A Vernacular for Coherent Logic

We propose a simple, yet expressive proof representation from which proofs for different proof assistants can easily be generated. The representation uses only a few inference rules and is based on a frag- ment of first-order logic called coherent logic. Coherent logic has been recognized by a number of researchers as a suitable logic for many ev- eryday mathematical developments. The proposed proof representation is accompanied by a corresponding XML format and by a suite of XSL transformations for generating formal proofs for Isabelle/Isar and Coq, as well as proofs expressed in a natural language form (formatted in LATEX or in HTML). Also, our automated theorem prover for coherent logic exports proofs in the proposed XML format. All tools are publicly available, along with a set of sample theorems.Comment: CICM 2014 - Conferences on Intelligent Computer Mathematics (2014

Poincaré on the Foundation of Geometry in the Understanding

This paper is about Poincaré’s view of the foundations of geometry. According to the established view, which has been inherited from the logical positivists, Poincaré, like Hilbert, held that axioms in geometry are schemata that provide implicit definitions of geometric terms, a view he expresses by stating that the axioms of geometry are “definitions in disguise.” I argue that this view does not accord well with Poincaré’s core commitment in the philosophy of geometry: the view that geometry is the study of groups of operations. In place of the established view I offer a revised view, according to which Poincaré held that axioms in geometry are in fact assertions about invariants of groups. Groups, as forms of the understanding, are prior in conception to the objects of geometry and afford the proper definition of those objects, according to Poincaré. Poincaré’s view therefore contrasts sharply with Kant’s foundation of geometry in a unique form of sensibility. According to my interpretation, axioms are not definitions in disguise because they themselves implicitly define their terms, but rather because they disguise the definitions which imply them

Alcohol Policies and Alcoholic Cirrhosis Mortality in the United States

Introduction Stronger alcohol policies predict decreased alcohol consumption and binge drinking in the United States. We examined the relation- ship between the strength of states’ alcohol policies and alcoholic cirrhosis mortality rates. Methods We used the Alcohol Policy Scale (APS), a validated assessment of policies of the 50 US states and Washington DC, to quantify the efficacy and implementation of 29 policies. State APS scores (the- oretical range, 0–100) for each year from 1999 through 2008 were compared with age-adjusted alcoholic cirrhosis death rates that oc- curred 3 years later. We used Poisson regression accounting for state-level clustering and adjusting for race/ethnicity, college edu- cation, insurance status, household income, religiosity, policing rates, and urbanization. Results Age-adjusted alcoholic cirrhosis mortality rates varied signific- antly across states; they were highest among males, among resid- ents in states in the West census region, and in states with a high proportion of American Indians/Alaska Natives (AI/ANs). Higher APS scores were associated with lower mortality rates among fe- males (adjusted incidence rate ratio [IRR], 0.91 per 10-point in- crease in APS score; 95% confidence interval [95% CI], 0.84–0.99) but not among males (adjusted IRR, 0.97; 95% CI, 0.90–1.04). Among non-AI/AN decedents, higher APS scores were also associated with lower alcoholic cirrhosis mortality rates among both sexes combined (adjusted IRR, 0.89; 95% CI, 0.82–0.97). Policies were more strongly associated with lower mortality rates among those living in the Northeast and West census regions than in other regions. Conclusions Stronger alcohol policy environments are associated with lower al- coholic cirrhosis mortality rates. Future studies should identify un- derlying reasons for racial/ethnic and regional differences in this relationship

Proceedings of the International Haemophilia Prophylaxis Study Group Meeting, November 2003, Montreal, PQ, Canada

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72691/1/j.1365-2516.2005.01053.x.pd

TuneTracker: Tensions in the Surveillance of Traditional Music

We describe the design and deployment of the first system ever to dynamically track and publish records of folk music playing. TuneTracker is a software system that has been, at time of writing, deployed at a pub in Dublin, Ireland for five months. It captures, stores, and posts the names of tunes played in Irish traditional music sessions on a public website. This paper makes two contributions: (1) drawing from a two year ethnographic study of trad musicians, it details the design and development of a system to track and publish traditional musicians’ practices while respecting the ethos of tradition, and (2) it presents a discussion of professional musicians’ reactions to having their music practices surveilled. This latter fieldwork revealed divergent viewpoints on the effect that TuneTracker would have on local sessions and the process of tradition

Determining significance of pairwise co-occurrences of events in bursty sequences

<p>Abstract</p> <p>Background</p> <p>Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes and therefore potentially more binding sites, while in some, possibly very long regions, hardly any events occur. Also some types of events may occur in the sequence more often than others.</p> <p>Tendencies of co-occurrence of binding sites of two or more TFs are interesting, as they may imply a co-operative role between the TFs in regulatory processes. Determining a numerical value to summarize the tendency for co-occurrence between two TFs can be done in a number of ways. However, testing for the significance of such values should be done with respect to a relevant null model that takes into account the global sequence structure.</p> <p>Results</p> <p>We extend the existing techniques that have been considered for determining the significance of co-occurrence patterns between a pair of event types under different null models. These models range from very simple ones to more complex models that take the burstiness of sequences into account. We evaluate the models and techniques on synthetic event sequences, and on real data consisting of potential transcription factor binding sites.</p> <p>Conclusion</p> <p>We show that simple null models are poorly suited for bursty data, and they yield many false positives. More sophisticated models give better results in our experiments. We also demonstrate the effect of the window size, i.e., maximum co-occurrence distance, on the significance results.</p

Preparation of anti-vicinal amino alcohols: asymmetric synthesis of D-erythro-Sphinganine, (+)-spisulosine and D-ribo-phytosphingosine

Two variations of the Overman rearrangement have been developed for the highly selective synthesis of anti-vicinal amino alcohol natural products. A MOM-ether directed palladium(II)-catalyzed rearrangement of an allylic trichloroacetimidate was used as the key step for the preparation of the protein kinase C inhibitor D-erythro-sphinganine and the antitumor agent (+)-spisulosine, while the Overman rearrangement of chiral allylic trichloroacetimidates generated by asymmetric reduction of an alpha,beta-unsaturated methyl ketone allowed rapid access to both D-ribo-phytosphingosine and L-arabino-phytosphingosine

Preparation of amino-substituted indenes and 1,4-dihydronaphthalenes using a one-pot multireaction approach: total synthesis of oxybenzo[c]phenanthridine alkaloids

Allylic trichloroacetimidates bearing a 2-vinyl or 2-allylaryl group have been designed as substrates for a one-pot, two-step multi-bond-forming process leading to the general preparation of aminoindenes and amino-substituted 1,4-dihydronaphthalenes. The synthetic utility of the privileged structures formed from this one-pot process was demonstrated with the total synthesis of four oxybenzo[c]phenanthridine alkaloids, oxychelerythrine, oxysanguinarine, oxynitidine, and oxyavicine. An intramolecular biaryl Heck coupling reaction, catalyzed using the Hermann–Beller palladacycle was used to effect the key step during the synthesis of the natural products

STELLAR: fast and exact local alignments

<p>Abstract</p> <p>Background</p> <p>Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches.</p> <p>Results</p> <p>We present here the local pairwise aligner STELLAR that has full sensitivity for <it>ε</it>-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments.</p> <p>Conclusions</p> <p>STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at <url>http://www.seqan.de/projects/stellar</url>. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at <url>http://www.seqan.de</url>.</p