Building an Academic Cloud for 500,000 Users

Under the brand name “sciebo – the Campuscloud” (derived from “science box”) a consortium of more than 20 research and applied science universities started a large scale cloud service for about 500,000 students and researchers in North Rhine-Westphalia, Germany’s most populous state. Starting with the much anticipated data privacy compliant sync & share functionality, sciebo offers the potential to become a more general cloud platform for collaboration and research data management which will be actively pursued in upcoming scientific and infrastructural projects. This project report describes the formation of the venture, its targets and the technical and the legal solution as well as the current status and the next steps.

J-Quizmaker

Lehrvideos erfreuen sich dank aktueller Entwicklungen im Bereich der Online-Lehre (Videoplattformen, MOOCs) auf der einen Seite und einer riesigen Auswahl sowie einer einfachen Produktion und Distribution auf der anderen Seite großer Beliebtheit bei der Wissensvermittlung. Trotzdem bringen Videos einen entscheidenden Nachteil mit sich, welcher in der Natur des Datenformats liegt. So sind die Suche nach konkreten Sachverhalten in einem Video sowie die semantische Aufbereitung zur automatisierten Verknüpfung mit weiteren spezifischen Inhalten mit hohem Aufwand verbunden. Daher werden die lernerfolg-orientierte Selektion von Lehrsegmenten und ihr Arrangement zur auf Lernprozesse abgestimmten Steuerung gehemmt. Beim Betrachten des Videos werden unter Umständen bereits bekannte Sachverhalte wiederholt bzw. können nur durch aufwendiges manuelles Spulen übersprungen werden. Selbiges Problem besteht auch bei der gezielten Wiederholung von Videoabschnitten. Als Lösung dieses Problems wird eine Webapplikation vorgestellt, welche die semantische Aufbereitung von Videos hin zu adaptiven Lehrinhalten ermöglicht: mittels Integration von Selbsttestaufgaben mit definierten Folgeaktionen können auf Basis des aktuellen Nutzerwissens Videoabschnitte automatisiert übersprungen oder wiederholt und externe Inhalte verlinkt werden. Der präsentierte Ansatz basiert somit auf einer Erweiterung der behavioristischen Lerntheorie der Verzweigten Lehrprogramme nach Crowder, die auf den Lernverlauf angepasste Sequenzen von Lerneinheiten beinhaltet. Gleichzeitig werden mittels regelmäßig eingeschobener Selbsttestaufgaben Motivation sowie Aufmerksamkeit des Lernenden nach Regeln der Programmierten Unterweisung nach Skinner und Verstärkungstheorie gefördert. Durch explizite Auszeichnung zusammengehöriger Abschnitte in Videos können zusätzlich die enthaltenden Informationen maschinenlesbar gestaltet werden, sodass weitere Möglichkeiten zum Auffinden und Verknüpfen von Lerninhalten geschaffen werden.

Extraktion und kartographische Visualisierung von Informationen aus Weblogs

Beim Information Retrieval ist in Anbetracht der Informationsflut entscheidend, relevante Informationen zu finden. Ein vielversprechender Ansatz liegt im Semantischen Web, wobei dem System die Bedeutung von Informationen ontologiebasiert beigebracht wird. Sucht der Benutzer nach Stichworten, werden ihm anhand der Ontologie verwandte Begriffe angezeigt und er kann mittels Mensch-Maschine-Interaktion seine relevanten Informationen extrahieren. Um eine solche Interaktion zu fördern, werden die Ergebnisse visuell aufgearbeitet. Dabei liegt der Mehrwert darin, dass der Benutzer anstelle von Tausenden von Suchresultaten in einer fast endlosen Liste, ein kartographisch visualisiertes Suchresultat geliefert bekommt. Dabei hilft die Visualisierung, unvorhergesehene Beziehungen zu entdecken und zu erforschen.

Geschichte und Trends im IR

Diese Seminararbeit wurde im Rahmen des Seminars Angewandtes Information Retrievalgeschrieben und beschäftigt sich mit der Geschichte der Daten, der Internetgeschichte und dem untrennbar dazugehörenden Information Retrieval, welches als Wiedergewinnung vonbereits zur Verfügung stehenden Daten gesehen werden kann.In einem ersten Teil befasst sich diese Arbeit mit der Geschichte der menschlichen Daten-sammlung und Speicherung. Hier wird die Geschichte von den Anfängen der Datensammlungbis hin zur heutigen digitalen Zeit durchlaufen.Im zweiten Teil werden die Evolution und Funktionsweise verschiedener Systeme vorgestellt,wobei eine Trennung vorgenommen wird in die Geschichte des Information Retrieval, alsAntwort auf die Datenmengen, welche durch die Evolution hervorgebracht wurde, und dannwird auf heutige Trends des Information Retrievals eingegangen. Hierbei werde ich nocheinmal die grundlegenden Probleme der Informationssuche aufzeigen und die aktuellen For-schungen in diesem Gebiet erwähnen.Danach wird ein Fazit gezogen und kritisch Stellung bezüglich der aktuellen Trends einge-nommen. In meinem Schlusswort gebe ich meine Vision einer Suchmaschine wieder, wiediese in Zukunft aussehen könnte

Pilot Project: Use of Wikis to Supplement Student Orientation

Background: During the orientation process, new students are often inundated with manuals, maps, and other materials essential to their success as students. The experience can leave students feeling overwhelmed, unable to sift through the substantial amount of information that has been given to them. Wikis, in contrast, are well-suited for facilitating userinteraction with vast amounts of diverse information. [See PDF for complete abstract]

A day in the life of PubMed: analysis of a typical day's query log.

OBJECTIVE: To characterize PubMed usage over a typical day and compare it to previous studies of user behavior on Web search engines. DESIGN: We performed a lexical and semantic analysis of 2,689,166 queries issued on PubMed over 24 consecutive hours on a typical day. MEASUREMENTS: We measured the number of queries, number of distinct users, queries per user, terms per query, common terms, Boolean operator use, common phrases, result set size, MeSH categories, used semantic measurements to group queries into sessions, and studied the addition and removal of terms from consecutive queries to gauge search strategies. RESULTS: The size of the result sets from a sample of queries showed a bimodal distribution, with peaks at approximately 3 and 100 results, suggesting that a large group of queries was tightly focused and another was broad. Like Web search engine sessions, most PubMed sessions consisted of a single query. However, PubMed queries contained more terms. CONCLUSION: PubMed's usage profile should be considered when educating users, building user interfaces, and developing future biomedical information retrieval systems.

U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3' end processing

The 3' cleavage generating non-polyadenylated animal histone mRNAs depends on the base pairing between U7 snRNA and a conserved histone pre-mRNA downstream element. This interaction is enhanced by a 100 kDa zinc finger protein (ZFP100) that forms a bridge between an RNA hairpin element upstream of the processing site and the U7 small nuclear ribonucleoprotein (snRNP). The N-terminus of Lsm11, a U7-specific Sm-like protein, was shown to be crucial for histone RNA processing and to bind ZFP100. By further analysing these two functions of Lsm11, we find that Lsm11 and ZFP100 can undergo two interactions, i.e. between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and between the N-terminus of ZFP100 and the Sm domain of Lsm11, respectively. Both interactions are not specific for the two proteins in vitro, but the second interaction is sufficient for a specific recognition of the U7 snRNP by ZFP100 in cell extracts. Furthermore, clustered point mutations in three phylogenetically conserved regions of the Lsm11 N-terminus impair or abolish histone RNA processing. As these mutations have no effect on the two interactions with ZFP100, these protein regions must play other roles in histone RNA processing, e.g. by contacting the pre-mRNA or additional processing factors.

Molecular beacons with a homo-DNA stem: improving target selectivity

Molecular beacons (MBs) are stem-loop DNA probes used for identifying and reporting the presence and localization of nucleic acid targets in vitro and in vivo via target-dependent dequenching of fluorescence. A drawback of conventional MB design is present in the stem sequence that is necessary to keep the MBs in a closed conformation in the absence of a target, but that can participate in target binding in the open (target-on) conformation, giving rise to the possibility of false-positive results. In order to circumvent these problems, we designed MBs in which the stem was replaced by an orthogonal DNA analog that does not cross-pair with natural nucleic acids. Homo-DNA seemed to be specially suited, as it forms stable adenine-adenine base pairs of the reversed Hoogsteen type, potentially reducing the number of necessary building blocks for stem design to one. We found that MBs in which the stem part was replaced by homo-adenylate residues can easily be synthesized using conventional automated DNA synthesis. As conventional MBs, such hybrid MBs show cooperative hairpin to coil transitions in the absence of a DNA target, indicating stable homo-DNA base pair formation in the closed conformation. Furthermore, our results show that the homo-adenylate stem is excluded from DNA target binding, which leads to a significant increase in target binding selectivity

Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast

The budding yeast multi-K homology domain RNA-binding protein Scp160p binds to > 1000 messenger RNAs (mRNAs) and polyribosomes, and its mammalian homolog vigilin binds transfer RNAs (tRNAs) and translation elongation factor EF1alpha. Despite its implication in translation, studies on Scp160p's molecular function are lacking to date. We applied translational profiling approaches and demonstrate that the association of a specific subset of mRNAs with ribosomes or heavy polysomes depends on Scp160p. Interaction of Scp160p with these mRNAs requires the conserved K homology domains 13 and 14. Transfer RNA pairing index analysis of Scp160p target mRNAs indicates a high degree of consecutive use of iso-decoding codons. As shown for one target mRNA encoding the glycoprotein Pry3p, Scp160p depletion results in translational downregulation but increased association with polysomes, suggesting that it is required for efficient translation elongation. Depletion of Scp160p also decreased the relative abundance of ribosome-associated tRNAs whose codons show low potential for autocorrelation on mRNAs. Conversely, tRNAs with highly autocorrelated codons in mRNAs are less impaired. Our data indicate that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of tRNA pairing.

Nuclear antisense effects in cyclophilin A pre-mRNA splicing by oligonucleotides: A comparison of tricyclo-DNA with LNA

The nuclear antisense properties of a series of tricyclo(tc)-DNA oligonucleotide 9-15mers, targeted against the 3' and 5' splice sites of exon 4 of cyclophilin A (CyPA) pre-mRNA, were evaluated in HeLa cells and compared with those of corresponding LNA-oligonucleotides. While the 9mers showed no significant antisense effect, the 11-15mers induced exon 4 skipping and exon 3+4 double skipping to about an equal extent upon lipofectamine mediated transfection in a sequence and dose dependent manner, as revealed by a RT-PCR assay. The antisense efficacy of the tc-oligonucleotides was found to be superior to that of the LNA-oligonucleotides in all cases by a factor of at least 4-5. A tc-oligonucleotide 15mer completely abolished CyPA mRNA production at 0.2‘M concentration. The antisense effect was confirmed by western blot analysis which revealed a reduction of CyPA protein to 13% of its normal level. Fluorescence microscopic investigations with a fluorescein labeled tc-15mer revealed a strong propensity for homogeneous nuclear localization of this backbone type after lipofectamine mediated transfection, while the corresponding lna 15mer showed a less clear cellular distribution pattern. Transfection without lipid carrier showed no significant internalization of both tc- and LNA-oligonucleotides. The obtained results confirm the power of tricyclo-DNA for nuclear antisense applications. Morover, CyPA may become an interesting therapeutic target due to its important role in the early steps of the viral replication of HIV-1.

Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion

During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control.

A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and eliminated by nonsense-mediated mRNA decay (NMD). NMD substrates can be degraded by different routes that all require phosphorylated UPF1 (P-UPF1) as a starting point. The endonuclease SMG6, which cleaves mRNA near the PTC, is one of the three known NMD factors thought to be recruited to nonsense mRNAs via an interaction with P-UPF1, leading to eventual mRNA degradation. By artificial tethering of SMG6 and mutants thereof to a reporter mRNA combined with knockdowns of various NMD factors, we demonstrate that besides its endonucleolytic activity, SMG6 also requires UPF1 and SMG1 to reduce reporter mRNA levels. Using in vivo and in vitro approaches, we further document that SMG6 and the unique stalk region of the UPF1 helicase domain, along with a contribution from the SQ domain, form a novel interaction and we also show that this region of the UPF1 helicase domain is critical for SMG6 function and NMD. Our results show that this interaction is required for NMD and for the capability of tethered SMG6 to degrade its bound RNA, suggesting that it contributes to the intricate regulation of UPF1 and SMG6 enzymatic activities.

Chromatin structure and DNase I hypersensitivity in the transcriptionally active and inactive porcine tumor necrosis factor gene locus

We have analyzed the chromatin structure of the porcine tumor necrosis factor gene locus (TNF-alpha and TNF-beta). Nuclei from porcine peripheral blood mononuclear cells were digested with different nucleases. As assessed with micrococcal nuclease, the two TNF genes displayed slightly faster digestion kinetics than bulk DNA. Studies with DNaseI revealed distinct DNaseI hypersensitive sites (DH-sites) within the porcine TNF locus. Four DH-sites could be observed in the promoter and mRNA leader regions of the TNF-beta gene. Two DH-sites could be observed for the TNF-alpha gene, one located in the promoter region close to the TATA-box and the other site in intron 3. This pattern of DH-sites was present independently of the activation state of the cells. Interestingly in a porcine macrophage-like cell line, we found that the TNF-alpha promoter DH-site disappeared and another DH-site appeared in the region of intron 1. Additionally, the DH-site of intron 3 could be enhanced by PMA-stimulation in these cells. TNF-beta sites were not detected in this cell line. However, DH-sites were totally absent in fibroblasts (freshly isolated from testicles) and in porcine kidney cells (PK15 cell line) both of which do not transcribe the TNF genes. Therefore, the pattern of DH-sites corresponds to the transcriptional activity of analyzed cells.

A complete-pelvis segmentation framework for image-free total hip arthroplasty (THA): methodology and clinical study

Background Complete-pelvis segmentation in antero-posterior pelvic radiographs is required to create a patient-specific three-dimensional pelvis model for surgical planning and postoperative assessment in image-free navigation of total hip arthroplasty. Methods A fast and robust framework for accurately segmenting the complete pelvis is presented, consisting of two consecutive modules. In the first module, a three-stage method was developed to delineate the left hemipelvis based on statistical appearance and shape models. To handle complex pelvic structures, anatomy-specific information processing techniques were employed. As the input to the second module, the delineated left hemi-pelvis was then reflected about an estimated symmetry line of the radiograph to initialize the right hemi-pelvis segmentation. The right hemi-pelvis was segmented by the same three-stage method, Results Two experiments conducted on respectively 143 and 40 AP radiographs demonstrated a mean segmentation accuracy of 1.61±0.68 mm. A clinical study to investigate the postoperative assessment of acetabular cup orientations based on the proposed framework revealed an average accuracy of 1.2°±0.9° and 1.6°±1.4° for anteversion and inclination, respectively. Delineation of each radiograph costs less than one minute. Conclusions Despite further validation needed, the preliminary results implied the underlying clinical applicability of the proposed framework for image-free THA.