The impact of transitive annotation on the training of taxonomic classifiers

IntroductionA common task in the analysis of microbial communities involves assigning taxonomic labels to the sequences derived from organisms found in the communities. Frequently, such labels are assigned using machine learning algorithms that are trained to recognize individual taxonomic groups based on training data sets that comprise sequences with known taxonomic labels. Ideally, the training data should rely on labels that are experimentally verified—formal taxonomic labels require knowledge of physical and biochemical properties of organisms that cannot be directly inferred from sequence alone. However, the labels associated with sequences in biological databases are most commonly computational predictions which themselves may rely on computationally-generated data—a process commonly referred to as “transitive annotation.”MethodsIn this manuscript we explore the implications of training a machine learning classifier (the Ribosomal Database Project’s Bayesian classifier in our case) on data that itself has been computationally generated. We generate new training examples based on 16S rRNA data from a metagenomic experiment, and evaluate the extent to which the taxonomic labels predicted by the classifier change after re-training.ResultsWe demonstrate that even a few computationally-generated training data points can significantly skew the output of the classifier to the point where entire regions of the taxonomic space can be disturbed.Discussion and conclusionsWe conclude with a discussion of key factors that affect the resilience of classifiers to transitively-annotated training data, and propose best practices to avoid the artifacts described in our paper

Mechanistic Elucidation of the Arylation of Non-Spectator N-Heterocyclic Carbenes at Copper Using a Combined Experimental and Computational Approach

CuI(NHC)Br complexes (NHC = N-heterocyclic carbene) undergo a direct reaction with iodobenzene to give 2-arylated benzimidazolium products. The nature of the N-substituent on the NHC ligand influences the reactivity of the CuI(NHC)Br complex toward arylation. N-Benzyl or N-phenyl substituents facilitate arylation, whereas N-mesityl substituents hinder arylation. Density functional theory calculations show that an oxidative addition/reductive elimination pathway involving CuIII species is energetically feasible. A less hindered CuI(NHC)Br complex with N-benzyl groups is susceptible to oxidation reactions to give 1,3-dibenzylbenzimidazolium cations containing a CuIBr anion (various polymorphs). The results described herein are of relevance to C–H functionalization of (benz)azoles

Bioheterojunction Effect on Fluorescence Origin and Efficiency Improvement of Firefly Chromophores

We propose the heterojunction effect in the analysis of the fluorescence mechanism of the firefly chromophore. Following this analysis, and with respect to the HOMO-LUMO gap alignment between the chromophore's functional fragments, three main heterojunction types (I, II, and I*) are identified. Time-dependent density-functional theory optical absorption calculations for the firefly chromophore show that the strongest excitation appears in the deprotonated anion state of the keto form. This can be explained by its high HOMO-LUMO overlap due to strong bio-heterojunction confinement. It is also found that the nitrogen atom in the thiazolyl rings, due to its larger electronegativity, plays a key role in the emission process, its importance growing when HOMO and LUMO overlap at its location. This principle is applied to enhance the chromophore's fluorescence efficiency and to guide the functionalization of molecular optoelectronic devices.Comment: 7 pages, 6 figure

A new technical aspect of ultrasound-guided liver surgery

Nowadays, resective hepatic surgery should be considered an echo-guided surgical procedure to guarantee that effective anatomical resection is accomplished. We describe a simple and original technique guided by intraoperative ultrasonography (IOUS), called the hooking technique, that enables the ligation sites of the intrahepatic vessels during systematic segmentectomy to be chosen precisely. Together with other IOUS-guided techniques described previously, the hooking technique provides a further guarantee for the successful execution of anatomical and radical liver resection

La terapia dell'infezione da virus dell'epatite C in soggetti candidati o sottoposti a trapianto di rene

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