The use of analysis of variance (ANOVA) in applied microbiology

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the number of replications required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the DF of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for each error term of the ANOVA. Finally, it is important to consider the design of the experiment because this determines the appropriate ANOVA to use. Some of the most common experimental designs used in the biosciences and their relevant ANOVAs are discussed by. If there is doubt about which ANOVA to use, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Quantitative assessment of the pharmacotherapy of biopolar disorder and schizophrenia

The work present in this thesis was aimed at assessing the efficacy of lithium in the acute treatment of mania and for the prophylaxis of bipolar disorder, and investigating the value of plasma haloperidol concentration for predicting response to treatment in schizophrenia. The pharmacogenetics of psychotropic drugs is critically appraised to provide insights into interindividual variability in response to pharmacotherapy, In clinical trials of acute mania, a number of measures have been used to assess the severity of illness and its response to treatment. Rating instruments need to be validated in order for a clinical study to provide reliable and meaningful estimates of treatment effects, Eight symptom-rating scales were identified and critically assessed, The Mania Rating Scale (MRS) was the most commonly used for assessing treatment response, The advantage of the MRS is that there is a relatively extensive database of studies based on it and this will no doubt ensure that it remains a gold standard for the foreseeable future. Other useful rating scales are available for measuring mania but further cross-validation and validation against clinically meaningful global changes are required. A total of 658 patients from 12 trials were included in an evaluation of the efficacy of lithium in the treatment of acute mania. Treatment periods ranged from 3 to 4 weeks. Efficacy was estimated using (i) the differences in the reduction in mania severity scores, and (ii) the ratio and difference in improvement response rates. The response rate ratio for lithium against placebo was 1.95 (95% CI 1.17 to 3.23). The mean number needed to treat was 5 (95% CI 3 to 20). Patients were twice as likely to obtain remission with lithium than with chlorpromazine (rate ratio = 1.96, 95% CI 1.02 to 3.77). The mean number needed to treat (NNT) was 4 (95% CI 3 to 9). Neither carbamazepine nor valproate was more effective than lithium. The response rate ratios were 1.01 (95% CI 0.54 to 1.88) for lithium compared to carbarnazepine and 1.22 (95% CI 0.91 to 1.64) for lithium against valproate. Haloperidol was no better than lithium on the basis of improvement based on assessment of global severity. The differences in effects between lithium and risperidone were -2.79 (95% CI -4.22 to -1.36) in favour of risperidone with respect to symptom severity improvement and -0.76 (95% CI -1.11 to -0,41) on the basis of reduction in global severity of disease. Symptom and global severity was at least as well controlIed with lithium as with verapamil. Lithium caused more side-effects than placebo and verapamil, but no more than carbamazepine or valproate. A total of 554 patients from 13 trials were included in the statistical analysis of lithium's efficacy in the prophylaxis of bipolar disorder. The mean follow-up period was 5-34 months. The relapse risk ratio for lithium versus placebo was 0.47 (95% CI 0.26 to 0.86) and the NNT was 3 (95% CI 2 to 7). The relapse risk ratio for lithium versus imipramine was 0.62 (95% CI 0.46 to 0.84) and the NNT was 4 (951% Cl 3 to 7), The combination of lithium and imipramine was no more effective than lithium alone. The risk of relapse was greater with lithium alone than with the lithium-divalproate combination. A risk difference of 0.60 (95% CI 0.21 to 0.99) and an NNT of 2 (95% CI 1 to 5) were obtained. Lithium was as effective as carbamazepine. Based on individual data concerning plasma haloperidol concentration and percent improvement in psychotic symptoms, our results suggest an acceptable concentration range of 11.20-30.30 ng/mL A minimum of 2 weeks should be allowed before evaluating therapeutic response. Monitoring of drug plasma levels seems not to be necessary unless behavioural toxicity or noncompliance is suspected. Pharmacokinetics and pharmacodynamics, which are mainly determined by genetic factors, contribute to interindividual and interethnic variations in clinical response to drugs. These variations are primarily due to differences in drug metabolism. Variability in pharmacokinetics of a number of drugs is associated with oxidation polymorphism. Debrisoquine/sparteine hydroxylase (CYP2D6) and the S-mephenytoin hydroxylase (CYP2C19) are polymorphic P450 enzymes with particular importance in psychopharmacotherapy. The enzymes are responsible for the metabolism of many commonly used antipsychotic and antidepressant drugs. The incidence of poor metabolisers of debrisoquine and S-mephenytoin varies widely among populations. Ethnic variations in polymorphic isoenzymes may, at least in part, explain ethnic differences in response to pharmacotherapy of antipsychotics and antidepressant drugs.

Accommodation in young adults wearing multifocal soft contact lenses under long- and short- wavelength lighting

Purpose: Several studies have suggested accommodative lags may serve as a stimulus for myopic growth, and while a blurred foveal image is believed to the main stimulus for accommodation, spectral composition of the retinal image is also believed to influence accommodative accuracy. Of particular interest is how altering spectral lighting conditions influences accommodation in the presence of soft multifocal contact lenses, which are currently being used off-label for myopia control. Methods: Accommodative responses were assessed using a Grand Seiko WAM-5500 autorefractor for four target distances: 25, 33, 50, and 100cm for 30 young adult subjects (14 myopic, 16 emmetropic; mean refractive errors (±SD, D) -4.22±2.04 and -0.15±0.67 respectively). Measurements were obtained with four different soft contact lenses, Single vision distance (SVD), Single vision near (SVN), Centre-Near (CN) and Centre-Distance (CD) (+1.50 add), and three different lighting conditions: red (peak λ 632nm), blue (peak λ 460nm), and white (peak λ 560nm). Corrections for chromatic differences in refraction were made prior to calculating accommodative errors. Results: The size of accommodative errors was significantly affected by lens design (p<0.001), lighting (p=0.027), and target distance (p=0.009). Mean accommodative errors were significantly larger with the SV lenses compared to the CD and CN designs (p<0.001). Errors were also significantly larger under blue light compared to white (p=0.004) and a significant interaction noted between lens design and lighting (p<0.001). Blue light generally decreased accommodative lags and increased accommodative leads relative to white and red light, the opposite was true of red light (p≤0.001). Lens design also significantly influenced direction of accommodative error (i.e. lag or lead) (p<0.001). Interactions with or between refractive groups were not found to be statistically significant for either the magnitude or direction of accommodative error (p>0.05 for all). Conclusions: Accuracy of accommodation is affected by both lens design and by wavelength of lighting. These accommodative lag data lend some support to recent speculation about the potential therapeutic value of lighting with a spectral bias towards blue during near work for myopia, although such treatment effects are likely to be more subtle under broad compared to the narrow spectrum lighting conditions used here.

The development and analysis of a field project model curriculum and its impact on achievement and attitude toward science and the environment with at-risk eleventh and twelfth grade students

This study was an evaluation of a Field Project Model Curriculum and its impact on achievement, attitude toward science, attitude toward the environment, self-concept, and academic self-concept with at-risk eleventh and twelfth grade students. One hundred eight students were pretested and posttested on the Piers-Harris Children's Self-Concept Scale, PHCSC (1985); the Self-Concept as a Learner Scale, SCAL (1978); the Marine Science Test, MST (1987); the Science Attitude Inventory, SAI (1970); and the Environmental Attitude Scale, EAS (1972). Using a stratified random design, three groups of students were randomly assigned according to sex and stanine level, to three treatment groups. Group one received the field project method, group two received the field study method, and group three received the field trip method. All three groups followed the marine biology course content as specified by Florida Student Performance Objectives and Frameworks. The intervention occurred for ten months with each group participating in outside-of-classroom activities on a trimonthly basis. Analysis of covariance procedures were used to determine treatment effects. F-ratios, p-levels and t-tests at p $<$.0062 (.05/8) indicated that a significant difference existed among the three treatment groups. Findings indicated that groups one and two were significantly different from group three with group one displaying significantly higher results than group two. There were no significant differences between males and females in performance on the five dependent variables. The tenets underlying environmental education are congruent with the recommendations toward the reform of science education. These include a value analysis approach, inquiry methods, and critical thinking strategies that are applied to environmental issues. ^

Can a Broader Education Narrow the Gap? Evidence on Non-Academic Features of Schooling

Empirical studies of education programs and systems, by nature, rely upon use of student outcomes that are measurable. Often, these come in the form of test scores. However, in light of growing evidence about the long-run importance of other student skills and behaviors, the time has come for a broader approach to evaluating education. This dissertation undertakes experimental, quasi-experimental, and descriptive analyses to examine social, behavioral, and health-related mechanisms of the educational process. My overarching research question is simply, which inside- and outside-the-classroom features of schools and educational interventions are most beneficial to students in the long term? Furthermore, how can we apply this evidence toward informing policy that could effectively reduce stark social, educational, and economic inequalities?

The first study of three assesses mechanisms by which the Fast Track project, a randomized intervention in the early 1990s for high-risk children in four communities (Durham, NC; Nashville, TN; rural PA; and Seattle, WA), reduced delinquency, arrests, and health and mental health service utilization in adolescence through young adulthood (ages 12-20). A decomposition of treatment effects indicates that about a third of Fast Track’s impact on later crime outcomes can be accounted for by improvements in social and self-regulation skills during childhood (ages 6-11), such as prosocial behavior, emotion regulation and problem solving. These skills proved less valuable for the prevention of mental and physical health problems.

The second study contributes new evidence on how non-instructional investments – such as increased spending on school social workers, guidance counselors, and health services – affect multiple aspects of student performance and well-being. Merging several administrative data sources spanning the 1996-2013 school years in North Carolina, I use an instrumental variables approach to estimate the extent to which local expenditure shifts affect students’ academic and behavioral outcomes. My findings indicate that exogenous increases in spending on non-instructional services not only reduce student absenteeism and disciplinary problems (important predictors of long-term outcomes) but also significantly raise student achievement, in similar magnitude to corresponding increases in instructional spending. Furthermore, subgroup analyses suggest that investments in student support personnel such as social workers, health services, and guidance counselors, in schools with concentrated low-income student populations could go a long way toward closing socioeconomic achievement gaps.

The third study examines individual pathways that lead to high school graduation or dropout. It employs a variety of machine learning techniques, including decision trees, random forests with bagging and boosting, and support vector machines, to predict student dropout using longitudinal administrative data from North Carolina. I consider a large set of predictor measures from grades three through eight including academic achievement, behavioral indicators, and background characteristics. My findings indicate that the most important predictors include eighth grade absences, math scores, and age-for-grade as well as early reading scores. Support vector classification (with a high cost parameter and low gamma parameter) predicts high school dropout with the highest overall validity in the testing dataset at 90.1 percent followed by decision trees with boosting and interaction terms at 89.5 percent.

Patient-reported quality-of-life analysis of radium-223 dichloride from the phase III ALSYMPCA study

BACKGROUND: Radium-223 dichloride (radium-223), a first-in-class α-emitting radiopharmaceutical, is recommended in both pre- and post-docetaxel settings in patients with castration-resistant prostate cancer (CRPC) and symptomatic bone metastases based on overall survival benefit demonstrated in the phase III ALSYMPCA study. ALSYMPCA included prospective measurements of health-related quality of life (QOL) using two validated instruments: the general EuroQoL 5D (EQ-5D) and the disease-specific Functional Assessment of Cancer Therapy-Prostate (FACT-P).

PATIENTS AND METHODS: Analyses were conducted to determine treatment effects of radium-223 plus standard of care (SOC) versus placebo plus SOC on QOL using FACT-P and EQ-5D. Outcomes assessed were percentage of patients experiencing improvement, percentage of patients experiencing worsening, and mean QOL scores during the study.

RESULTS: Analyses were carried out on the intent-to-treat population of patients randomized to receive radium-223 (n = 614) or placebo (n = 307). The mean baseline EQ-5D utility and FACT-P total scores were similar between treatment groups. A significantly higher percentage of patients receiving radium-223 experienced meaningful improvement in EQ-5D utility score on treatment versus placebo {29.2% versus 18.5%, respectively; P = 0.004; odds ratio (OR) = 1.82 [95% confidence interval (CI) 1.21-2.74]}. Findings were similar for FACT-P total score [24.6% versus 16.1%, respectively; P = 0.020; OR = 1.70 (95% CI 1.08-2.65)]. A lower percentage of patients receiving radium-223 experienced meaningful worsening versus placebo measured by EQ-5D utility score and FACT-P total score. Prior docetaxel use and current bisphosphonate use did not affect these findings. Treatment was a significant predictor of EQ-5D utility score, with radium-223 associated with higher scores versus placebo (0.56 versus 0.50, respectively; P = 0.002). Findings were similar for FACT-P total score (99.08 versus 95.22, respectively; P = 0.004).

CONCLUSIONS: QOL data from ALSYMPCA demonstrated that improved survival with radium-223 is accompanied by significant QOL benefits, including a higher percentage of patients with meaningful QOL improvement and a slower decline in QOL over time in patients with CRPC.

Sequential Morphological Changes in the CNV Net after Intravitreal Anti-VEGF Evaluated with OCT Angiography

PURPOSE: To assess and describe sequential morphological changes in the choroidal neovascularization (CNV) net using optical coherence tomography angiography (OCTA) in patients undergoing treatment with intravitreal antivascular endothelial growth factor (VEGF). METHODS: Prospective cohort study. OCTA was performed sequentially: before (t0), 1 h (t1), 1 week (t2) and 1 month after the injection (t3), using Avanti RTVue XR equipped with the AngioVue® software (Optovue, Calif., USA). All images were classified by two independent graders. RESULTS: Ten eyes of 10 patients, with a mean age of 72.4 ± 10.5 years, were included. CNV morphology was described as tree-like in 5 eyes, glomerular in 1 and fragmented in 4. A fibrovascular capsule surrounding the CNV net was found in 4 eyes and a feeder trunk was noticed in 6. No changes were observed at t1. Loss of peripheral capillaries, vessel fragmentation and decreased vessel density were evident in 8 eyes at t2. The CNV capillary density and the peripheral anastomosis increased in all of these at t3. Two eyes remained unchanged through the whole length of follow-up. CONCLUSIONS: Significant changes in the CNV net can be observable in OCTA at least 1 week after intravitreal anti-VEGF. The safety of frequent examinations may provide a method of gauging treatment effects.

Recovering Natural History: Modeling Cardiovascular Biomarkers in the Presence of Endogenous Medication Use

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

Stepped Wedge Design for Multiple Interventions

Thesis (Master's)--University of Washington, 2016-08

Estimating the effect of the 2008 financial crisis on GNI in Greece and Iceland: A synthetic control approach

The purpose of this thesis is to conduct a comparative study in order to estimate the impact of the financial crisis to the GNI of Greece and Iceland. By applying synthetic control matching (a relatively new methodology) the study intends to compare the two countries, thus deducting conclusions about good or bad measures adopted. The results indicate that in both cases the adopted measures were not the optimal ones, since the synthetic counterfactual appear to perform better than the actual Greece and Iceland. Moreover, it is shown that Iceland reacted better to the shock it was exposed. However, different characteristics of the two countries impede the application of Icelandic actions in the Greek case.

Sequential Morphological Changes in the CNV Net after Intravitreal Anti-VEGF Evaluated with OCT Angiography

PURPOSE: To assess and describe sequential morphological changes in the choroidal neovascularization (CNV) net using optical coherence tomography angiography (OCTA) in patients undergoing treatment with intravitreal antivascular endothelial growth factor (VEGF). METHODS: Prospective cohort study. OCTA was performed sequentially: before (t0), 1 h (t1), 1 week (t2) and 1 month after the injection (t3), using Avanti RTVue XR equipped with the AngioVue® software (Optovue, Calif., USA). All images were classified by two independent graders. RESULTS: Ten eyes of 10 patients, with a mean age of 72.4 ± 10.5 years, were included. CNV morphology was described as tree-like in 5 eyes, glomerular in 1 and fragmented in 4. A fibrovascular capsule surrounding the CNV net was found in 4 eyes and a feeder trunk was noticed in 6. No changes were observed at t1. Loss of peripheral capillaries, vessel fragmentation and decreased vessel density were evident in 8 eyes at t2. The CNV capillary density and the peripheral anastomosis increased in all of these at t3. Two eyes remained unchanged through the whole length of follow-up. CONCLUSIONS: Significant changes in the CNV net can be observable in OCTA at least 1 week after intravitreal anti-VEGF. The safety of frequent examinations may provide a method of gauging treatment effects.

Características bioquímicas da carne de bubalinos Mediterrâneo terminados em confinamento e abatidos em diferentes pesos

Este trabalho teve como objetivo avaliar as características bioquímicas da carne de bubalinos Mediterrâneo terminados em confinamento e abatidos em diferentes pesos. Foram utilizados 28 bubalinos Mediterrâneo jovens, com idade de 9 meses, e peso vivo médio inicial de 240kg. Os animais foram alimentados com ração total à vontade em regime de confinamento até atingirem pesos de abate de 450, 480, 510 e 540kg de peso vivo (tratamentos). Os valores de pH e temperatura dos músculos Longissimus dorsi e Bíceps femoris foram coletados a intervalos de duas horas durante 24 horas após o abate. Determinou-se a cor da carne pelos métodos subjetivo e objetivo. Não houve efeito de interação entre tratamento e tempo de coleta. Não houve diferença significativa entre os tratamentos em relação ao pH e à temperatura nos dois músculos estudados (Longissimus dorsi e Bíceps femoris) durante o processo de resfriamento das carcaças. Os valores médios de pH inicial e pH final dos músculos Longissimus dorsi e Bíceps femoris foram de 6,6 e 5,4; e de 6,3 e 5,5, respectivamente. Os valores médios de temperatura inicial e final dos músculos Longissimus dorsi e Bíceps femoris foram 39,7°C e 4,1°C; 40,4°C e 7,0°C, respectivamente. Quanto à cor da carne, pelo método subjetivo, não houve diferença significativa entre os tratamentos estudados, obtendo-se a média geral de 3,41 pontos. em relação à cor da carne pelo método objetivo, não houve diferença significativa entre os tratamentos estudados. Os valores médios encontrados foram : L*= 35,16; a*=12,43 e b*=5,29. A carne bubalina, apesar de se apresentar mais escura que a carne bovina, não traz prejuízos quanto ao aspecto visual para o consumidor.

The timing and interval of mate encounter affects investment during mating

The benefits obtained from mating are usually condition-dependent, favouring the evolution of flexible investment during copulation, for instance, in terms of invested time, energy, or sperm. Flexible investment strategies are predicted to depend on the likelihood of acquiring alternative mates and therefore they should depend on the timing of mate encounter. However, scarce experimental evidence for this hypothesis exists. Here we manipulated the time delay until first mating and the interval between first and second mating in the polygynandrous common lizard, Zootoca vivipara. We determined treatment effects on fertilisation success and copulation duration, the latter being a proxy for investment in mating and for quantity of transferred sperm. The duration of the second copulation decreased with increasing inter-mating interval and depended on the fertilisation success of first mates. The former provides evidence for time-dependent investment strategies, most likely resulting from the progression of the female's reproductive cycle. Fertilisation success of first mates increased with increasing inter-mating interval and was higher when females were closer to ovulation, showing that flexible investment strategies significantly affected male reproductive success. This points to fertilisation assurance, which may mitigate negative effects of low population density on reproductive success, e.g. Allee effects.

Use of ordinal outcomes in vascular prevention trials: comparison with binary outcomes in published trials

Background and Purpose—Vascular prevention trials mostly count “yes/no” (binary) outcome events, eg, stroke/no stroke. Analysis of ordered categorical vascular events (eg, fatal stroke/nonfatal stroke/no stroke) is clinically relevant and could be more powerful statistically. Although this is not a novel idea in the statistical community, ordinal outcomes have not been applied to stroke prevention trials in the past. Methods—Summary data on stroke, myocardial infarction, combined vascular events, and bleeding were obtained by treatment group from published vascular prevention trials. Data were analyzed using 10 statistical approaches which allow comparison of 2 ordinal or binary treatment groups. The results for each statistical test for each trial were then compared using Friedman 2-way analysis of variance with multiple comparison procedures. Results—Across 85 trials (335 305 subjects) the test results differed substantially so that approaches which used the ordinal nature of stroke events (fatal/nonfatal/no stroke) were more efficient than those which combined the data to form 2 groups (P0.0001). The most efficient tests were bootstrapping the difference in mean rank, Mann–Whitney U test, and ordinal logistic regression; 4- and 5-level data were more efficient still. Similar findings were obtained for myocardial infarction, combined vascular outcomes, and bleeding. The findings were consistent across different types, designs and sizes of trial, and for the different types of intervention. Conclusions—When analyzing vascular events from prevention trials, statistical tests which use ordered categorical data are more efficient and are more likely to yield reliable results than binary tests. This approach gives additional information on treatment effects by severity of event and will allow trials to be smaller. (Stroke. 2008;39:000-000.)

An in-depth characterisation of neonatal seizures by early continuous video-EEG analysis

Introduction Seizures are harmful to the neonatal brain; this compels many clinicians and researchers to persevere further in optimizing every aspects of managing neonatal seizures. Aims To delineate the seizure profile between non-cooled versus cooled neonates with hypoxic-ischaemic encephalopathy (HIE), in neonates with stroke, the response of seizure burden to phenobarbitone and to quantify the degree of electroclinical dissociation (ECD) of seizures. Methods The multichannel video-EEG was used in this research study as the gold standard to detect seizures, allowing accurate quantification of seizure burden to be ascertained in term neonates. The entire EEG recording for each neonate was independently reviewed by at least 1 experienced neurophysiologist. Data were expressed in medians and interquartile ranges. Linear mixed models results were presented as mean (95% confidence interval); p values <0.05 were deemed as significant. Results Seizure burden in cooled neonates was lower than in non-cooled neonates [60(39-224) vs 203(141-406) minutes; p=0.027]. Seizure burden was reduced in cooled neonates with moderate HIE [49(26-89) vs 162(97-262) minutes; p=0.020] when compared with severe HIE. In neonates with stroke, the background pattern showed suppression over the infarcted side and seizures demonstrated a characteristic pattern. Compared with 10 mg/kg, phenobarbitone doses at 20 mg/kg reduced seizure burden (p=0.004). Seizure burden was reduced within 1 hour of phenobarbitone administration [mean (95% confidence interval): -14(-20 to -8) minutes/hour; p<0.001], but seizures returned to pre-treatment levels within 4 hours (p=0.064). The ECD index in cooled, non-cooled neonates with HIE, stroke and in neonates with other diagnoses were 88%, 94%, 64% and 75% respectively. Conclusions Further research exploring the treatment effects on seizure burden in the neonatal brain is required. A change to our current treatment strategy is warranted as we continue to strive for more effective seizure control, anchored with use of the multichannel EEG as the surveillance tool.