RTPrimerDB: the portal for real-time PCR primers and probes

RTPrimerDB (http://www.rtprimerdb.org) is a freely accessible database and analysis tool for real-time quantitative PCR assays. RTPrimerDB includes records with user submitted assays that are linked to genome information from reference databases and quality controlled using an in silico assay evaluation system. The primer evaluation tools intended to assess the specificity and to detect features that could negatively affect the amplification efficiency are combined into a pipeline to test custom-designed primer and probe sequences. An improved user feedback system guides users and submitters to enter practical remarks and details about experimental evaluation analyses. The database is linked with reference databases to allow the submission of assays for all genes and organisms officially registered in Entrez Gene and RefSeq. Records in RTPrimerDB are assigned unique and stable identifiers. The content is provided via an interactive web-based search system and is available for download in the recently developed RDML format and as bulk export file. RTPrimerDB is a one-stop portal for high-quality and highly annotated real-time PCR assays

Beleidsevaluaties tussen methode en praktijk: Naar een meer realistische evaluatiebenadering

__Abstract__ Het idee dat evaluatie kan bijdragen aan het verbeteren van beleid is niets nieuws onder de zon. Al in de jaren ’80 van de vorige eeuw bloeide evaluatie op met de bedoeling beleidsformulering en beleidsuitvoering te informeren, en in het hedendaagse ‘evidence-based’ tijdperk is evaluatie meer dan ooit een bloeiende praktijk. 1 Nederland volgde historisch weliswaar een ander en sneller traject dan Belgie¨, waar evaluatie slechts na de millenniumwisseling algemeen ingang vond.2 De potentie van evaluatie is tegenwoordig niettemin grotendeels (h)erkend en wordt gevat in adagia als ‘leren van evalueren’. Er worden met regelmaat evaluatiestudies uitgevoerd, maar opvallend is dat deze in toenemende mate ook het gebruik van evaluatieonderzoek zelf betreffen

Does touch matter? The impact of stroking versus non-stroking maternal touch on cardio-respiratory processes in mothers and infants

The beneficial effects of touch in development were already observed in different types of skin-to-skin care. In the current study, we aimed at studying potential underlying mechanisms of these effects in terms of parasympatho-inhibitory regulation. We examined the specific impact of affective maternal stroking versus non-stroking touch on the cardio-respiration of both mothers and infants in terms of respiratory sinus arrhythmia (RSA). We compared a 3-min TOUCH PERIOD (stroking or non-stroking touch) with a baseline before (PRE-TOUCH) and after (POST-TOUCH) in 45 dyads (24 stroking/21 non-stroking touch) with infants aged 4–16 weeks. We registered mother-infant ECG, respiration and made video-recordings. We calculated RR-interval (RRI), respiration rate (fR) and (respiratory corrected) RSA and analyzed stroking mean velocity rate (MVR) of the mothers. ANOVA-tests showed a significant different impact on infants' respiratory corrected RSA of stroking touch (increase) versus non-stroking touch (decrease). Further, during and after stroking touch, RRI significantly increased whereas fR significantly decreased. Non-stroking touch had no significant impact on infants' RRI and fR. In the mothers, RRI significantly decreased and fR significantly increased during the TOUCH PERIOD. The mothers' MVR occurred within the range of 1–10 cm/s matching with the optimal afferent stimulation range of a particular class of cutaneous unmyelinated, low-threshold mechano-sensitive nerves, named c-tactile (CT) afferents. We suggest CT afferents to be the a potential missing link between the processing of affective touch and the development of physiological and emotional self-regulation. The results are discussed with regard to the potential role of CT afferents within the building of early self-regulation as part of a multisensory intuitive parenting system and the importance to respect this ecological context of an infant in research and clinical applications

Impact of long-term daylight deprivation on retinal light sensitivity, circadian rhythms and sleep during the Antarctic winter.

Long-term daylight deprivation such as during the Antarctic winter has been shown to lead to delayed sleep timing and sleep fragmentation. We aimed at testing whether retinal sensitivity, sleep and circadian rest-activity will change during long-term daylight deprivation on two Antarctic bases (Concordia and Halley VI) in a total of 25 healthy crew members (mean age: 34 ± 11y; 7f). The pupil responses to different light stimuli were used to assess retinal sensitivity changes. Rest-activity cycles were continuously monitored by activity watches. Overall, our data showed increased pupil responses under scotopic (mainly rod-dependent), photopic (mainly L-/M-cone dependent) as well as bright-blue light (mainly melanopsin-dependent) conditions during the time without direct sunlight. Circadian rhythm analysis revealed a significant decay of intra-daily stability, indicating more fragmented rest-activity rhythms during the dark period. Sleep and wake times (as assessed from rest-activity recordings) were significantly delayed after the first month without sunlight (p < 0.05). Our results suggest that during long-term daylight deprivation, retinal sensitivity to blue light increases, whereas circadian rhythm stability decreases and sleep-wake timing is delayed

Postmortem pump-driven reperfusion of the vascular system of porcine lungs: towards a new model for surgical training

PURPOSE: The objective of this experiment is to establish a continuous postmortem circulation in the vascular system of porcine lungs and to evaluate the pulmonary distribution of the perfusate. This research is performed in the bigger scope of a revascularization project of Thiel embalmed specimens. This technique enables teaching anatomy, practicing surgical procedures and doing research under lifelike circumstances. METHODS: After cannulation of the pulmonary trunk and the left atrium, the vascular system was flushed with paraffinum perliquidum (PP) through a heart-lung machine. A continuous circulation was then established using red PP, during which perfusion parameters were measured. The distribution of contrast-containing PP in the pulmonary circulation was visualized on computed tomography. Finally, the amount of leak from the vascular system was calculated. RESULTS: A reperfusion of the vascular system was initiated for 37 min. The flow rate ranged between 80 and 130 ml/min throughout the experiment with acceptable perfusion pressures (range: 37-78 mm Hg). Computed tomography imaging and 3D reconstruction revealed a diffuse vascular distribution of PP and a decreasing vascularization ratio in cranial direction. A self-limiting leak (i.e. 66.8% of the circulating volume) towards the tracheobronchial tree due to vessel rupture was also measured. CONCLUSIONS: PP enables circulation in an isolated porcine lung model with an acceptable pressure-flow relationship resulting in an excellent recruitment of the vascular system. Despite these promising results, rupture of vessel walls may cause leaks. Further exploration of the perfusion capacities of PP in other organs is necessary. Eventually, this could lead to the development of reperfused Thiel embalmed human bodies, which have several applications

Mangroves facing climate change: landward migration potential in response to projected scenarios of sea level rise

Mangrove forests prominently occupy an intertidal boundary position where the effects of sea level rise will be fast and well visible. This study in East Africa (Gazi Bay, Kenya) addresses the question of whether mangroves can be resilient to a rise in sea level by focusing on their potential to migrate towards landward areas. The combinatory analysis between remote sensing, DGPS-based ground truth and digital terrain models (DTM) unveils how real vegetation assemblages can shift under different projected (minimum (+9 cm), relative (+20 cm), average (+48 cm) and maximum (+88 cm)) scenarios of sea level rise (SLR). Under SLR scenarios up to 48 cm by the year 2100, the landward extension remarkably implies an area increase for each of the dominant mangrove assemblages except for Avicennia marina and Ceriops tagal, both on the landward side. On the one hand, the increase in most species in the first three scenarios, including the socio-economically most important species in this area, Rhizophora mucronata and C. tagal on the seaward side, strongly depends on the colonisation rate of these species. On the other hand, a SLR scenario of +88 cm by the year 2100 indicates that the area flooded only by equinoctial tides strongly decreases due to the topographical settings at the edge of the inhabited area. Consequently, the landward Avicennia-dominated assemblages will further decrease as a formation if they fail to adapt to a more frequent inundation. The topography is site-specific; however non-invadable areas can be typical for many mangrove settings