Learning from reproducing computational results: introducing three principles and the Reproduction Package.

We carry out efforts to reproduce computational results for seven published articles and identify barriers to computational reproducibility. We then derive three principles to guide the practice and dissemination of reproducible computational research: (i) Provide transparency regarding how computational results are produced; (ii) When writing and releasing research software, aim for ease of (re-)executability; (iii) Make any code upon which the results rely as deterministic as possible. We then exemplify these three principles with 12 specific guidelines for their implementation in practice. We illustrate the three principles of reproducible research with a series of vignettes from our experimental reproducibility work. We define a novel Reproduction Package, a formalism that specifies a structured way to share computational research artifacts that implements the guidelines generated from our reproduction efforts to allow others to build, reproduce and extend computational science. We make our reproduction efforts in this paper publicly available as exemplar Reproduction Packages. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Clinical applicability of robot-guided contact-free laser osteotomy in cranio-maxillo-facial surgery: in-vitro simulation and in-vivo surgery in minipig mandibles.

Laser was being used in medicine soon after its invention. However, it has been possible to excise hard tissue with lasers only recently, and the Er:YAG laser is now established in the treatment of damaged teeth. Recently experimental studies have investigated its use in bone surgery, where its major advantages are freedom of cutting geometry and precision. However, these advantages become apparent only when the system is used with robotic guidance. The main challenge is ergonomic integration of the laser and the robot, otherwise the surgeon's space in the operating theatre is obstructed during the procedure. Here we present our first experiences with an integrated, miniaturised laser system guided by a surgical robot. An Er:YAG laser source and the corresponding optical system were integrated into a composite casing that was mounted on a surgical robotic arm. The robot-guided laser system was connected to a computer-assisted preoperative planning and intraoperative navigation system, and the laser osteotome was used in an operating theatre to create defects of different shapes in the mandibles of 6 minipigs. Similar defects were created on the opposite side with a piezoelectric (PZE) osteotome and a conventional drill guided by a surgeon. The performance was analysed from the points of view of the workflow, ergonomics, ease of use, and safety features. The integrated robot-guided laser osteotome can be ergonomically used in the operating theatre. The computer-assisted and robot-guided laser osteotome is likely to be suitable for clinical use for ostectomies that require considerable accuracy and individual shape.

TRIPLE Q: a three channel quantum cascade laser absorption spectrometer for fast multiple species concentration measurements.

A compact and transportable three channel quantum cascade laser system (TRIPLE Q) based on mid-infrared absorption spectroscopy has been developed for time-resolved plasma diagnostics. The TRIPLE Q spectrometer encompasses three independently controlled quantum cascade lasers (QCLs), which can be used for chemical sensing, particularly for gas phase analysis of plasmas. All three QCLs are operated in the intra-pulse mode with typical pulse lengths of the order of 150 ns. Using a multiplexed detection, a time resolution shorter than 1 µs can be achieved. Hence, the spectrometer is well suited to study kinetic processes of multiple infrared active compounds in reactive plasmas. A special data processing and analysis technique has been established to account for time jitter effects of the infrared emission of the QCLs. The performance of the TRIPLE Q system has been validated in pulsed direct current plasmas containing N(2)O/air and NO(2)/air.

An integrated approach for bioaccumulation assessment in mussels: towards the development of Environmental Quality Standards for biota.

The possible use of chemical concentrations measured in mussels (Mytillus galloprovincialis) for compliance checking against Environmental Quality Standards (EQS) established for biota is analyzed with the help of an integrated model. The model consists of a 3D planktonic module that provides biomasses in the different compartments, i.e., phytoplankton, zooplankton and bacteria; a 3D fate module that provides the concentrations of contaminants in the water column and in the sediments; and a 3D bioaccumulation module that calculates internal concentrations in relevant biotic compartments. These modules feed a 0D growth and bioaccumulation module for mussels, based on the Dynamic Energy Budget (DEB) approach. The integrated model has been applied to study the bioaccumulation of persistent organic pollutants (POPs) in the Thau lagoon (France). The model correctly predicts the concentrations of polychlorinated biphenyls (PCBs) and polychlorinated dibenzodioxins and dibenzofurans (PCDD/Fs) in mussels as a function of the concentrations in the water column and in phytoplankton. It also sheds light on the origin of the complexity associated with the use of EQS for biota and their conversion to water column concentrations. The integrated model is potentially useful for regulatory purposes, for example in the context of the European Water Framework (WFD) and Marine Strategy Framework Directives (MSFD).

A 3D hydrodynamic fate and transport model for herbicides in Sacca di Goro coastal lagoon (Northern Adriatic).

Sacca di Goro is a shallow coastal microtidal lagoon with a surface area of 26 km2, and an average depth of about 1.5m. Fresh water pollutant loads from Po River branches and several drainage canals lead to anthropogenic eutrophication, frequent summer anoxia crises and chemical contamination. Such events not only affect the lagoon ecosystem but also cause serious economic losses, the lagoon being the second largest producer of clams in Italy. The present work aims at using a fate model coupled with COHERENS 3D hydrodynamic model to simulate and to explain the spatial distribution and temporal variations of s-triazines herbicides in the Sacca di Goro lagoon. The simulation results of spatial and temporal dynamic behaviour of atrazine, simazine and terbuthylazine have been compared with experimental data obtained during an annual monitoring programme.

Monitoring of road-traffic emissions with a mobile photoacoustic system.

Ammonia and ethene are pollutants which are arousing concern as regards their environmental impact, e.g. as greenhouse gases. Road traffic is an increasingly important emission source for these gases. As part of an atmospheric pollution measurement campaign, we performed in situ measurements of NH3, C2H4 and CO2 concentrations at the mouth of a freeway tunnel with a time resolution of 1 min using a mobile laser-based photoacoustic system. Measurements were performed over a period of 5 weeks. In good temporal correlation with traffic counts, we observed peak concentrations of >600 ppb (>1200 ppb for Friday afternoon peaks) for NH3, of up to 400 ppb for C2H4 and >2000 ppm for CO2. Preliminary comparisons with previous measurements at the same location indicate a considerable increase in ammonia and CO2 peak concentrations (greater than the increase in traffic over the same period) and a less pronounced increase in C2H4 concentrations.

[Zollinger-Ellison syndrome]. / Vurkhu sindroma na Zollinger-Ellison.

Three patients with Zollinger-Ellison syndrome are reported. In the first one, on the base of fibroduodenoscopy, an ulceriform cancer was found in the region of Vater's papilla in duodenum, with a penetration to pancreas and the elimination of gastrinoma (duodenectomy with right-side pancreas resection) led to the clinical healing, normalization of stomach secretion and the rest of the laboratory tests. Six years after the operation, the patient had no complaints and is with well preserved capacity for work. A gastrinoma, hazel-nut size, localized in the distal end of Wirsung's canal was concerned in the other two patients, that led to multiple recidivation and complications (hemorrhages and fistulas) of the duodenal peptic ulcer. One of the patients, due to the complications, underwent 7 resections and the other -- 3 but in neither of the two a radical operative intervention was performed (gastrinoma elimination or total gastrectomy) due to which one of them died four years and the other -- 8 years after the first operation and the onset of the clinical manifestations. Only the present radical operation treatment could lead to permanent results.