Query Technologies and Applications for Program Comprehension

Industrial software systems are large and complex, both in terms of the software entities and their relationships. Consequently, understanding how a software system works requires the ability to pose queries over the design-level entities of the system. Traditionally, this task has been supported by simple tools (e.g., grep) combined with the programmer's intuition and experience. Recently, however, specialized code query technologies have matured to the point where they can be used in industrial situations, providing more intelligent, timely, and efficient responses to developer queries. This working session aims to explore the state of the art in code query technologies, and discover new ways in which these technologies may be useful in program comprehension. The session brings together researchers and practitioners. We survey existing techniques and applications, trying to understand the strengths and weaknesses of the various approaches, and sketch out new frontiers that hold promise.

Simultaneous bilateral hip replacement reveals superior outcome and fewer complications than two-stage procedures: a prospective study including 1819 patients and 5801 follow-ups from a total joint replacement registry

Background Total joint replacements represent a considerable part of day-to-day orthopaedic routine and a substantial proportion of patients undergoing unilateral total hip arthroplasty require a contralateral treatment after the first operation. This report compares complications and functional outcome of simultaneous versus early and delayed two-stage bilateral THA over a five-year follow-up period. Methods The study is a post hoc analysis of prospectively collected data in the framework of the European IDES hip registry. The database query resulted in 1819 patients with 5801 follow-ups treated with bilateral THA between 1965 and 2002. According to the timing of the two operations the sample was divided into three groups: I) 247 patients with simultaneous bilateral THA, II) 737 patients with two-stage bilateral THA within six months, III) 835 patients with two-stage bilateral THA between six months and five years. Results Whereas postoperative hip pain and flexion did not differ between the groups, the best walking capacity was observed in group I and the worst in group III. The rate of intraoperative complications in the first group was comparable to that of the second. The frequency of postoperative local and systemic complication in group I was the lowest of the three groups. The highest rate of complications was observed in group III. Conclusions From the point of view of possible intra- and postoperative complications, one-stage bilateral THA is equally safe or safer than two-stage interventions. Additionally, from an outcome perspective the one-stage procedure can be considered to be advantageous.

Object-Oriented Legacy System Trace-based Logic Testing

When reengineering legacy systems, it is crucial to assess if the legacy behavior has been preserved or how it changed due to the reengineering effort. Ideally if a legacy system is covered by tests, running the tests on the new version can identify potential differences or discrepancies. However, writing tests for an unknown and large system is difficult due to the lack of internal knowledge. It is especially difficult to bring the system to an appropriate state. Our solution is based on the acknowledgment that one of the few trustable piece of information available when approaching a legacy system is the running system itself. Our approach reifies the execution traces and uses logic programming to express tests on them. Thereby it eliminates the need to programatically bring the system in a particular state, and handles the test-writer a high-level abstraction mechanism to query the trace. The resulting system, called TESTLOG, was used on several real-world case studies to validate our claims.

Querying Runtime Information in the IDE

Code queries focus mainly on the static structure of a system. To comprehend the dynamic behavior of a system however, a software engineer needs to be able to reason about the dynamics of this system, for instance by querying a database of dynamic information. Such a querying mechanism should be directly available in the IDE where the developers implements, navigates and reasons about the software system. We propose (i) concepts to gather dynamic information, (ii) the means to query this information, and (iii) tools and techniques to integrate querying of dynamic information in the IDE, including the presentation of results generated by queries.

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

The MQN-mapplet is a Java application giving access to the structure of small molecules in large databases via color-coded maps of their chemical space. These maps are projections from a 42-dimensional property space defined by 42 integer value descriptors called molecular quantum numbers (MQN), which count different categories of atoms, bonds, polar groups, and topological features and categorize molecules by size, rigidity, and polarity. Despite its simplicity, MQN-space is relevant to biological activities. The MQN-mapplet allows localization of any molecule on the color-coded images, visualization of the molecules, and identification of analogs as neighbors on the MQN-map or in the original 42-dimensional MQN-space. No query molecule is necessary to start the exploration, which may be particularly attractive for nonchemists. To our knowledge, this type of interactive exploration tool is unprecedented for very large databases such as PubChem and GDB-13 (almost one billion molecules). The application is freely available for download at www.gdb.unibe.ch.

Integration of WSNs into enterprise systems based on semantic physical business entities

Internet of Things based systems are anticipated to gain widespread use in industrial applications. Standardization efforts, like 6L0WPAN and the Constrained Application Protocol (CoAP) have made the integration of wireless sensor nodes possible using Internet technology and web-like access to data (RESTful service access). While there are still some open issues, the interoperability problem in the lower layers can now be considered solved from an enterprise software vendors' point of view. One possible next step towards integration of real-world objects into enterprise systems and solving the corresponding interoperability problems at higher levels is to use semantic web technologies. We introduce an abstraction of real-world objects, called Semantic Physical Business Entities (SPBE), using Linked Data principles. We show that this abstraction nicely fits into enterprise systems, as SPBEs allow a business object centric view on real-world objects, instead of a pure device centric view. The interdependencies between how currently services in an enterprise system are used and how this can be done in a semantic real-world aware enterprise system are outlined, arguing for the need of semantic services and semantic knowledge repositories. We introduce a lightweight query language, which we use to perform a quantitative analysis of our approach to demonstrate its feasibility.

Fuzzy Online Reputation Analysis Framework

The fuzzy online reputation analysis framework, or “foRa” (plural of forum, the Latin word for marketplace) framework, is a method for searching the Social Web to find meaningful information about reputation. Based on an automatic, fuzzy-built ontology, this framework queries the social marketplaces of the Web for reputation, combines the retrieved results, and generates navigable Topic Maps. Using these interactive maps, communications operatives can zero in on precisely what they are looking for and discover unforeseen relationships between topics and tags. Thus, using this framework, it is possible to scan the Social Web for a name, product, brand, or combination thereof and determine query-related topic classes with related terms and thus identify hidden sources. This chapter also briefly describes the youReputation prototype (www.youreputation.org), a free web-based application for reputation analysis. In the course of this, a small example will explain the benefits of the prototype.

Implementing the UNESCO Convention in EU's Internal Policies

This briefing note was prepared by invitation from the European Parliament's Committee on Culture and Education. It provides an analysis of how the existent EU internal policies reflect the spirit and the letter of the UNESCO Convention on Cultural Diversity. The note suggests further ideas on how the EU may calibrate current practices and explores in a forward-looking manner the possibilities for the Convention’s implementation in future internal policies, understood both as hard and soft EU legal instruments. Particular attention in this query is paid to digital media and their regulatory implications.

Supersymmetric quantum mechanics on the lattice: I. Loop formulation

Simulations of supersymmetric field theories on the lattice with (spontaneously) broken supersymmetry suffer from a fermion sign problem related to the vanishing of the Witten index. We propose a novel approach which solves this problem in low dimensions by formulating the path integral on the lattice in terms of fermion loops. For N=2 supersymmetric quantum mechanics the loop formulation becomes particularly simple and in this paper – the first in a series of three – we discuss in detail the reformulation of this model in terms of fermionic and bosonic bonds for various lattice discretisations including one which is Q-exact.

On the similarity of Sturm-Liouville operators with non-Hermitian boundary conditions to self-adjoint and normal operators

We consider one-dimensional Schrödinger-type operators in a bounded interval with non-self-adjoint Robin-type boundary conditions. It is well known that such operators are generically conjugate to normal operators via a similarity transformation. Motivated by recent interests in quasi-Hermitian Hamiltonians in quantum mechanics, we study properties of the transformations and similar operators in detail. In the case of parity and time reversal boundary conditions, we establish closed integral-type formulae for the similarity transformations, derive a non-local self-adjoint operator similar to the Schrödinger operator and also find the associated “charge conjugation” operator, which plays the role of fundamental symmetry in a Krein-space reformulation of the problem.

An welchen Vorerfahrungen sollten Planende und Durchführende von Weiterbildungen mit ihren Angeboten zu E-Learning ansetzen, um Lehrende in berufsbegleitenden Studienangeboten zu erreichen?

Obwohl E-Learning-Anteile im Studium ein unverzichtbares Element für das zeit- und ortsunabhängige Lernen für berufstätige Studierende sind, setzen die Lehrenden in den berufsbegleitenden Studiengängen der Technischen Hochschule Ingolstadt (THI) E-Learning wenig bis kaum ein. Weiterbildungen zu dieser Thematik bestehen, führen aber zurzeit nicht zu den gewünschten Änderungen der Lehre. Im Forschungs- und Entwicklungsprojekt „Offene Hochschule Oberbayern (OHO)“ wird daher unter anderem die Frage beantwortet, an welchen Vorerfahrungen in Hinblick auf technische und didaktische Einsatzmöglichkeiten von ELearning, aber auch in Hinblick auf die Haltung gegenüber Online-Lehre, für die Gestaltung von Weiterbildungen für Lehrende angesetzt werden kann. Eine mehrstufige Bedarfsanalyse im „OHO“-Projekt liefert hier Ergebnisse, die ein aus hochschuldidaktischer Sicht entwickeltes Weiterbildungskonzept um die Sicht der Studierenden, der Institution und der Lehrenden anreichert.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Firearm legislation and firearm mortality in the USA: a cross-sectional, state-level study.

BACKGROUND In an effort to reduce firearm mortality rates in the USA, US states have enacted a range of firearm laws to either strengthen or deregulate the existing main federal gun control law, the Brady Law. We set out to determine the independent association of different firearm laws with overall firearm mortality, homicide firearm mortality, and suicide firearm mortality across all US states. We also projected the potential reduction of firearm mortality if the three most strongly associated firearm laws were enacted at the federal level. METHODS We constructed a cross-sectional, state-level dataset from Nov 1, 2014, to May 15, 2015, using counts of firearm-related deaths in each US state for the years 2008-10 (stratified by intent [homicide and suicide]) from the US Centers for Disease Control and Prevention's Web-based Injury Statistics Query and Reporting System, data about 25 firearm state laws implemented in 2009, and state-specific characteristics such as firearm ownership for 2013, firearm export rates, and non-firearm homicide rates for 2009, and unemployment rates for 2010. Our primary outcome measure was overall firearm-related mortality per 100 000 people in the USA in 2010. We used Poisson regression with robust variances to derive incidence rate ratios (IRRs) and 95% CIs. FINDINGS 31 672 firearm-related deaths occurred in 2010 in the USA (10·1 per 100 000 people; mean state-specific count 631·5 [SD 629·1]). Of 25 firearm laws, nine were associated with reduced firearm mortality, nine were associated with increased firearm mortality, and seven had an inconclusive association. After adjustment for relevant covariates, the three state laws most strongly associated with reduced overall firearm mortality were universal background checks for firearm purchase (multivariable IRR 0·39 [95% CI 0·23-0·67]; p=0·001), ammunition background checks (0·18 [0·09-0·36]; p<0·0001), and identification requirement for firearms (0·16 [0·09-0·29]; p<0·0001). Projected federal-level implementation of universal background checks for firearm purchase could reduce national firearm mortality from 10·35 to 4·46 deaths per 100 000 people, background checks for ammunition purchase could reduce it to 1·99 per 100 000, and firearm identification to 1·81 per 100 000. INTERPRETATION Very few of the existing state-specific firearm laws are associated with reduced firearm mortality, and this evidence underscores the importance of focusing on relevant and effective firearms legislation. Implementation of universal background checks for the purchase of firearms or ammunition, and firearm identification nationally could substantially reduce firearm mortality in the USA. FUNDING None.