On the accuracy of spectrum-based fault localization

Spectrum-based fault localization shortens the test- diagnose-repair cycle by reducing the debugging effort. As a light-weight automated diagnosis technique it can easily be integrated with existing testing schemes. However, as no model of the system is taken into account, its diagnostic accuracy is inherently limited. Using the Siemens Set benchmark, we investigate this diagnostic accuracy as a function of several parameters (such as quality and quantity of the program spectra collected during the execution of the system), some of which directly relate to test design. Our results indicate that the superior performance of a particular similarity coefficient, used to analyze the program spectra, is largely independent of test design. Furthermore, near- optimal diagnostic accuracy (exonerating about 80% of the blocks of code on average) is already obtained for low-quality error observations and limited numbers of test cases. The influence of the number of test cases is of primary importance for continuous (embedded) processing applications, where only limited observation horizons can be maintained

Granular cell tumor of the breast: correlations between imaging and pathology findings

OBJECTIVE: To review the imaging features of granular cell tumors of the breast (on mammography, ultrasound, and magnetic resonance imaging), establishing a pathological correlation, in order to familiarize radiologists with this entity and make them aware of the differential diagnoses, other than malignancy, of lesions with spiculated margins. MATERIALS AND METHODS: We reviewed the medical records (from a clinical-pathology database and picture archiving and communication system) of five patients with a pathologically confirmed diagnosis of granular cell tumor of the breast, treated at the Portuguese Oncology Institute of Lisbon, in the city of Lisbon, Portugal, between January 2012 and December 2018. RESULTS: All five tumors exhibited imaging features highly suggestive of malignancy (BI-RADS 5 lesions), namely spiculated margins, significant depth, and posterior acoustic shadowing (on ultrasound). One tumor showed a kinetic curve indicative of washout on magnetic resonance imaging, two were adherent to the pectoralis muscle, and one was accompanied by skin retraction. Pathology provided the definitive diagnosis in all cases. CONCLUSION: Granular cell tumors of the breast pose a diagnostic challenge because they can present with clinical and imaging features mimicking malignancy, and the diagnosis is therefore provided by pathology. Radiologists should be familiarized with this entity, so they can be aware of the fact that breast lesions with spiculated margins can be indicative of diagnoses other than malignancy.info:eu-repo/semantics/publishedVersio

Diagnosis of embedded software using program spectra

Automated diagnosis of errors detected during software testing can improve the efficiency of the debugging process, and can thus help to make software more reliable. In this paper we discuss the application of a specific automated debugging technique, namely software fault localization through the analysis of program spectra, in the area of embedded software in high-volume consumer electronics products. We discuss why the technique is particularly well suited for this application domain, and through experiments on an industrial test case we demonstrate that it can lead to highly accurate diagnoses of realistic errors

Blood-retinal barrier permeability and its relation to progression of retinopathy in patients with type 2 diabetes. A four-year follow-up study.

Forty patients with late-onset diabetes (age at diagnosis 30 years or more) and minimal retinopathy as found by fundus photography were followed prospectively by repeated examination (baseline, 1 year, and 4 years). The study shows that early retinopathy changes are not permanent or invariably progressive. In the 1st year of follow-up microaneurysms worsened in 25%, improved in 10%, and remained stabilized in 65%. Vitreous fluorometry was able to detect an overall increase of 0.84 +/- 1.06 x 10(-6) min-1 in blood-retinal barrier (BRB) penetration ratios. After 4 years, 16 of the 40 patients had undergone photocoagulation (focal photo-coagulation in 11 and pan retinal photocoagulation in 5). The eyes that needed photocoagulation were the eyes that had higher fluorometry penetration ratios at the patient's entry into the study and showed a higher rate of deterioration during the 1st year of the study (5.54 +/- 1.97 vs 3.11 +/- 1.22 x 10(-6) min-1, P < 0.001, initial values; 1.52 +/- 0.76 vs 0.45 +/- 0.99 x 10(-6) min-1, P < 0.001, annual increase in leakage). The eyes that did not need photocoagulation, 24 out of 40, showed stable fluorometry readings within the 4-year period of follow-up (+0.02 +/- 0.98 10(-6) min-1). Abnormally high vitreous fluorometry values and their rapid increase over time appear to be good indicators of rapid progression and worsening of the retinopathy

Progression of retinopathy and alteration of the blood-retinal barrier in patients with type 2 diabetes: a 7-year prospective follow-up study

BACKGROUND: The study was carried out to evaluate the correlation between blood-retinal barrier (BRB) permeability and the progression of diabetic retinopathy (DR), defined by development of "need for photocoagulation", over a 7-year period by means of vitreous fluorometry (VF). METHODS: Forty type 2 diabetic patients with minimal or no retinopathy, aged 40-65 years (mean 53.9 + 7.3 years), were followed up prospectively for 7 years. Investigations including standard ophthalmological examination, fundus photography, fluorescein angiography and VF were performed at entry and 1, 4, 5 and 7 years later. Only one eye per patient was included in the study. Need for photocoagulation was based on Early Treatment Diabetic Retinopathy Study protocols and decided by the attending ophthalmologist. RESULTS: After 7 years of follow-up a total of 22 of the 40 eyes had received photocoagulation. The eyes that needed photocoagulation were those that had higher VF values at the entry of the study and showed higher rates of deterioration (initial values 5.1 + 1.9 vs 2.8 + 1.5 x 10(-6) min-1, P < 0.001; annual increase in leakage for the first year, 1.5 + 0.8 vs 0.5 + 1.0 x 10(-6) min-1, P < 0.001,). The eyes that did not need photocoagulation during the 7 years of follow-up showed stable VF readings (-0.1 + 1.2 x 10(-6) min-1, difference between initial values and 7 years later). CONCLUSIONS: Abnormally high VF values and their rapid increase over time are good indicators of progression and worsening of the retinopathy in diabetes type 2

Video enhancement using adaptive spatio-temporal connective filter and piecewise mapping

This paper presents a novel video enhancement system based on an adaptive spatio-temporal connective (ASTC) noise filter and an adaptive piecewise mapping function (APMF). For ill-exposed videos or those with much noise, we first introduce a novel local image statistic to identify impulse noise pixels, and then incorporate it into the classical bilateral filter to form ASTC, aiming to reduce the mixture of the most two common types of noises - Gaussian and impulse noises in spatial and temporal directions. After noise removal, we enhance the video contrast with APMF based on the statistical information of frame segmentation results. The experiment results demonstrate that, for diverse low-quality videos corrupted by mixed noise, underexposure, overexposure, or any mixture of the above, the proposed system can automatically produce satisfactory results

Theoretical Aspects of Particle Production

These lectures describe some of the latest data on particle production in high-energy collisions and compare them with theoretical calculations and models based on QCD. The main topics covered are: fragmentation functions and factorization, small-x fragmentation, hadronization models, differences between quark and gluon fragmentation, current and target fragmentation in deep inelastic scattering, and heavy quark fragmentation.Comment: 26 pages, 27 figures. Lectures at International Summer School on Particle Production Spanning MeV and TeV Energies, Nijmegen, The Netherlands, August 199

Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma

The lung is a complex ecosystem of host cells and microbes often disrupted in pathological conditions. Although bacteria have been hypothesized as agents of carcinogenesis, little is known about microbiota profile of the most prevalent cancer subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). To characterize lung cancer (LC) microbiota a first a screening was performed through a pooled sequencing approach of 16S ribosomal RNA gene (V3-V6) using a total of 103 bronchoalveaolar lavage fluid samples. Then, identified taxa were used to inspect 1009 cases from The Cancer Genome Atlas and to annotate tumor unmapped RNAseq reads. Microbial diversity was analyzed per cancer subtype, history of cigarette smoking and airflow obstruction, among other clinical data. We show that LC microbiota is enriched in Proteobacteria and more diverse in SCC than ADC, particularly in males and heavier smokers. High frequencies of Proteobacteria were found to discriminate a major cluster, further subdivided into well-defined communities’ associated with either ADC or SCC. Here, a SCC subcluster differing from other cases by a worse survival was correlated with several Enterobacteriaceae. Overall, this study provides first evidence for a correlation between lung microbiota and cancer subtype and for its influence on patient life expectancy.We would like to thank all patients for donating their samples and for collaborating in this study. IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT). This work was supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds through the FCT (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274, fellowships SFRH/BPD/77646/2011 and SFRH/BPD/120777/2016 to S.G. and P.I.M., respectively, grant PTDC/BEXGMG/0242/2012 to S.S. and by Programa Operacional Regional do Norte (ON.2 – O Novo Norte and Norte 2020), through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN; projects NORTE-07-0162-FEDER-00018 and NORTE-070162-FEDER-000067, and NORTE-01-0145-FEDER-000029)

Phenomenology of event shapes at hadron colliders

We present results for matched distributions of a range of dijet event shapes at hadron colliders, combining next-to-leading logarithmic (NLL) accuracy in the resummation exponent, next-to-next-to leading logarithmic (NNLL) accuracy in its expansion and next-to-leading order (NLO) accuracy in a pure alpha_s expansion. This is the first time that such a matching has been carried out for hadronic final-state observables at hadron colliders. We compare our results to Monte Carlo predictions, with and without matching to multi-parton tree-level fixed-order calculations. These studies suggest that hadron-collider event shapes have significant scope for constraining both perturbative and non-perturbative aspects of hadron-collider QCD. The differences between various calculational methods also highlight the limits of relying on simultaneous variations of renormalisation and factorisation scale in making reliable estimates of uncertainties in QCD predictions. We also discuss the sensitivity of event shapes to the topology of multi-jet events, which are expected to appear in many New Physics scenarios.Comment: 70 pages, 25 figures, additional material available from http://www.lpthe.jussieu.fr/~salam/pp-event-shapes

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters

<p>Abstract</p> <p>Background</p> <p>Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters.</p> <p>Implementation</p> <p>MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections.</p> <p>Conclusion</p> <p>MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.</p