academic years, the student work conducted outside the classroom consisted of undertaking a psychological assessment that was written and handed in at the end of the course. From this the student obtained a qualification and a review if they applied for it In accordance with the European Credits for Higher Education, this subject was reduced to 9 credits, which is the equivalent of a total of 255 hours of in-class work and outside the classroom. In the 2006-07 academic year we created a guide to manage the student’s experiences outside the classroom, with the objective of encouraging the application of problem solving/critical thinking (Bloom, 1975), in line with the recommendations of the Catalonia Agency for University System Quality (2005). The guide includes: learning objectives, evaluation criterions, a description of activities, work week timetable for the whole course, programmed tutorials to review all steps of the psychological assessment process, and the use of a web-based virtual forum for the transfer of knowledge, analysis and constructive critiques of the assessment done by themselves and their colleagues

The motivation to learn as a self-presentation tool among Swiss high school students : The moderating role of mastery goals' perceived social value on learning

Although it has been assumed that the motivation to learn - or mastery goal endorsement - positively predicts learning achievement, most empirical findings fail to demonstrate this relationship. In the present research, conducted in a Swiss high school, we adopted a social value approach to test the hypothesis that adolescent students' mastery goals do in fact predict learning, but only if these goals are perceived as highly useful for scholarly success (high social utility), and are not endorsed as a means to be appreciated by the teachers (low social desirability), a finding that has previously been observed among college students and on teacher-graded achievement measures only. Results demonstrate that in spite of potential peculiarities of an adolescent population, individual differences in mastery goals' perceived social utility and desirability moderate the mastery goal endorsement-learning achievement relation. Findings are discussed with regard to both theory development and educational practice.

Identifying Specific Cues and Contexts Related to Smoking Craving for the Development of Effective Virtual Environments

Craving is considered the main variable associated with relapse after smoking cessation. Cue Exposure Therapy (CET) consists of controlled and repeated exposure to drug-related cues with the aim of extinguishing craving responses. Some virtual reality (VR) environments, such as virtual bars or parties, have previously shown their efficacy as tools for eliciting smoking craving. However, in order to adapt this technology to smoking cessation interventions, there is a need for more diverse environments that enhance the probability of generalization of extinction in real life. The main objective of this study was to identify frequent situations that produce smoking craving, as well as detecting specific craving cues in those contexts. Participants were 154 smokers who responded to an ad hoc self-administered inventory for assessing craving level in 12 different situations. Results showed that having a drink in a bar/pub at night, after having lunch/dinner in a restaurant and having a coffee in a cafe or after lunch/dinner at home were reported as the most craving-inducing scenarios. Some differences were found with regard to participants' gender, age, and number of cigarettes smoked per day. Females, younger people, and heavier smokers reported higher levels of craving in most situations. In general, the most widely cited specific cues across the contexts were people smoking, having a coffee, being with friends, and having finished eating. These results are discussed with a view to their consideration in the design of valid and reliable VR environments that could be used in the treatment of nicotine addicts who wish to give up smoking.

Self, mémoire épisodique et narration chez l'enfant de 6 à 9 ans

Le self est une notion polysémique qui fait l'objet d'un consensus relatif dans plusieurs domaines, dont la psychologie du développement. Elle rend compte de la faculté de s'éprouver le même au fil du temps et de distinguer le « je » qui regarde du « moi » regardé. C'est le garant d'un sens de soi plus ou moins cohérent au fil du temps, en dépit des changements qui surviennent au cours de la vie. Le self combine des processus de réflexivité et d'intersubjectivité. Nous en avons analysé trois composantes fonctionnelles : la mémoire de travail, la mémoire épisodique et la narration, à partir d'un protocole expérimental témoignant de son ontogenèse chez des enfants de 6 à 9 ans (n=24 répartis en deux groupes de 6‐7 et 8-9 ans). Nous avons créé le « jeu informatique du lutin » qui propose un parcours semiorienté dans un monde imaginaire. C'est une narration de soi, opérant la mise en sens des temporalités et des espaces auxquels les événements se réfèrent. Deux semaines après cette « aventure », on recueille la narration des souvenirs épisodiques de cette histoire. Nous avons également utilisé un test de mémoire de travail visuospatiale non verbale. Des différences développementales affectent les dimensions narratives de la mémoire de l'épisode du jeu, comme l'efficacité de la mémoire de travail visuospatiale. Ces développements témoignent d'une augmentation de « l'épaisseur temporelle de la conscience» entre 6 et 9 ans. L'épaisseur de la conscience renvoie fondamentalement à la faculté du self de vivre le temps dans une cyclicité incluant le passé, le présent et le futur anticipé. Le développment observé élargit les possibilités de mettre en lien des mémoires et des scénarios futurs, tout comme les mises en sens des relations aux autres et à soi-­même. Self is a polysemic concept of common use in various scientific fields, among which developmental psychology. It accounts for the capacity to maintain the conviction to be « oneself », always the same through circumstances and throughout my life. This important function contributes in maintaining coherence and some sorte of Ariadne's thread in memory. To analyse the ontogeny of the self, we have focused upon three components : working memory, episodic memory and narration in children aged between 6 and 9 years. We used a non verbal working memory task. It was completed by a video game specially designed for our purpose, in which children were engaged in moving an elf in a landscape changing through seasons, in order to deliver a princess from a mischievous wizard. Two weeks after the game, the children had to tell what happened while they moved the elf. It is a self-narrative that creates a link‐up of temporality and spaces to which the events refer. The narrated episode was assessed for its coherence and continuity dimensions. Developmental differences affect the narrative dimensions of the memory of the episode of the game, as the effectiveness of visuospatial working memory. These developments show an increase in "temporal thickness of consciousness" between 6 and 9 years. The thickness of consciousness basically refers to the ability of the self to live in a cyclical time including past, present and anticipated future. The observed development broadens the possibilities to link memories and future scenarios, like setting sense of relations with others and with oneself.

The personal research portal : web 2.0 driven individual commitment with open access for development

Peer-reviewed

Health-related quality of life in the Cambridge City over-75s Cohort (CC75C): development of a dementia-specific scale and descriptive analyses.

BACKGROUND: The assessment of Health Related Quality of Life (HRQL) is important in people with dementia as it could influence their care and support plan. Many studies on dementia do not specifically set out to measure dementia-specific HRQL but do include related items. The aim of this study is to explore the distribution of HRQL by functional and socio-demographic variables in a population-based setting. METHODS: Domains of DEMQOL's conceptual framework were mapped in the Cambridge City over 75's Cohort (CC75C) Study. HRQL was estimated in 110 participants aged 80+ years with a confirmed diagnosis of dementia with mild/moderate severity. Acceptability (missing values and normality of the total score), internal consistency (Cronbach's alpha), convergent, discriminant and known group differences validity (Spearman correlations, Wilcoxon Mann-Whitney and Kruskal-Wallis tests) were assessed. The distribution of HRQL by socio-demographic and functional descriptors was explored. RESULTS: The HRQL score ranged from 0 to 16 and showed an internal consistency Alpha of 0.74. Validity of the instrument was found to be acceptable. Men had higher HRQL than women. Marital status had a greater effect on HRQL for men than it did for women. The HRQL of those with good self-reported health was higher than those with fair/poor self-reported health. HRQL was not associated with dementia severity. CONCLUSIONS: To our knowledge this is the first study to examine the distribution of dementia-specific HRQL in a population sample of the very old. We have mapped an existing conceptual framework of dementia specific HRQL onto an existing study and demonstrated the feasibility of this approach. Findings in this study suggest that whereas there is big emphasis in dementia severity, characteristics such as gender should be taken into account when assessing and implementing programmes to improve HRQL.

Development of an instrument to measure the degree of critical patient's satisfaction with nursing care: research protocol

Aim: To investigate and understand patient's satisfaction with nursing care in the intensive care unit to identify the dimensions of the concept of"satisfaction" from the patient's point of view. To design and validate a questionnaire that measures satisfaction levels in critical patients. Background: There are many instruments capable of measuring satisfaction with nursing care; however, they do not address the reality for critical patients nor are they applicable in our context. Design: A dual approach study comprising: a qualitative phase employing Grounded Theory and a quantitative and descriptive phase to prepare and validate the questionnaire. Methods: Data collection in the qualitative phase will consist of: in-depth interview after theoretical sampling, on-site diary and expert discussion group. The sample size will depend on the expected theoretical saturation n = 27-36. Analysis will be based on Grounded Theory. For the quantitative phase, the sampling will be based on convenience (n = 200). A questionnaire will be designed on the basis of qualitative data. Descriptive and inferential statistics will be used. The validation will be developed on the basis of the validity of the content, the criteria of the construct and reliability of the instrument by the Cronbach's alpha and test-retest approach. Approval date for this protocol was November 2010. Discussion: Self-perceptions, beliefs, experiences, demographic, socio-cultural epistemological and political factors are determinants for satisfaction, and these should be taken into account when compiling a questionnaire on satisfaction with nursing care among critical patients.

A Development and Application of a Three-Dimensional Model for a CFB Gasifier

The developing energy markets and rising energy system costs have sparked the need to find new forms of energy production and increase the self-sufficiency of energy production. One alternative is gasification, whose principles have been known for decades, but it is only recently when the technology has become a true alternative. However, in order to meet the requirements of modern energy production methods, it is necessary to study the phenomenon thoroughly. In order to understand the gasification process better and optimize it from the viewpoint of ecology and energy efficiency, it is necessary to develop effective and reliable modeling tools for gasifiers. The main aims of this work have been to understand gasification as a process and furthermore to develop an existing three-dimensional circulating fluidized bed modeling tool for modeling of gasification. The model is applied to two gasification processes of 12 and 50 MWth. The results of modeling and measurements have been compared and subsequently reviewed. The work was done in co-operation with Lappeenranta University of Technology and Foster Wheeler Energia Oy.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Mental Well-being at Work. A Sign of a Healthy Organisation and a Necessary Precondition for Organisational Development

One of the aims of the study was to clarify the reliability and validity of the Job Diagnostic Survey (JDS) and the Eigenzustand (EZ) method as measures of the objective characteristics of work and short-term mental work load in the Finnish data. The reliability and validity were examined taking into consideration the theoretical backgrounds of the methods and the reliability of the measurements. The methods were used for finding out the preconditions for organisational development based on self-improvement and clarifying the impacts of working environment (organisational functioning and job characteristics) on a worker’s mental state and health. The influences were examined on a general level - regardless of individual personal or specific contextual factors. One aim was also to clarify how cognitions and emotions are intertwined and how they influence a person’s perception of the working environment. The data consisted of 15 blue-collar organisations in the public sector. The organisations were divided in target and comparison groups depending on the research frames. The data was collected by questionnaires by post. The exploratory and confirmatory factor analyses (Lisrel) were used as the main statistical methods in examining the structures of the methods and impacts between the variables. It was shown that it is possible for organisations to develop their working conditions themselves on specific preconditions. The advance of the development processes could be shown by the amount of the development activity as well as by the changes of the mental well-being (ability to act) and sick absenteeism of the personnel. It was found that the JDS and the EZ methods were reliable and valid measures in the Finnish data. It was shown that, in addition to the objective working environment (organisational functioning and job characteristics), also such a personal factor as selfesteem influences a person’s perception of mental work load. However, the influence did not seem to be direct. The importance of job satisfaction as a general indicator of perceived working conditions was emphasised. Emotional and cognitive factors were found to be functionally intertwined constituting a common factor. Organisational functioning and the characteristics of work had connections with a person’s health measured by sick absenteeism.

Competence in intensive and critical care nursing - development of a basic assessment scale for graduating nursing students

Intensive and critical care nursing is a speciality in its own right and with its own nature within the nursing profession. This speciality poses its own demands for nursing competencies. Intensive and critical care nursing is focused on severely ill patients and their significant others. The patients are comprehensively cared for, constantly monitored and their vital functions are sustained artificially. The main goal is to win time to cure the cause of the patient’s situation or illness. The purpose of this empirical study was i) to describe and define competence and competence requirements in intensive and critical care nursing, ii) to develop a basic measurement scale for competence assessment in intensive and critical care nursing for graduating nursing students, and iii) to describe and evaluate graduating nursing students’ basic competence in intensive and critical care nursing by seeking the reference basis of self-evaluated basic competence in intensive and critical care nursing from ICU nurses. However, the main focus of this study was on the outcomes of nursing education in this nursing speciality. The study was carried out in different phases: basic exploration of competence (phase 1 and 2), instrumentation of competence (phase 3) and evaluation of competence (phase 4). Phase 1 (n=130) evaluated graduating nursing students’ basic biological and physiological knowledge and skills for working in intensive and critical care with Basic Knowledge Assessment Tool version 5 (BKAT-5, Toth 2012). Phase 2 focused on defining competence in intensive and critical care nursing with the help of literature review (n=45 empirical studies) as well as competence requirements in intensive and critical care nursing with the help of experts (n=45 experts) in a Delphi study. In phase 3 the scale Intensive and Critical Care Nursing Competence Scale (ICCN-CS) was developed and tested twice (pilot test 1: n=18 students and n=12 nurses; pilot test 2: n=56 students and n=54 nurses). Finally, in phase 4, graduating nursing students’ competence was evaluated with ICCN-CS and BKAT version 7 (Toth 2012). In order to develop a valid assessment scale of competence for graduating nursing students and to evaluate and establish the competence of graduating nursing students, empirical data were retrieved at the same time from both graduating nursing students (n=139) and ICU nurses (n=431). Competence can be divided into clinical and general professional competence. It can be defined as a specific knowledge base, skill base, attitude and value base and experience base of nursing and the personal base of an intensive and critical care nurse. Personal base was excluded in this self-evaluation based scale. The ICCN-CS-1 consists of 144 items (6 sum variables). Finally, it became evident that the experience base of competence is not a suitable sum variable in holistic intensive and critical care competence scale for graduating nursing students because of their minor experience in this special nursing area. ICCN-CS-1 is a reliable and tolerably valid scale for use among graduating nursing students and ICU nurses Among students, basic competence of intensive and critical care nursing was self-rated as good by 69%, as excellent by 25% and as moderate by 6%. However, graduating nursing students’ basic biological and physiological knowledge and skills for working in intensive and critical care were poor. The students rated their clinical and professional competence as good, and their knowledge base and skill base as moderate. They gave slightly higher ratings for their knowledge base than skill base. Differences in basic competence emerged between graduating nursing students and ICU nurses. The students’ self-ratings of both their basic competence and clinical and professional competence were significantly lower than the nurses’ ratings. The students’ self-ratings of their knowledge and skill base were also statistically significantly lower than nurses’ ratings. However, both groups reported the same attitude and value base, which was excellent. The strongest factor explaining students’ conception of their competence was their experience of autonomy in nursing. Conclusions: Competence in intensive and critical care nursing is a multidimensional concept. Basic competence in intensive and critical care nursing can be measured with self-evaluation based scale but alongside should be used an objective evaluation method. Graduating nursing students’ basic competence in intensive and critical care nursing is good but their knowledge and skill base are moderate. Especially the biological and physiological knowledge base is poor. Therefore in future in intensive and critical care nursing education should be focused on both strengthening students’ biological and physiological knowledge base and on strengthening their overall skill base. Practical implications are presented for nursing education, practice and administration. In future, research should focus on education methods and contents, mentoring of clinical practice and orientation programmes as well as further development of the scale.

Self-Assessement Report for International Accreditation - Bachelor's and Master's degree programmes in Energy Technology

Self-Assessment Report was made for the accreditation of degree programmes in Energy Technology. The report includes the following items: the content,concept and implementation of of the degree programmes, the resources, the quality management and further development of the degree programmes.

Self-Assessment Report for International Accreditation - Bachelor’s and Master’s degree programmes in Environmental Technology

Ympäristötekniikan kandidaatin ja diplomi-insinöörin tutkinto-ohjelmien itsearviointiraportissa käsitellään tutkinto-ohjelmien osaamistavoitteita ja niiden saavuttamista. Raportissa käydään läpi myös käytössä olevat resurssit sekä tutkinto-ohjelmiin liittyviä tunnuslukuja. Itsearviointi on toteutettu kansainvälisen akkreditointijärjestön kriteerien mukaisesti (ASIIN ja EUR-ACE).

Professional development among educators pursuing a B.Ed. program in special education in Tanzania : a study of motives and perceived outcomes

Implementation of different policies and plans aiming at providing education for all is a challenge in Tanzania. The need for educators and professionals with relevant knowledge and qualifications in special education is substantial. Teacher education does not equip educators with sufficient knowledge and skills in special education and professional development programs in special education are few in number. Up to 2005 no degree programs in special education at university level were available in Tanzania. The B.Ed. Special Education program offered by the Open University of Tanzania in collaboration with Åbo Akademi University in Finland was one of the efforts aimed at addressing the big national need for teachers and other professionals with degree qualifications in special education. This pilot program offered unique possibilities to study professional development in Tanzania. The research group in this study consisted of the group of students who participated in the degree program 2005-2007. The study is guided by three theoretical perspectives: individual, social and societal. The individual perspective emphasizes psychological factors as motives, motivation, achievement, self-directed behavior and personal growth. Within social perspective, professional development is viewed as situated within the social and cultural context. The third perspective, the societal, focuses on change, reforms, innovations and transformation of school systems and societies. Accordingly, professional development is viewed as an individual, social and societal phenomenon. The overall aim of the study is to explore the participants’ motives for participating in a B.Ed. Special Education program and the perceived outcomes of the program in terms of professional development. In order to achieve the objectives of the study, a case study approach was adopted. Questionnaires and semi-structured interviews were administered in three waves between January 2007 and February 2009 to the 35 educators participating in the B.Ed. Special Education program. The findings of the study reveal that the participants expressed motives which were related to job performance, knowledge, skills, academic degree and career. Also altruistic motives were expressed by the participants in terms of helping and supporting students with special needs and their communities. The perceived outcomes of the program were in line with the expressed motives. However, the results indicate that the participants also learned new skills, as interaction skills and guidance and counseling skills. Increased self-confidence was also mentioned as an outcome. The participants also got deepened understanding of disability issues. In addition, they learned strategies for creating awareness of persons with disability in the communities. Thus the findings of the study indicate positive outcomes of the program in terms of professional development. The conclusion of the study is that individual, social and societal factors interact when it comes to explaining why Tanzanian educators in special education choose to pursue a degree program in special education. The individual motives, as increased knowledge and better prospects of career development interact with the social and societal motives to help and support vulnerable student groups. The study contributes to increased understanding of the complexity of professional development and of the realities educators meet when educational reforms are implemented in a developing country.