Master of Science / Department of Animal Sciences and Industry / Jeffrey S. Stevenson / Our objective was to determine the optimal time to inseminate artificially cows following the standard CO-Synch protocol that also included a progesterone-releasing intravaginal controlled internal drug release (CIDR) insert. Lactating females from 3 Kansas locations were utilized. Crossbred Angus cows (n = 212) from the Agriculture Research Center in Hays (ARCH; location 1); Angus-Hereford crossbred cows (n = 249) from the Kansas State University Cow-Calf Unit (location 2); and purebred Angus, Hereford, and Simmental cows (n = 144) from the Kansas State University Purebred Beef Unit (location 3) were used in this study. Cows within each location were blocked by parity and assigned randomly within blocks to be artificially inseminated (AI) at 4 different times after the PGF2[Alpha] injection of the protocol: 48, 56, 64, or 72 h. Pregnancy diagnosis occurred at 32 and 63 d after insemination. Blood samples were collected 9 to 10 d and just before the first GnRH injection. Radioimmunoassays were performed on the blood sera samples to determine progesterone concentrations. Progesterone concentrations determined that approximately 60% of cows were cycling at the initiation of the study. A difference in cyclicity was observed with regards to age as well as body condition score. Pregnancies per AI (P/AI) at d 32 varied according to location and cycling status. Pregnancy loss between d 32 and 63 also was greatest for cows inseminated at 48 and 72 h. As pregnancy rates at d 63 increased with the 56- and 64-h treatments, pregnancy loss decreased. A significant difference in calving interval was detected among treatments, the shortest calving interval at 56 h. Results indicated that in most situations, the 56- and 64-h treatments presented the most desirable outcomes. The 56-h treatment presented the greatest number of P/AI for younger cows (≤ 3 yr), but for older cows, inseminations anytime 56 h or later produced the most P/AI. Overall pregnancy rates at d 63 were greatest for the 56-h treatment, with the fewest pregnancy losses. Given the interactions that seem to exist among location, cycling status, and age, further work is necessary to better define these relationships with the applied protocol.

In the field of formal verification of real-time systems, major developments have been recorded in the last fifteen years. It is about logics, automata, process algebra, programming languages, etc. From the beginning, a formalism has played an important role: timed automata and their natural extension,hybrid automata. Those models allow the definition of real-time constraints using real-valued clocks, or more generally analog variables whose evolution is governed by differential equations. They generalize finite automata in that their semantics defines timed words where each symbol is associated with an occurrence timestamp. The decidability and algorithmic analysis of timed and hybrid automata have been intensively studied in the literature. The central result for timed automata is that they are positively decidable. This is not the case for hybrid automata, but semi-algorithmic methods are known when the dynamics is relatively simple, namely a linear relation between the derivatives of the variables. With the increasing complexity of nowadays systems, those models are however limited in their classical semantics, for modelling realistic implementations or dynamical systems. In this thesis, we study the algorithmics of complex semantics for timed and hybrid automata. On the one hand, we propose implementable semantics for timed automata and we study their computational properties: by contrast with other works, we identify a semantics that is implementable and that has decidable properties. On the other hand, we give new algorithmic approaches to the analysis of hybrid automata whose dynamics is given by an affine function of its variables.

<p>Regular inference is a research direction in machine learning. The goal of regular inference is to construct a representation of a regular language in the form of deterministic finite automaton (DFA) based on the set of positive and negative examples. DFAs take strings of symbols (words) as input, and produce a binary classification as output, indicating whether the word belongs to the language or not. There are two types of learning algorithms for DFAs: passive and active learning algorithms. In passive learning, the set of positive and negative examples is given and not chosen by inference algorithm. In contrast, in active learning, the learning algorithm chooses examples from which a model is constructed.</p><p>Active learning was introduced in 1987 by Dana Angluin. She presented the L* algorithm for learning DFAs by asking membership and equivalence queries to a teacher who knows the regular language accepted by DFA to be learned. A membership query checks whether a word belongs to the language or not. An equivalence query checks whether a hypothesized model is equivalent to the DFA to be learned.The L* algorithm has been found to be useful in different areas, including black box checking, compositional verification and integration testing. There are also other algorithms similar to L* for regular inference. However, the learning of timed systems has not been studied before. This thesis presents algorithms for learning timed systems in an active learning framework.</p><p>As a model of timed system we choose event-recording automata (ERAs), a determinizable subclass of the widely used timed automata. The advantages of ERA in comparison with timed automata, is that it is known priori the set of clocks of an ERA and when clocks are reset. The contribution of this thesis is four algorithms for learning deterministic event-recording automaton (DERA). Two algorithms learn a subclass of DERA, called event-deterministic ERA (EDERA) and two algorithms learn general DERA.</p><p>The problem with DERAs that they do not have canonical form. Therefore we focus on subclass of DERAs that have canonical representation, EDERA, and apply the L* algorithm to learn EDERAs. The L* algorithm in timed setting requires a procedure that learns clock guards of DERAs. This approach constructs EDERAs which are exponentially bigger than automaton to be learned. Another procedure can be used to lean smaller EDERAs, but it requires to solve NP-hard problem.</p><p>We also use the L* algorithm to learn general DERA. One drawback of this approach that inferred DERAs have a form of region graph and there is blow-up in the number of transitions. Therefore we introduce an algorithm for learning DERA which uses a new data structure for organising results of queries, called a timed decision tree, and avoids region graph construction. Theoretically this algorithm can construct bigger DERA than the L* algorithm, but in the average case we expect better performance.</p>

Real-time Embedded Systems (RTESs) have an increasing role in controlling society infrastructures that we use on a day-to-day basis. RTES behaviour is not based solely on the interactions it might have with its surrounding environment, but also on the timing requirements it induces. As a result, ensuring that an RTES behaves correctly is non-trivial, especially after adding time as a new dimension to the complexity of the testing process. This research addresses the problem of testing RTESs from Timed Automata (TA) specification by the following. First, a new Priority-based Approach (PA) for testing RTES modelled formally as UPPAAL timed automata (TA variant) is introduced. Test cases generated according to a proposed timed adequacy criterion (clock region coverage) are divided into three sets of priorities, namely boundary, out-boundary and in-boundary. The selection of which set is most appropriate for a System Under Test (SUT) can be decided by the tester according to the system type, time specified for the testing process and its budget. Second, PA is validated in comparison with four well-known timed testing approaches based on TA using Specification Mutation Analysis (SMA). To enable the validation, a set of timed and functional mutation operators based on TA is introduced. Three case studies are used to run SMA. The effectiveness of timed testing approaches are determined and contrasted according to the mutation score which shows that our PA achieves high mutation adequacy score compared with others. Third, to enhance the applicability of PA, a new testing tool (GeTeX) that deploys PA is introduced. In its current version, GeTeX supports Control Area Network (CAN) applications. GeTeX is validated by developing a prototype for that purpose. Using GeTeX, PA is also empirically validated in comparison with some TA testing approaches using a complete industrial-strength test bed. The assessment is based on fault coverage, structural coverage, the length of generated test cases and a proposed assessment factor. The assessment is based on fault coverage, structural coverage, the length of generated test cases and a proposed assessment factor. The assessment results confirmed the superiority of PA over the other test approaches. The overall assessment factor showed that structural and fault coverage scores of PA with respect to the length of its tests were better than the others proving the applicability of PA. Finally, an Analytical Hierarchy Process (AHP) decision-making framework for our PA is developed. The framework can provide testers with a systematic approach by which they can prioritise the available PA test sets that best fulfils their testing requirements. The AHP framework developed is based on the data collected heuristically from the test bed and data collected by interviewing testing experts. The framework is then validated using two testing scenarios. The decision outcomes of the AHP framework were significantly correlated to those of testing experts which demonstrated the soundness and validity of the framework.

Objectives were to: 1) Evaluate the effectiveness of presynchronization with GnRH before the CO‐Synch + CIDR protocol with timed AI (TAI) at 66 h in Bos indicus‐influenced cattle; 2) Characterize ovarian events associated with the presynchronization; 3) Evaluate the efficacy of measuring vaginal electrical resistance (VER) to assess follicular maturity at TAI; and 4) Compare serum concentrations of progesterone (P4) in ovariectomized cows bearing new or previously used CIDR devices with or without autoclaving. In Exp. 1 and 2, cattle received either GnRH or saline on day ‐7. The CO‐Synch + CIDR protocol included a CIDR insert and GnRH (GnRH‐1; day 0), removal of CIDR and PGF2α on day 7, and GnRH (GnRH‐2) and TAI 66 h after CIDR removal. In Exp. 1, pregnancy rate of females with BCS ≥ 5 tended to differ (P=0.085) between Presynch (38%) and CO‐Synch + CIDR (54%). In Exp. 2, ovulatory response to GnRH‐1 was greater (P<0.01) in the Presynchronization (58%) than in the CO‐Synch + CIDR (27.1%) group. Emergence of a follicular wave after GnRH‐1 and ovulation rate after GnRH‐2 did not differ between groups. More (P<0.01) females that developed a follicular wave after GnRH‐1 ovulated (82%) after GnRH‐2, compared to those that did not (29%). Mean VER (ohms) was greatest (101.4±0.8) on day 0 and declined (P<0.01) to 95.2±0.8 and 82±0.8, respectively, on days 7 and 10. We observed a low negative but significant relationship (r=0.38; P<0.001) between VER and follicular size on day 0, 7, and 10. VER difference (day 10 minus day 7) did not differ between females with small and large follicles at TAI. Mean concentrations of P4 during the 7‐day insertion period were greater (P<0.03) for new (3.7 ng/ml) and re‐used autoclaved (3.4 ng/ml) than for re‐used disinfected CIDRs (2.8 ng/ml). In summary, Presynch improved ovulation rate after GnRH‐1, but did not improve pregnancy rates compared to CO‐Synch + CIDR. Follicular maturity estimation was not feasible using VER as applied in this study. Autoclaving may be the best option when re‐using CIDR inserts because it creates greater concentrations of P4 during the first 48 h.

La thèse se situe à la charnière de l'informatique théorique et de la logique mathématique. Elle se concentre en particulier sur les aspects mathématiques de la vérification et du contrôle. La thèse se focalise sur l'étude de deux sous-classes d'automates hybrides: les automates temporisés pondérés et les automates hybrides o-minimaux. Concernant les automates temporisés pondérés, en introduisant un nouvel algorithme, nous donnons une caractérisation exacte de la complexité du problème d'atteignabilité optimal en prouvant qu'il est PSpace-complet. Nous prouvons que le model-checking de la logique WCTL est en général indécidable. Nous nous intéressons alors à une restriction de la logique WCTL. Nous montrons que la décidabilité du model-checking de WCTL restreint dépend de la dimension de l'automate et du fait que le temps soit discret ou dense. Finalement pour, nous prouvons que le problème de contrôle optimal est en général indécidable. Nous prouvons cependant que ce même problème est décidable pour les automates temporisés pondérés de dimension 1. En ce qui concerne les automates hybrides o-minimaux, à l'aide d'un encodage symbolique des trajectoires par des mots, nous sommes parvenus à prouver l'existence d'une bisimulation finie pour ces automates. De plus (toujours en utilisant nos encodages des trajectoires par des mots), nous avons obtenu des résultats de décidabilité pour des problèmes de jeux sur ces mêmes automates hybrides o-minimaux. Pour une classe d'automates hybrides o-minimaux, nous avons prouvé (i) que l'existence de stratégie gagnante pouvait être décidée et (ii) que ces stratégies gagnantes pouvaient être synthétisées.

Rule-based systems implemented as event-condition-action (ECA) rules utilize a powerful and flexible paradigm when it comes to specifying systems that need to react to complex situation in their environment. Rules can be specified to react to combinations of events occurring at any time in any order. However, the behavior of a rule based system is notoriously hard to analyze due to the rules ability to interact with each other. Formal methods are not utilized in their full potential for enhancing software quality in practice. We argue that seamless support in a high-level paradigm specific tool is a viable way to provide industrial system designers with powerful verification techniques. This thesis targets the issue of formally verifying that a set of specified rules behaves as indented. The prototype tool REX (Rule and Event eXplorer) is developed as a proof of concept of the results of this thesis. Rules and events are specified in REX which is acting as a rule-based front-end to the existing timed automata CASE tool UPPAAL. The rules, events and requirements of application design are specified in REX. To support formal verification, REX automatically transforms the specified rules to timed automata, queries the requirement properties in the model-checker provided by UPPAAL and returns results to the user of REX in terms of rules and events. The results of this thesis consist of guidelines for modeling and verifying rules in a timed automata model-checker and experiences from using and building a tool implementing the proposed guidelines. Moreover, the result of an industrial case study is presented, validating the ability to model and verify a system of industrial complexity using the proposed approach. / Avhandlingen presenterar en ny ansats för att formellt verifiera regel-baserade system. En verktygsprototyp, REX, är utvecklad inom ramen för detta projekt i syfte att stödja ansatsen genom realisering av de teoretiska resultaten. De regler som avses är Event-Condition-Action (ECA) regler, vilket betyder att en regel exekverar ett stycke kod (Action) om ett villkor (Condition) är sant när en specifik händelse (Event) inträffar. ECA-regler är användbara för att speci¯cera beteendet av system som måste reagera på komplexa situationer i sin interagerande miljö. En regel kan till exempel reagera på en kombination av händelser som kan inträffa när som helst och i vilken ordning som helst. Avhandlingen fokuserar på hur man med hjälp av formella metoder kan påvisa att en regelmängd beter sig som förväntat. Användandet av formella metoder för att öka kvalitén på mjukvara är inte så utbrett som det skulle kunna vara. Några av anledningarna kan vara att formella metoder anses svåra att använda och att de kräver extra tid och kunskap. Avhandlingen handlar om en approach där utvecklare kan uttrycka sitt system i ett för dem enkelt språk och där detaljer rörande det formella verktyget döljs av ett verktyg som sköter interaktionen med det formella verktyget. Regler och händelser specificeras som indata till verktyget REX som agerar som en regelbaserad front-end till det formella verktyget UPPAAL. Regler, händelser och egenskaper som modellen ska uppfylla specificeras i REX. Formell verifiering stöds genom att REX automatiskt överför regler och egenskaper till en tidsautomat som kan verifieras av Uppaal. REX startar model-checkern i UPPAAL och returnerar resultatet från analysen till användaren. Resultatet från avhandlingen består av riktlinjer för hur man kan modellera och verifiera regler i en tidsautomat samt erfarenheter från att bygga och använda ett verktyg som implementerar dessa riktlinjer. Därutöver presenteras resultat från experiment och en fallstudie som genomförts för att validera den framtagna ansatsen.

This work presents a static instruction allocation scheme for the precision timed architecture’s (PRET) scratchpad memory. Since PRET provides timing instructions to control the temporal execution of programs, the objective of the allocation scheme is to ensure that the explicitly specified temporal requirements are met. Furthermore, this allocation incorporates instructions from multiple hardware threads of the PRET architecture. We formulate the allocation as an integer-linear programming problem, and we implement a tool that takes binaries, constructs a control-flow graph, performs the allocation, rewrites the binary with the new allocation, and generates an output binary for the PRET architecture. We carry out experiments on a modified version of the Malardalen benchmarks to illustrate that commonly known ACET and WCET based approaches cannot be directly applied to meet explicit timing requirements. We also show the advantage of performing the allocation across multiple threads. We present a real time benchmark controlling an Unmanned Air Vehicle as the case study.

Detecting contingency relationships between causal events allows us to adapt to and control these events. However, research has shown age-related impairments in this ability. The goal of this study was to examine how reduced processing speed in older adults affects contingency learning. Manipulating the time during which to generate the response, to test the limited time mechanism of processing speed, had little effect on contingency judgments. Varying the temporal contiguity of events, to test the simultaneity mechanism of processing speed, affected young adults’ contingency judgments. Older adults’ judgments were less accurate overall, and young adults’ judgments were similarly less accurate when there was less temporal contiguity of events. These findings lend support for a processing speed theory of contingency learning.

Two trials were conducted to quantify the effects of GnRH and prostaglandin in conjunction with a 7-d CIDR on estrus and on pregnancy rate in comparison with a traditional synchronization protocol. In trial 1, ewes (n=12) were randomly allotted to one of three treatments: CIDR (7 d) with administration of GnRH (Cystorelin®, 50μg, im) at CIDR insertion and PGF2α (Lutalyse®, 20 mg, im) on d 6.5 (GnRH1); the GnRH1 protocol with a second injection of GnRH 30 h after CIDR removal (GnRH2); and CIDR (11 d) with administration of PGF2α at CIDR insertion and PMSG (400 iu) at CIDR removal (PMSG). A blood sample was obtained every 2 h for 42 h after CIDR removal for serum LH analysis. On d 8 after CIDR removal, blood samples were obtained at 12 h intervals for 36 h for serum P4 analysis. One ewe in the GnRH1 group did not retain the CIDR device and was excluded from the analysis. Mean LH concentration did not differ (P = 0.48) among groups. Time and time x treatment affected (P < 0.001) mean LH concentration. Mean P4 concentration was not affected (P = 0.26) by time, treatment or their interaction. In trial 2, ewes (n=72) were randomly allotted to one of the three treatments described in trial 1. At CIDR removal, three ewes per treatment were joined with a single ram fitted with a marking harness in each of 8 pens. Ewes were monitored every hour for estrus activity and ultrasounded transabdominally 60 d after CIDR removal for pregnancy. Estrus activity did not differ (P > 0.05) among the groups. Marking frequency was 92 percent, 75 percent, and 88 percent for GnRH1, GnRH2, and PMSG groups, respectively. Mean interval to estrus was shorter (P < 0.05) for the GnRH2 than for the PMSG group and tended to be reduced (P < 0.10) compared with the GnRH1 group. Pregnancy rate differed (P < 0.05) among treatments (79 percent, 58 percent and 38 percent for GnRH1, GnRH2, and PMSG groups, respectively). These results indicate that synchrony of estrus and pregnancy rate to natural service can be increased in response to a CIDR protocol when combined with administration of GnRH rather than PMSG.