Formal modeling and analysis techniques for high level Petri nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. ^ There are two issues in using HLPNs—modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. ^ For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. ^ For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. ^ The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.^

Formal Modeling and Analysis Techniques for High Level Petri Nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. There are two issues in using HLPNs - modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.

Preimplantation genetic diagnosis: Analysis of gene expression, nuclear DNA and cytoplasmic DNA

Preimplantation genetic diagnosis (PGD) following in vitro fertilization (IVF) offers couples at risk for transmitting genetic disorders the opportunity to identify affected embryos prior to replacement. In particular, embryo gender determination permits screening for X-linked diseases of unknown etiology. Analysis of embryos can be performed by polymerase chain reaction (PCR) amplification of material obtained by micromanipulation. This approach provides an alternative to the termination of an established pregnancy following chorionic villi sampling or amniocentesis. ^ Lately, the focus of preimplantation diagnosis and intervention has been shifting toward an attempt to correct cytoplasmic deficiencies. Accordingly, it is the aim of this investigation to develop methods to permit the examination of single cells or components thereof for clinical evaluation. In an attempt to lay the groundwork for precise therapeutic intervention for age related aneuploidy, transcripts encoding proteins believed to be involved in the proper segregation of chromosomes during human oocyte maturation were examined and quantified. Following fluorescent rapid cycle RT-PCR analysis it was determined that the concentration of cell cycle checkpoint gene transcripts decreases significantly as maternal age increases. Given the well established link between increasing maternal age and the incidence of aneuploidy, these results suggest that the degradation of these messages in aging oocytes may be involved with inappropriate chromosome separation during meiosis. ^ In order to investigate the cause of embryonic rescue observed following clinical cytoplasmic transfer procedures and with the objective of developing a diagnostic tool, mtDNA concentrations in polar bodies and subcellular components were evaluated. First, the typical concentration of mtDNA in human and mouse oocytes was determined by fluorescent rapid cycle PCR. Some disparity was noted between the copy numbers of individual cytoplasmic samples which may limit the use of the current methodology for the clinical assessment of the corresponding oocyte. ^

Time spent with children and working parents' willingness to medicate ADHD-like behaviors

ADHD, which refers to one of the most common behavioral problems among children, is subject to controversial arguments surrounding its nature and its primary treatment with psychiatric medications. At the heart of the problem are parents, whose responsibility includes providing pivotal information to clinicians for the diagnosis and deciding whether their children will receive medications. This study investigates the relationship between working parents' willingness to medicate ADHD-like behaviors and the time they are able to spend with their children during a regular workday. The importance of time spent with children derives from the observation that it is likely to influence not only parents' judgments of their children's behaviors but the behaviors themselves. The relationship was investigated using a subsample of 551 working parents (452 parents reporting no child with problems and 99 parents reporting child with problems) drawn from a population-based telephone survey of parents in the Miami-Dade and Broward counties of Florida. A series of path analyses, controlling for selected socio-demographic and family variables, showed that spending more time with their children during a regular workday was significantly related to being less willing to medicate ADHD-like behaviors. The association was stronger for parents reporting having a child with emotional and behavioral problems (β = −.20) and faint for other parents (β = −.06). The interpretation of the study findings emphasizes the vagueness surrounding the nature of ADHD and the events and procedures leading to the diagnosing of a child, as well as the delicate situations in which parents find themselves.

The clinical competency of practicing and nonpracticing faculty of associate degree schools of nursing

This study assesses and describes the perception of clinical competency and the relationship to clinical practice of full-time nursing faculty in the associate degree nursing programs in the state of Florida. The study was developed around one major hypothesis and four research questions. The Hygiene-Motivators Theory proposed by Herzberg, Mausner, and Snyderman (1959) provided the conceptual framework to explain factors that would motivate a person to expand workload and maintain job satisfaction.^ Data were collected from the 244 faculty members teaching full-time at the 15 associate degree schools of nursing accredited by the National League for Nursing in the state of Florida. A total of 186 faculty (76%) responded and 175 (72%) cases were used for data analysis.^ Two instruments were modified and combined for the investigation. The instruments were the Faculty Perception of Practice Questionnaire (Parascenzo, 1983) and a three-part Attributes Deemed Necessary for Faculty to Proclaim Clinical Competency (Smith, 1991) scale. Computer analyses employing descriptive and inferential statistics were performed.^ The findings revealed that faculty were closely divided as to practice activities with more faculty nonpracticing than practicing. Factors identified as impediments to increased clinical practice were identified as teaching load and personal/family responsibilities that lead to a lack of time and lack of opportunity. Those faculty who practice did so as moonlighters in positions that would not require advanced training. Both the practicing and nonpracticing faculty reported a high level of satisfaction with their activities as a means of maintaining clinical practice. While both groups reported a high level of expertise, those practicing faculty perceived themselves to be more clinically competent on the attributes of knowledge, skills, and on the total attribute scale. It was further revealed that perception of competency declined with the length of time spent out of practice. There was no difference in the two groups on the attributes of values/attitude. ^

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

Background: Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results: We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion: Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Elementary music and classroom teachers' time -use: A comparison by grade level, time of day, and day of the week

This study investigated time-use of elementary music teachers and elementary classroom teachers to determine: (1) whether there was a relationship between grade level, time of day, and day of the week and teachers' time-use in teaching, monitoring, and non-curricular, and (2) whether ethnicity, training, and years of experience affect teacher time-use. Sixty-nine music teachers and 55 classroom teachers participated. ^ A MANOVA was used to examine the hypothesized relationship. ANOVA results were significant for time spent teaching, monitoring, and non-curricular. An independent t test revealed a significance difference (t (302) = 5.20, p < .001) between the two groups of teachers. A significant difference was found for teaching, t (302) = 5.20, p < .001: music teachers spent more time actively teaching than did classroom teachers. There was a significant difference for monitoring (t (302) = 13.62, p < .001): classroom teachers allocated more time to monitoring than did music teachers. A significant difference was also found for non-curricular (t (302) = 7.03, p < .001): music teachers spent more time in this category of activities than did classroom teachers. ^ Analyses of the activities subsumed under the major categories indicated significant differences between elementary music teachers and elementary classroom teachers, overall, in subject matter (p < .001), discussion (p < .05), school-wide activities (p < .001), seatwork (p < .001), giving directions (p < .001), changing activities (p < .001), lunch (p < .05), planning (p < .001) and interruption (p < .001). Analyses of the relationship and ethnicity, training, degree, experience indicated significant difference for main effect, ethnicity (F(2, 116) = 4.22, p < .017). Time-use for black non-Hispanic teachers was higher than time-use for those who were Hispanic and white non-Hispanic. ^ Analyses of time-use by grade showed no increase for either group as grade level increased. A statistically significant Wilks Lambda ( F (1,294) = .917 p < .013) was found for the independent variable day of the week. ANOVA indicated that elementary classroom teachers monitored more on Thursdays and Fridays: music teachers allocated more time to non-curricular activities on Fridays. ^

The effects of student -centered and traditional models of teaching on reading skills

A pre-test, post-test, quasi-experimental design was used to examine the effects of student-centered and traditional models of reading instruction on outcomes of literal comprehension and critical thinking skills. The sample for this study consisted of 101 adult students enrolled in a high-level developmental reading course at a large, urban community college in the Southeastern United States. The experimental group consisted of 48 students, and the control group consisted of 53 students. Students in the experimental group were limited in the time spent reading a course text of basic skills, with instructors using supplemental materials such as poems, news articles, and novels. Discussions, the reading-writing connection, and student choice in material selection were also part of the student-centered curriculum. Students in the control group relied heavily on a course text and vocabulary text for reading material, with great focus placed on basic skills. Activities consisted primarily of multiple-choice questioning and quizzes. The instrument used to collect pre-test data was Descriptive Tests of Language Skills in Reading Comprehension; post-test data were taken from the Florida College Basic Skills Exit Test. A MANCOVA was used as the statistical method to determine if either model of instruction led to significantly higher gains in literal comprehension skills or critical thinking skills. A paired samples t-test was also used to compare pre-test and post-test means. The results of the MANCOVA indicated no significant difference between instructional models on scores of literal comprehension and critical thinking. Neither was there any significant difference in scores between subgroups of age (under 25 and 25 and older) and language background (native English speaker and second-language learner). The results of the t-test indicated, however, that students taught under both instructional models made significant gains in on both literal comprehension and critical thinking skills from pre-test to post-test.

Elementary music and classroom teachers' time-use: a comparison by grade level, time of day, and day of the week

This study investigated time-use of elementary music teachers and elementary classroom teachers to determine: (1) whether there was a relationship between grade level, time of day, and day of the week and teachers' time-use in teaching, monitoring, and non-curricular, and (2) whether ethnicity, training, and years of experience affect teacher time-use. Sixty-nine music teachers and 55 classroom teachers participated. A MANOVA was used to examine the hypothesized relationship. ANOVA results were significant for time spent teaching, monitoring, and non-curricular. An independent t test revealed a significance difference (t (302) = 5.20, p Analyses of the activities subsumed under the major categories indicated significant differences between elementary music teachers and elementary classroom teachers, overall, in subject matter ( p teachers was higher than time-use for those who were Hispanic and white non-Hispanic. Analyses of time-use by grade showed no increase for either group as grade level increased. A statistically significant Wilks Lambda ( F (1,294) = .917 p < .013 ) was found for the independent variable day of the week. ANOVA indicated that elementary classroom teachers monitored more on Thursdays and Fridays: music teachers allocated more time to non-curricular activities on Fridays.

Effect of Pavement-Vehicle Interaction on Highway Fuel Consumption and Emission

Vehicle fuel consumption and emission are two important effectiveness measurements of sustainable transportation development. Pavement plays an essential role in goals of fuel economy improvement and greenhouse gas (GHG) emission reduction. The main objective of this dissertation study is to experimentally investigate the effect of pavement-vehicle interaction (PVI) on vehicle fuel consumption under highway driving conditions. The goal is to provide a better understanding on the role of pavement in the green transportation initiates. Four study phases are carried out. The first phase involves a preliminary field investigation to detect the fuel consumption differences between paired flexible-rigid pavement sections with repeat measurements. The second phase continues the field investigation by a more detailed and comprehensive experimental design and independently investigates the effect of pavement type on vehicle fuel consumption. The third study phase calibrates the HDM-IV fuel consumption model with data collected in the second field phase. The purpose is to understand how pavement deflection affects vehicle fuel consumption from a mechanistic approach. The last phase applies the calibrated HDM-IV model to Florida’s interstate network and estimates the total annual fuel consumption and CO2 emissions on different scenarios. The potential annual fuel savings and emission reductions are derived based on the estimation results. Statistical results from the two field studies both show fuel savings on rigid pavement compared to flexible pavement with the test conditions specified. The savings derived from the first phase are 2.50% for the passenger car at 112km/h, and 4.04% for 18-wheel tractor-trailer at 93km/h. The savings resulted from the second phase are 2.25% and 2.22% for passenger car at 93km/h and 112km/h, and 3.57% and 3.15% for the 6-wheel medium-duty truck at 89km/h and 105km/h. All savings are statistically significant at 95% Confidence Level (C.L.). From the calibrated HDM-IV model, one unit of pavement deflection (1mm) on flexible pavement can cause an excess fuel consumption by 0.234-0.311 L/100km for the passenger car and by 1.123-1.277 L/100km for the truck. The effect is more evident at lower highway speed than at higher highway speed. From the network level estimation, approximately 40 million gallons of fuel (combined gasoline and diesel) and 0.39 million tons of CO2 emission can be saved/reduced annually if all Florida’s interstate flexible pavement are converted to rigid pavement with the same roughness levels. Moreover, each 1-mile of flexible-rigid conversion can result in a reduction of 29 thousand gallons of fuel and 258 tons of CO2 emission yearly.