Gülnur Birol

A modular simulation package for fed-batch fermentation: penicillin production

Simulation software based on a detailed unstructured model for penicillin production in a fed-batch fermentor has been developed. The model extends the mechanistic model of Bajpai and Reuss by adding input variables such as pH, temperature, aeration rate, agitation power, and feed flow rate of substrate and introducing the CO2 evolution term. The simulation package was then used for monitoring and fault diagnosis of a typical penicillin fermentation process. The simulator developed may be used for both research and educational purposes and is available at the web site: http://www.chee.iit.edu/ � /control/software.html. # 2002 Elsevier Science Ltd. All rights reserved.

The Colorado Learning Attitudes about Science Survey (CLASS) for Use in Biology

This paper describes a newly adapted instrument for measuring novice-to-expert-like perceptions about biology: the Colorado Learning Attitudes about Science Survey for Biology (CLASS-Bio). Consisting of 31 Likert-scale statements, CLASS-Bio probes a range of perceptions that vary between experts and novices, including enjoyment of the discipline, propensity to make connections to the real world, recognition of conceptual connections underlying knowledge, and problem-solving strategies. CLASS-Bio has been tested for response validity with both undergraduate students and experts (biology PhDs), allowing student responses to be directly compared with a consensus expert response. Use of CLASS-Bio to date suggests that introductory biology courses have the same challenges as introductory physics and chemistry courses: namely, students shift toward more novice-like perceptions following instruction. However, students in upper-division biology courses do not show the same novice-like shifts. CLASS-Bio can also be paired with other assessments to: 1) examine how student perceptions impact learning and conceptual understanding of biology, and 2) assess and evaluate how pedagogical techniques help students develop both expertise in problem solving and an expert-like appreciation of the nature of biology.

Effects of Photocoagulation on Intraretinal Po2 in Cat

PURPOSE To test the hypothesis that intraretinal Po(2) increases after photocoagulation. METHODS Anesthetized cats underwent retinal argon laser photocoagulation. At least 4 weeks after treatment, Po(2)-sensitive microelectrodes were used to record intraretinal Po(2) profiles from healed photocoagulation lesions in anesthetized cats breathing air. Histopathologic examination of the retinas was used to confirm that the photoreceptors were destroyed and that the inner retinal layers were preserved, though somewhat disorganized, as in human panretinal photocoagulation (PRP). RESULTS The retina and tapetum were thinner in the lesioned retina than in the nonphotocoagulated retina. Average Po(2) across the inner 50% of the retina was higher (22 +/- 10 mm Hg) in photocoagulated retina than in untreated retina (14 +/- 7 mm Hg; P < 0.01; n = 13 cats). The minimum Po(2) was also significantly higher, whereas choroidal Po(2) was significantly lower in the photocoagulated retina than in untreated retina. No significant difference was found in the preretinal vitreous. After lesions, inner retinal Po(2) could also be maintained above zero, even in the absence of retinal circulation. CONCLUSIONS Previous measurements showed increased Po(2) in the preretinal vitreous of rabbits and pigs (but not cats) after photocoagulation of the outer retina. These intraretinal measurements in cats provide further evidence for a chronic increase in inner retinal Po(2) in lesioned areas during air breathing.

A hybrid supervisory knowledge-based system for monitoring penicillin fermentation

Batch and fed-batch bioprocesses generally exhibit batch-to-batch variation. Multivariate statistical monitoring of these processes based on the use of empirical models developed from the multiway principal component analysis was performed by using contribution, T/sup 2/ and square prediction error plots. To cope with uncertainties in the fermentation process and to provide more effective supervision, a knowledge-based system was developed allowing the coupling of quantitative statistical information with the qualitative domain expertise (heuristic knowledge). This hybrid system (PenExpert) aims to perform old-of-batch process monitoring as well as online process monitoring and fault diagnosis.

Simulation studies on the dynamics of diabetes mellitus

Glucose-insulin interaction in an insulin-dependent diabetic patient has been simulated using an overall and a detailed model based on pharmacokinetic diagrams of insulin and glucose. Both models are capable of predicting the blood glucose and insulin levels, total glucose uptake and the renal glucose excretion. The simulator is integrated with a graphical user interface to provide a user-friendly environment. The package may be used to perform virtual experiments with various characteristics, diet and exercise conditions.

Development of a Meiosis Concept Inventory

A 17-question Meiosis Concept Inventory (Meiosis CI) was designed, developed, and validated to diagnose student misconceptions on meiosis, a fundamental concept in genetics. The Meiosis CI targets large introductory biology and genetics courses.

Metabolic Responses to Light in Monkey Photoreceptors

Purpose: Transient changes in intraretinal oxygen tension (PO2) in response to light stimuli were studied in order to understand the dynamics of light-evoked changes in photoreceptor oxidative metabolism. Methods: PO2 changes during illumination were recorded by double-barreled microelectrodes in the outer part of the perifoveal retina in five macaques (Rhesus and Cynomolgus) and were fitted to a single exponential equation to obtain the time constant (τ) and maximum PO2 change. Results: At the onset of light, PO2 increased at all illuminations in all animals. The magnitude of the light-evoked PO2 change increased with increasing illumination over 3–4 log units but decreased in all animals at the maximum illumination. The median time constant of the PO2 change (τ) was 26 sec and was not correlated with illumination. The time constant for the return to darkness was similar for illuminations below rod saturation. Since O2 diffusion is fast over the short distance from the choroid to the inner segments, τ reflects the time course of the underlying change in oxidative metabolism. Conclusions: Previous results suggested that two competing processes influence the change in photoreceptor oxidative metabolism with light, Na+/K+ pumping and cyclic guanosine monophosphate (cGMP) turnover. Because a single exponential fitted the PO2 data, it appears that these processes have time constants that differ by no more than a few seconds in primate. In monkeys, τ is longer than previously reported values for cat and rat. Longer time constants are related to larger photoreceptor volume, possibly because metabolic rate is controlled by intracellular Na+, and a change in intracellular Na+ after the onset of illumination occurs more slowly in larger photoreceptors. The “metabolic threshold” illumination that reduced oxygen consumption by about 10% is approximately the same as the illumination that closes 10% of the light-dependent cation channels that are open in the dark.

Development of the Biological Experimental Design Concept Inventory (BEDCI)

The Biological Experimental Design Concept Inventory (BEDCI) is a carefully designed diagnostic tool. The process of development and assessment of reliability and validity of the instrument are documented. BEDCI can be used to identify non-expert-like conceptions, inform teaching practices, and measure the effectiveness of targeted instruction.

Longitudinal Study of Student Attitudes in a Biology Program.

This study is among the first to report longitudinal results of student attitudes across a university program. Biology students become significantly more expert‐like from the first year to the fourth year of the program, but students are still far from expert‐like for problem solving–related attitudes. Also, after four years, high‐performing students displayed significantly more expert-like attitudes than low‐performing students.

Glucosim: a simulator for education on the dynamics of diabetes mellitus

Glucose-insulin interactions in healthy and insulin-dependent diabetic humans are simulated using an overall and a detailed model based on pharmacokinetic diagrams of insulin and glucose. Both models are capable of predicting blood glucose and insulin levels, total glucose uptake and renal glucose excretion. The simulator is integrated with a graphical user interface to provide a user-friendly environment for performing virtual experiments with various characteristics, diet and exercise conditions.