Scientific workflows with the jABC framework

The jABC is a framework for process modelling and execution according to the XMDD (eXtreme model-driven design) paradigm, which advocates the rigorous use of user-level models in the software development process and software life cycle. We have used the jABC in the domain of scientific workflows for more than a decade now—an occasion to look back and take stock of our experiences in the field. On the one hand, we discuss results from the analysis of a sample of nearly 100 scientific workflow applications that have been implemented with the jABC. On the other hand, we reflect on our experiences and observations regarding the workflow development process with the framework. We then derive and discuss ongoing further developments and future perspectives for the framework, all with an emphasis on simplicity for end users through increased domain specificity. Concretely, we describe how the use of the PROPHETS synthesis plugin can enable a semantics-based simplification of the workflow design process, how with the jABC4 and DyWA frameworks more attention is paid to the ease of data management, and how the Cinco SCCE Meta-Tooling Suite can be used to generate tailored workflow management tools.     

Intrasphincteric injection of botulinum toxin is effective in long-term treatment of esophageal achalasia

We investigated the long-term efficacy and safety of intrasphincteric injections of botulinum toxin (100 U) in 57 patients with esophageal achalasia. One month after treatment, 50 patients had improved (88%); both symptom score and LES pressure were significantly reduced (P < 0.001). After a mean follow-up of 24+/-15 months (range 6-48), 43 patients (75%) are still in remission, although repeat injections of toxin were needed to achieve a stable effect on symptoms.     

Static analysis of Linear Logic programming

Linear Logic is gaining momentum in computer science because it offers a unified framework and a common vocabulary for studying and analyzing different aspects of programming and computation. We focus here on models where computation is identified with proof search in the sequent system of Linear Logic. A proof normalization procedure, called “focusing”, has been proposed to make the problem of proof search tractable. Correspondingly, there is a normalization procedure mapping formulae of Linear Logic into a syntactic fragment of that logic, calledLinLog, where the focusing normalization for proofs can be most conveniently expressed. In this paper, we propose to push this compilation/normalization process further, by applying abstract interpretation and partial evaluation techniques to (focused) proofs inLinLog. These techniques provide information concerning the evolution of the computational resources (formulae) during the execution (proof construction). The practical outcome that we expect from this theoretical effort is the definition of a general tool for statically analyzing and reasoning about the runtime behavior of programs in frameworks where computations can be accounted for in terms of proof search in Linear Logic.     

Calibration Transfer from Micro NIR Spectrometer to Hyperspectral Imaging: a Case Study on Predicting Soluble Solids Content of Bananito Fruit (<Emphasis Type="Italic">Musa acuminata</Emphasis>)

Calibration transfer from a handheld micro NIR spectrometer (NIR-point, 939–1602 nm, 6.2 nm) to a desktop hyperspectral imaging (NIR-HSI) for predicting soluble solids content (SSC) of bananito flesh was investigated in the study. Different spectral pre-processing and standardization methods were employed for correcting spectra so as to minimise spectral differences between NIR-point and NIR-HSI. Results show that application of standard normal variate (SNV) reduced spectral differences from 31.49 to 8.96%. The best standardization method was developed based on piecewise direct standardization (PDS) algorithm using ten transfer samples. The developed PLS model yielded a high prediction performance (R ² _p = 0.922 and RMSEP = 1.451%) for predicting SSC of validation samples using the NIR-point spectra. After SNV and standardization, the model was successfully transferred to NIR-HSI data, giving a comparable prediction accuracy of R ² _p = 0.925 and RMSEP = 1.592%. The results illustrated the potential of transferring calibration models from a simple and easy-available micro NIR spectrometer to a more expensive and sophisticated hyperspectral imaging system, when the spatial distribution of quality information is required.     

Partial dealcoholisation of red wines by membrane contactor technique: influence on colour, phenolic compounds and saliva precipitation index

In this study, red wines from different grape varieties (Merlot, Aglianico and Piedirosso) and containing different alcoholic level (from 13.67 to 15.46% v/v) were treated to diminish the alcoholic percentage of 2, 3 and 5% v/v by a polypropylene hollow fibre membrane contactor apparatus. The wines were analysed before and after partial dealcoholisation. Colour indexes and phenolics were analysed by spectrophotometric methods and HPLC. Wine astringency was evaluated by an astringency index based on the ability of treated wines to precipitate salivary proteins (SPI, Saliva Precipitation Index). For all the levels of dealcoholisation studied, changes in chromatic characteristics, Folin–Ciocalteu index and vanillin reactive flavans were below the methodological errors of the analyses. A loss of malvidin 3-monoglucoside was detected after the dealcoholisation process. Decreasing the ethanol content of wines caused an increase in SPI values.     

HPLC-ESI-MS/MS assessment of the tetrahydro-metabolites of cortisol and cortisone in bovine urine: promising markers of dexamethasone and prednisolone treatment

The effects of long-term administration of low doses of dexamethasone (DX) and prednisolone (PL) on the metabolism of endogenous corticosteroids were investigated in veal calves. In addition to cortisol (F) and cortisone (E), whose interconversion is regulated by 11β-hydroxysteroid dehydrogenases (11βHSDs), special attention was paid to tetrahydrocortisol (THF), allo-tetrahydrocortisol (aTHF), tetrahydrocortisone (THE) and allo-tetrahydrocortisone (aTHE), which are produced from F and E by catalytic activity of 5α and 5β-reductases. A specifically developed HPLC-ESI-MS/MS method achieved the complete chromatographic separation of two pairs of diastereoisomers (THF/aTHF and THE/aTHE), which, with appropriate mass fragmentation patterns, provided an unambiguous conformation. The method was linear (r² > 0.9905; 0.5–25 ng ml^?1), with LOQQ of 0.5 ng ml^?1. Recoveries were in range 75–114%, while matrix effects were minimal. The experimental study was carried out on three groups of male Friesian veal calves: group PL (n = 6, PL acetate 15 mg day^–1 p.o. for 31 days); group DX (n = 5, 5 mg of estradiol (E2) i.m., weekly, and 0.4 mg day^–1 of DX p.o. for 31 days) and a control group (n = 8). Urine was collected before, during (twice) and at the end of treatment. During PL administration, the tetrahydro-metabolite levels decreased gradually and remained low after the suspension of treatment. DX reduced urinary THF that persisted after the treatment, while THE levels decreased during the experiment, but rebounded substantially after the DX was withdrawn. Both DX and PL significantly interfered with the production of F and E, leading to their complete depletion. Taken together, the results demonstrate the influence of DX and PL administration on 11βHSD activity and their impact on dysfunction of the 5-reductase pathway. In conclusion, profiling tetrahydro-metabolites of F and E might serve as an alternative, indirect but reliable, non-invasive procedure for assessing the impact of synthetic glucocorticosteroids administration.     

Oxidative stabilization of ultra-high omega-3 concentrates as ethyl esters or triacylglycerols

A comparative study of the oxidative stability of “ultra-high” ω3 concentrates (80%) from fish oils as triacylglycerols (TAG) or ethyl esters (EE), as well as their stabilization by supercritical extracts of rosemary (SER), α-tocopherol or their mixture, by Rancimat method and throughout storage time, was carried out. No significant differences were found between EE and TAG on oxidative stability when measured by Rancimat conditions in the range of 50?90 °C. However, storage experiments revealed a poor stability of the EE concentrate form, measured by the monitorization of peroxide and p-anisidine values. Concerning the stabilization by antioxidants, there was a lack of antioxidant effect of evaluated compounds when Rancimat assays were performed at 70 °C, whereas an antioxidant effect began to evidence at 60 °C, and a clearest antioxidant protection was measured at 50 °C for the mixture of the SER plus α-tocopherol in both EE and TAG forms. This selected binary mixture efficiently stabilized the ω3-TAG concentrate throughout 50 days of storage conditions, whereas the stabilization of ω3-EE concentrate was worse. Therefore, the combination of SER and α-tocopherol seemed to be a good antioxidant mixture for the efficient stabilization of extremely labile ultra-high ω3 concentrates, especially in the form of ω3 TAG oils.     

Behaviour of Saccharomyces cerevisiae wine strains during adaptation to unfavourable conditions of fermentation on synthetic medium: cell lipid composition, membrane integrity, viability and fermentative activity

During must fermentation wine strains are exposed to a variety of biotic and abiotic stresses which, when prevailing over the cellular defence systems, can affect cell viability with negative consequences on the progression of the fermentative process. To investigate the ability of wine strains to survive and adapt to unfavourable conditions of fermentation, the lipid composition, membrane integrity, cell viability and fermentative activity of three strains of Saccharomyces cerevisiae were analysed during hypoxic growth in a sugar-rich medium lacking lipid nutrients. These are stressful conditions, not unusual during must fermentation, which, by affecting lipid biosynthesis may exert a negative effect on yeast viability. The results obtained showed that the three strains were able to modulate cell lipid composition during fermentation. However, only two of them, which showed highest viability and membrane integrity at the end of the fermentation process, reached a fatty acid composition which seemed to be optimal for a successful adaptation. In particular, C16/TFA and UFA/TFA ratios, more than total lipid and ergosterol contents, seem to be involved in yeast adaptation.