Comparison and Evaluation of Clone Detection Tools

Many techniques for detecting duplicated source code (software clones) have been proposed in the past. However, it is not yet clear how these techniques compare in terms of recall and precision as well as space and time requirements. This paper presents an experiment that evaluates six clone detectors based on eight large C and Java programs (altogether almost 850 KLOC). Their clone candidates were evaluated by one of the authors as an independent third party. The selected techniques cover the whole spectrum of the state-of-the-art in clone detection. The techniques work on text, lexical and syntactic information, software metrics, and program dependency graphs

Assessing minipig compact jawbone quality at the microscale

Preclinical studies often require animal models for in vivo experiments. Particularly in dental research, pig species are extensively used due to their anatomical similarity to humans. However, there is a considerable knowledge gap on the multiscale morphological and mechanical properties of the miniature pigs’ jawbones, which is crucial for implant studies and a direct comparison to human tissue. In the present work, we demonstrate a multimodal framework to assess the jawbone quantity and quality for a minipig animal model that could be further extended to humans. Three minipig genotypes, commonly used in dental research, were examined: Yucatan, G ̈ottingen, and Sinclair. Three animals per genotype were tested. Cortical bone samples were extracted from the premolar region of the mandible, opposite to the teeth growth. Global morphological, compositional, and mechanical properties were assessed using micro-computed tomography (micro-CT) together with Raman spectroscopy and nano- indentation measurements, averaged over the sample area. Local mineral-mechanical relationships were investigated with the site-matched Raman spectroscopy and micropillar compression tests. For this, a novel femtosecond laser ablation protocol was developed, allowing high-throughput micropillar fabrication and testing without exposure to high vacuum. At the global averaged sample level, bone relative mineralization demonstrated a significant difference between the genotypes, which was not observed from the complementary micro-CT measurements. Moreover, bone hardness measured by nanoindentation showed a positive trend with the relative mineralization. For all genotypes, significant differences between the relative mineralization and elastic properties were more pronounced within the osteonal regions of cortical bone. Site-matched micropillar compression and Raman spectroscopy highlighted the differences between the genotypes’ yield stress and mineral to matrix ratios. The methods used at the global level (averaged over sample area) could be potentially correlated to the medical tools used to assess jawbone toughness and morphology in clinics. On the other hand, the local analysis methods can be applied to quantify compressive bone mechanical properties and their relationship to bone mineralization

Sidus Stem-Free Shoulder System for primary osteoarthritis: short-term results of a multicenter study

BACKGROUND: The aim of this prospective multicenter study was to evaluate clinical and radiologic results of a new metaphyseal anchored system. This system features a different anchor geometry that potentially leads to better bony integration and less loosening. METHODS: From November 2012 until December 2015, 148 patients (151 shoulders) were treated with the Sidus Stem-Free Shoulder System at 9 centers in Europe. The main indication was primary osteoarthritis (80.1%). This analysis only includes patients diagnosed with primary osteoarthritis (n = 121). A clinical evaluation was performed using the Constant-Murley score, Subjective Shoulder Value, American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form, and range of motion. Radiologic assessment was based on the occurrence of radiolucent lines and signs of implant migration, osteolysis, loosening, and heterotopic ossification. RESULTS: We evaluated 105 patients after a follow-up period of 2 years. There were 53 women and 52 men. The average age was 64 years. Total shoulder arthroplasty was performed in 73 cases and hemiarthroplasty in 32. The Constant-Murley score improved from 26 points preoperatively to 70 points at 2 years' follow-up (P < .001). The Subjective Shoulder Value increased from 34% to 84% (P < .001), and the American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form increased from 34 points to 86 points (P < .001). Radiologically, neither migration nor loosening was found. However, radiolucent lines of 2 mm or greater could be detected around the glenoid in 2 cases, but none of them have had clinical relevance yet. The overall complication rate was 6.7%, and the revision rate was 0%. CONCLUSION: Patients with the Sidus Stem-Free Shoulder System achieve good clinical and radiologic short-term results that are comparable with the results of other stem-free shoulder implants

Northern lights assay: a versatile method for comprehensive detection of DNA damage.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked DownloadDNA damage assays have various limitations in types of lesions detected, sensitivity, specificity and samples that can be analyzed. The Northern Lights Assay (NLA) is based on 2D Strandness-Dependent Electrophoresis (2D-SDE), a technique that separates nucleic acids based on length, strandness, structure and conformation changes induced by damage. NLA is run on a microgel platform in 20-25 min. Each specimen is analyzed in pairs of non-digested DNA to detect single- and double-stranded breaks (DSBs) and Mbo I-digested DNA to detect other lesions. We used NLA to evaluate DNA in solution and isolated from human cells treated with various genotoxic agents. NLA detected and distinguished between single- and DSBs, interstrand and intrastrand DNA crosslinks, and denatured single-stranded DNA. NLA was sufficiently sensitive to detect biologically relevant amount of DNA damage. NLA is a versatile, sensitive and simple method for comprehensive and simultaneous analysis of multiple types of damage, both in purified DNA and in DNA isolated from cells and body fluids. NLA can be used to evaluate DNA quality in biosamples, monitor complex molecular procedures, assess genotoxicity, diagnose genome instability, facilitate cancer theranostics and in basic nucleic acids research.University of Iceland Research Fund Landspitali University Hospital Research Fund Icelandic Center for Research Funds Lifeind ehf. University of Iceland Research Fun

Peri-operative red blood cell transfusion in neonates and infants: NEonate and Children audiT of Anaesthesia pRactice IN Europe: A prospective European multicentre observational study

BACKGROUND: Little is known about current clinical practice concerning peri-operative red blood cell transfusion in neonates and small infants. Guidelines suggest transfusions based on haemoglobin thresholds ranging from 8.5 to 12 g dl-1, distinguishing between children from birth to day 7 (week 1), from day 8 to day 14 (week 2) or from day 15 (≥week 3) onwards. OBJECTIVE: To observe peri-operative red blood cell transfusion practice according to guidelines in relation to patient outcome. DESIGN: A multicentre observational study. SETTING: The NEonate-Children sTudy of Anaesthesia pRactice IN Europe (NECTARINE) trial recruited patients up to 60 weeks' postmenstrual age undergoing anaesthesia for surgical or diagnostic procedures from 165 centres in 31 European countries between March 2016 and January 2017. PATIENTS: The data included 5609 patients undergoing 6542 procedures. Inclusion criteria was a peri-operative red blood cell transfusion. MAIN OUTCOME MEASURES: The primary endpoint was the haemoglobin level triggering a transfusion for neonates in week 1, week 2 and week 3. Secondary endpoints were transfusion volumes, 'delta haemoglobin' (preprocedure - transfusion-triggering) and 30-day and 90-day morbidity and mortality. RESULTS: Peri-operative red blood cell transfusions were recorded during 447 procedures (6.9%). The median haemoglobin levels triggering a transfusion were 9.6 [IQR 8.7 to 10.9] g dl-1 for neonates in week 1, 9.6 [7.7 to 10.4] g dl-1 in week 2 and 8.0 [7.3 to 9.0] g dl-1 in week 3. The median transfusion volume was 17.1 [11.1 to 26.4] ml kg-1 with a median delta haemoglobin of 1.8 [0.0 to 3.6] g dl-1. Thirty-day morbidity was 47.8% with an overall mortality of 11.3%. CONCLUSIONS: Results indicate lower transfusion-triggering haemoglobin thresholds in clinical practice than suggested by current guidelines. The high morbidity and mortality of this NECTARINE sub-cohort calls for investigative action and evidence-based guidelines addressing peri-operative red blood cell transfusions strategies. TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT02350348

A Product Line Asset Management Tool

Abstract. When developing a software product line, software engineers are confronted with the task of configuration and revision management for the product line as a whole. Furthermore, both on domain and product level explicit variation management has to be provided for. While there are partial solutions to these tasks, there is no integrated support for the product line developers. In this paper we present a tool for the integrated management of software assets for software product line development. We address the problems of configuration and revision management, explicit variation point handling, and the differences in domain and product development. In our approach, the available solutions to specific tasks are integrated to provide a new solution.

MADSTRESS: A linear approach for evaluating scattering and absorption coefficients of samples measured using time-resolved spectroscopy in reflection

Time-resolved spectroscopy is a powerful technique permitting the separation of the scattering properties from the chemical absorption properties of a sample. The reduced scattering coefficient and the absorption coefficient are usually obtained by fitting diffusion or Monte Carlo models to the measured data using numerical optimization techniques. However, these methods do not take the spectral dimension of the data into account during the evaluation procedure, but evaluate each wavelength separately. A procedure involving multivariate methods may seem more appealing for people used to handling conventional near-infrared data. In this study we present a new method for processing TRS spectra in order to compute the absorption and reduced scattering coefficients. This approach, MADSTRESS, is based on linear regression and a twodimensional (2D) interpolation procedure. The method has allowed us to calculate absorption and scattering coefficients of apples and fructose powder. The accuracy of the method was good enough to provide the identification of fructose absorption peaks in apple absorption spectra and the construction of a calibration model predicting the sugar content of apples

Micro- to nano-scale investigation of Precambrian metasediments: biogenicity and preservation in the 3.22 Ga Moodies Group (Barberton Greenstone Belt, S. Africa) and the 2.46 Ga Brockman Iron Formation (Hamersley Basin, W. Australia)

Abstract Precambrian metasediments provide a unique archive for understanding Earth’s earliest biosphere, however traces of microbial life preserved in ancient rocks are often controversial. In this study we leveraged several micro- to nano-scale techniques to study filamentous structures previously reported in clastic sediments of the 3.22 Ga Moodies Group, Barberton Greenstone Belt, S. Africa. We performed petrographic, mineralogical, electron microprobe, confocal fluorescence and electron microscopy analyses of these structures in order to evaluate their biogenicity and syngenecity. We also examined drill core samples of deep-water iron formations from the 2.46 Ga Joffre member of the Brockman Iron Formation (Hamersley Basin, W. Australia) to better understand their potential biogenicity. In both cases, we aimed to resolve primary vs. secondary mineral assemblages and their relation to filamentous or sedimentary structures. In the Moodies Group samples, filamentous structures were resolved by confocal imaging and revealed to be crosscut by later metamorphic phases, highlighting their syngenetic nature. Three-dimensional imaging reveals that while the filamentous structures are not necessarily associated with grain boundaries (e.g., as organic coatings), they form both sheets and filaments, complicating their interpretation but not ruling out a biological origin. No organic microstructures appeared to be preserved in our Dales Gorge samples. We also examined the possible application of electron paramagnetic resonance spectroscopy (EPR) to carbonaceous matter in ancient silica-rich matrices, similar to Bourbin et al. (2013), using samples from the Brockman iron formation. While resonance associated with organic matter was largely unresolvable in the Brockman iron formation samples due to their low organic matter contents, large effects on the EPR spectra were apparent stemming from the presence of magnetic iron minerals, highlighting the need to carefully consider sample composition in EPR analyses targeting ancient organic matter. Collectively, this study highlights the added value of micro- to nano-scale techniques as applied to Precambrian metasediments containing traces of ancient life, for example in revealing the pre-metamorphic emplacement and three-dimensional structure of filaments in the Moodies Group, but also the potential drawbacks and pitfalls, such as the case of strong magnetic mineral interference in EPR analysis of organic matter in trace abundance in the Dales Gorge

Evaluation of manual vs semi-automated delineation of liver lesions on CT images

In this paper we compare a semi-automated delineation method with totally manual delineation for area quantification, with respect to efficiency, quality, and intra- and interobserver variability. Liver lesions on 28 CT images were delineated by three observers, twice using completely manual delineation and twice using a semi-automated method. Quantitative comparisons were performed with respect to delineated area and time required for the delineation tasks. Subjective comparisons were performed with respect to efficiency and perceived quality of the semi-automated method. The areas obtained using semi-automated delineation were significantly smaller (11 %) than those obtained using totally manual delineation. Intraobserver and interobserver variability with the semi-automated method were approximately three times lower than with manual delineation. Efficiency of the semi-automated method was subjectively rated favorable, although further improvements are possible. With respect to quality, the semi-automated method was ranked better than the manual method in 73 % of cases.status: publishe