And the beak shall inherit - evolution in response to invasion

The increased demographic performance of biological invaders may often depend on their escape from specifically adapted enemies. Here we report that native taxa in colonized regions may swiftly evolve to exploit such emancipated exotic species because of selection caused by invaders. A native Australian true bug has expanded it host range to include a vine imported from tropical America that has become a serious environmental weed. Based on field comparisons and historical museum specimens, we show that over the past 30-40 years, seed feeding soapberry bugs have evolved 5-10% longer mouthparts, better suited to attack the forest-invading balloon vines, which have large fruits. Laboratory experiments show that these differences are genetically based, and result in a near-doubling of the rate at which seeds are attacked. Thus a native biota that initially permits invasion may rapidly respond in ways that ultimately facilitate control.

Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic

The Paraneoptera (Hemipteroid Assemblage) comprises the orders Thysanoptera (thrips), Hemiptera (bugs), Phthiraptera (lice) and Psocoptera (booklice and barklice). The phylogenetic relationships among the Psocodea (Phthiraptera and Psocoptera), Thysanoptera and Hemiptera are unresolved, as are some relationships within the Psocodea. Here, we present phylogenetic hypotheses inferred from SSU rDNA sequences; the most controversial of which is the apparent paraphyly of the Phthiraptera, which are parasites of birds and mammals, with respect to one family of Psocoptera, the Liposcelididae. The order Psocoptera and the suborder that contains the Liposcelididae, the Troctomorpha, are also paraphyletic. The two remaining psocopteran suborders, the Psocomorpha and the Trogiomorpha, are apparently monophyletic. The Liposcelididae is most closely related to lice from the suborder Amblycera. These results suggest that the taxonomy of the Psocodea needs revision. In addition, there are implications for the evolution of parasitism in insects; parasitism may have evolved twice in lice or have evolved once and been subsequently lost in the Liposcelididae.

Influence of Observer Presence on Pacific Damsel Bug Behavior: Who is Watching Whom?

When direct observations are used to study animal behavior the presence of the observer may alter the animal and hence influence the data being collected, yet few studies have quantified this effect. We conducted direct observation studies in the glasshouse to assess the relative influence of observer presence on the behavior of Pacific damsel bugs, Nabis kinbergii, a potentially important predator of crop pests. Comparisons of predator activity, predator distribution, prey (Helicoverpa armigera) mortality and prey distribution between frequently observed and minimally observed treatments, during diurnal and nocturnal observation sessions showed that the frequency of observer presence had no apparent impact on Pacific damsel bug behavior. This is the first documented test of the impact of observer presence in an insect system. To place our results in context, we reviewed 15 papers on the influence of observer presence in a range of animals. We established that just over half of these papers found evidence for an effect. Nevertheless, direct observations should be useful in further studies of Pacific damsel bug behavior, and researchers using direct observations to study the behavior of other animals should be cognizant of observer effects during design and interpretation of their study.

The species composition of true bug assemblages extracted with Berlese funnels (Data to the knowledge on the ground-living Heteroptera of Hungary, No 1)

A rich collection of Heteroptera extracted with Berlese funnel by Dr. I. Loksa between 1953–1974 in Hungary, has been examined. Altogether 157 true bug species have been identified. The great majority of them have been found in very low number, there are only 27 species of which more than 10 adult individuals have been found. Some species considered to be rare or very rare in Hungary have been collected in relatively great number (Ceratocombus coleoptratus, Cryptostemma pusillimum, C. waltli, Acalypta carinata, A. platycheila, Loricula ruficeps, Myrmedobia exilis). The three families, which are more or less rich in species and have the highest ratio of extracted species, were Rhyparochromidae, Tingidae and Nabidae. Out of them, the family Rhyparochromidae has been found to be most diverse and most characteristic at the ground-level. Individuals of the families Tingidae, Hebridae and Rhyparochromidae have been found in greatest number. The occurrence of the lace bug Campylosteira orientalis Horváth, 1881 in Hungary has been verified by a voucher specimen. In respect to the environmental changes through the country, parallel changes have been observed in the zoogeographical distribution of the ground-living bugs.

Ecology of the Acalypta species occurring in Hungary Insecta Heteroptera Tingidae data to the knowledge on the ground-living Heteroptera of Hungary, No 3

As a third part of a series of papers on the ground-living true bugs of Hungary, the species belonging to the lace bug genus Acalypta Westwood, 1840 (Insecta: Heteroptera: Tingidae) were studied. Extensive materials collected with Berlese funnels during about 20 years all over Hungary were identified. Based on these sporadic data of many years, faunistic notes are given on some Hungarian species. The seasonal occurrence of the species are discussed. The numbers of specimens of different Acalypta species collected in diverse plant communities are compared with multivariate methods. Materials collected with pitfall traps between 1979–1982 at Bugac, Kiskunság National Park were also processed. In this area, only A. marginata and A. gracilis occurred, both in great number. The temporal changes of the populations are discussed. Significant differences could be observed between the microhabitat distribution of the two species: both species occurred in very low number in traps placed out in patches colonized by dune-slack purple moorgrass meadow; Acalypta gracilis preferred distinctly the Pannonic dune open grassland patches; A. marginata occurred in almost equal number in Pannonic dune open grassland and in Pannonic sand puszta patches.

The effects of intellectual property rights on knowledge spillovers and innovation: An empirical investigation

FDI is believed to be a conduit of new technologies between countries. The first chapter of this dissertation studies the advantages of outward FDI for the home country of multinationals conducting research and development abroad. We use patent citations as a proxy for technology spillovers and we bring empirical evidence that supports the hypothesis that a U.S. subsidiary conducting research and development overseas facilitates the flow of knowledge between its host and home countries.^ The second chapter examines the impact of intellectual property rights (IPR) reforms on the technology flows between the U.S. and host countries of U.S. affiliates. We again use patent citations to examine whether the diffusion of new technology between the host countries and the U.S. is accelerated by the reforms. Our results suggest that the reforms favor innovative efforts of domestic firms in the reforming countries rather than U.S. affiliates efforts. In other words, reforms mediate the technology flows from the U.S. to the reforming countries.^ The third chapter deals with another form of IPR, open source (OS) licenses. These differ in the conditions under which licensors and OS contributors are allowed to modify and redistribute the source code. We measure OS project quality by the speed with which programming bugs are fixed and test whether the license chosen by project leaders influences bug resolution rates. In initial regressions, we find a strong correlation between the hazard of bug resolution and the use of highly restrictive licenses. However, license choices are likely to be endogenous. We instrument license choice using (i) the human language in which contributors operate and (ii) the license choice of the project leaders for a previous project. We then find weak evidence that restrictive licenses adversely affect project success.^

An approach for design and analysis of User-centric Communication Middleware

Today, the development of domain-specific communication applications is both time-consuming and error-prone because the low-level communication services provided by the existing systems and networks are primitive and often heterogeneous. Multimedia communication applications are typically built on top of low-level network abstractions such as TCP/UDP socket, SIP (Session Initiation Protocol) and RTP (Real-time Transport Protocol) APIs. The User-centric Communication Middleware (UCM) is proposed to encapsulate the networking complexity and heterogeneity of basic multimedia and multi-party communication for upper-layer communication applications. And UCM provides a unified user-centric communication service to diverse communication applications ranging from a simple phone call and video conferencing to specialized communication applications like disaster management and telemedicine. It makes it easier to the development of domain-specific communication applications. The UCM abstraction and API is proposed to achieve these goals. The dissertation also tries to integrate the formal method into UCM development process. The formal model is created for UCM using SAM methodology. Some design errors are found during model creation because the formal method forces to give the precise description of UCM. By using the SAM tool, formal UCM model is translated to Promela formula model. In the dissertation, some system properties are defined as temporal logic formulas. These temporal logic formulas are manually translated to promela formulas which are individually integrated with promela formula model of UCM and verified using SPIN tool. Formal analysis used here helps verify the system properties (for example multiparty multimedia protocol) and dig out the bugs of systems.

Methods for modeling and analyzing concurrent software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.

The Relationship of Heteroptera Species Richness, Abundance, and Morphology to Elevation Gradients and Land-use Regimes on Mt. Kilimanjaro

Insect biodiversity is unevenly distributed on local, regional, and global scales. Elevation is a key factor in the uneven distribution of insect diversity, serving as a proxy for a host of environmental variables. My study examines the relationship of Heteroptera (true bugs) species diversity, abundance, and morphology to elevational gradients and land-use regimes on Mt. Kilimanjaro, Tanzania, East Africa. Heteroptera specimens were collected from 60 research sites covering an elevational range of 3684m (866-4550m above sea level). Thirty of the sites were classified as natural, while the remaining 30 were classified as disturbed (e.g., agricultural use or converted to grasslands). I measured aspects of the body size of adult specimens and recorded their location of origin. I used regression models to analyze the relationships of Heteroptera species richness, abundance, and body measurements to elevation and land-use regime. Richness and abundance declined with greater elevation, controlling for land use. The declines were linear or logarithmic in form, depending on the model. Richness and abundance were greater in natural than disturbed sites, controlling for elevation. According to an interaction, richness decreased more in natural than disturbed sites with rising elevation. Body length increased as a quadratic function of elevation, adjusting for land use. Body width X length decreased as a logarithmic function of elevation, while leg length/body length decreased as a quadratic function. Leg length/body length was greater in disturbed than natural sites. Interactions indicated that body length and body width X length were greater in natural than disturbed sites as elevation rose, although the general trend was downward. Future research should examine the relative importance of land area, temperature, and resource constraints for Heteroptera diversity and morphology on Mt. Kilimanjaro.

An Exploration of the challenges associated with software logging in large systems

Over the past few years, logging has evolved from from simple printf statements to more complex and widely used logging libraries. Today logging information is used to support various development activities such as fixing bugs, analyzing the results of load tests, monitoring performance and transferring knowledge. Recent research has examined how to improve logging practices by informing developers what to log and where to log. Furthermore, the strong dependence on logging has led to the development of logging libraries that have reduced the intricacies of logging, which has resulted in an abundance of log information. Two recent challenges have emerged as modern software systems start to treat logging as a core aspect of their software. In particular, 1) infrastructural challenges have emerged due to the plethora of logging libraries available today and 2) processing challenges have emerged due to the large number of log processing tools that ingest logs and produce useful information from them. In this thesis, we explore these two challenges. We first explore the infrastructural challenges that arise due to the plethora of logging libraries available today. As systems evolve, their logging infrastructure has to evolve (commonly this is done by migrating to new logging libraries). We explore logging library migrations within Apache Software Foundation (ASF) projects. We i find that close to 14% of the pro jects within the ASF migrate their logging libraries at least once. For processing challenges, we explore the different factors which can affect the likelihood of a logging statement changing in the future in four open source systems namely ActiveMQ, Camel, Cloudstack and Liferay. Such changes are likely to negatively impact the log processing tools that must be updated to accommodate such changes. We find that 20%-45% of the logging statements within the four systems are changed at least once. We construct random forest classifiers and Cox models to determine the likelihood of both just-introduced and long-lived logging statements changing in the future. We find that file ownership, developer experience, log density and SLOC are important factors in determining the stability of logging statements.

Type-Aware Programming Models for Distributed Applications

Thesis (Ph.D.)--University of Washington, 2016-08

Automatiserade regressionstester avseende arbetsflöden och behörigheter i ProjectWise. : En fallstudie om ProjectWise på Trafikverket

Test av mjukvara görs i syfte att se ifall systemet uppfyller specificerade krav samt för att hitta fel. Det är en viktig del i systemutveckling och involverar bland annat regressionstestning. Regressionstester utförs för att säkerställa att en ändring i systemet inte medför att andra delar i systemet påverkas negativt. Dokumenthanteringssystem hanterar ofta känslig data hos organisationer vilket ställer höga krav på säkerheten. Behörigheter i system måste därför testas noggrant för att säkerställa att data inte hamnar i fel händer. Dokumenthanteringssystem gör det möjligt för flera organisationer att samla sina resurser och kunskaper för att nå gemensamma mål. Gemensamma arbetsprocesser stöds med hjälp av arbetsflöden som innehåller ett antal olika tillstånd. Vid dessa olika tillstånd gäller olika behörigheter. När en behörighet ändras krävs regressionstester för att försäkra att ändringen inte har gjort inverkan på andra behörigheter. Denna studie har utförts som en kvalitativ fallstudie vars syfte var att beskriva utmaningar med regressionstestning av roller och behörigheter i arbetsflöden för dokument i dokumenthanteringssystem. Genom intervjuer och en observation så framkom det att stora utmaningar med dessa tester är att arbetsflödens tillstånd följer en förutbestämd sekvens. För att fullfölja denna sekvens så involveras en enorm mängd behörigheter som måste testas. Det ger ett mycket omfattande testarbete avseende bland annat tid och kostnad. Studien har riktat sig mot dokumenthanteringssystemet ProjectWise som förvaltas av Trafikverket. Beslutsunderlag togs fram för en teknisk lösning för automatiserad regressionstestning av roller och behörigheter i arbetsflöden åt ProjectWise. Utifrån en kravinsamling tillhandahölls beslutsunderlag som involverade Team Foundation Server (TFS), Coded UI och en nyckelordsdriven testmetod som en teknisk lösning. Slutligen jämfördes vilka skillnader den tekniska lösningen kan utgöra mot manuell testning. Utifrån litteratur, dokumentstudie och förstahandserfarenheter visade sig testautomatisering kunna utgöra skillnader inom ett antal identifierade problemområden, bland annat tid och kostnad.

FRAMEWORK SYNTHESIS FOR SYMBOLIC EXECUTION OF EVENT-DRIVEN FRAMEWORKS

Symbolic execution is a powerful program analysis technique, but it is very challenging to apply to programs built using event-driven frameworks, such as Android. The main reason is that the framework code itself is too complex to symbolically execute. The standard solution is to manually create a framework model that is simpler and more amenable to symbolic execution. However, developing and maintaining such a model by hand is difficult and error-prone. We claim that we can leverage program synthesis to introduce a high-degree of automation to the process of framework modeling. To support this thesis, we present three pieces of work. First, we introduced SymDroid, a symbolic executor for Android. While Android apps are written in Java, they are compiled to Dalvik bytecode format. Instead of analyzing an app’s Java source, which may not be available, or decompiling from Dalvik back to Java, which requires significant engineering effort and introduces yet another source of potential bugs in an analysis, SymDroid works directly on Dalvik bytecode. Second, we introduced Pasket, a new system that takes a first step toward automatically generating Java framework models to support symbolic execution. Pasket takes as input the framework API and tutorial programs that exercise the framework. From these artifacts and Pasket's internal knowledge of design patterns, Pasket synthesizes an executable framework model by instantiating design patterns, such that the behavior of a synthesized model on the tutorial programs matches that of the original framework. Lastly, in order to scale program synthesis to framework models, we devised adaptive concretization, a novel program synthesis algorithm that combines the best of the two major synthesis strategies: symbolic search, i.e., using SAT or SMT solvers, and explicit search, e.g., stochastic enumeration of possible solutions. Adaptive concretization parallelizes multiple sub-synthesis problems by partially concretizing highly influential unknowns in the original synthesis problem. Thanks to adaptive concretization, Pasket can generate a large-scale model, e.g., thousands lines of code. In addition, we have used an Android model synthesized by Pasket and found that the model is sufficient to allow SymDroid to execute a range of apps.

A User Interaction Bug Analyzer Based on Image

Context: Mobile applications support a set of user-interaction features that are independent of the application logic. Rotating the device, scrolling, or zooming are examples of such features. Some bugs in mobile applications can be attributed to user-interaction features. Objective: This paper proposes and evaluates a bug analyzer based on user-interaction features that uses digital image processing to find bugs. Method: Our bug analyzer detects bugs by comparing the similarity between images taken before and after a user-interaction. SURF, an interest point detector and descriptor, is used to compare the images. To evaluate the bug analyzer, we conducted a case study with 15 randomly selected mobile applications. First, we identified user-interaction bugs by manually testing the applications. Images were captured before and after applying each user-interaction feature. Then, image pairs were processed with SURF to obtain interest points, from which a similarity percentage was computed, to finally decide whether there was a bug. Results: We performed a total of 49 user-interaction feature tests. When manually testing the applications, 17 bugs were found, whereas when using image processing, 15 bugs were detected. Conclusions: 8 out of 15 mobile applications tested had bugs associated to user-interaction features. Our bug analyzer based on image processing was able to detect 88% (15 out of 17) of the user-interaction bugs found with manual testing.