Syntes och analys av tidigare kravspecifikationer för upphandlingar av LMS inom den svenska högskolan 2000-2004

Högskolan i Borås gavs 2004-11-01 i uppdrag av Myndigheten för Sveriges nätuniversitet att sammanställa och analysera tidigare kravspecifikationer, framtagna av högskolor och universitet, i samband med LMS-upphandlingar (Learning Management System). Material har ställts till förfogande från Högskolan i Borås, Chalmers tekniska högskola, IT-universitetet i Göteborg, Karlstads universitet, Högskolan i Kristianstad, Luleå tekniska universitet, Malmö högskola, Umeå universitet samt Uppsala universitet. Målet med rapporten är att underlätta en nationell upphandling av en eller flera utbildningsplattformar inom den svenska högskolan och främja ett långvarigt erfarenhetsutbyte, inom den svenska högskolesektorn, rörande frågor knutna mot LMS/VLE (Virtual Learning Environment). Rapporten bygger på såväl kravspecifikationer som tidigare använts vid upphandlingar av LMS: s som sådana som är/var tänkta att ligga till grund för en framtida upphandling. Rapporten är utformad på ett sådant sätt att det skall vara möjligt att, med relativt små justeringar, använda materialet i ett gemensamt nationellt upphandlingsuppdrag. Det innebär att läsaren får ha en viss förståelse för hur framförallt kapitel tre, som är en sammanställning av olika krav, är uppbyggt. En uppdelning har gjorts i skall-krav och i bör-krav . De förstanämnda kraven måste ett system uppfylla för att över huvudtaget bli aktuellt i en upphandling, de senare är sådana som är önskvärda, men inte direkt tvingande. Vidare har varje krav åsatts ett visst viktningsvärde. Det skall noteras att olika lärosäten kan ha givit samma krav olika vikt, beroende på det enskilda lärosätets prioriteringar. Även om det utförs en syntes så bör det finnas en enkelhet i att på ett effektivt sätt kunna organisera alla variabler som ingår i en sådan syntes därav konstruktionen av ett system med en så kallad mall för ingående variabler. I syntesen har framförallt de senaste årens underlag använts. På grund av den expansiva teknikutvecklingen finns det brister i de tidigare underlagen. Inte på så sätt att dessa skulle vara undermåliga utan mer anpassade efter den teknik som fanns att tillgå i slutet av 1990-talet och i början av 2000-talet. Det går inte att bortse ifrån att många tidigare bör-krav numera är standard och därmed ett skall-krav

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

<p>Abstract</p> <p>Background</p> <p>The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either <it>hupW </it>or <it>hoxW</it>, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria <it>Nostoc punctiforme </it>ATCC 29133 and <it>Nostoc </it>sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively.</p> <p>Results</p> <p>In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of <it>hupW </it>in <it>Nostoc punctiforme </it>ATCC 29133 and <it>hupW </it>and <it>hoxW </it>in <it>Nostoc </it>sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (<it>hupW</it>) and LexA (<it>hoxW</it>). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase.</p> <p>Conclusion</p> <p>Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.</p

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120

<p>Abstract</p> <p>Background</p> <p>The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by <it>hypABCDEF </it>and a hydrogenase specific protease, encoded either by <it>hupW </it>or <it>hoxW</it>. The N₂-fixing cyanobacterium <it>Nostoc </it>sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of <it>hyp</it>-genes in <it>Nostoc </it>sp. strain PCC 7120.</p> <p>Results</p> <p>RT-PCRs demonstrated that the six <it>hyp</it>-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from <it>hypF </it>and 445 bp upstream of <it>hypC</it>, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between <it>hupSL</it>, encoding the small and large subunits of the uptake hydrogenase, and the <it>hyp</it>-operon, and two downstream ORFs from the <it>hyp</it>-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between <it>hupSL</it>, and the <it>hyp </it>genes are found in several other N₂-fixing cyanobacteria, but are absent in non N₂-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended <it>hyp</it>-operon, appearing between 11 and 79 times in the genome.</p> <p>Conclusion</p> <p>This study demonstrated that five ORFs upstream of the <it>hyp</it>-gene cluster are co-transcribed with the <it>hyp</it>-genes, and identified three TSPs in the extended <it>hyp</it>-gene cluster in <it>Nostoc </it>sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.</p

Validity of Stokes-Einstein Relation in Soft Colloids up to the Glass Transition

We investigate the dynamics of kinetically frozen block copolymer micelles of different softness across a wide range of particle concentrations, from the fluid to the onset of glassy behavior, through a combination of rheology, dynamic light scattering and pulsed field gradient NMR spectroscopy. We additionally perform Brownian dynamics simulations based on an ultrasoft coarse-grained potential, which are found to be in quantitative agreement with experiments, capturing even the very details of dynamic structure factors S(Q, t) on approaching the glass transition. We provide evidence that for these systems the Stokes-Einstein relation holds up to the glass transition; given that it is violated for dense suspensions of hard colloids, our findings suggest that its validity is an intriguing signature of ultrasoft interactions.Comment: 5 pages, 4 figures, Supplementary Information, Accepted to Physical Review Letters (PRL) (2015

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, fc(q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of fc(q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with fc(q, t), there is indication of long-time exponential decay of fc(q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of fc(q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for fc(q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, fs(q, t), and its non-Gaussian parameter α2(t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from fc(q, t) is theoretically validated.Fil: Banchio, Adolfo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; ArgentinaFil: Heinen, Marco. Universidad de Guanajuato; MéxicoFil: Holmqvist, Peter. Lund University; SueciaFil: Nägele, Gerhard. Universitat Dusseldorf; Alemania. Helmholtz Gemeinschaft. Forschungszentrum Jülich; Alemani

Characterization of the hupSL promoter activity in Nostoc punctiforme ATCC 29133

<p>Abstract</p> <p>Background</p> <p>In cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, H₂, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures H₂and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce H₂.<it>Nostoc punctiforme </it>ATCC 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. Generally, little is known about the transcriptional regulation of the cyanobacterial uptake hydrogenases. In this study gel shift assays showed that NtcA has a specific affinity to a region of the <it>hupSL </it>promoter containing a predicted NtcA binding site. The predicted NtcA binding site is centred at 258.5 bp upstream the transcription start point (tsp). To further investigate the <it>hupSL </it>promoter, truncated versions of the <it>hupSL </it>promoter were fused to either <it>gfp </it>or <it>luxAB</it>, encoding the reporter proteins Green Fluorescent Protein and Luciferase, respectively.</p> <p>Results</p> <p>Interestingly, all <it>hupsSL </it>promoter deletion constructs showed heterocyst specific expression. Unexpectedly the shortest promoter fragment, a fragment covering 57 bp upstream and 258 bp downstream the tsp, exhibited the highest promoter activity. Deletion of the NtcA binding site neither affected the expression to any larger extent nor the heterocyst specificity.</p> <p>Conclusion</p> <p>Obtained data suggest that the <it>hupSL </it>promoter in <it>N. punctiforme </it>is not strictly dependent on the upstream NtcA cis element and that the shortest promoter fragment (-57 to tsp) is enough for a high and heterocyst specific expression of <it>hupSL</it>. This is highly interesting because it indicates that the information that determines heterocyst specific gene expression might be confined to this short sequence or in the downstream untranslated leader sequence.</p

Nematic-Isotropic Spinodal Decomposition Kinetics of Rod-like Viruses

We investigate spinodal decomposition kinetics of an initially nematic dispersion of rod-like viruses (fd virus). Quench experiments are performed from a flow-stabilized homogeneous nematic state at high shear rate into the two-phase isotropic-nematic coexistence region at zero shear rate. We present experimental evidence that spinodal decomposition is driven by orientational diffusion, in accordance with a very recent theory.Comment: 17 pages, 6 figures, accepted in Phys. Rev.

Design and control of chromatography step in an integrated column sequence

Integration of the purification steps in downstream processing is one way to minimize the number of storage tanks and reduce hold-up time. The result is an integrated column sequence that performs straight through processing of the target protein, with minimal time from expression to formulation. This paper discusses the overall integration design and its expected performance, together with a more detailed analysis of the step behavior based on column simulations. The optimal design of the individual steps in the sequence is presented, both with robustness margins and local control system, as well as with and without local recycle. An optimization methodology for chromatography steps is used to quantify the performance of the integrated sequence. The propagation of disturbances in connected column sequences forces an open-loop control strategy to be unnecessary conservative. The optimization is modified to also handle disturbances which makes it possible to find the robust optimum. The introduction of local control for disturbance compensation and for guarantee of optimal robust performance is shown for transient control of the dynamic cyclic steady-state. For some separation problems, it is attractive to introduce local recycles in the process, such as in MCSGP, to enhance the yield of the target protein. These recycles are also introduced in the optimization methodology of separation steps in integrated column sequences, generating optimal robust solutions with recycles. The result shows the advantages and disadvantages of local recycles for the case study analyzed in the work

Conveying clinical reasoning based on visual observation via eye-movement modelling examples

Jarodzka, H., Balslev, T., Holmqvist, K., Nyström, M., Scheiter, K., Gerjets, P., & Eika, B. (2012). Conveying clinical reasoning based on visual observation via eye-movement modelling examples. Instructional Science, 40(5), 813-827. doi:10.1007/s11251-012-9218-5Complex perceptual tasks, like clinical reasoning based on visual observations of patients, require not only conceptual knowledge about diagnostic classes but also the skills to visually search for symptoms and interpret these observations. However, medical education so far has focused very little on how visual observation skills can be efficiently conveyed to novices. The current study applied a novel instructional method to teach these skills by showing the learners how an expert model visually searches and interprets symptoms (i.e., eye-movement modelling examples; EMMEs). Case videos of patients were verbally explained by a model (control condition) and presented to students. In the experimental conditions, the participants received a recording of the model’s eye movements superimposed on the case videos. The eye movements were displayed by either highlighting the features the model focused on with a circle (the circle condition) or by blurring the features the model did not focus on (the spotlight condition). Compared to the other two conditions, results show that a spotlight on the case videos better guides the students’ attention towards the relevant features. Moreover, when testing the students’ clinical reasoning skills with videos of new patient cases without any guidance participants studying EMMEs with a spotlight showed improved their visual search and enhanced interpretation performance of the symptoms in contrast to participants in either the circle or the control condition. These findings show that a spotlight EMME can successfully convey clinical reasoning based on visual observations