Biobank quality management in the BBMRI.be network

From as early as 2005, different guidelines and quality standards covering biobank activities and sample handling methods have been developed to improve and guarantee the reproducibility of biomarker research. Ten years on, the BBMRI.be Quality working group wanted to gauge the current situation of these aspects in the biobanks of the BBMRI.be network. To this end, two online surveys were launched (fall 2017 and fall 2018) to the biobank quality managers in the BBMRI.be network to determine the status and setup of their current quality management system (QMS) and how their QMS and related practices have evolved over a 14 month time period. All biobanks addressed by the two surveys provided a complete response (12 and 13, respectively). A QMS was implemented in 85% of biobanks, with 4 standards emerging as primary basis. Supplementary guidelines were used, with a strong preference for the ISBER best practices for biobanks. The Standard Preanalytical Code-an indicator of the preanalytical lifecycle of a biospecimen impacting the downstream analysis results-was already implemented in 50% of the biobanks while the other half intends future implementation. To assess and maintain the quality of their QMS, 62% of biobanks used self-assessment tools and 71% participated in proficiency testing schemes. The majority of biobanks had implemented procedures for general and biobank specific activities. However, policies regarding the business and sustainability aspect of biobank were only implemented in a limited number of biobanks. A clear desire for a peer-review audit was expressed by 69% of biobanks, with over half of them intending to implement the recently published biobank standard ISO20387. Overall, the biobanks of the BBMRI.be network have actively implemented a solid quality approach in their practices. The implementation of ISO 20387 may bring further professionalization of activities. Based on the needs expressed in this survey, the Quality working group will be setting up an audit program for the BBMRI.be biobanks, to enhance, harmonize and streamline their activities. On the whole, the biobanks in the BBMRI.be network are able to substantially contribute to translational research, as a primary facilitator guaranteeing high quality standards and reproducibility

La vitrification en une seule étape d’embryons murins définit de nouveaux standards de cryopréservation

La cryopréservation d’embryons est un des outils les plus efficaces, économiques et utiles au niveau éthique pour préserver indéfiniment la génétique des animaux de laboratoire. Les bénéfices liés à son utilisation sont nombreux, et incluent la réduction des coûts associés à la pérennisation de lignées, la limitation de l’apparition et de la dissémination de mutations non voulues, la facilité et la sécurité pour les transferts internationaux, et la réduction du nombre d’animaux à élever en captivité. La vitrification a été démontrée comme étant plus efficace que la congélation lente en procréation médicalement assistée humaine, où elle constitue maintenant la méthode de référence. Il en va de même pour la cryopréservation des embryons de souris, où la vitrification préserve mieux l’intégrité de la chromatine, réduit la pénétration intracytoplasmique d’agents cryoprotecteurs potentiellement toxiques, et in fine permet une meilleure survie et un meilleur développement après réchauffement que la congélation lente. Cependant, pour être efficaces, les méthodes actuelles de vitrification nécessitent plusieurs étapes d’exposition des embryons à des solutions spécifiques avant le refroidissement, mais aussi au cours de leur réchauffement ultérieur. Cette relative complexité peut s’avérer difficile à gérer de manière optimale quand un grand nombre d’embryons doivent être traités au cours d’une même session. Nous avons développé et breveté une technologie de vitrification d’embryons en une étape (« one-step ») qui est aussi efficace que les meilleures méthodes de vitrification multi-étapes. De plus, nos milieux sont chimiquement définis (sans sérum ou autre composant biologique non défini), et des supports permettant la vitrification aseptique peuvent être utilisés sans perte de rendement. Notre technologie de vitrification one-step d’embryons de rongeurs répond ainsi aux problèmes d’ergonomie liés aux méthodes classiques de vitrification, et fournit ainsi aux scientifiques une solution efficace, biologiquement sûre et facile à utiliser pour la cryopréservation d’embryons de rongeurs. Elle rend ainsi l’efficacité de la vitrification plus aisément applicable aux rongeurs de laboratoire, contribuant ainsi à la réduction du nombre d’animaux nécessaires à la pérennisation et à la diffusion de lignées ou de colonies utiles.Vitricell: développement et valorisation de kits de vitrification de cellules en conditions aseptiques et chimiquement définie

Quantitative analysis of the strength generating C-S-H-phase in concrete by IR-spectroscopy

The C-S-H-phase is the most important strength generating phase in concrete and other cementitious materials. The analysis of C-S-H is therefore an important instrument of innovations in the field of concrete and its durability and sustainability. The quantification and insights in C-S-H are hindered by the predominantly amorphous structure of C-S-H. Only the time consuming and expensive solid state nuclear magnetic resonance spectroscopy (NMR) gives a chance to get results, but is restricted to model substances. A new technique, based on the cheap and widespread infrared-spectroscopy (IR) was developed. The quantitative analysis is based on the silicon content in the different structural units of C-S-H and a calibration with natural and synthetic materials with known silicon content in these units. The technique allows to investigate specimens from real structures. Specimens with quartz or limestone aggregate can be analyzed directly. In other cases the aggregates must be separated, for example with heavy liquid separation. Tests with different mortars showed a good correspondence of measured and expected values of C-S-H concentration

From oligomers towards a racemic crystal: molecular simulation of DL-norleucine crystal nucleation from solution

We elucidate the evolution of forming nuclei leading towards a racemic molecular crystal by means of computer simulation. Our simulations start with the association of individual D- and L-norleucine molecules and subsequent formation of aggregates and thus provide molecular scale insights into the early stages of nucleation from (octanol) solution. During aggregate evolution from micelles to bilayers and eventually nanoparticles comprising staggered bilayers we identified a step-wise increase in molecular ordering. While the key structural motifs in the early aggregates are given by hydrogen bonded dimers, after association of ~150 molecules a solid–solid phase transition leads to ordering of the hydrogen-bonded network in favour of the final crystal structure. This secondary nucleation event seems to be of key importance for changing the initially random arrangement of D and L enantiomers in the small (<150 molecules) aggregates to an ordered arrangement, that is alternating -D-D- and -L-L-alignments within the staggered bilayers of the molecular crystal

A phase I radiation dose-escalation study to determine the maximal dose of radiotherapy in combination with weekly gemcitabine in patients with locally advanced pancreatic adenocarcinoma

<p>Abstract</p> <p>Background</p> <p>The primary objective of this study was to determine the maximum tolerated dose (MTD) of escalating doses of radiotherapy (RT) concomitantly with a fixed dose of gemcitabine (300 mg/m²/week) within the same overall treatment time.</p> <p>Methods</p> <p>Thirteen patients were included. Gemcitabine 300 mg/m²/week was administered prior to RT. The initial dose of RT was 45 Gy in 1.8 Gy fractions, escalated by adding 5 fractions of 1.8 Gy (one/week) to a dose of 54 Gy with a total duration kept at 5 weeks. All patients received a dynamic MRI to assess the pancreatic respiratory related movements. Toxicity was scored using the RTOG-EORTC toxicity criteria.</p> <p>Results</p> <p>Three of six patients experienced an acute dose limiting toxicity (DLT) at the 54 Gy dose level. For these patients a grade III gastro-intestinal toxicity (GI) was noted. Patients treated at the 45 Gy dose level tolerated therapy without DLT. The 54 Gy dose level was designated as the MTD and was deemed not suitable for further investigation.</p> <p>Between both dose levels, there was a significant difference in percentage weight loss (p = 0.006) and also in cumulative GI toxicity (p = 0.027). There was no grade 3 toxicity in the 45 Gy cohort versus 4 grade 3 toxicity events in the 54 Gy cohort. The mean dose to the duodenum was significantly higher in the 54 Gy cohort (38.45 Gy vs. 51.82 Gy; p = 0.001).</p> <p>Conclusion</p> <p>Accelerated dose escalation to a total dose of 54 Gy with 300 mg/m²/week gemcitabine was not feasible. GI toxicity was the DLT. Retrospectively, the dose escalation of 9 Gy by accelerated radiotherapy might have been to large. A dose of 45 Gy is recommended. Considering the good patient outcomes, there might be a role for the investigation of a fixed dose of gemcitabine and concurrent RT with small fractions (1.8 Gy/day) in borderline resectable or unresectable non-metastatic locally advanced pancreatic cancer.</p

Validation of Calcein Violet as a New Marker of Semen Membrane Integrity in Domestic Animals

peer reviewedMany fluorochromes routinely used in semen quality analysis emit in the green and red channels, limiting their possible combination for multiple parameter analysis. The use of fluorophores emitting in different light channels broadens the possibilities of combination to expand the range of simultaneously evaluated criteria. This is of great interest in cases of small ejaculated volumes, such as those naturally occurring in roosters, small dog breeds and drones (Apis mellifera). The purpose of this experiment is to establish Calcein Violet (CaV), a blue fluorochrome, as a marker of viability and acrosomal integrity in domestic animals in order to free the red and green channels. SYBR®14/Propidium Iodide (PI) was used as reference dye, heat-treated samples as negative controls, serial staining combination for validation and epifluorescence microscopy for observation. Dead spermatozoa marked in red with PI showed no blue fluorescence either from the head or the tail. Live spermatozoa showed a decreasing blue emission from head to tail when single stained with CaV. Unreacted acrosomes showed intense blue fluorescence irrespective of plasma membrane integrity. This needs to be further confirmed for species with small and difficult to observe heads. Establishment of CaV as a marker of membrane integrity by fluorescence microscopy is a decisive first step towards further technical development and use with flow cytometry

Optimizing copious activity type classes based on classi cation accuracy and entropy retention

Despite the advantages, big transport data are characterized by a considerable disadvantage as well. Personal and activity-travel information are often lacking, making it necessary to deduce this information with data mining techniques. However, some studies predict many unique activity type classes (ATCs), while others merge multiple activity types into larger ATCs. This action enhances the activity inference estimation, but destroys important activity information. Previous studies do not provide a strong justification for this practice. An objectively optimized set of ATCs, balancing model prediction accuracy and preserving activity information from the original data, becomes essential. Previous research developed a classification methodology in which the optimal set of ATCs was identified by analyzing all possible ATC combinations. However, this approach is practically impossible in a finite amount of time for e.g. the US National Household Travel Survey (NHTS) 2009 data set, which comprises 36 ATCs (home activity excluded), since there would be 3.82•1030 unique combinations (an exponential increase). The aim of this paper is to optimize which original ATCs should be grouped into a new class, and this for data sets for which it is impossible or impractical to simply calculate all ATC combinations. The proposed method defines an optimization parameter U (based on classification accuracy and information retention) which is maximized in an iterative local search algorithm. The optimal set of ATCs for the NHTS 2009 data set was determined. A comparison finds that this optimum is considerably better than many expert opinion activity type classification systems. Convergence was confirmed and large performance gains were found

Developing an optimised activity type annotation method based on classification accuracy and entropy indices

The generation of substantial amounts of travel and mobility related data has spawned the emergence of the era of big data. However, this data generally lacks activity-travel information such as trip purpose. This deficiency led to the development of trip purpose inference (activity type imputation / annotation) techniques, of which the performance depends on the available input data and the (number of) activity type classes to infer. Aggregating activity types strongly increases the inference accuracy and is usually left to the discretion of the researcher. As this is open for interpretation, it undermines the reported inference accuracy. This study developed an optimised classification methodology by identifying classes of activity types with an optimal balance between improving model accuracy, and preserving activity information from the original data set. A sensitivity analysis was performed. Additionally, several machine learning algorithms are experimented with. The proposed method may be applied to any study area