GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Separation and Execution of graphical engine on a cross platform IDE to enhance performance

“Biosim” is a simulation software which works to simulate the harvesting system.This system is able to design a model for any logistic problem with the combination of several objects so that the artificial system can show the performance of an individual model. The system will also describe the efficiency, possibility to be chosen for real life application of that particular model. So, when any one wish to setup a logistic model like- harvesting system, in real life he/she may be noticed about the suitable prostitution for his plants and factories as well as he/she may get information about the least number of objects, total time to complete the task, total investment required for his model, total amount of noise produced for his establishment in advance. It will produce an advance over view for his model. But “Biosim” is quite slow .As it is an object based system, it takes long time to make its decision. Here the main task is to modify the system so that it can work faster than the previous. So, the main objective of this thesis is to reduce the load of “Biosim” by making some modification of the original system as well as to increase its efficiency. So that the whole system will be faster than the previous one and performs more efficiently when it will be applied in real life. Theconcept is to separate the execution part of ”Biosim” form its graphical engine and run this separated portion in a third generation language platform. C++ is chosenhere as this external platform. After completing the proposed system, results with different models have been observed. The results show that, for any type of plants of fields, for any number of trucks, the proposed system is faster than the original system. The proposed system takes at least 15% less time “Biosim”. The efficiency increase with the complexity of than the original the model. More complex the model, more efficient the proposed system is than original “Biosim”.Depending on the complexity of a model, the proposed system can be 56.53 % faster than the original “Biosim”.

IT support for administrative planning of clinical practice.

The administration of clinical practice placements for nursing students is a highly complex and information driven task. This demonstration is intended to give insight into the web based system KliPP (a Swedish acronym for Clinical Practice Planning) and to discuss the possibilities for further development and use.

Akademisk kvalitet, vad är det? : Om utarmningen av den akademiska autonomin

What is academic quality? On the decline of academic autonomy In light of the transformations that universities currently undergo, with Bologna as a keyword, the following questions are put: What ideals lie behind the assessment of academic “excellence” and “quality”? What agents have the ability to define what is good science and education today? These questions are approached through Pierre Bourdieus concept of field. Looking at the development the last decade, traditional academic values, such as the ideal of universal knowledge as (personal and collective) enrichment and the intellectual independence “of all political authority and economic power”, as stated in the Magna Charta Universitatum, seem to have emerged into the shadow of employability, knowledge control, competitiveness, and economic benefit. In connection with the formation of concepts such as “the knowledge society” and “knowledge based economies” the university has received a somewhat different and more central role in society. The university has come to take the role more of a knowledge producing enterprise clearly directed towards the surrounding society. There are higher demands on academic knowledge to contribute to economic, regional or national development and competitiveness. When the university is regarded as a knowledge company whose task is to accoun tfor the requests of the students, the labour market, and the business world it undertakes to follow trends and short term social phases rather than to critically examine them, which has been a traditional task for the university. If the academic work is guided by the market economical principle, that the client requests decide what quality is, instead of the experts on the academic field themselves (i.e. the scientists,) it is obviously not scientific ideals that constitute the criteria for what is good science and education.

Narration in Swedish pre- and primary school : a recourse for language development and multilingualism

Increased immigration in Europe and worldwide has led to more pre- and primary school students being educated through the medium of a second language, and there is considerable research, much of it coming from Australia, to suggest that in order to cope with this situation, children will need to begin to acquire, from their earliest years in pre-school, a variety of knowledge-based language skills that will be sufficient to carry them through the subject-based education they will encounter in their subsequent schooling. This is particularly important for L2-students who are less likely to meet academic language outside the school. In this paper, based on transcripts of oral interactions in the classroom, it is argued that conversational and story-telling skills, oral and written, provide a rich environment for the development of academic school language, while at the same time promoting and making good use of the cultural diversity that is increasingly a feature of pre-primary and primary classrooms.

A web application for follow-up of results from a mobile device test battery for parkinson’s disease patients

Background: A test battery consisting of self-assessments and motor tests (tapping and spiral drawing) was developed for a hand computer with touch screen in a telemedicine setting. Objectives: To develop and evaluate a web-based system that delivers decision support information to the treating clinical staff for assessing PD symptoms in their patients based on the test battery data. Methods: The test battery is currently being used in a clinical trial (DAPHNE, EudraCT No. 2005-002654-21) by sixty five patients with advanced Parkinson’s disease (PD) on 9991 test occasions (four tests per day during in all 362 week-long test periods) at nine clinics around Sweden. Test results are sent continuously from the hand unit over a mobile net to a central computer and processed with statistical methods. They are summarized into scores for different dimensions of the symptom state and an ‘overall test score’ reflecting the overall condition of the patient during a test period. The information in the web application is organized and presented graphically in a way that the general overview of the patient performance per test period is emphasized. Focus is on the overall test score, symptom dimensions and daily summaries. In a recent preliminary user evaluation, the web application was demonstrated to the fifteen study nurses who had used the test battery in the clinical trial. At least one patient per clinic was shown. Results: In general, the responses from nurses were positive. They claimed that the test results shown in the system were consistent with their own clinical observations. They could follow complications, changes and trends within their patients. Discussion: In conclusion, the system is able to summarise the various time series of motor test results and self-assessments during test periods and present them in a useful manner. Its main contribution is a novel and reliable way to capture and easily access symptom information from patients’ home environment. The convenient access to current symptom profile as well as symptom history provides a basis for individualized evaluation and adjustment of treatments.

Mobile systems for monitoring Parkinson's disease

A challenge for the clinical management of Parkinson's disease (PD) is the large within- and between-patient variability in symptom profiles as well as the emergence of motor complications which represent a significant source of disability in patients. This thesis deals with the development and evaluation of methods and systems for supporting the management of PD by using repeated measures, consisting of subjective assessments of symptoms and objective assessments of motor function through fine motor tests (spirography and tapping), collected by means of a telemetry touch screen device. One aim of the thesis was to develop methods for objective quantification and analysis of the severity of motor impairments being represented in spiral drawings and tapping results. This was accomplished by first quantifying the digitized movement data with time series analysis and then using them in data-driven modelling for automating the process of assessment of symptom severity. The objective measures were then analysed with respect to subjective assessments of motor conditions. Another aim was to develop a method for providing comparable information content as clinical rating scales by combining subjective and objective measures into composite scores, using time series analysis and data-driven methods. The scores represent six symptom dimensions and an overall test score for reflecting the global health condition of the patient. In addition, the thesis presents the development of a web-based system for providing a visual representation of symptoms over time allowing clinicians to remotely monitor the symptom profiles of their patients. The quality of the methods was assessed by reporting different metrics of validity, reliability and sensitivity to treatment interventions and natural PD progression over time. Results from two studies demonstrated that the methods developed for the fine motor tests had good metrics indicating that they are appropriate to quantitatively and objectively assess the severity of motor impairments of PD patients. The fine motor tests captured different symptoms; spiral drawing impairment and tapping accuracy related to dyskinesias (involuntary movements) whereas tapping speed related to bradykinesia (slowness of movements). A longitudinal data analysis indicated that the six symptom dimensions and the overall test score contained important elements of information of the clinical scales and can be used to measure effects of PD treatment interventions and disease progression. A usability evaluation of the web-based system showed that the information presented in the system was comparable to qualitative clinical observations and the system was recognized as a tool that will assist in the management of patients.

Kravsammanställning samt utvärdering avbildvisningsprogramför diagnostik inom telepatologi : En fallstudiemed SIV-metoden som tillvägagångssätt

De flesta har i sin närhet någon som drabbats av cancer och sjukdomsfallen har ökat genom åren. Den yrkesgrupp som ställer diagnos av denna sjukdom är patologer. Bristen på patologer är idagsläget stor och det finns därför ett behov av att finna effektiva lösningar för att möta denna brist och en ökande mängd patienter. För att digitalisera vävnadsproven som diagnostiseras, scannas dessa in med en glasscanner. Dessa digitala bildfiler kan sedan visas i ett bildvisningsprogram och delas digitalt mellan patologer på distans. Detta begrepp kallas för telepatologi. Studien utgår utifrån följande frågeställningar: Vilka krav är väsentliga och bör ingå i en utvärdering för bildvisningsprogram avsedda för diagnostik inom telepatologi? Vilket bildvisningsprogram är mest lämpat att implementeras i ett webbaserat system baserat på dessa väsentliga krav? Syftet med studien är att undersöka vilka krav som är väsentliga och bör ingå i en utvärdering av bildvisningsprogram avsedda för diagnostik inom telepatologi, samt att utföra en utvärdering av ett urval bildvisningsprogramvaror med hjälp av dessa krav. En fallstudie genomfördes med datainsamlingsmetoderna: intervjuer med två personer från studiens samarbetspartner CGM, Frågeformulär där Sveriges patologer var respondenter samt dokumentstudier för att samla in information gällande bildvisningsprogrammen. Studien tillämpar utvalda delar ur Anders G. Nilssons SIV-metod som tillvägagångsätt för att samla in krav samt för att göra ett urval av bildvisningsprogram som sedan utvärderas gentemot dessa krav. Resultaten av datainsamlingarna analyserades och ledde till ett kravdokument med väsentliga krav.Tre så kallade utslagsgivande faktorer bland dessa krav var att bildvisningsprogrammet måste vara webbaserat utan installation på klient, funktioner för in- och ut-zoomning samt panorering måste finnas. Utvärderingen av utvalda bildvisningsprogram visade slutligen att OpenSlide var mest lämpad att implementeras i ett webbaserat system.

Automatic and objective assessment of alternating tapping performance in Parkinson’s disease

This paper presents the development and evaluation of a method for enabling quantitative and automatic scoring of alternating tapping performance of patients with Parkinson’s disease (PD). Ten healthy elderly subjects and 95 patients in different clinical stages of PD have utilized a touch-pad handheld computer to perform alternate tapping tests in their home environments. First, a neurologist used a web-based system to visually assess impairments in four tapping dimensions (‘speed’, ‘accuracy’, ‘fatigue’ and ‘arrhythmia’) and a global tapping severity (GTS). Second, tapping signals were processed with time series analysis and statistical methods to derive 24 quantitative parameters. Third, principal component analysis was used to reduce the dimensions of these parameters and to obtain scores for the four dimensions. Finally, a logistic regression classifier was trained using a 10-fold stratified cross-validation to map the reduced parameters to the corresponding visually assessed GTS scores. Results showed that the computed scores correlated well to visually assessed scores and were significantly different across Unified Parkinson’s Disease Rating Scale scores of upper limb motor performance. In addition, they had good internal consistency, had good ability to discriminate between healthy elderly and patients in different disease stages, had good sensitivity to treatment interventions and could reflect the natural disease progression over time. In conclusion, the automatic method can be useful to objectively assess the tapping performance of PD patients and can be included in telemedicine tools for remote monitoring of tapping.

Evaluation of a thermally driven heat pump for solar heating and cooling applications

Exploiting solar energy technology for both heating and cooling purposes has the potential of meeting an appreciable portion of the energy demand in buildings throughout the year. By developing an integrated, multi-purpose solar energy system, that can operate all twelve months of the year, a high utilisation factor can be achieved which translates to more economical systems. However, there are still some techno-economic barriers to the general commercialisation and market penetration of such technologies. These are associated with high system and installation costs, significant system complexity, and lack of knowledge of system implementation and expected performance. A sorption heat pump module that can be integrated directly into a solar thermal collector has thus been developed in order to tackle the aforementioned market barriers. This has been designed for the development of cost-effective pre-engineered solar energy system kits that can provide both heating and cooling. This thesis summarises the characterisation studies of the operation of individual sorption modules, sorption module integrated solar collectors and a full solar heating and cooling system employing sorption module integrated collectors. Key performance indicators for the individual sorption modules showed cooling delivery for 6 hours at an average power of 40 W and a temperature lift of 21°C. Upon integration of the sorption modules into a solar collector, measured solar radiation energy to cooling energy conversion efficiencies (solar cooling COP) were between 0.10 and 0.25 with average cooling powers between 90 and 200 W/m2 collector aperture area. Further investigations of the sorption module integrated collectors implementation in a full solar heating and cooling system yielded electrical cooling COP ranging from 1.7 to 12.6 with an average of 10.6 for the test period. Additionally, simulations were performed to determine system energy and cost saving potential for various system sizes over a full year of operation for a 140 m2 single-family dwelling located in Madrid, Spain. Simulations yielded an annual solar fraction of 42% and potential cost savings of €386 per annum for a solar heating and cooling installation employing 20m2 of sorption integrated collectors.

När det inte blir som man har tänkt sig : - En fallstudie av undervisningssituationer med elever med behov av särskilt stöd

Fallstudien beskriver och diskuterar några lektioner med elever som har specifika inlärnings-svårigheter, utifrån skolverkets Allmänna råd, och belyser vilka pedagogiskt svårhanterliga problem och dilemman som kan uppstå när det inte blir som läraren har planerat. Teorin om den proximala utvecklingszonen åskådliggörs. Aktivitetens betydelse för inlärning belyses. Komplexiteten kring lärarskap och ledarskap illustreras. Skolverkets teori om kunskap genom progression, enligt givna årskurser med givet innehåll, stämmer inte alltid med erfarenheterna hos några av verklighetens elever. Samspelet mellan lärare och elever belyses i studien. Be-skrivningar av utvecklingsrelaterade funktionsnedsättningar och psykiskt sårbara barn visar ytterligare hur elevers individuella förutsättningar kan ge konsekvenser för inlärning.

Designing Agent-Oriented Systems by Analysing Agent Interactions

We propose a preliminary methodology for agent-oriented software engineering based on the idea of agent interaction analysis. This approach uses interactions between undetermined agents as the primary component of analysis and design. Agents as a basis for software engineering are useful because they provide a powerful and intuitive abstraction which can increase the comprehensiblity of a complex design. The paper describes a process by which the designer can derive the interactions that can occur in a system satisfying the given requirements and use them to design the structure of an agent-based system, including the identification of the agents themselves. We suggest that this approach has the flexibility necessary to provide agent-oriented designs for open and complex applications, and has value for future maintenance and extension of these systems.

Granularity and disaggregation in compositional modelling with applications to ecological systems

In the past decade, compositional modelling (CM) has established itself as the predominant knowledge-based approach to construct mathematical (simulation) models automatically. Although it is mainly applied to physical systems, there is a growing interest in applying CM to other domains, such as ecological and socio-economic systems. Inspired by this observation, this paper presents a method for extending the conventional CM techniques to suit systems that are fundamentally presented by interacting populations of individuals instead of physical components or processes. The work supports building model repositories for such systems, especially in addressing the most critical outstanding issues of granularity and disaggregation in ecological systems modelling.

On Arbitrary Selection Strategies for Basic Superposition

For first-order Horn clauses without equality, resolution is complete with an arbitrary selection of a single literal in each clause [dN 96]. Here we extend this result to the case of clauses with equality for superposition-based inference systems. Our result is a generalization of the result given in [BG 01]. We answer their question about the completeness of a superposition-based system for general clauses with an arbitrary selection strategy, provided there exists a refutation without applications of the factoring inference rule.

Determining the Trustworthiness of New Electronic Contracts

Expressing contractual agreements electronically potentially allows agents to automatically perform functions surrounding contract use: establishment, fulfilment, renegotiation etc. For such automation to be used for real business concerns, there needs to be a high level of trust in the agent-based system. While there has been much research on simulating trust between agents, there are areas where such trust is harder to establish. In particular, contract proposals may come from parties that an agent has had no prior interaction with and, in competitive business-to-business environments, little reputation information may be available. In human practice, trust in a proposed contract is determined in part from the content of the proposal itself, and the similarity of the content to that of prior contracts, executed to varying degrees of success. In this paper, we argue that such analysis is also appropriate in automated systems, and to provide it we need systems to record salient details of prior contract use and algorithms for assessing proposals on their content. We use provenance technology to provide the former and detail algorithms for measuring contract success and similarity for the latter, applying them to an aerospace case study.