mizar-items: Exploring fine-grained dependencies in the Mizar Mathematical Library

The Mizar Mathematical Library (MML) is a rich database of formalized mathematical proofs (see http://mizar.org). Owing to its large size (it contains more than 1100 "articles" summing to nearly 2.5 million lines of text, expressing more than 50000 theorems and 10000 definitions using more than 7000 symbols), the nature of its contents (the MML is slanted toward pure mathematics), and its classical foundations (first-order logic, set theory, natural deduction), the MML is an especially attractive target for research on foundations of mathematics. We have implemented a system, mizar-items, on which a variety of such foundational experiements can be based. The heart of mizar-items is a method for decomposing the contents of the MML into fine-grained "items" (e.g., theorem, definition, notation, etc.) and computing dependency relations among these items. mizar-items also comes equipped with a website for exploring these dependencies and interacting with them.Comment: Accepted at CICM 2011: Conferences in Intelligent Computer Mathematics, Track C: Systems and Project

To correct or not correct?: Teachers\u27 behavior and students\u27 perception

Recent, well-known explorations of the role of models in science suggest a theory of scientific innovation which links innovation to a creative extension of knowledge brought about by the invokation of a metaphor. At the same time, concrete evidence about actual procedures of scientific investigation have for the first time become available from anthropological observation studies of scientific laboratories. This paper draws upon one year of observations done in 1976-77 in a group working on chemical, microbiological, toxicological and technological aspects of plant proteins and plant protein generation at a research institute employing more than 300 scientists in Berkeley, Ca. and upon interviews done with scientists of various other groups at the same institute. The paper attempts to reconsider the role of metaphor in the light of the observer's account of the research process in the laboratory, and in the light of the scientists' accounts of research efforts they considered innovative. Both the scientists' and the observer's account suggest that reference to metaphor needs to be extended to include, in accordance with some earlier conceptual investigations, the more general phenomenon of analogical reasoning. At the same time they suggest that the metaphor- or analogytheory needs to be restricted in its claim to account for innovation, and that innovation must be linked to the active constructions of the process of production and reproduction of research

Oscillatory Bursting as a Mechanism for Temporal Coupling and Information Coding

© Copyright © 2020 Tal, Neymotin, Bickel, Lakatos and Schroeder. Even the simplest cognitive processes involve interactions between cortical regions. To study these processes, we usually rely on averaging across several repetitions of a task or across long segments of data to reach a statistically valid conclusion. Neuronal oscillations reflect synchronized excitability fluctuations in ensembles of neurons and can be observed in electrophysiological recordings in the presence or absence of an external stimulus. Oscillatory brain activity has been viewed as sustained increase in power at specific frequency bands. However, this perspective has been challenged in recent years by the notion that oscillations may occur as transient burst-like events that occur in individual trials and may only appear as sustained activity when multiple trials are averaged together. In this review, we examine the idea that oscillatory activity can manifest as a transient burst as well as a sustained increase in power. We discuss the technical challenges involved in the detection and characterization of transient events at the single trial level, the mechanisms that might generate them and the features that can be extracted from these events to study single-trial dynamics of neuronal ensemble activity

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Haptoglobin Polymorphism: A Novel Genetic Risk Factor for Celiac Disease Development and Its Clinical Manifestations

Background: Haptoglobin (Hp) α-chain alleles 1 and 2 account for 3 phenotypes that may influence the course of inflammatory diseases via biologically important differences in their antioxidant, scavenging, and immunomodulatory properties. Hp1-1 genotype results in the production of small dimeric, Hp2-1 linear, and Hp2-2 cyclic polymeric haptoglobin molecules. We investigated the haptoglobin polymorphism in patients with celiac disease and its possible association to the presenting symptoms. Methods: We studied 712 unrelated, biopsy-proven Hungarian celiac patients (357 children, 355 adults; severe malabsorption 32.9%, minor gastrointestinal symptoms 22.8%, iron deficiency anemia 9.4%, dermatitis herpetiformis 15.6%, silent disease 7.2%, other 12.1%) and 384 healthy subjects. We determined haptoglobin phenotypes by gel electrophoresis and assigned corresponding genotypes. Results: Hp2-1 was associated with a significant risk for celiac disease (P = 0.0006, odds ratio [OR] 1.54, 95% CI 1.20–1.98; prevalence 56.9% in patients vs 46.1% in controls). It was also overrepresented among patients with mild symptoms (69.2%) or silent disease (72.5%). Hp2-2 was less frequent in patients than in controls (P = 0.0023), but patients having this phenotype were at an increased risk for severe malabsorption (OR 2.21, 95% CI 1.60–3.07) and accounted for 45.3% of all malabsorption cases. Celiac and dermatitis herpetiformis patients showed similar haptoglobin phenotype distributions. Conclusions: The haptoglobin polymorphism is associated with susceptibility to celiac disease and its clinical presentations. The predominant genotype in the celiac population was Hp2-1, but Hp2-2 predisposed to a more severe clinical course. The phenotype-dependent effect of haptoglobin may result from the molecule’s structural and functional properties