Computer-Supported Research: Konzeptpapier zum CoSRe-Projekt

Die Wissenschaften befinden sich am Beginn zu einem neuen Zeitalter: neue Messverfahren erzeugen riesige Mengen experimenteller Daten, Computer gestatten die Exploration dieser Daten, immer größere und komplexere Modelle erlauben präzise Vorhersagen, das Internet führt zu einer weltweiten Kollaboration, der Innovationszyklus wird immer schneller. Jim Gray bezeichnet dies als „vierten wissenschaftlichen Paradigma“ Diese Datengetriebenheit stellt die Wissenschaften aber auch vor neue Herausforderungen. Zwar werden immer mehr Routineaufgaben von Computern übernommen. Für die Bewältigung der Informationsflut ist aber eine Computer-Unterstützung des gesamten wissenschaftlichen Zyklus notwendig: von der experimentellen Datenerhebung über die Datenanalyse und anschließende Modellbildung bis hin zur Simulation und einer Modellrevision auf Grund der Simulationsergebnisse. Wissenschaftliches Arbeiten, das von einer solchen Art der Computer-Unterstützung getragen wird, bezeichnen wir als Computer-Supported Research. Zwei Beobachtungen sind für die Unterstützung des gesamten wissenschaftlichen Zyklus sehr hilfreich: Zum einen ist es für die Verarbeitung von Daten unwichtig, ob sie aus Experimenten in der realen Welt oder aus Simulationen stammen. Zum anderen werden Modelle selbst heute mehr und mehr als First-Class-Objekte, d.h. als Daten behandelt: sie werden zwischen Programmen ausgetauscht, in Datenbanken gespeichert, über das Internet verschickt und durch Programme manipuliert

Differential CRH expression level determines efficiency of Cre- and Flp-dependent recombination

Corticotropin-releasing hormone expressing (CRH+) neurons are distributed throughout the brain and play a crucial role in shaping the stress responses. Mouse models expressing site-specific recombinases (SSRs) or reporter genes are important tools providing genetic access to defined cell types and have been widely used to address CRH+ neurons and connected brain circuits. Here, we investigated a recently generated CRH-FlpO driver line expanding the CRH system-related tool box. We directly compared it to a previously established and widely used CRH-Cre line with respect to the FlpO expression pattern and recombination efficiency. In the brain, FlpO mRNA distribution fully recapitulates the expression pattern of endogenous Crh. Combining both Crh locus driven SSRs driver lines with appropriate reporters revealed an overall coherence of respective spatial patterns of reporter gene activation validating CRH-FlpO mice as a valuable tool complementing existing CRH-Cre and reporter lines. However, a substantially lower number of reporter-expressing neurons was discerned in CRH-FlpO mice. Using an additional CRH reporter mouse line (CRH-Venus) and a mouse line allowing for conversion of Cre into FlpO activity (CAG-LSL-FlpO) in combination with intersectional and subtractive mouse genetic approaches, we were able to demonstrate that the reduced number of tdTomato reporter expressing CRH+ neurons can be ascribed to the lower recombination efficiency of FlpO compared to Cre recombinase. This discrepancy particularly manifests under conditions of low CRH expression and can be overcome by utilizing homozygous CRH-FlpO mice. These findings have direct experimental implications which have to be carefully considered when targeting CRH+ neurons using CRH-FlpO mice. However, the lower FlpO-dependent recombination efficiency also entails advantages as it provides a broader dynamic range of expression allowing for the visualization of cells showing stress-induced CRH expression which is not detectable in highly sensitive CRH-Cre mice as Cre-mediated recombination has largely been completed in all cells generally possessing the capacity to express CRH. These findings underscore the importance of a comprehensive evaluation of novel SSR driver lines prior to their application

Safety and immunogenicity of inactivated poliovirus vaccine when given with measles–rubella combined vaccine and yellow fever vaccine and when given via diff erent administration routes: a phase 4, randomised, non-inferiority trial in The Gambia

Background The introduction of the inactivated poliovirus vaccine (IPV) represents a crucial step in the polio eradication endgame. This trial examined the safety and immunogenicity of IPV given alongside the measles–rubella and yellow fever vaccines at 9 months and when given as a full or fractional dose using needle and syringe or disposable-syringe jet injector. Methods We did a phase 4, randomised, non-inferiority trial at three periurban government clinics in west Gambia. Infants aged 9–10 months who had already received oral poliovirus vaccine were randomly assigned to receive the IPV, measles–rubella, and yellow fever vaccines, singularly or in combination. Separately, IPV was given as a full intramuscular or fractional intradermal dose by needle and syringe or disposable-syringe jet injector at a second visit. The primary outcomes were seroprevalence rates for poliovirus 4–6 weeks post-vaccination and the rate of seroconversion between baseline and post-vaccination serum samples for measles, rubella, and yellow fever; and the post-vaccination antibody titres generated against each component of the vaccines. We did a per-protocol analysis with a non-inferiority margin of 10% for poliovirus seroprevalence and measles, rubella, and yellow fever seroconversion, and (⅓) log2 for log2-transformed antibody titres. This trial is registered with ClinicalTrials.gov, number NCT01847872. Findings Between July 10, 2013, and May 8, 2014, we assessed 1662 infants for eligibility, of whom 1504 were enrolled into one of seven groups for vaccine interference and one of four groups for fractional dosing and alternative route of administration. The rubella and yellow fever antibody titres were reduced by co-administration but the seroconversion rates achieved non-inferiority in both cases (rubella, –4·5% [95% CI –9·5 to –0·1]; yellow fever, 1·2% [–2·9 to 5·5]). Measles and poliovirus responses were unaff ected (measles, 6·8% [95% CI –1·4 to 14·9]; poliovirus serotype 1, 1·6% [–6·7 to 4·7]; serotype 2, 0·0% [–2·1 to 2·1]; serotype 3, 0·0% [–3·8 to 3·9]). Poliovirus seroprevalence was universally high (>97%) after vaccination, but the antibody titres generated by fractional intradermal doses of IPV did not achieve non-inferiority compared with full dose. The number of infants who seroconverted or had a four-fold rise in titres was also lower by the intradermal route. There were no safety concerns. Interpretation The data support the future co-administration of IPV, measles–rubella, and yellow fever vaccines within the Expanded Programme on Immunization schedule at 9 months. The administration of single fractional intradermal doses of IPV by needle and syringe or disposable-syringe jet injector compromises the immunity generated, although it results in a high post-vaccination poliovirus seroprevalence

Chronic Q fever diagnosis—consensus guideline versus expert opinion

Chronic Q fever, caused by Coxiella burnetii, has high mortality and morbidity rates if left untreated. Controversy about the diagnosis of this complex disease has emerged recently. We applied the guideline from the Dutch Q Fe­ver Consensus Group and a set of diagnostic criteria pro­posed by Didier Raoult to all 284 chronic Q fever patients included in the Dutch National Chronic Q Fever Database during 2006–2012. Of the patients who had proven cas­es of chronic Q fever by the Dutch guideline, 46 (30.5%) would not have received a diagnosis by the alternative cri­teria designed by Raoult, and 14 (4.9%) would have been considered to have possible chronic Q fever. Six patients with proven chronic Q fever died of related causes. Until results from future studies are available, by which current guidelines can be modified, we believe that the Dutch lit­erature-based consensus guideline is more sensitive and easier to use in clinical practice

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology

The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed “single topology” or “dual topology”. As the terminology is often used ambiguously in the literature, a systematic categorization of the system representations is proposed here. In the dual-topology approach, the molecules are simulated as separate molecules. Such an approach is relatively easy to automate for high-throughput RBFE calculations compared to the single-topology approach. Distance restraints are commonly applied to prevent the molecules from drifting apart, thereby improving the sampling efficiency. In this study, we introduce the program RestraintMaker, which relies on a greedy algorithm to find (locally) optimal distance restraints between pairs of atoms based on geometric measures. The algorithm is further extended for multi-state methods such as enveloping distribution sampling (EDS) or multi-site λ-dynamics. The performance of RestraintMaker is demonstrated for toy models and for the calculation of relative hydration free energies. The Python program can be used in script form or through an interactive GUI within PyMol. The selected distance restraints can be written out in GROMOS or GROMACS file formats. Additionally, the program provides a human-readable JSON format that can easily be parsed and processed further. The code of RestraintMaker is freely available on GitHub https://github.com/rinikerlab/restraintmaker.ISSN:0920-654XISSN:1573-495

Rapid dynamic R1/R2*/temperature assessment: a method with potential for monitoring drug delivery

Local drug delivery by hyperthermia-induced drug release from thermosensitive liposomes (TSLs) may reduce the systemic toxicity of chemotherapy, whilst maintaining or increasing its efficacy. Relaxivity contrast agents can be co-encapsulated with the drug to allow the visualization of the presence of liposomes, by means of R 2 *, as well as the co-release of the contrast agent and the drug, by means of R 1, on heating. Here, the mathematical method used to extract both R 2 * and R 1 from a fast dynamic multi-echo spoiled gradient echo (ME-SPGR) is presented and analyzed. Finally, this method is used to monitor such release events. R 2 * was obtained from a fit to the ME-SPGR data. Absolute R 1 was calculated from the signal magnitude changes corrected for the apparent proton density changes and a baseline Look–Locker R 1 map. The method was used to monitor nearly homogeneous water bath heating and local focused ultrasound heating of muscle tissue, and to visualize the release of a gadolinium chelate from TSLs in vitro. R 2 *, R 1 and temperature maps were measured with a 5-s temporal resolution. Both R 2 *and R 1 measured were found to change with temperature. The dynamic R 1 measurements after heating agreed with the Look–Locker R 1 values if changes in equilibrium magnetization with temperature were considered. Release of gadolinium from TSLs was detected by an R 1 increase near the phase transition temperature, as well as a shallow R 2 * increase. Simultaneous temperature, R 2 * and R 1 mapping is feasible in real time and has the potential for use in image-guided drug delivery studies

Rapid Dynamic Temperature/R1/R2* Assessment : A Method With Potential For Monitoring Drug Delivery

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