Scaling up algorithmic debugging with virtual execution trees

Declarative debugging is a powerful debugging technique that has been adapted to practically all programming languages. However, the technique suffers from important scalability problems in both time and memory. With realistic programs the huge size of the execution tree handled makes the debugging session impractical and too slow to be productive. In this work, we present a new architecture for declarative debuggers in which we adapt the technique to work with incomplete execution trees. This allows us to avoid the problem of loading the whole execution tree in main memory and solve the memory scalability problems. We also provide the technique with the ability to debug execution trees that are only partially generated. This allows the programmer to start the debugging session even before the execution tree is computed. This solves the time scalability problems. We have implemented the technique and show its practicality with several experiments conducted with real applications.Insa Cabrera, D.; Silva Galiana, JF. (2011). Scaling up algorithmic debugging with virtual execution trees. En Logic-Based Program Synthesis and Transformation. Springer Verlag (Germany). 6564:149-163. doi:10.1007/978-3-642-20551-4_10S1491636564Av-Ron, E.: Top-Down Diagnosis of Prolog Programs. PhD thesis, Weizmanm Institute (1984)Binks, D.: Declarative Debugging in Gödel. PhD thesis, University of Bristol (1995)Caballero, R.: A Declarative Debugger of Incorrect Answers for Constraint Functional-Logic Programs. In: Proc. of the 2005 ACM SIGPLAN Workshop on Curry and Functional Logic Programming (WCFLP 2005), pp. 8–13. ACM Press, New York (2005)Caballero, R.: Algorithmic Debugging of Java Programs. In: Proc. of the 2006 Workshop on Functional Logic Programming (WFLP 2006). Electronic Notes in Theoretical Computer Science, pp. 63–76 (2006)Caballero, R., Martí-Oliet, N., Riesco, A., Verdejo, A.: A declarative debugger for maude functional modules. Electronic Notes Theoretical Computer Science 238(3), 63–81 (2009)Davie, T., Chitil, O.: Hat-delta: One Right Does Make a Wrong. In: Seventh Symposium on Trends in Functional Programming, TFP 2006 (April 2006)Girgis, H., Jayaraman, B.: JavaDD: a Declarative Debugger for Java. Technical Report 2006-07, University at Buffalo (March 2006)Kokai, G., Nilson, J., Niss, C.: GIDTS: A Graphical Programming Environment for Prolog. In: Workshop on Program Analysis For Software Tools and Engineering (PASTE 1999), pp. 95–104. ACM Press, New York (1999)MacLarty, I.: Practical Declarative Debugging of Mercury Programs. PhD thesis, Department of Computer Science and Software Engineering, The University of Melbourne (2005)Sun Microsystems. Java Platform Debugger Architecture - JPDA (2010), http://java.sun.com/javase/technologies/core/toolsapis/jpda/Nilsson, H., Fritzson, P.: Algorithmic Debugging for Lazy Functional Languages. Journal of Functional Programming 4(3), 337–370 (1994)Shapiro, E.Y.: Algorithmic Program Debugging. MIT Press, Cambridge (1982)Silva, J.: An Empirical Evaluation of Algorithmic Debugging Strategies. Technical Report DSIC-II/10/09, UPV (2009), http://www.dsic.upv.es/~jsilva/research.htm#techsSilva, J.: Algorithmic debugging strategies. In: Proc. of International Symposium on Logic-based Program Synthesis and Transformation (LOPSTR 2006), pp. 134–140 (2006)Silva, J.: A Comparative Study of Algorithmic Debugging Strategies. In: Puebla, G. (ed.) LOPSTR 2006. LNCS, vol. 4407, pp. 143–159. Springer, Heidelberg (2007

Wettability characteristics of an Al2O3/SiO2-based ceramic modified with CO2, Nd:YAG, excimer and high-power diode lasers

Interaction of CO2, Nd:YAG, excimer and high power diode laser (HPDL) radiation with the surface of an Al2O3/SiO2 based ceramic was found to effect significant changes in the wettability characteristics of the material. It was observed that interaction with CO2, Nd:YAG and HPDL radiation reduced the enamel contact angle from 1180 to 310, 340 and 330 respectively. In contrast, interaction with excimer laser radiation resulted an increase in the contact angle to 1210. Such changes were identified as being due to: (i) the melting and partial vitrification of the Al2O3/SiO2 based ceramic surface as a result of interaction with CO2, Nd:YAG HPDL radiation. (ii) the surface roughness of the Al2O3/SiO2 based ceramic increasing after interaction with excimer laser radiation. (iii) the surface oxygen content of the Al2O3/SiO2 based ceramic increasing after interaction with CO2, Nd:YAG and HPDL radiation. The work has shown that the wettability characteristics of the Al2O3/SiO2 based ceramic could be controlled and/or modified with laser surface treatment. In particular, whether the laser radiation had the propensity to cause surface melting. However, a wavelength dependance of the change of the wetting properties could not be deduced from the findings of this work

Two-site recognition of Staphylococcus aureus peptidoglycan by lysostaphin SH3b

Lysostaphin is a bacteriolytic enzyme targeting peptidoglycan, the essential component of the bacterial cell envelope. It displays a very potent and specific activity toward staphylococci, including methicillin-resistant Staphylococcus aureus. Lysostaphin causes rapid cell lysis and disrupts biofilms, and is therefore a therapeutic agent of choice to eradicate staphylococcal infections. The C-terminal SH3b domain of lysostaphin recognizes peptidoglycans containing a pentaglycine crossbridge and has been proposed to drive the preferential digestion of staphylococcal cell walls. Here we elucidate the molecular mechanism underpinning recognition of staphylococcal peptidoglycan by the lysostaphin SH3b domain. We show that the pentaglycine crossbridge and the peptide stem are recognized by two independent binding sites located on opposite sides of the SH3b domain, thereby inducing a clustering of SH3b domains. We propose that this unusual binding mechanism allows synergistic and structurally dynamic recognition of S. aureus peptidoglycan and underpins the potent bacteriolytic activity of this enzyme

Development of a High Intensity Neutron Source at the European Spallation Source: The HighNESS project

The European Spallation Source (ESS), presently under construction in Lund, Sweden, is a multidisciplinary international laboratory that will operate the world's most powerful pulsed neutron source. Supported by a 3M Euro Research and Innovation Action within the EU Horizon 2020 program, a design study (HighNESS) is now underway to develop a second neutron source below the spallation target. Compared to the first source, located above the spallation target and designed for high cold and thermal brightness, the new source will provide higher intensity, and a shift to longer wavelengths in the spectral regions of cold (2 /- 20 {\AA}), very cold (VCN, 10 /- 120 {\AA}), and ultra cold (UCN, > 500 {\AA}) neutrons. The core of the second source will consist of a large liquid deuterium moderator to deliver a high flux of cold neutrons and to serve secondary VCN and UCN sources, for which different options are under study. The features of these new sources will boost several areas of condensed matter research and will provide unique opportunities in fundamental physics. Part of the HighNESS project is also dedicated to the development of future instruments that will make use of the new source and will complement the initial suite of instruments in construction at ESS. The HighNESS project started in October 2020. In this paper, the ongoing developments and the results obtained in the first year are described.Comment: 10 pages, 10 figures, 14th International Topical Meeting on Nuclear Applications of Accelerators, November 30 to December 4, 2021, Washington, D

Apolipoprotein E4 Frequencies in a Japanese Population with Alzheimer's Disease and Dementia with Lewy Bodies

BACKGROUND: The apolipoprotein E (APOE) ε4 allele has been reported to be a risk factor for Alzheimer's disease (AD) and dementia with Lewy bodies (DLB). Previous neuropathological studies have demonstrated similar frequencies of the APOE ε4 allele in AD and DLB. However, the few ante-mortem studies on APOE allele frequencies in DLB have shown lower frequencies than post-mortem studies. One reason for this may be inaccuracy of diagnosis. We examined APOE genotypes in subjects with AD, DLB, and a control group using the latest diagnostic criteria and MRI, SPECT, and MIBG myocardial scintigraphy. METHODS: The subjects of this study consisted of 145 patients with probable AD, 50 subjects with probable DLB, and a control group. AD subjects were divided into two groups based on age of onset: early onset AD (EOAD) and late onset AD (LOAD). All subjects had characteristic features on MRI, SPECT, and/or myocardial scintigraphy. RESULTS: The rate of APOE4 carrier status was 18.3% and the frequency of the ε4 allele was 9.7% in controls. The rate of APOE4 carrier status and the frequency of the ε4 allele were 47% and 27% for LOAD, 50% and 31% for EOAD, and 42% and 31% for DLB, respectively. CONCLUSION: The APOE4 genotypes in this study are consistent with previous neuropathological studies suggesting accurate diagnosis of AD and DLB. APOE4 genotypes were similar in AD and DLB, giving further evidence that the ε4 allele is a risk factor for both disorders

Phosphorylated tyrosine-containing proteins in primary lung cancer correlates with proliferation and prognosis

To determine the usefulness of tyrosine phosphorylation in evaluating biological characteristics, we attempted to evaluate the relationship between the amount of phosphorylated tyrosine-containing proteins and clinicopathological factors, cell proliferation and outcome in non-small cell lung cancer. To evaluate phosphorylated tyrosine-containing proteins we used 96 surgically resected materials of non-small cell lung cancer and normal peripheral lung, while immunohistochemical evaluation was performed. Cell proliferating ability was evaluated using the labelling index of proliferating cell nuclear antigen-positive nuclear staining cells. There were statistically significant differences between the expression levels of phosphorylated tyrosine-containing proteins of normal and cancerous tissues (P<0.0001). Evaluations based on clinicopathological factors apart from histopathological differentiation, showed no statistically significant differences of phosphorylated tyrosine-containing proteins expression. However, phosphorylated tyrosine-containing proteins correlated with cell proliferation activity evaluated (P(Low, High)<0.0001; P(Low, Int) <0.0001; P(Int, High)<0.0001). Furthermore, non-small cell lung cancer cases with high expression and intermediate expression of phosphorylated tyrosine-containing proteins had a significantly shorter disease-free postoperative survival than those with low expression of phosphorylated tyrosine-containing proteins using log-rank analysis (P(Low, Int) <0.0028; P(Low, High)=0.0002). Furthermore, phosphorylated tyrosine-containing proteins expression level statistically contributed to disease-free survival in Cox's proportional hazard model. Therefore, phosphorylated tyrosine-containing proteins in non-small cell lung cancer tissues seem to reflect its biological malignancy, and this evaluation may be valuable for constructing the most appropriate therapeutic strategy

Tyrosine kinase signalling in breast cancer: ErbB family receptor tyrosine kinases

ERBB family receptor tyrosine kinases are overexpressed in a significant subset of breast cancers. One of these receptors, HER2/neu, or ErbB-2, is the target for a new rational therapeutic antibody, Herceptin. Other inhibitors that target this receptor, and another family member, the epidermal growth factor (EGF) receptor, are moving into clinical trials. Both of these receptors are sometimes overexpressed in breast cancer, and still subject to regulation by hormones and other physiological regulators. Optimal use of therapeutics targeting these receptors will require consideration of the several modes of regulation of these receptors and their interactions with steroid receptors

New high-sensitivity searches for neutrons converting into antineutrons and/or sterile neutrons at the HIBEAM/NNBAR experiment at the European Spallation Source

The violation of baryon number, B, is an essential ingredient for the preferential creation of matter over antimatter needed to account for the observed baryon asymmetry in the Universe. However, such a process has yet to be experimentally observed. The HIBEAM/NNBAR program is a proposed two-stage experiment at the European Spallation Source to search for baryon number violation. The program will include high-sensitivity searches for processes that violate baryon number by one or two units: free neutron-antineutron oscillation (n -> (n) over bar) via mixing, neutron-antineutron oscillation via regeneration from a sterile neutron state (n -> [n',(n) over bar'] -> (n) over bar), and neutron disappearance (n -> n'); the effective Delta B = 0 process of neutron regeneration (n ->[n',(n) over bar'] -> n) is also possible. The program can be used to discover and characterize mixing in the neutron, antineutron and sterile neutron sectors. The experiment addresses topical open questions such as the origins of baryogenesis and the nature of dark matter, and is sensitive to scales of new physics substantially in excess of those available at colliders. A goal of the program is to open a discovery window to neutron conversion probabilities (sensitivities) by up to three orders of magnitude compared with previous searches. The opportunity to make such a leap in sensitivity tests should not be squandered. The experiment pulls together a diverse international team of physicists from the particle (collider and low energy) and nuclear physics communities, while also including specialists in neutronics and magnetics.Peer reviewe