Implementation of Quantitative Reaction-based Model Refinement

Building a computational model for complex biological systems is an iterative process. It starts from an abstraction of the process and then incorporates more details regarding the specific biochemical reactions which results in the change of the model fit. Meanwhile, the model’s numerical properties such as its numerical fit and validation should be preserved. However, refitting the model after each refinement iteration is computationally expensive resource-wise. There is an alternative approach which ensures the model fit preservation without the need to refit the model after each refinement iteration. And this approach is known as quantitative model refinement. The aim of this thesis is to develop and implement a tool called ModelRef which does the quantitative model refinement automatically. It is both implemented as a stand-alone Java application and as one of Anduril framework components. ModelRef performs data refinement of a model and generates the results in two different well known formats (SBML and CPS formats). The development of this tool successfully reduces the time and resource needed and the errors generated as well by traditional reiteration of the whole model to perform the fitting procedure.

Quantitative characteristics of fruits and seeds of Pouteria pachycarpa Pires - Sapotaceae

Pouteria pachycarpa is a tree species, found in the Brazilian Amazon and Bolivia whose wood has been exploited from the native forest. The present research describes the quantitative characteristics of fruits and seeds and quantifies the seed germination of this species. The fruit and seed color were characterized and measurements taken of the mass, length, diameter and number of seeds per fruit, the seed length, width and thickness, the germination percentage, abnormal seedlings and dead seeds. Sowing was carried out on a substrate containing sand and sawdust (1:1), in four replications of 50 seeds. The predominant fruit and seed colors were vivid yellowish orange (9YR) and dark grayish brown (6YR), respectively. Fruit mass, length and diameter ranged from 37.7 to 192.4g, 41.3 to 87.3mm and 39.7 to 71.7mm, respectively. Fruits had from two to seven seeds, and 42.6% were damaged by insects. Seed length, width and thickness ranged from 22.4 to 35.2mm, 9.7 to 15.5mm and 5.5 to 10.8mm, respectively. Seedling emergence began 18 days after sowing. Maximum germination, 86%, was recorded 33 days after sowing. The germination curve was sigmoid, similar to the majority of species. The percentage of abnormal seedlings and dead seeds were 3% and 11%, respectively. Both fruits and seeds show great variation in quantitative characteristics and the germination is slow and non-uniform.

Cardiac Imaging in the Diagnosis of Coronary Artery Disease: The Value of Quantitative Imaging of Myocardial Perfusion and Deformation

Atherosclerosis is a chronic and progressive disease of the vasculature. Increasing coronary atherosclerosis can lead to obstructive coronary artery disease (CAD) or myocardial infarction. Computed tomography angiography (CTA) allows noninvasive assessment of coronary anatomy and quantitation of atherosclerotic burden. Myocardial blood flow (MBF) can be accurately measured in absolute terms (mL/g/min) by positron emission tomography (PET) with [15O] H O as a radiotracer. We studied the coronary microvascular dysfunction as a risk factor for future coronary calcification in healthy young men by measuring the coronary flow reserve (CFR) which is the ratio between resting and hyperemic MBF. Impaired vasodilator function was not linked with accelerated atherosclerosis 11 years later. Currently, there is a global interest in quantitative PET perfusion imaging. We established optimal thresholds of [15O] H O PET perfusion for diagnosis of CAD (hyperemic MBF of 2.3 mL/g/min and CFR of 2.5) in the first multicenter study of this type (Turku, Amsterdam and Uppsala). In myocardial bridging a segment of the coronary artery travels inside the myocardium and can be seen as intramural course (CTA) or systolic compression (invasive coronary angiography). Myocardial bridging is frequently linked with proximal atherosclerotic plaques. We used quantitative [15O] H O PET perfusion to evaluate the hemodynamic effects of myocardial bridging. Myocardial bridging was not associated with decreased absolute MBF or increased atherosclerotic burden. Speckle tracking allows quantitative echocardiographic imaging of myocardial deformation. Speckle tracking during dobutamine stress echocardiography was feasible and comparable to subjective wall motion analysis in the diagnosis of CAD. In addition, it correctly risk stratified patients with multivessel disease and extensive ischemia.

GIS-based approach for optimization of onshore wind park infrastructure alignment in Finland

Wind power is a rapidly developing, low-emission form of energy production. In Fin-land, the official objective is to increase wind power capacity from the current 1 005 MW up to 3 500–4 000 MW by 2025. By the end of April 2015, the total capacity of all wind power project being planned in Finland had surpassed 11 000 MW. As the amount of projects in Finland is record high, an increasing amount of infrastructure is also being planned and constructed. Traditionally, these planning operations are conducted using manual and labor-intensive work methods that are prone to subjectivity. This study introduces a GIS-based methodology for determining optimal paths to sup-port the planning of onshore wind park infrastructure alignment in Nordanå-Lövböle wind park located on the island of Kemiönsaari in Southwest Finland. The presented methodology utilizes a least-cost path (LCP) algorithm for searching of optimal paths within a high resolution real-world terrain dataset derived from airborne lidar scannings. In addition, planning data is used to provide a realistic planning framework for the anal-ysis. In order to produce realistic results, the physiographic and planning datasets are standardized and weighted according to qualitative suitability assessments by utilizing methods and practices offered by multi-criteria evaluation (MCE). The results are pre-sented as scenarios to correspond various different planning objectives. Finally, the methodology is documented by using tools of Business Process Management (BPM). The results show that the presented methodology can be effectively used to search and identify extensive, 20 to 35 kilometers long networks of paths that correspond to certain optimization objectives in the study area. The utilization of high-resolution terrain data produces a more objective and more detailed path alignment plan. This study demon-strates that the presented methodology can be practically applied to support a wind power infrastructure alignment planning process. The six-phase structure of the method-ology allows straightforward incorporation of different optimization objectives. The methodology responds well to combining quantitative and qualitative data. Additional-ly, the careful documentation presents an example of how the methodology can be eval-uated and developed as a business process. This thesis also shows that more emphasis on the research of algorithm-based, more objective methods for the planning of infrastruc-ture alignment is desirable, as technological development has only recently started to realize the potential of these computational methods.

Bone properties and skeletal maturity in adolescent males, as assessed by quantitative ultrasound

ABSTRACT Background: Previous studies have implied that weight-bearing, intense and prolonged physical activities optimize bone accretion during the grow^ing years. The majority of past inquiries have used dual-energy X-ray absorptiometry (DXA) to examine bone strength and hand-wrist radiography to determine skeletal maturity in children. Recently, quantitative ultrasound (QUS) technologies have been developed to examine bone properties and skeletal maturity in a safe, noninvasive and cost-effective manner. Objective: The purpose of this study was to compare bone properties and skeletal maturity in competitive male child and adolescent athletes with minimallyactive, age-matched controls, using QUS technology. >. Methods: In total, 224 males were included in the study. The 115 pre-pubertal boys aged 10-12 years consisted of control, minimally-active children (n=34), soccer players (n=26), gymnasts (n=25) and hockey players (n=30). In addition, the 109 late-pubertal boys aged 14-16 years consisted of control, minimally-active adolescents (n=31), soccer players (n=30), gymnasts (n=17) and hockey players (n=31). The athletic groups were elite level players that predominantly trained year-round. Physical activity, nutrition and sports participation were assessed with various questionnaires. Anthropometries, such as height, weight and relative body fat percentage (BF%) were assessed using standard measures. Skeletal strength and age were evaluated using bone QUS. Lastly, salivary testosterone (sT) concentration was measured using Radioimmunoassay (RIA). Results: Within each age group, there were no significant differences between the activity groups in age and pubertal stage. An age effect was apparent in all variables, as expected. A sport effect was noted in all physical characteristics: the child and adolescent gymnasts were shorter and lighter than other sports groups. Adiposity was greater in the controls and in the hockey players. All child subjects were pubertal stage (fanner) I or II, while adolescent subjects were pubertal stage IV or V. There were no differences in daily energy and mineral intakes between sports groups. In both age groups, gymnasts had a higher training volume than other athletic groups. Bone speed of sound (50s) was higher in adolescents compared with the children. Gymnasts had signifieantly higher radial 50S than controls, hockey and soccer players in both age cohorts. Hockey athletes also had higher radial 50S than controls and soccer players in the child and adolescent groups, respectiyely. Child gymnasts and soccer players had greater tibial 50S compared with the hockey players and control groups. Likewise, adolescent gymnasts and soccer players had higher tibial SoS compared with the control group. No interaction was apparent between age and type of activity in any of the bone measures. » Lastly, maturity as assessed by sT and secondary sex characteristics (Tanner stage) was not different between sports group within each age group. Despite the similarity in chronological age, androgen levels and sexual maturity, differences between activity groups were noted in skeletal maturity. In the younger group, hockey players had the highest bone age while the soccer players had the lowest bone age. In the adolescent group, gymnasts and hockey players were characterized by higher skeletal maturity compared with controls. An interaction between the age and sport type effects was apparent in skeletal maturity, reflecting the fact that among the children, the soccer players were significantly less mature than the rest of the groups, while in the adolescents, the controls were the least skeletally mature. Summary and Conclusions: In summary, radial and tibial SOS are enhanced by the unique loading pattern in each sport (i.e, upper and lower extremities in gymnastics, lower extremities in soccer), with no cumulative effect between childhood and adolescence. That is, the effect of sport participation on bone SOS was apparent already among the young athletes. Enhanced bone properties among athletes of specific sports suggest that participation in these sports can improve bone strength and potential bone health.

Synthesis of isotope-labelled methoxypyrazine compounds as internal standards and quantitative determination of aroma methoxypyrazines in water and wines by solid-phase extraction with isotope dilution-GC-MS /

An efficient way of synthesizing the deuterium labelled analogues of three methoxypyrazine compounds: 2-d3-methoxy-3-isopropylpyrazine, 2-d3-methoxy-3- isobutylpyrazine, and 2-d3-methoxy-3-secbutylpyrazine, has been developed. To confirm that the deuterium labels had been incorporated into the expected positions in the molecules synthesized, the relevant characterization by NMR, HRMS and GC/MS analysis was conducted. Another part of this work involved quantitative determination of methoxypyrazines in water and wines. Solid-phase extraction (SPE) proved to be a suitable means for the sample separation and concentration prior to GC/MS analysis.Such factors as the presence of ethanol, salt, and acid have been investigated which can influence the recovery by SPE for the pyrazines from the water matrix. Significantly, in this work comparatively simple fractional distillation was attempted to replace the conventional steam distillation for pre-concentrating a sample with a relatively large volume prior to SPE. Finally, a real wine sample spiked with the relevant isotope-labelled methoxypyrazines was quantitatively analyzed, revealing that the wine with 10 beetles per litre contained 138 ppt of 2-methoxy-3-isopropylpyrazine. Interestingly, we have also found that 2-methoxy-3-secbutylpyrazine exhibits an extremely low detection limit in GC/MS analysis compared with the detection limit of the other two methoxypyrazines: 2- methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine.

Composition analysis of high-Tc superconducting thin films by quantitative x-ray fluorescence

A method is presented for determining the composition of thin films containing the elements Bi, Sr, Br, Cu, and Ca. Quantitative x-ray fluorescence (XRF) consisting of radioactive sources (secondary foil excitor 241Am-Mo source and 55Pe source), a Si(Li) detector, and a multichannel analyzer were employed. The XRF system was calibrated by using sol gel thin films of known element composition and also by sputtered thin films analyzed by the conventional Rutherford Back Scattering (RBS). The XRF system has been used to assist and optimize the sputter target composition required to produce high-Tc BiSrCaCuO films with the desired metal composition.

Studies on the insecticide - nematicide-oxamyl and its quantitative determination by gas chromatographic method

Ox amyl , an insecticide/nematicide with the chemical name; methyl ~'. ~·-dimethyl-~-(methylcarbamoyl)oxy-l-thiooxamimidate, and its major degradation compound; oxime or oximino compound, methyl ~',~'-dimethyl-~-hydroxy-l-thiooxamimidate were studied in this work. NMR and mass spectrometry were utilized in the structural studies. An attempt was made to explain the fragmentation patterns of some major peaks in the mass spectra of oxamyl and oxime. A new gas chromatographic method for the detection and determination of submicrogram levels of intact oxamyl using a electron-capture detector was developed. The principle of this method is to produce a derivative which is highly sensitive to an electron-capture detector. The derivative described is dinitrophenyl methylamine( DNPMA ) • Experimental conditions such as pH , reaction temperature , reaction time, the amount of reagent ( Dinitrofluaro benzene) etc. were thoroughly investigated and optimized. This method was successfully applied to the determination of oxamyl residues in tobacco leaves and soil. Throughout this J9D:oject , thin layer chromatography was also used in the separation:and clean up of oxamyl and oxime samples.

Exploring Chinese-Canadians' perspectives on health : a quantitative study

Chinese have unique perspectives on health and illness, which is mostly umecognized by western medicine. Immigration may contribute to problems with health consultations, inconvenience, and dissatisfaction. As the largest visible minority in Canada, Chinese- Canadians' perspectives on health should be studied in order to help Chinese immigrants adapt to a new health-care and health-promotion system, and keep them healthy. A quantitative questionnaire was designed based on the findings from a pilot study and previous literature. A hundred participants were recruited from Toronto, Vancouver, Halifax, and St. Catharines. Descriptive analysis and correlation analysis were used to investigate the structure of the variables. Findings indicated that most oftheir attitudes and corresponding practices to the different health aspects were positive. The relation between dietary practices and attitude was only found in small cities. Their attitudes were impacted by their length of stay in Canada. Their attitudes to regularly timed meals and psychological consultation were related to their acculturation level, as was the regularity of their practice of dental flossing. Their self-evaluated general health levels were also found to be affected by their medical history, education level, feeling to talk about • sexual health, and smoking, particularly in the male subjects of the study. In conclusion, they realized that each health aspect w~s important to their health. However, their practices did not bear a strong relation to their beliefs. Traditional thoughts about health reseeded with time. Acculturation level did not affect most of their attitudes or practices. Under pressure, the priority of the daily health practices decreased. Older persons, those with low incomes, lower education levels or families under stress need to pay more attention to their health level. In-depth future research was recommended.

A Quantitative Study of Social Capital Components, Self-Reported Health Status and Social Determinants of Health

This quantitative descriptive co-relational study used telephone survey interviews and stratified random sampling to collect data related to Social Capital (SC) and its components (trust and safety, reciprocity, civic engagement and collective action) and selected determinants of health variables in Niagara Region, Canada. Among the four components of social capital, trust and safety levels were highest among all participants (m=5.42, SD=1.0), with community engagement yielding the lowest mean score for the sample (m=1.93, SD=.8). Reciprocity had the strongest association with all other components of SC (r=0.51). Those most likely to report low levels of SC and health were unattached and low-income females. Males were more likely to report higher trust and safety levels and higher levels of self-rated health. In this study, a linear relationship between self-reported health status and SC was not found. Marital and employment status were associated with differences in mean scores of SC and self-reported health.

Learning and Experiential Outcomes of Face-to-Face Versus Online Communications Courses

Higher education is rapidly trending toward the implementation of online (OL) courses and a blended facilitation style that incorporates both OL and face-to-face (FTF) classes. Though previous studies have explored the benefits and pitfalls of OL and blended learning formats from institutional, teacher, and student perspectives, scant research has examined learning outcomes for OL and FTF courses sharing identical content. This study used an explanatory mixed methods design—including pre- and post-test assessments, a questionnaire, and interviews—to explore similarities and differences in participant and teacher perceptions and outcomes (gain scores and final grades) of OL versus traditional FTF Communications courses, and to examine effects of students’ age and gender on learning preference and performance. Data collection occurred over a 4-month period and involved 183 student and 2 professor participants. The study used an SPSS program for data analysis and created a Microsoft Excel document to record themes derived from the questionnaire and interviews. Quantitative findings suggest there are no significant differences in gain scores, final grades, or other learning outcomes when comparing OL and FTF versions of identical Communications courses; however, qualitative findings indicate differences between facilitation styles based on student and professor perception. The study sheds light on student and faculty perceptions of facilitation styles and suggests areas for potential improvements in FTF- and OL-facilitated courses. The study ultimately recommends that students and faculty should have options when it comes to preferred delivery of course material.

A Quantitative and Qualitative Inquiry Into Positive Involvement Trends of Contemporary Fathers and Influence of Parenting Programs

Parent education programs offered by a variety of public health services are effective support and knowledge resources that enhance positive parenting competencies in early childhood and adolescence. However, parenting education programs are less effective and encompass fewer benefits for fathers in comparison to mothers. This study sought to investigate trends of paternal involvement in early childhood and to compare the influence of parenting education programs on paternal involvement and conceptualization of fathers. A sample of 52 fathers, between the ages of 19 to 54, with children 6 years old and younger completed an electronic or hard copy version of a survey questionnaire reporting on their fathering and experiences as a dad. Findings indicate the sample of Canadian fathers self-reported high levels of paternal involvement, including many who favoured play-based interactions with their children. Although no significant difference in levels of involvement was noted between fathers who had versus those who had not previously participated in a parenting education program, half of the Canadian fathers indicated that supports are needed to strengthen their role as fathers. Results suggest that future initiatives to strengthen parent education program services available in Canada should specifically consider the father’s role.

Factors Contributing to Reading Performance: An In-Depth Analysis of the “Boy Crisis”

This research used a quantitative study approach to investigate the “boy crisis” in Canada. Boy crisis advocates suggest that boys are being surpassed by girls on reading assessments and promote strategies to assist male students. A feminist framework was used in this study that allowed for an investigation and discussion of the factors that mediate between gender and success at reading comprehension, interpretation, and response to text without ignoring female students. Reading scores and questionnaire data compiled by the Pan-Canadian Assessment Program were used in this research, specifically the PCAP-13 2007 assessment of approximately 30,000 13-year-old students from all Canadian provinces and Yukon Territory (CMEC, 2008). Approximately 20,000 participants wrote the reading assessment, while 30,000 students completed the questionnaire responses. Predictor variables were tested using parametric tests such as independent samples t-test, one-way ANOVA, chi-square analysis, and Pearson r. Findings from this study indicate that although boys scored lower than girls on the PCAP-13 2007 reading assessment, factors were found to influence the reading scores of both male and female students to varying degrees. Socioeconomic status, perceptions of the reading material used in language arts classrooms, reading preference, reading interest, parental involvement, parental encouragement for reading, and self-efficacy were all found to affect the reading performance of boys and girls. Relationships between variables were also found and are discussed in this research. The analysis presented in this study allows parents, educators, and policy makers to begin to critically examine and re-evaluate boy crisis literature and offers suggestions on how to improve reading performance for all students of all socioeconomic backgrounds.