Does replication groups scoring reduce false positive rate in SNP interaction discovery?

BACKGROUNG. Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008) proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups), rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions. RESULTS. A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups) reported fewer false positives. CONCLUSIONS. With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse

Does replication groups scoring reduce false positive rate in SNP interaction discovery?

<p>Abstract</p> <p>Background</p> <p>Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008) proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups), rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions.</p> <p>Results</p> <p>A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups) reported fewer false positives.</p> <p>Conclusions</p> <p>With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse.</p

The Chemistry of Organo Halogenic Molecules. 155. The Role of Reagent Structure in Halogenation of 9-Substituted Phenanthrenes

9-Substituted phenanthrenes were used as target molecules in investigations of the effect of the reagent structure and reaction conditions on halogenation with bromine (1), CsSO4F (2) and F-TEDA (1-chloromethyl-4-fluoro-1,4-diazoniabicycloe[2,2,2]octane bis(tetra- fluoroborate), (3). 9-Methoxyphenanthrene (4) was converted to 9- bromo-10-methoxyphenanthrene (6a) and 9-bromo-10-hydroxy- phenanthrene (7a), while the amount of dealkylation depended on the solvent and was more pronounced in methanol than in acetonitrile, but no adduct was observed. Addition reaction became a major process in fluorination with CsS04F (2) in methanol and 88% of 9-fluoro-10,10-dimethoxy-9,10-dihydrophenanthrene (8b) was formed, while dealkylation occurred in acetonitrile. The course of fluorination of 9-methoxyphenanthrene with F-TEDA (3) could be completely manipulated by the choice of solvent and 9,9-difluoro- 10-oxo-9,10-dihydrophenanthrene (9b) was formed in acetonitrile, 9-fluoro-10-methoxyphenanthrene (6b) in trifluoroacetic acid and 9-fluoro-10,10-dimethoxy-9,10-dihydrophenanthrene (8b) in methanol. Bromination of 9-hydroxyphenanthrene (5) in acetonitrile resulted only in the substitution process, while 9-fluoro-10-hydroxyphenanthrene (7b) formed in the reaction with CsSO4F and F-TEDA was more reactive than the starting hydroxy derivative and, using a 2 molar ratio of F-TEDA, only 9,9-difluoro-10-oxo- 9,10-dihydrophenanthrene (9b) was formed

Fractionation of potentially toxic elements in urban soils from five European cities by means of a harmonised sequential extraction procedure

The revised (four-step) BCR sequential extraction procedure has been applied to fractionate the chromium, copper, iron, manganese, nickel, lead and zinc contents in urban soil samples from public-access areas in five European cities. A preliminary inter-laboratory comparison was conducted and showed that data obtained by different laboratories participating in the study were sufficiently harmonious for comparisons to be made between cities and land types (e.g. parks, roadside, riverbanks, etc.). Analyte recoveries by sequential extraction, with respect to direct aqua regia digestion, were generally acceptable (100 ± 15%). Iron, nickel and, at most sites, chromium were found mainly in association with the residual phase of the soil matrix. Copper was present in the reducible, oxidisable and residual fractions, whilst zinc was found in all four sequential extracts. Manganese was strongly associated with reducible material as, in some cities, was lead. This is of concern because high lead concentrations were present in some soils (>500 mg kg−1) and the potential exists for remobilisation under reducing conditions. As would be expected, extractable metal contents were generally highest in older, more heavily industrialised cities. Copper, lead and zinc showed marked (and often correlated) variations in concentrations between sites within the same city whereas manganese and, especially, iron, did not. No overall relationships were, however, found between analyte concentrations and land use, nor between analyte partitioning and land use

Antithrombotic management in patients undergoing cardiac implantable electronic device implantation

Cardiac implantable electronic devices (CIEDs) are an established treatment option for arrhythmias, sudden cardiac death prevention, and heart failure. Approximately 1000 devices are implanted per million inhabitants in European countries each year. However, the main concern in patients with an indication for CIED implantation is frequently associated with comorbidities requiring antithrombotic medications. The invasive device implantation procedure represents a bleeding risk ranging from pocket hematoma to cardiac tamponade. On the other hand, temporary interruption of antithrombotic therapy increases the risk for thromboembolic events. Implanting CIEDs in patients on antithrombotic medications incites several clinical dilemmas of balancing thromboembolic risk against bleeding risk, as complications are associated with higher mortality rates in both aspects. The most common bleeding complication is pocket haematoma formation, which is associated with a prolonged hospital stay, higher cost, higher risk of pocket infection, and thus higher morbidity and mortality. Studies have shown that the heparin bridging strategy in patients on oral anticoagulants imposes a greater risk for pocket haematoma formation and no benefit in reducing thromboembolic events. Most procedures of CIED implantation can be performed safely with uninterrupted oral anticoagulants. Dual antiplatelet therapy increases the risk of pocket haematoma and should be avoided whenever possible

Snowmass Theory Frontier: Effective Field Theory

We summarize recent progress in the development, application, and understanding of effective field theories and highlight promising directions for future research. This Report is prepared as the TF02 "Effective Field Theory" topical group summary for the Theory Frontier as part of the Snowmass 2021 process.Comment: 12 page

Novi i značajni podaci o biljkama, algama i gljivama iz JI Evrope i susednih regiona, 10

This paper presents new records and noteworthy data on the following taxa in SE Europe and adjacent regions: red algae Lemanea rigida and Paralemanea torulosa, mycorrhizal fungi Amanita simulans and Terfezia pseudoleptoderma, parasitic fungus Microbotryum vinosum, saprotrophic fungus Sarcoscypha jurana, stonewort Chara tenuispina, mosses Brachytheciastrum collinum and Meesia longiseta, monocots Dactylorhiza romana and Neotinea maculata and dicots Adenophora liliifolia, Ambrosia artemisiifolia and Tanacetum corymbosum subsp. cinereum are given within SE Europe and adjacent regions.U radu su prikazani novi i značajni podaci sa područja JI Evrope i susednih regiona o sledećim taksonima: crvenim algama Lemanea rigida i Paralemanea torulosa, mikorizalnim gljivama Amanita simulans i Terfezia pseudoleptoderma, parazitskoj gljivi Microbotryum vinosum, saprofitnoj gljivi Sarcoscypha jurana, pršljenčici Chara tenuispina, mahovinama Brachytheciastrum collinum i Meesia longiseta, monokotilama Dactylorhiza romana i Neotinea maculata i dikotilama Adenophora liliifolia, Ambrosia artemisiifolia i Tanacetum corymbosum subsp. cinereum

How Can We Advance Integrative Biology Research in Animal Science in 21st Century?:Experience at University of Ljubljana from 2002 to 2022

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health