Towards an Interaction-based Integration of MKM Services into End-User Applications

The Semantic Alliance (SAlly) Framework, first presented at MKM 2012, allows integration of Mathematical Knowledge Management services into typical applications and end-user workflows. From an architecture allowing invasion of spreadsheet programs, it grew into a middle-ware connecting spreadsheet, CAD, text and image processing environments with MKM services. The architecture presented in the original paper proved to be quite resilient as it is still used today with only minor changes. This paper explores extensibility challenges we have encountered in the process of developing new services and maintaining the plugins invading end-user applications. After an analysis of the underlying problems, I present an augmented version of the SAlly architecture that addresses these issues and opens new opportunities for document type agnostic MKM services.Comment: 14 pages, 7 figure

Search Interfaces for Mathematicians

Access to mathematical knowledge has changed dramatically in recent years, therefore changing mathematical search practices. Our aim with this study is to scrutinize professional mathematicians' search behavior. With this understanding we want to be able to reason why mathematicians use which tool for what search problem in what phase of the search process. To gain these insights we conducted 24 repertory grid interviews with mathematically inclined people (ranging from senior professional mathematicians to non-mathematicians). From the interview data we elicited patterns for the user group "mathematicians" that can be applied when understanding design issues or creating new designs for mathematical search interfaces.Comment: conference article "CICM'14: International Conference on Computer Mathematics 2014", DML-Track: Digital Math Libraries 17 page

Using RNA-seq to characterize responses to 4 hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

Background: Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause crippling yield losses for both maize (Zea mays L.) and soybean (Glycine max L. Merr). In 2011, 4-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicide resistance was first reported in two waterhemp populations. Since the discovery of HPPD-herbicide resistance, studies have identified the mechanism of resistance and described the inheritance of the herbicide resistance. However, no studies have examined genome-wide gene expression changes in response to herbicide treatment in herbicide resistant and susceptible waterhemp. Results: We conducted RNA-sequencing (RNA-seq) analyses of two waterhemp populations (HPPD-herbicide resistant and susceptible), from herbicide-treated and mock-treated leaf samples at three, six, twelve, and twenty-four hours after treatment (HAT). We performed a de novo transcriptome assembly using all sample sequences. Following assessments of our assembly, individual samples were mapped to the de novo transcriptome allowing us to identify transcripts specific to a genotype, herbicide treatment, or time point. Our results indicate that the response of HPPDherbicide resistant and susceptible waterhemp genotypes to HPPD-inhibiting herbicide is rapid, established as soon as 3 hours after herbicide treatment. Further, there was little overlap in gene expression between resistant and susceptible genotypes, highlighting dynamic differences in response to herbicide treatment. In addition, we used stringent analytical methods to identify candidate single nucleotide polymorphisms (SNPs) that distinguish the resistant and susceptible genotypes. Conclusions: The waterhemp transcriptome, herbicide-responsive genes, and SNPs generated in this study provide valuable tools for future studies by numerous plant science communities. This collection of resources is essential to study and understand herbicide effects on gene expression in resistant and susceptible weeds. Understanding how herbicides impact gene expression could allow us to develop novel approaches for future herbicide development. Additionally, an increased understanding of the prolific traits intrinsic in weed success could lead to crop improvement

A Survey on Retrieval of Mathematical Knowledge

We present a short survey of the literature on indexing and retrieval of mathematical knowledge, with pointers to 72 papers and tentative taxonomies of both retrieval problems and recurring techniques.Comment: CICM 2015, 20 page

SALL4 Expression in Gonocytes and Spermatogonial Clones of Postnatal Mouse Testes

The spermatogenic lineage is established after birth when gonocytes migrate to the basement membrane of seminiferous tubules and give rise to spermatogonial stem cells (SSC). In adults, SSCs reside within the population of undifferentiated spermatogonia (Aundiff) that expands clonally from single cells (Asingle) to form pairs (Apaired) and chains of 4, 8 and 16 Aaligned spermatogonia. Although stem cell activity is thought to reside in the population of Asingle spermatogonia, new research suggests that clone size alone does not define the stem cell pool. The mechanisms that regulate self-renewal and differentiation fate decisions are poorly understood due to limited availability of experimental tools that distinguish the products of those fate decisions. The pluripotency factor SALL4 (sal-like protein 4) is implicated in stem cell maintenance and patterning in many organs during embryonic development, but expression becomes restricted to the gonads after birth. We analyzed the expression of SALL4 in the mouse testis during the first weeks after birth and in adult seminiferous tubules. In newborn mice, the isoform SALL4B is expressed in quiescent gonocytes at postnatal day 0 (PND0) and SALL4A is upregulated at PND7 when gonocytes have colonized the basement membrane and given rise to spermatogonia. During steady-state spermatogenesis in adult testes, SALL4 expression overlapped substantially with PLZF and LIN28 in Asingle, Apaired and Aaligned spermatogonia and therefore appears to be a marker of undifferentiated spermatogonia in mice. In contrast, co-expression of SALL4 with GFRα1 and cKIT identified distinct subpopulations of Aundiff in all clone sizes that might provide clues about SSC regulation. Collectively, these results indicate that 1) SALL4 isoforms are differentially expressed at the initiation of spermatogenesis, 2) SALL4 is expressed in undifferentiated spermatogonia in adult testes and 3) SALL4 co-staining with GFRα1 and cKIT reveals distinct subpopulations of Aundiff spermatogonia that merit further investigation. © 2013 Gassei, Orwig

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

A Foundational View on Integration Problems

The integration of reasoning and computation services across system and language boundaries is a challenging problem of computer science. In this paper, we use integration for the scenario where we have two systems that we integrate by moving problems and solutions between them. While this scenario is often approached from an engineering perspective, we take a foundational view. Based on the generic declarative language MMT, we develop a theoretical framework for system integration using theories and partial theory morphisms. Because MMT permits representations of the meta-logical foundations themselves, this includes integration across logics. We discuss safe and unsafe integration schemes and devise a general form of safe integration

Subcutaneous vitamin B12 administration using a portable infusion pump in cobalamin-related remethylation disorders: a gentle and easy to use alternative to intramuscular injections

BACKGROUND Cobalamin (cbl)-related remethylation disorders are a heterogeneous group of inherited disorders comprising the remethylation of homocysteine to methionine and affecting multiple organ systems, most prominently the nervous system and the bone marrow. To date, the parenteral, generally intramuscular, lifelong administration of hydroxycobalamin (OHCbl) is the mainstay of therapy in these disorders. The dosage and frequency of OHCbl is titrated in each patient to the minimum effective dose in order to account for the painful injections. This may result in undertreatment, a possible risk factor for disease progression and disease-related complications. RESULTS We describe parenteral administration of OHCbl using a subcutaneous catheter together with a portable infusion pump in a home therapy setting in four pediatric patients with remethylation disorders, two patients with cblC, one patient with cblG, and one patient with cblE deficiency, in whom intramuscular injections were not or no longer feasible. The placement of the subcutaneous catheters and handling of the infusion pump were readily accomplished and well accepted by the patients and their families. No adverse events occurred. The use of a small, portable syringe driver pump allowed for a most flexible administration of OHCbl in everyday life. The concentrations of total homocysteine levels were determined at regular patient visits and remained within the therapeutic target range. This approach allowed for the continuation of OHCbl therapy or the adjustment of therapy required to improve metabolic control in our patients. CONCLUSIONS Subcutaneous infusion using a subcutaneous catheter system and a portable pump for OHCbl administration in combined and isolated remethylation disorders is safe, acceptable, and effective. It decreases disease burden in preventing frequent single injections and providing patient independence. Thus, it may promote long-term adherence to therapy in patients and parents

Large Formal Wikis: Issues and Solutions

We present several steps towards large formal mathematical wikis. The Coq proof assistant together with the CoRN repository are added to the pool of systems handled by the general wiki system described in \cite{DBLP:conf/aisc/UrbanARG10}. A smart re-verification scheme for the large formal libraries in the wiki is suggested for Mizar/MML and Coq/CoRN, based on recently developed precise tracking of mathematical dependencies. We propose to use features of state-of-the-art filesystems to allow real-time cloning and sandboxing of the entire libraries, allowing also to extend the wiki to a true multi-user collaborative area. A number of related issues are discussed.Comment: To appear in The Conference of Intelligent Computer Mathematics: CICM 201

Mathematical practice, crowdsourcing, and social machines

The highest level of mathematics has traditionally been seen as a solitary endeavour, to produce a proof for review and acceptance by research peers. Mathematics is now at a remarkable inflexion point, with new technology radically extending the power and limits of individuals. Crowdsourcing pulls together diverse experts to solve problems; symbolic computation tackles huge routine calculations; and computers check proofs too long and complicated for humans to comprehend. Mathematical practice is an emerging interdisciplinary field which draws on philosophy and social science to understand how mathematics is produced. Online mathematical activity provides a novel and rich source of data for empirical investigation of mathematical practice - for example the community question answering system {\it mathoverflow} contains around 40,000 mathematical conversations, and {\it polymath} collaborations provide transcripts of the process of discovering proofs. Our preliminary investigations have demonstrated the importance of "soft" aspects such as analogy and creativity, alongside deduction and proof, in the production of mathematics, and have given us new ways to think about the roles of people and machines in creating new mathematical knowledge. We discuss further investigation of these resources and what it might reveal. Crowdsourced mathematical activity is an example of a "social machine", a new paradigm, identified by Berners-Lee, for viewing a combination of people and computers as a single problem-solving entity, and the subject of major international research endeavours. We outline a future research agenda for mathematics social machines, a combination of people, computers, and mathematical archives to create and apply mathematics, with the potential to change the way people do mathematics, and to transform the reach, pace, and impact of mathematics research.Comment: To appear, Springer LNCS, Proceedings of Conferences on Intelligent Computer Mathematics, CICM 2013, July 2013 Bath, U