Fingerprints of biocomplexity: Taxon‐specific growth of phytoplankton in relation to environmental factors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110012/1/lno2004494part21446.pd

Measure-Based Inconsistency-Tolerant Maintenance of Database Integrity

[EN] To maintain integrity, constraint violations should be prevented or repaired. However, it may not be feasible to avoid inconsistency, or to repair all violations at once. Based on an abstract concept of violation measures, updates and repairs can be checked for keeping inconsistency bounded, such that integrity violations are guaranteed to never get out of control. This measure-based approach goes beyond conventional methods that are not meant to be applied in the presence of inconsistency. It also generalizes recently introduced concepts of inconsistency-tolerant integrity maintenance.Partially supported by FEDER and the Spanish grants TIN2009-14460-C03 and TIN2010-17139Decker, H. (2013). Measure-Based Inconsistency-Tolerant Maintenance of Database Integrity. Lecture Notes in Computer Science. 7693:149-173. https://doi.org/10.1007/978-3-642-36008-4_7S1491737693Abiteboul, S., Hull, R., Vianu, V.: Foundations of Databases. Addison-Wesley (1995)Abiteboul, S., Vianu, V.: A transaction-based approach to relational database specification. JACM 36(4), 758–789 (1989)Afrati, F., Kolaitis, P.: Repair checking in inconsistent databases: algorithms and complexity. In: 12th ICDT, pp. 31–41. ACM Press (2009)Arenas, M., Bertossi, L., Chomicki, J.: Consistent query answers in inconsistent databases. In: PODS 1999, pp. 68–79. ACM Press (1999)Arieli, O., Denecker, M., Bruynooghe, M.: Distance semantics for database repair. Ann. Math. Artif. Intell. 50, 389–415 (2007)Arni-Bloch, N., Ralyté, J., Léonard, M.: Service–Driven Information Systems Evolution: Handling Integrity Constraints Consistency. In: Persson, A., Stirna, J. (eds.) PoEM 2009. LNBIP, vol. 39, pp. 191–206. Springer, Heidelberg (2009)Bauer, H.: Maß- und Integrationstheorie, 2. Auflage. De Gruyter (1992)Besnard, P., Hunter, A.: Quasi-Classical Logic: Non-Trivializable Classical Reasoning from Inconsistent Information. In: Froidevaux, C., Kohlas, J. (eds.) ECSQARU 1995. LNCS, vol. 946, pp. 44–51. Springer, Heidelberg (1995)Bohanon, P., Fan, W., Flaster, M., Rastogi, R.: A Cost-Based Model and Effective Heuristic for Repairing Constraints by Value Modification. In: Proc. SIGMOD 2005, pp. 143–154. ACM Press (2005)Ceri, S., Cochrane, R., Widom, J.: Practical Applications of Triggers and Constraints: Success and Lingering Issues. In: Proc. 26th VLDB, pp. 254–262. Morgan Kaufmann (2000)Chakravarthy, U., Grant, J., Minker, J.: Logic-based Approach to Semantic Query Optimization. Transactions on Database Systems 15(2), 162–207 (1990)Chomicki, J.: Consistent Query Answering: Five Easy Pieces. In: Schwentick, T., Suciu, D. (eds.) ICDT 2007. LNCS, vol. 4353, pp. 1–17. Springer, Heidelberg (2006)Christiansen, H., Martinenghi, D.: On simplification of database integrity constraints. Fundamenta Informaticae 71(4), 371–417 (2006)Clark, K.: Negation as Failure. In: Gallaire, H., Minker, J. (eds.) Logic and Data Bases, pp. 293–322. Plenum Press (1978)Curino, C., Moon, H., Deutsch, A., Zaniolo, C.: Update Rewriting and Integrity Constraint Maintenance in a Schema Evolution Support System: PRISM++. PVLDB 4, 117–128 (2010)Dawson, J.: The compactness of first-order logic: From Gödel to Lindström. History and Philosophy of Logic 14(1), 15–37 (1993)Decker, H.: The Range Form of Databases and Queries or: How to Avoid Floundering. In: Proc. 5th ÖGAI. Informatik-Fachberichte, vol. 208, pp. 114–123. Springer (1989)Decker, H.: Drawing Updates From Derivations. In: Kanellakis, P.C., Abiteboul, S. (eds.) ICDT 1990. LNCS, vol. 470, pp. 437–451. Springer, Heidelberg (1990)Decker, H.: Extending Inconsistency-Tolerant Integrity Checking by Semantic Query Optimization. In: Bhowmick, S.S., Küng, J., Wagner, R. (eds.) DEXA 2008. LNCS, vol. 5181, pp. 89–96. Springer, Heidelberg (2008)Decker, H.: Answers That Have Integrity. In: Schewe, K.-D., Thalheim, B. (eds.) SDKB 2010. LNCS, vol. 6834, pp. 54–72. Springer, Heidelberg (2011)Decker, H.: Causes of the Violation of Integrity Constraints for Supporting the Quality of Databases. In: Murgante, B., Gervasi, O., Iglesias, A., Taniar, D., Apduhan, B.O. (eds.) ICCSA 2011, Part V. LNCS, vol. 6786, pp. 283–292. Springer, Heidelberg (2011)Decker, H.: Inconsistency-tolerant Integrity Checking based on Inconsistency Metrics. In: König, A., Dengel, A., Hinkelmann, K., Kise, K., Howlett, R.J., Jain, L.C. (eds.) KES 2011, Part II. LNCS, vol. 6882, pp. 548–558. Springer, Heidelberg (2011)Decker, H.: Partial Repairs that Tolerate Inconsistency. In: Eder, J., Bielikova, M., Tjoa, A.M. (eds.) ADBIS 2011. LNCS, vol. 6909, pp. 389–400. Springer, Heidelberg (2011)Decker, H.: Consistent Explanations of Answers to Queries in Inconsistent Knowledge Bases. In: Roth-Berghofer, T., Tintarev, N., Leake, D. (eds.) Explanation-aware Computing, Proc. IJCAI 2011 Workshop ExaCt 2011, pp. 71–80 (2011), http://exact2011.workshop.hm/index.phpDecker, H., Martinenghi, D.: Classifying integrity checking methods with regard to inconsistency tolerance. In: Proc. PPDP 2008, pp. 195–204. ACM Press (2008)Decker, H., Martinenghi, D.: Modeling, Measuring and Monitoring the Quality of Information. In: Heuser, C.A., Pernul, G. (eds.) ER 2009. LNCS, vol. 5833, pp. 212–221. Springer, Heidelberg (2009)Decker, H., Martinenghi, D.: Inconsistency-tolerant Integrity Checking. IEEE TKDE 23(2), 218–234 (2011)Decker, H., Muñoz-Escoí, F.D.: Revisiting and Improving a Result on Integrity Preservation by Concurrent Transactions. In: Meersman, R., Dillon, T., Herrero, P. (eds.) OTM 2010 Workshops. LNCS, vol. 6428, pp. 297–306. Springer, Heidelberg (2010)Dung, P., Kowalski, R., Toni, F.: Dialectic Proof Procedures for Assumption-based Admissible Argumentation. Artificial Intelligence 170(2), 114–159 (2006)Ebbinghaus, H.-D., Flum, J.: Finite Model Theory, 2nd edn. Springer (2006)Embury, S., Brandt, S., Robinson, J., Sutherland, I., Bisby, F., Gray, A., Jones, A., White, R.: Adapting integrity enforcement techniques for data reconciliation. Information Systems 26, 657–689 (2001)Enderton, H.: A Mathematical Introduction to Logic, 2nd edn. Academic Press (2001)Eiter, T., Fink, M., Greco, G., Lembo, D.: Repair localization for query answering from inconsistent databases. ACM TODS 33(2), article 10 (2008)Furfaro, F., Greco, S., Molinaro, C.: A three-valued semantics for querying and repairing inconsistent databases. Ann. Math. Artif. Intell. 51(2-4), 167–193 (2007)Grant, J., Hunter, A.: Measuring the Good and the Bad in Inconsistent Information. In: Proc. 22nd IJCAI, pp. 2632–2637 (2011)Greco, G., Greco, S., Zumpano, E.: A logical framework for querying and repairing inconsistent databases. IEEE TKDE 15(6), 1389–1408 (2003)Guessoum, A., Lloyd, J.: Updating knowledge bases. New Generation Computing 8(1), 71–89 (1990)Guessoum, A., Lloyd, J.: Updating knowledge bases II. New Generation Computing 10(1), 73–100 (1991)Gupta, A., Sagiv, Y., Ullman, J., Widom, J.: Constraint checking with partial information. In: Proc. PODS 1994, pp. 45–55. ACM Press (1994)Hunter, A.: Measuring Inconsistency in Knowledge via Quasi-Classical Models. In: Proc. 18th AAAI &14th IAAI, pp. 68–73 (2002)Hunter, A., Konieczny, S.: Approaches to Measuring Inconsistent Information. In: Bertossi, L., Hunter, A., Schaub, T. (eds.) Inconsistency Tolerance. LNCS, vol. 3300, pp. 191–236. Springer, Heidelberg (2005)Hunter, A., Konieczny, S.: Measuring inconsistency through minimal inconsistent sets. In: Brewka, G., Lang, J. (eds.) Principles of Knowledge Representation and Reasoning (Proc. 11th KR), pp. 358–366. AAAI Press (2008)Hunter, A., Konieczny, S.: On the measure of conflicts: Shapley Inconsistency Values. Artificial Intelligence 174, 1007–1026 (2010)Kakas, A., Mancarella, P.: Database updates through abduction. In: Proc. 16th VLDB, pp. 650–661. Morgan Kaufmann (1990)Kakas, A., Kowalski, R., Toni, F.: The role of Abduction in Logic Programming. In: Gabbay, D., Hogger, C., Robinson, J.A. (eds.) Handbook of Logic in Artificial Intelligence and Logic Programming, vol. 5, pp. 235–324. Oxford University Press (1998)Lee, S.Y., Ling, T.W.: Further improvements on integrity constraint checking for stratifiable deductive databases. In: Proc. VLDB 1996, pp. 495–505. Morgan Kaufmann (1996)Lehrer, K.: Relevant Deduction and Minimally Inconsistent Sets. Journal of Philosophy 3(2,3), 153–165 (1973)Mu, K., Liu, W., Jin, Z., Bell, D.: A Syntax-based Approach to Measuring the Degree of Inconsistency for Belief Bases. J. Approx. Reasoning 52(7), 978–999 (2011)Lloyd, J., Sonenberg, L., Topor, R.: Integrity constraint checking in stratified databases. J. Logic Programming 4(4), 331–343 (1987)Lozinskii, E.: Resolving contradictions: A plausible semantics for inconsistent systems. J. Automated Reasoning 12(1), 1–31 (1994)Ma, Y., Qi, G., Hitzler, P.: Computing inconsistency measure based on paraconsistent semantics. J. Logic Computation 21(6), 1257–1281 (2011)Martinenghi, D., Christiansen, H.: Transaction Management with Integrity Checking. In: Andersen, K.V., Debenham, J., Wagner, R. (eds.) DEXA 2005. LNCS, vol. 3588, pp. 606–615. Springer, Heidelberg (2005)Martinenghi, D., Christiansen, H., Decker, H.: Integrity Checking and Maintenance in Relational and Deductive Databases and Beyond. In: Ma, Z. (ed.) Intelligent Databases: Technologies and Applications, pp. 238–285. IGI Global (2006)Martinez, M.V., Pugliese, A., Simari, G.I., Subrahmanian, V.S., Prade, H.: How Dirty Is Your Relational Database? An Axiomatic Approach. In: Mellouli, K. (ed.) ECSQARU 2007. LNCS (LNAI), vol. 4724, pp. 103–114. Springer, Heidelberg (2007)Meyer, J., Wieringa, R. (eds.): Deontic Logic in Computer Science. Wiley (1994)Nicolas, J.M.: Logic for improving integrity checking in relational data bases. Acta Informatica 18, 227–253 (1982)Plexousakis, D., Mylopoulos, J.: Accommodating Integrity Constraints During Database Design. In: Apers, P.M.G., Bouzeghoub, M., Gardarin, G. (eds.) EDBT 1996. LNCS, vol. 1057, pp. 495–513. Springer, Heidelberg (1996)Rahm, E., Do, H.: Data Cleaning: Problems and Current Approaches. Data Engineering Bulletin 23(4), 3–13 (2000)Sadri, F., Kowalski, R.: A theorem-proving approach to database integrity. In: Minker, J. (ed.) Foundations of Deductive Databases and Logic Programming, pp. 313–362. Morgan Kaufmann (1988)Thimm, M.: Measuring Inconsistency in Probabilistic Knowledge Bases. In: Proc. 25th UAI, pp. 530–537. AUAI Press (2009)Vardi, M.: On the integrity of databases with incomplete information. In: Proc. 5th PODS, pp. 252–266. ACM Press (1986)Wijsen, J.: Database repairing using updates. ACM Trans. Database Syst. 30(3), 722–768 (2005

Treatment retention of infliximab and etanercept originators versus their corresponding biosimilars : Nordic collaborative observational study of 2334 biologics naive patients with spondyloarthritis

Objective Although clinical trials support equivalence of originator products and biosimilars for etanercept and infliximab, real-world studies among biologics-naive patients with spondyloarthritis (SpA) are lacking. The objectives were to compare treatment retention in biologics-naive patients with SpA starting either the originator product or a biosimilar of infliximab and etanercept, and to explore the baseline characteristics of these patients. Methods Patients with SpA (ankylosing spondylitis/non-radiographical axial SpA/undifferentiated SpA), starting infliximab or etanercept as their first-ever biological disease-modifying antirheumatic drug during January 2014-June 2017 were identified in five Nordic biologics-rheumatology registers. Baseline characteristics were retrieved from each registry; comorbidity data were identified through linkage to national health registers. Country-specific data were pooled, and data on infliximab and etanercept were analysed separately. Comparisons of treatment retention between originators and biosimilars were assessed through survival probability curves, retention rates (2 years for infliximab/1 year for etanercept) and Hazard Ratios (HR). Results We included 1319 patients starting infliximab (24% originator/76% biosimilar), and 1015 patients starting etanercept (49% originator/51% biosimilar). Baseline characteristics were largely similar for the patients treated with the originators compared with the corresponding biosimilars. Survival probability curves were highly similar for the originator and its biosimilar, as were retention rates: infliximab 2-year retention originator, 44% (95% CI 38% to 50%)/biosimilar, 46% (95% CI: 42% to 51%); and etanercept 1-year retention originator, 66% (95% CI 61% to 70%)/biosimilar, 73% (95% CI 68% to 78%). HRs were not statistically significant. Conclusion This observational study of biologics-naive patients with SpA from five Nordic countries showed similar baseline characteristics and very similar retention rates in patients treated with originators versus biosimilars, for both infliximab and etanercept, indicating comparable effectiveness in clinical practice.Peer reviewe

The sequences of 150,119 genomes in the UK Biobank

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data(1,2). Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank(3). This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation

Predictors of ASDAS-CRP inactive disease in axial spondyloarthritis during treatment with TNF-inhibitors : Data from the EuroSpA collaboration

Correction: Volume 58, Article Number 152141 DOI: 10.1016/j.semarthrit.2022.152141 Published: FEB 2023Objectives: In patients with axial spondyloarthritis (axSpA) initiating their first tumor necrosis factor alpha-inhibitor (TNFi), we aimed to identify common baseline predictors of Ankylosing Spondylitis Disease Activity Score (ASDAS-CRP) inactive disease (primary objective) and clinically important improvement (CII) at 6 months, and drug retention at 12-months across 15 European registries. Methods: Baseline demographic and clinical characteristics were collected. Outcomes were investigated per registry and in pooled data using logistic regression analyses on multiply imputed data. Results: The consistency of baseline predictors in individual registries justified pooling the data. In the pooled dataset (n = 21,196), the 6-month rates for ASDAS inactive disease and ASDAS CII were 26% and 51%, and the 12-month drug retention rate 65% in patients with available data (n = 9,845, n = 6,948 and n = 21,196, respectively). Nine common baseline predictors of ASDAS inactive disease, ASDAS CII and 12-month drug retention were identified, and the odds ratios (95%-confidence interval) for ASDAS inactive disease were: age, per year: 0.97 (0.97-0.98), men vs. women: 1.88 (1.60-2.22), current vs. non-smoking: 0.76 (0.63-0.91), HLA-B27 positive vs. negative: 1.51 (1.20-1.91), TNF start year 2015-2018 vs. 2009-2014: 1.24 (1.06-1.45), CRP > 10 vs.Peer reviewe

Potential Effects of a Statutory Minimum Wage on the Gender Pay Gap A Simulation-Based Study for Germany

In a simulation-based study with data from the German Socio-Economic Panel Study (SOEP), we analyze the effects of the newly introduced statutory minimum wage of 8.50 Euro per working hour in Germany on the gender wage gap. In our first scenario where we abstain from employment effects, the pay differential is reduced by 2.5 percentage points from 19.6 % to 17.1 %, due to a reduction of the sticky-floor effect at the bottom of the wage distribution. In more realistic scenarios where we incorporate minimum wage effects on labor demand, a further reduction of the pay gap by 0.2 pp (1.2 pp) in case of a monopsonistic (neoclassical) labor market is achieved. However, this comes at the cost of job losses by which women are more strongly affected than men. The magnitude of job losses ranges between 0.2 % and 3.0 % of all employees. It is higher in a neoclassical market setting and positively related to the assumed wage elasticity

Predictors of ASDAS-CRP inactive disease in axial spondyloarthritis during treatment with TNF-inhibitors: Data from the EuroSpA collaboration

ObjectivesIn patients with axial spondyloarthritis (axSpA) initiating their first tumor necrosis factor alpha-inhibitor (TNFi), we aimed to identify common baseline predictors of Ankylosing Spondylitis Disease Activity Score (ASDAS-CRP) inactive disease (primary objective) and clinically important improvement (CII) at 6 months, and drug retention at 12-months across 15 European registries.MethodsBaseline demographic and clinical characteristics were collected. Outcomes were investigated per registry and in pooled data using logistic regression analyses on multiply imputed data.ResultsThe consistency of baseline predictors in individual registries justified pooling the data. In the pooled dataset (n = 21,196), the 6-month rates for ASDAS inactive disease and ASDAS CII were 26% and 51%, and the 12-month drug retention rate 65% in patients with available data (n = 9,845, n = 6,948 and n = 21,196, respectively). Nine common baseline predictors of ASDAS inactive disease, ASDAS CII and 12-month drug retention were identified, and the odds ratios (95%-confidence interval) for ASDAS inactive disease were: age, per year: 0.97 (0.97–0.98), men vs. women: 1.88 (1.60–2.22), current vs. non-smoking: 0.76 (0.63–0.91), HLA-B27 positive vs. negative: 1.51 (1.20–1.91), TNF start year 2015–2018 vs. 2009–2014: 1.24 (1.06–1.45), CRP>10 vs. ≤10 mg/l: 1.49 (1.25–1.77), one unit increase in health assessment questionnaire (HAQ): 0.77 (0.58–1.03), one-millimeter (mm) increase in Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) fatigue and spinal pain: 0.99 (0.99–1.00) and 0.99 (0.99–1.99), respectivelyConclusionCommon baseline predictors of treatment response and adherence to TNFi could be identified across data from 15 European registries, indicating that they may be universal across different axSpA populations.</p

Synergism between basic Asp49 and Lys49 phospholipase A2 myotoxins of viperid snake venom in vitro and in vivo

artículo (arbitrado) -- Universidad de Costa Rica, Instituto de investigaciones Clodomiro Picado. 2014Two subtypes of phospholipases A2 (PLA2s) with the ability to induce myonecrosis, ‘Asp49’ and ‘Lys49’ myotoxins, often coexist in viperid snake venoms. Since the latter lack catalytic activity, two different mechanisms are involved in their myotoxicity. A synergism between Asp49 and Lys49 myotoxins from Bothrops asper was previously observed in vitro, enhancing Ca2+ entry and cell death when acting together upon C2C12 myotubes. These observations are extended for the first time in vivo, by demonstrating a clear enhancement of myonecrosis by the combined action of these two toxins in mice. In addition, novel aspects of their synergism were revealed using myotubes. Proportions of Asp49 myotoxin as low as 0.1% of the Lys49 myotoxin are sufficient to enhance cytotoxicity of the latter, but not the opposite. Sublytic amounts of Asp49 myotoxin also enhanced cytotoxicity of a synthetic peptide encompassing the toxic region of Lys49 myotoxin. Asp49 myotoxin rendered myotubes more susceptible to osmotic lysis, whereas Lys49 myotoxin did not. In contrast to myotoxic Asp49 PLA2, an acidic non-toxic PLA2 from the same venom did not markedly synergize with Lys49 myotoxin, revealing a functional difference between basic and acidic PLA2 enzymes. It is suggested that Asp49 myotoxins synergize with Lys49 myotoxins by virtue of their PLA2 activity. In addition to the membrane-destabilizing effect of this activity, Asp49 myotoxins may generate anionic patches of hydrolytic reaction products, facilitating electrostatic interactions with Lys49 myotoxins. These data provide new evidence for the evolutionary adaptive value of the two subtypes of PLA2 myotoxins acting synergistically in viperid venoms.Funding support by the Graduate Studies Program, Universidad de Costa Rica; International Centre for Genetic Engineering and Biotechnology, Italy (CRP/COS13-01); and Vicerrectoria de Investigacion, Universidad de Costa Rica (741-B4-100).UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto Clodomiro Picado (ICP