Monitoring data in R with the lumberjack package

Monitoring data while it is processed and transformed can yield detailed insight into the dynamics of a (running) production system. The lumberjack package is a lightweight package allowing users to follow how an R object is transformed as it is manipulated by R code. The package abstracts all logging code from the user, who only needs to specify which objects are logged and what information should be logged. A few default loggers are included with the package but the package is extensible through user-defined logger objects.Comment: Accepted for publication in the Journal of Statistical Softwar

Mass transfer characteristics in structured packing for CO2 emission reduction processes

Acid gas treating and CO2 capture from flue gas by absorption have gained wide importance over the past few decades. With the implementation of more stringent environmental regulations and the awareness of the greenhouse effect, the need for efficient removal of acid gases such as CO2 (carbon dioxide) has increased significantly. Therefore, additional effort for research in this field is inevitable. For flue gas processes the ratio of absorption solvent to gas throughput is very different compared to acid gas treating processes owing to the atmospheric pressures and the dilution effect of combustion air. Moreover, in flue gas applications pressure drop is a very important process parameter. Packing types are required that allow for low pressure drop in combination with high interfacial areas at low liquid loading per square meter. The determination of interfacial areas in gas-liquid contactors by means of the chemical method (Danckwerts, P. V. Gas-liquid reactions; McGraw-Hill: London, 1970) has been very frequently applied. Unfortunately, many of the model systems proposed in the literature are reversible and therefore this condition possibly is not met. Versteeg et al. (Versteeg, G. F.; Kuipers, J. A. M.; Beckum, F. P. H.; van Swaaij, W. P. M. Chem. Eng. Sci. 1989, 44, 2292) have demonstrated that for reversible reactions the conditions for the determination of the interfacial area by means of the chemical method are much more severe. In a study by Raynal et al. (Raynal, L.; Ballaguet, J. P.; Berrere-Tricca, C. Chem. Eng. Sci. 2004, 59, 5395), it has been shown that there is a dependency of the interfacial area on the packing height. Unfortunately, most model systems used, e.g., CO2-caustic soda (as used by Raynal et al.), are much more complex and consist of (a set of) reversible reaction(s). The natures of these systems make the conditions at which the interfacial area can be determined much more severe and put more limitations on the process conditions and experimental equipment than a priori can be expected. Therefore, an extended absorption model is required to determine the conditions at which the interfacial area can be measured without detailed knowledge of the values of the liquid-side mass transfer coefficient, k1, beforehand.

Direct measurement of the radiative lifetime of vibrationally excited OH radicals

Neutral molecules, isolated in the gas-phase, can be prepared in a long-lived excited state and stored in a trap. The long observation time afforded by the trap can then be exploited to measure the radiative lifetime of this state by monitoring the temporal decay of the population in the trap. This method is demonstrated here and used to benchmark the Einstein $A$-coefficients in the Meinel system of OH. A pulsed beam of vibrationally excited OH radicals is Stark decelerated and loaded into an electrostatic quadrupole trap. The radiative lifetime of the upper $\Lambda$-doublet component of the $X ^2\Pi_{3/2}, v=1, J=3/2$ level is determined as $59.0 \pm 2.0$ ms, in good agreement with the calculated value of $57.7 \pm 1.0$ ms.Comment: 4 pages, 3 figures, submitted to Phys. Rev. Let

Standardisation of Environmental Enrichment for Laboratory Mice and Rats: Utilisation, Practicality and Variation in Experimental Results

Rats and mice are the most commonly used species as laboratory animal models of diseases in biomedical  research. Environmental factors such as cage size, number of cage mates and cage structure such as environmental  enrichment can affect the physiology and behavioural development of laboratory animals and  their well-being throughout their lives. Therefore compromising the animals’ well-being due to inadequate  environmental conditions would diminish the value of the research models. In order to improve laboratory  animals’ well-being and promote the quality of animal based biomedical research, it is fundamentally  important that the environment of the animals meets the animals’ species typical behavioural needs. Standardisation  of environmental enrichment for laboratory rats and mice therefore should provide possibilities  for the animals to engage in at least the essential behavioural needs such as social contact, nest building,  exploring and foraging. There is a wide variety of environmental enrichment items commercially available  for laboratory mice and rats. However, how these items are used by the animals, their practicality in the  laboratory and whether these enrichments might lead to increased variation in experimental results have  not been widely assessed. In this study, we implemented two standardised enrichment items (shelters, nesting  materials) for rats and mice at different animal units. We instructed the animal care staff in monitoring  the use of enrichment items by the animals by means of a daily score sheet system. The animal staff ’s  viewpoint on practicality of the standardised enrichment program was assessed with a monthly score sheet  survey. Also we assessed whether the enriched environment affected breeding results and contributed to an  increase in variation of experimental data from several participating current studies. Our results show that  the animals readily used the provided enrichment items. A slight increase in workload for the animal staff  was reported. However, the overall judgement was mainly reported as good. Breeding results and variation  in experimental data did not reveal differences as compared to data from previous housing and/or non enriched  housing conditions. Overall, the results indicate that standard environmental enrichment that is species  appropriate may enhance the animal’s well-being without undesirable side effects on the experimental  outcome and daily working routine of the animal care staff.

Male management : coping with aggression problems in male laboratory mice

Jaarlijks worden er in ons land ruim 700.000 proefdieren gebruikt, waarvan 45% muizen. Dit zijn sociaal levende dieren die over het algemeen gehuisvest worden in groepen van 6 tot 10 dieren. Bij groepshuisvesting van mannelijke muizen ontstaat echter vaak agressie. Deze kan dusdanig ernstige vormen aannemen, dat het welzijn van de dieren ernstig wordt geschaad en proefresultaten niet meer betrouwbaar zijn. Het in dit proefschrift beschreven onderzoek had tot doel om tot praktische oplossingen te komen voor het probleem van agressie tussen mannelijke laboratorium muizen. Allereerst is nagegaan of de aanpak zoals die nu vaak wordt gehanteerd, nl. het individueel huisvesten, een voor de muizen aanvaardbare oplossing is. Dit bleek echter niet zo te zijn. In een experiment waarin dieren konden kiezen tussen een kooi voor zich alleen, of denabijheid van een soortgenoot, brachten de muizen ongeveer 70% van hun tijd door bij hun soortgenoot, zelfs wanneer zij eerder met elkaar hadden gevochten. De aanwezigheid van een soortgenoot bleek duidelijk preferent boven individuele huisvesting. Daarom werd vervolgens gezocht naar mogelijkheden om binnen groepenmannelijke muizen het agressief gedrag te verlagen. Vastgesteld kon worden dat wanneer de muizen worden gehuisvest in kleinere groepen dan gebruikelijk, ze minder vaak vechten. Bij de in dit proefschrift onderzochte muizenstammen bleek het optimum aantal dieren 3 per kooi te zijn. Verder bleek ook de aanwezigheid van nestmateriaal in de kooi de agressie aanzienlijk te verlagen. Agressief gedrag treedt met name op wanneer de dieren verstoord worden, bijvoorbeeld na het verschonen van kooien. Wanneer het nestmateriaal (met daarin de eigen nestgeur) tijdens het verschonen van de kooien werd overgezet, kon de agressie nog verder worden verlaagd. De resultaten beschreven in dit proefschrift tonen aan dat door middel van eenvoudig toepasbare aanpassingen in huisvesting en verzorging agressief gedrag tussen mannelijke laboratoriummuizen kan worden verminderd. Deze resultaten dragen hiermee bij aan het verbeteren van het welzijn van laboratoriummuizen en daarmee tevens aan de betrouwbaarheid van proefresultaten

Data Validation Infrastructure for R

Checking data quality against domain knowledge is a common activity that pervades statistical analysis from raw data to output. The R package validate facilitates this task by capturing and applying expert knowledge in the form of validation rules: logical restrictions on variables, records, or data sets that should be satisfied before they are considered valid input for further analysis. In the validate package, validation rules are objects of computation that can be manipulated, investigated, and confronted with data or versions of a data set. The results of a confrontation are then available for further investigation, summarization or visualization. Validation rules can also be endowed with metadata and documentation and they may be stored or retrieved from external sources such as text files or tabular formats. This data validation infrastructure thus allows for systematic, user-defined definition of data quality requirements that can be reused for various versions of a data set or by data correction algorithms that are parameterized by validation rules