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

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

Students’ Evolving Meaning About Tangent Line with the Mediation of a Dynamic Geometry Environment and an Instructional Example Space

In this paper I report a lengthy episode from a teaching experiment in which fifteen Year 12 Greek students negotiated their definitions of tangent line to a function graph. The experiment was designed for the purpose of introducing students to the notion of derivative and to the general case of tangent to a function graph. Its design was based on previous research results on students’ perspectives on tangency, especially in their transition from Geometry to Analysis. In this experiment an instructional example space of functions was used in an electronic environment utilising Dynamic Geometry software with Function Grapher tools. Following the Vygotskian approach according to which students’ knowledge develops in specific social and cultural contexts, students’ construction of the meaning of tangent line was observed in the classroom throughout the experiment. The analysis of the classroom data collected during the experiment focused on the evolution of students’ personal meanings about tangent line of function graph in relation to: the electronic environment; the pre-prepared as well as spontaneous examples; students’ engagement in classroom discussion; and, the role of researcher as a teacher. The analysis indicated that the evolution of students’ meanings towards a more sophisticated understanding of tangency was not linear. Also it was interrelated with the evolution of the meaning they had about the inscriptions in the electronic environment; the instructional example space; the classroom discussion; and, the role of the teacher

Bohmian Mechanics and Quantum Information

Many recent results suggest that quantum theory is about information, and that quantum theory is best understood as arising from principles concerning information and information processing. At the same time, by far the simplest version of quantum mechanics, Bohmian mechanics, is concerned, not with information but with the behavior of an objective microscopic reality given by particles and their positions. What I would like to do here is to examine whether, and to what extent, the importance of information, observation, and the like in quantum theory can be understood from a Bohmian perspective. I would like to explore the hypothesis that the idea that information plays a special role in physics naturally emerges in a Bohmian universe.Comment: 25 pages, 2 figure

The Blazhko behaviour of RR Geminorum I - CCD photometric results in 2004

Extended CCD monitoring of RR Gem revealed that it is a Blazhko type RRab star with the shortest Blazhko period (7.23d) and smallest modulation amplitude (Delta Mmax<0.1 mag) currently known. The short period of the modulation cycle enabled us to obtain complete phase coverage of the pulsation at each phase of the modulation. This is the first multicolour observation of a Blazhko star which is extended enough to define accurate mean magnitudes and colours of the variable at different Blazhko phases. Small, but real, changes in the intensity mean colours at different Blazhko phases have been detected. The Fourier analysis of the light curves shows that, in spite of the mmag and smaller order of the amplitudes, the triplet structure is noticeable up to about the 14th harmonic. The modulation is concentrated to a very narrow, 0.2 phase range of the pulsation, centred on the supposed onset of the H emission during rising light. These observational results raise further complications for theoretical explanation of the long known but poorly understood Blazhko phenomenon.Comment: 10 pages, 12 figures, 3 tables. Accepted for publication in Astronomy and Astrophysic

Is early limited surgery associated with a more benign disease course in Crohn’s disease?

AIM: To analyze the difference in disease course and need for surgery in patients with Crohn's disease (CD). METHODS: Data of 506 patients with incident CD were analyzed (age at diagnosis: 31.5 ± 13.8 years). Both hospital and outpatient records were collected prospectively with a complete clinical follow-up and comprehensively reviewed in the population-based Veszprem province database, which includes incident CD patients diagnosed between January 1, 1977 and December 31, 2008. Follow-up data were collected until December 31, 2009. All patients included had at least 1 year of follow-up available. Patients with indeterminate colitis at diagnosis were excluded from the analysis. RESULTS: Overall, 73 patients (14.4%) required resective surgery within 1 year of diagnosis. Steroid exposure and need for biological therapy were lower in patients with early limited surgery (P < 0.001 and P = 0.09). In addition, surgery rates during follow-up in patients with and without early surgery differed significantly after matching on propensity scores (P < 0.001, HR = 0.23). The need for reoperation was also lower in patients with early limited resective surgery (P = 0.038, HR = 0.42) in a Kaplan-Meier and multivariate Cox regression (P = 0.04) analysis. However, this advantage was not observed after matching on propensity scores (P(Logrank) = 0.656, P(Breslow) = 0.498). CONCLUSION: Long-term surgery rates and overall exposure to steroids and biological agents were lower in patients with early limited resective surgery, but reoperation rates did not differ