Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We discuss a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from (global) static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be checked statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis.

Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We present a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be verified statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by means of user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis. In practice, this modularity allows detecting statically bugs in user programs even if they do not contain any assertions.

Programming with Global Analysis

Abstract is not available

Independence, Global analysis, and parallelism, in dinamically scheduled constraint logic programming.

El punto de vista de muchas otras aplicaciones que modifican las reglas de computación. En segundo lugar, y una vez generalizado el concepto de independencia, es necesario realizar un estudio exhaustivo de la efectividad de las herramientas de análisis en la tarea de la paralelizacion automática. Los resultados obtenidos de dicha evaluación permiten asegurar de forma empírica que la utilización de analizadores globales en la tarea de la paralelizacion automática es vital para la consecución de una paralelizarían efectiva. Por último, a la luz de los buenos resultados obtenidos sobre la efectividad de los analizadores de flujo globales basados en la interpretación abstracta, se presenta la generalización de las herramientas de análisis al contexto de los lenguajes lógicos restricciones y planificación dinámica.

Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin β6 subunit (β6−/−), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology

The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis.

Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors

The proteasome is a large protease complex consisting of multiple catalytic subunits that function simultaneously to digest protein substrates. This complexity has made deciphering the role each subunit plays in the generation of specific protein fragments difficult. Positional scanning libraries of peptide vinyl sulfones were generated in which the amino acid located directly at the site of hydrolysis (P1 residue) was held constant and sequences distal to that residue (P2, P3, and P4 positions) were varied across all natural amino acids (except cysteine and methionine). Binding information for each of the individual catalytic subunits was obtained for each library under a variety of different conditions. The resulting specificity profiles indicated that substrate positions distal to P1 are critical for directing substrates to active subunits in the complex. Furthermore, specificity profiles of IFN-γ-regulated subunits closely matched those of their noninducible counterparts, suggesting that subunit swapping may modulate substrate processing by a mechanism that does require a change in the primary sequence specificity of individual catalytic subunits in the complex. Finally, specificity profiles were used to design specific inhibitors of a single active site in the complex. These reagents can be used to further establish the role of each subunit in substrate processing by the proteasome.

A Global Analysis of of Imperfect Competition in the Banking Systems and the Latest Israeli Regulation Dealing with Market Failures. ACES Working Paper No. 3, 2007

The high concentration of the banking sector is a cross-border phenomenon that has high impact on local and global economies. This paper's main goal is to analyze the factors that impact concentration in the banking systems around the globe. The innovation of this paper is that we combined economic, "economic environment", and culture variables as explanatory variables for this analysis. We found among other things that regulation in the banking system is helpful in order to keep it competitive. We also found that when the society has more individual values rather than collective ones, its banking sector is less concentrated. In the second part of the paper we focused on the Israeli case, showing that although recent indicators of the Israeli banking system indicate a higher level of concentration and lower level of competition, it seems that the recent trend is moving toward less concentration and higher competition.

CYP2D6: a global analysis of phenotypic and genotypic variation in search of radical cure of Plasmodium vivax malaria

Thesis (Master's)--University of Washington, 2016-06

Carleson Measures and Logvinenko-Sereda sets on compact manifolds

Given a compact Riemannian manifold $M$ of dimension $m \geq 2$, we study the space of functions of $L^2(M)$generated by eigenfunctions ofeigenvalues less than $L \geq 1$ associated to the Laplace-Beltrami operator on $M$. On these spaces we give a characterization of the Carleson measures and the Logvinenko-Sereda sets.

National, regional, and global trends in fasting plasma glucose and diabetes prevalence since 1980: systematic analysis of health examination surveys and epidemiological studies with 370 country-years and 2·7 million participants.

BACKGROUND: Data for trends in glycaemia and diabetes prevalence are needed to understand the effects of diet and lifestyle within populations, assess the performance of interventions, and plan health services. No consistent and comparable global analysis of trends has been done. We estimated trends and their uncertainties in mean fasting plasma glucose (FPG) and diabetes prevalence for adults aged 25 years and older in 199 countries and territories. METHODS: We obtained data from health examination surveys and epidemiological studies (370 country-years and 2·7 million participants). We converted systematically between different glycaemic metrics. For each sex, we used a Bayesian hierarchical model to estimate mean FPG and its uncertainty by age, country, and year, accounting for whether a study was nationally, subnationally, or community representative. FINDINGS: In 2008, global age-standardised mean FPG was 5·50 mmol/L (95% uncertainty interval 5·37-5·63) for men and 5·42 mmol/L (5·29-5·54) for women, having risen by 0·07 mmol/L and 0·09 mmol/L per decade, respectively. Age-standardised adult diabetes prevalence was 9·8% (8·6-11·2) in men and 9·2% (8·0-10·5) in women in 2008, up from 8·3% (6·5-10·4) and 7·5% (5·8-9·6) in 1980. The number of people with diabetes increased from 153 (127-182) million in 1980, to 347 (314-382) million in 2008. We recorded almost no change in mean FPG in east and southeast Asia and central and eastern Europe. Oceania had the largest rise, and the highest mean FPG (6·09 mmol/L, 5·73-6·49 for men; 6·08 mmol/L, 5·72-6·46 for women) and diabetes prevalence (15·5%, 11·6-20·1 for men; and 15·9%, 12·1-20·5 for women) in 2008. Mean FPG and diabetes prevalence in 2008 were also high in south Asia, Latin America and the Caribbean, and central Asia, north Africa, and the Middle East. Mean FPG in 2008 was lowest in sub-Saharan Africa, east and southeast Asia, and high-income Asia-Pacific. In high-income subregions, western Europe had the smallest rise, 0·07 mmol/L per decade for men and 0·03 mmol/L per decade for women; North America had the largest rise, 0·18 mmol/L per decade for men and 0·14 mmol/L per decade for women. INTERPRETATION: Glycaemia and diabetes are rising globally, driven both by population growth and ageing and by increasing age-specific prevalences. Effective preventive interventions are needed, and health systems should prepare to detect and manage diabetes and its sequelae. FUNDING: Bill & Melinda Gates Foundation and WHO.

Adaptive strategy for the statistical analysis of connectomes.

We study an adaptive statistical approach to analyze brain networks represented by brain connection matrices of interregional connectivity (connectomes). Our approach is at a middle level between a global analysis and single connections analysis by considering subnetworks of the global brain network. These subnetworks represent either the inter-connectivity between two brain anatomical regions or by the intra-connectivity within the same brain anatomical region. An appropriate summary statistic, that characterizes a meaningful feature of the subnetwork, is evaluated. Based on this summary statistic, a statistical test is performed to derive the corresponding p-value. The reformulation of the problem in this way reduces the number of statistical tests in an orderly fashion based on our understanding of the problem. Considering the global testing problem, the p-values are corrected to control the rate of false discoveries. Finally, the procedure is followed by a local investigation within the significant subnetworks. We contrast this strategy with the one based on the individual measures in terms of power. We show that this strategy has a great potential, in particular in cases where the subnetworks are well defined and the summary statistics are properly chosen. As an application example, we compare structural brain connection matrices of two groups of subjects with a 22q11.2 deletion syndrome, distinguished by their IQ scores.

Bias and standard error for social reciprocity measurements

The directional consistency and skew-symmetry statistics have been proposed as global measurements of social reciprocity. Although both measures can be useful for quantifying social reciprocity, researchers need to know whether these estimators are biased in order to assess descriptive results properly. That is, if estimators are biased, researchers should compare actual values with expected values under the specified null hypothesis. Furthermore, standard errors are needed to enable suitable assessment of discrepancies between actual and expected values. This paper aims to derive some exact and approximate expressions in order to obtain bias and standard error values for both estimators for round-robin designs, although the results can also be extended to other reciprocal designs.

A Summary of the American Bar Association’s (ABA) Jurisdiction in Cyberspace Project: “Achieving Legal and Business Order in Cyberspace: A Report on Global Jurisdiction Issues Created by the Internet”

"Suite à plus de deux années de recherches, le projet de l’American Bar Association (ABA) concernant la juridiction du cyberespace, « Achieving Legal and Business Order in Cyberspace: A Report on Global Jurisdiction Issues Created by the Internet », a été publié dans l’édition du mois d’août 2000 de la revue juridique The Business Lawyer. Ce rapport poursuivait deux objectifs distincts : Tout d’abord, effectuer une analyse globale des complexités potentielles entourant les conflits juridictionnels découlant du commerce en ligne. Ensuite, élaborer une liste exhaustive des solutions pouvant être utilisées pour résoudre de tels conflits. Le présent article se veut un résumé concis et accessible des trois grandes sections du « Cyberspace Jurisdiction Report » : (1) les solutions proposées aux problèmes juridictionnels découlant des conflits résultant du commerce électronique ; (2) afin d’appuyer les solutions proposées : l’utilisation d’exemples d’occasions où la technologie a déjà, par le passé, causé la métamorphose de certains paradigmes juridictionnels; et (3) afin d’appuyer les solutions proposées : l’utilisation d’un contexte doctrinal."

Significance of Time Scales in Nonlinear Dynamical Analysis of Electroencephalogram Signals

We propose to show in this paper, that the time series obtained from biological systems such as human brain are invariably nonstationary because of different time scales involved in the dynamical process. This makes the invariant parameters time dependent. We made a global analysis of the EEG data obtained from the eight locations on the skull space and studied simultaneously the dynamical characteristics from various parts of the brain. We have proved that the dynamical parameters are sensitive to the time scales and hence in the study of brain one must identify all relevant time scales involved in the process to get an insight in the working of brain.