A Transformational Approach to Resource Analysis with Typed-Norms

In order to automatically infer the resource consumption of programs, analyzers track how data sizes change along a program s execution. Typically, analyzers measure the sizes of data by applying norms which are mappings from data to natural numbers that represent the sizes of the corresponding data. When norms are defined by taking type information into account, they are named typed-norms. The main contribution of this paper is a transformational approach to resource analysis with typed-norms. The analysis is based on a transformation of the program into an intermediate abstract program in which each variable is abstracted with respect to all considered norms which are valid for its type. We also sketch a simple analysis that can be used to automatically infer the required, useful, typed-norms from programs.This work was funded partially by the EU project FP7-ICT-610582 ENVISAGE: Engineering Virtualized Services (http://www.envisage-project.eu) and by the Spanish projects TIN2008-05624 and TIN2012-38137. Raúl Gutiérrez is also partially supported by a Juan de la Cierva Fellowship from the Spanish MINECO, ref. JCI-2012-13528.Albert Albiol, EM.; Genaim, S.; Gutiérrez Gil, R. (2014). A Transformational Approach to Resource Analysis with Typed-Norms. Lecture Notes in Computer Science. 8901:38-53. https://doi.org/10.1007/978-3-319-14125-1_3S38538901Albert, E., Arenas, P., Genaim, S., Gómez-Zamalloa, M., Puebla, G.: Cost Analysis of Concurrent OO Programs. In: Yang, H. (ed.) APLAS 2011. LNCS, vol. 7078, pp. 238–254. Springer, Heidelberg (2011)Albert, E., Arenas, P., Genaim, S., Puebla, G., Zanardini, D.: Cost Analysis of Java Bytecode. In: De Nicola, R. (ed.) ESOP 2007. LNCS, vol. 4421, pp. 157–172. Springer, Heidelberg (2007)Albert, E., Arenas, P., Genaim, S., Puebla, G., Zanardini, D.: Removing Useless Variables in Cost Analysis of Java Bytecode. In: Proc. of SAC 2008, pp. 368–375. ACM (2008)Alonso, D., Arenas, P., Genaim, S.: Handling Non-linear Operations in the Value Analysis of COSTA. In: Proc. of BYTECODE 2011. ENTCS, vol. 279, pp. 3–17. Elsevier (2011)Bossi, A., Cocco, N., Fabris, M.: Proving Termination of Logic Programs by Exploiting Term Properties. In: Proc. of TAPSOFT 1991. LNCS, vol. 494, pp. 153–180. Springer (1991)Bruynooghe, M., Codish, M., Gallagher, J., Genaim, S., Vanhoof, W.: Termination Analysis of Logic Programs through Combination of Type-Based norms. TOPLAS 29(2), Art. 10 (2007)Claessen, K., Hughes, J.: QuickCheck: A Lightweight Tool for Random Testing of Haskell Programs. In: Proc. of ICFP 2000, pp. 268–279. ACM (2000)Fähndrich, M.: Static Verification for Code Contracts. In: Cousot, R., Martel, M. (eds.) SAS 2010. LNCS, vol. 6337, pp. 2–5. Springer, Heidelberg (2010)Genaim, S., Codish, M., Gallagher, J.P., Lagoon, V.: Combining Norms to Prove Termination. In: Cortesi, A. (ed.) VMCAI 2002. LNCS, vol. 2294, pp. 123–138. Springer, Heidelberg (2002)Johnsen, E.B., Hähnle, R., Schäfer, J., Schlatte, R., Steffen, M.: ABS: A Core Language for Abstract Behavioral Specification. In: Aichernig, B.K., de Boer, F.S., Bonsangue, M.M. (eds.) Formal Methods for Components and Objects. LNCS, vol. 6957, pp. 142–164. Springer, Heidelberg (2011)King, A., Shen, K., Benoy, F.: Lower-bound Time-complexity Analysis of Logic Programs. In: Proc. of ILPS 1997, pp. 261–275. MIT Press (1997)Serrano, A., Lopez-Garcia, P., Bueno, F., Hermenegildo, M.: Sized Type Analysis for Logic Programs. In: Tech. Comms. of ICLP 2013. Cambridge U. Press (2013) (to appear)Spoto, F., Mesnard, F., Payet, É.: A Termination Analyser for Java Bytecode based on Path-Length. TOPLAS 32(3), Art. 8 (2010)Vallée-Rai, R., Hendren, L., Sundaresan, V., Lam, P., Gagnon, E., Co, P.: Soot - a Java Optimization Framework. In: Proc. of CASCON 1999. pp. 125–135. IBM (1999)Vasconcelos, P.: Space Cost Analysis using Sized Types. Ph.D. thesis, School of CS, University of St. Andrews (2008)Vasconcelos, P.B., Hammond, K.: Inferring Cost Equations for Recursive, Polymorphic and Higher-Order Functional Programs. In: Trinder, P., Michaelson, G.J., Peña, R. (eds.) IFL 2003. LNCS, vol. 3145, pp. 86–101. Springer, Heidelberg (2004)Wegbreit, B.: Mechanical Program Analysis. Commun. ACM 18(9), 528–539 (1975

Heritable patterns of tooth decay in the permanent dentition: principal components and factor analyses

<p>Abstract</p> <p>Background</p> <p>Dental caries is the result of a complex interplay among environmental, behavioral, and genetic factors, with distinct patterns of decay likely due to specific etiologies. Therefore, global measures of decay, such as the DMFS index, may not be optimal for identifying risk factors that manifest as specific decay patterns, especially if the risk factors such as genetic susceptibility loci have small individual effects. We used two methods to extract patterns of decay from surface-level caries data in order to generate novel phenotypes with which to explore the genetic regulation of caries.</p> <p>Methods</p> <p>The 128 tooth surfaces of the permanent dentition were scored as carious or not by intra-oral examination for 1,068 participants aged 18 to 75 years from 664 biological families. Principal components analysis (PCA) and factor analysis (FA), two methods of identifying underlying patterns without <it>a priori </it>surface classifications, were applied to our data.</p> <p>Results</p> <p>The three strongest caries patterns identified by PCA recaptured variation represented by DMFS index (correlation, r = 0.97), pit and fissure surface caries (r = 0.95), and smooth surface caries (r = 0.89). However, together, these three patterns explained only 37% of the variability in the data, indicating that <it>a priori </it>caries measures are insufficient for fully quantifying caries variation. In comparison, the first pattern identified by FA was strongly correlated with pit and fissure surface caries (r = 0.81), but other identified patterns, including a second pattern representing caries of the maxillary incisors, were not representative of any previously defined caries indices. Some patterns identified by PCA and FA were heritable (h²= 30-65%, p = 0.043-0.006), whereas other patterns were not, indicating both genetic and non-genetic etiologies of individual decay patterns.</p> <p>Conclusions</p> <p>This study demonstrates the use of decay patterns as novel phenotypes to assist in understanding the multifactorial nature of dental caries.</p

Liver cirrhosis, other liver diseases, and risk of hospitalisation for intracerebral haemorrhage: A Danish population-based case-control study

<p>Abstract</p> <p>Background</p> <p>Liver diseases are suspected risk factors for intracerebral haemorrhage (ICH). We conducted a population-based case-control study to examine risk of ICH among hospitalised patients with liver cirrhosis and other liver diseases.</p> <p>Methods</p> <p>We used data from the hospital discharge registries (1991–2003) and the Civil Registration System in Denmark, to identify 3,522 cases of first-time hospitalisation for ICH and 35,173 sex- and age-matched population controls. Among cases and controls we identified patients with a discharge diagnosis of liver cirrhosis or other liver diseases before the date of ICH. We computed odds ratios for ICH by conditional logistic regressions, adjusting for a number of confounding factors.</p> <p>Results</p> <p>There was an increased risk of ICH for patients with alcoholic liver cirrhosis (adjusted OR = 4.8, 95% CI: 2.7–8.3), non-alcoholic liver cirrhosis (adjusted OR = 7.7, 95% CI: 2.0–28.9) and non-cirrhotic alcoholic liver disease (adjusted OR = 5.4, 95%CI:3.1–9.5) but not for patients with non-cirrhotic non-alcoholic liver diseases (adjusted OR = 0.9, 95%CI:0.5–1.6). The highest risk was found among women with liver cirrhosis (OR = 8.9, 95%CI:2.9–26.7) and for patients younger than 70 years (OR = 6.1, 95%CI:3.4–10.9). There were no sex- or age-related differences in the association between other liver diseases (alcoholic or non-alcoholic) and hospitalisation with ICH.</p> <p>Conclusion</p> <p>Patients with liver cirrhosis and non-cirrhotic alcoholic liver disease have a clearly increased risk for ICH.</p

Effectiveness of second-generation antipsychotics: a naturalistic, randomized comparison of olanzapine, quetiapine, risperidone, and ziprasidone

<p>Abstract</p> <p>Background</p> <p>No clear recommendations exist regarding which antipsychotic drug should be prescribed first for a patient suffering from psychosis. The primary aims of this naturalistic study were to assess the head-to-head effectiveness of first-line second-generation antipsychotics with regards to time until drug discontinuation, duration of index admission, time until readmission, change of psychopathology scores and tolerability outcomes.</p> <p>Methods</p> <p>Patients ≥ 18 years of age admitted to the emergency ward for symptoms of psychosis were consecutively randomized to risperidone (n = 53), olanzapine (n = 52), quetiapine (n = 50), or ziprasidone (n = 58), and followed for up to 2 years.</p> <p>Results</p> <p>A total of 213 patients were included, of which 68% were males. The sample represented a diverse population suffering from psychosis. At admittance the mean Positive and Negative Syndrome Scale (PANSS) total score was 74 points and 44% were antipsychotic drug naïve. The primary intention-to-treat analyses revealed no substantial differences between the drugs regarding the times until discontinuation of initial drug, until discharge from index admission, or until readmission. Quetiapine was superior to risperidone and olanzapine in reducing the PANSS total score and the positive subscore. Quetiapine was superior to the other drugs in decreasing the PANSS general psychopathology subscore; in decreasing the Clinical Global Impression - Severity of Illness scale score (CGI-S); and in increasing the Global Assessment of Functioning - Split version, Functions scale score (GAF-F). Ziprasidone was superior to risperidone in decreasing the PANSS positive symptoms subscore and the CGI-S score, and in increasing the GAF-F score. The drugs performed equally with regards to most tolerability outcomes except a higher increase of hip-circumference per day for olanzapine compared to risperidone, and more galactorrhoea for risperidone compared to the other groups.</p> <p>Conclusions</p> <p>Quetiapine appears to be a good starting drug candidate in this sample of patients admitted to hospital for symptoms of psychosis.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov ID; URL: <url>http://www.clinicaltrials.gov/</url>: NCT00932529</p

Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice

Glycans on mucosal surfaces have an important role in host–microbe interactions. The locus encoding the blood-group-related glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) is subject to strong selective forces in natural house-mouse populations that contain a common allelic variant that confers loss of B4galnt2 gene expression in the gastrointestinal (GI) tract. We reasoned that altered glycan-dependent intestinal host–microbe interactions may underlie these signatures of selection. To determine whether B4galnt2 influences the intestinal microbial ecology, we profiled the microbiota of wild-type and B4galnt2-deficient siblings throughout the GI tract using 16S rRNA gene pyrosequencing. This revealed both distinct communities at different anatomic sites and significant changes in composition with respect to genotype, indicating a previously unappreciated role of B4galnt2 in host–microbial homeostasis. Among the numerous B4galnt2-dependent differences identified in the abundance of specific bacterial taxa, we unexpectedly detected a difference in the pathogenic genus, Helicobacter, suggesting Helicobacter spp. also interact with B4galnt2 glycans. In contrast to other glycosyltransferases, we found that the host intestinal B4galnt2 expression is not dependent on presence of the microbiota. Given the long-term maintenance of alleles influencing B4galnt2 expression by natural selection and the GI phenotypes presented here, we suggest that variation in B4galnt2 GI expression may alter susceptibility to GI diseases such as infectious gastroenteritis

Allogeneic blood transfusion and prognosis following total hip replacement: a population-based follow up study

<p>Abstract</p> <p>Background</p> <p>Allogeneic red blood cell transfusion is frequently used in total hip replacement surgery (THR). However, data on the prognosis of transfused patients are sparse. In this study we compared the risk of complications following THR in transfused and non-transfused patients.</p> <p>Methods</p> <p>A population-based follow-up study was performed using data from medical databases in Denmark. We identified 28,087 primary THR procedures performed from 1999 to 2007, from which we computed a propensity score for red blood cell transfusion based on detailed data on patient-, procedure-, and hospital-related characteristics. We were able to match 2,254 transfused with 2,254 non-transfused THR patients using the propensity score.</p> <p>Results</p> <p>Of the 28,087 THR patients, 9,063 (32.3%) received at least one red blood cell transfusion within 8 days of surgery. Transfused patients had higher 90-day mortality compared with matched non-transfused patients: the adjusted OR was 2.2 (95% confidence interval (CI): 1.2-3.8). Blood transfusion was also associated with increased odds of pneumonia (OR 2.1; CI: 1.2-3.8), whereas the associations with cardiovascular or cerebrovascular events (OR 1.4; CI: 0.9-2.2) and venous thromboembolism (OR 1.2; CI: 0.7-2.1) did not reach statistical significance. The adjusted OR of reoperation due to infection was 0.6 (CI: 0.1-2.9).</p> <p>Conclusions</p> <p>Red blood cell transfusion was associated with an adverse prognosis following primary THR, in particular with increased odds of death and pneumonia. Although the odds estimates may partly reflect unmeasured bias due to blood loss, they indicate the need for careful assessment of the risk versus benefit of transfusion even in relation to routine THR procedures.</p

Plasma phyto-oestrogens and prostate cancer in the European Prospective Investigation into Cancer and Nutrition

We examined plasma concentrations of phyto-oestrogens in relation to risk for subsequent prostate cancer in a case–control study nested in the European Prospective Investigation into Cancer and Nutrition. Concentrations of isoflavones genistein, daidzein and equol, and that of lignans enterolactone and enterodiol, were measured in plasma samples for 950 prostate cancer cases and 1042 matched control participants. Relative risks (RRs) for prostate cancer in relation to plasma concentrations of these phyto-oestrogens were estimated by conditional logistic regression. Higher plasma concentrations of genistein were associated with lower risk of prostate cancer: RR among men in the highest vs the lowest fifth, 0.71 (95% confidence interval (CI) 0.53–0.96, P trend=0.03). After adjustment for potential confounders this RR was 0.74 (95% CI 0.54–1.00, P trend=0.05). No statistically significant associations were observed for circulating concentrations of daidzein, equol, enterolactone or enterodiol in relation to overall risk for prostate cancer. There was no evidence of heterogeneity in these results by age at blood collection or country of recruitment, nor by cancer stage or grade. These results suggest that higher concentrations of circulating genistein may reduce the risk of prostate cancer but do not support an association with plasma lignans