Review: Use the examples below to help you define Polyhedra and Non-Polyhedra. Polyhedra Non-Polyhedra Polyhedra: a solid with flat faces Non-Polyhedra: solid with any surface that is not flat
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REFLECTIVE JOURNALING TOOLS Reflective J ournalingTools LEARNING: • How is practice different from theory? Did this exercise help you to understand your theory and the application of theory better? How? Why? • Did you learn anything that helped you to better understand a theory, the use of a test that you were taught in lectures/labs? • What did you learn that were not taught in lectures (e.g. communication with patients), and how did you cope or learn more about this to improve your performance? Or how can this be incorporated into lectures? • Did this exercise help you to remember or recall later other aspects of previous experiences that you have forgotten? • Did this exercise help you identify areas that need to be changed, improved etc. in yourself/peers/staff/clinical training etc. Why and how? • What actions did you take you take and what are the results (what did you learn)? SELF ASSESSMENT: • Did you identify areas/issues that you were unclear of, or disagreed with your supervisors/peers, or different from what you have learned in your past lectures? Justify the actions taken. Did this help you in your learning? How? • Have you been open to share with others and to listen what others have to say? • Have you paid attention to both your strong and weak points? Can you identify them? What are you going to do about them? • How did faculty supervision/RW help you in your clinical experiences in relation to your professional growth? (eg. did it encourage you to be more independent, to become more confident in professional activities and behaviors etc) • What have you noted about yourself, your learning altitude, your relationship with peers/supervisors etc. that has changed from doing this exercise? COMMUNICATION: • What have you learned from interacting with others (peers/supervisors/staff etc)? • Did your peers gain anything from YOUR involvement in this exercise and vice versa? • Did this exercise encourage and facilitate communication? • Did you clarify with your supervisors/peers about problematic issues identified? Why (not)? What are the results? • How could you/your peers/staff help you overcome negative emotions arising from your work? Did your show empathy for your peers? PROFESSIONALISM: • Did you learn that different situations call for different strategies in management? • What are the good and bad practices that you have identified? How would you suggest to handle the bad/poor practices identified (if any)? • Did you learn to accept and use constructive criticism? • Did you accept responsibility for your own actions? • Did you try to maintain high standard of performance? • Did you display a generally positive altitude and demonstrate self-confidence? • Did you demonstrate knowledge of the legal boundaries and ethics of contact lens practice? EMOTION & PERSONAL GROWTH: • Did you reflect on your feelings when dealing with the case/peers/supervisor (eg. frustration, embarrassment, fear) for this exercise? If not, why not? If yes, who should be responsible — you, your patient or your supervisor? Why? • Did you find reflection (as required for this exercise) helpful, challenging, and enjoyable, change the way you learn? How? Why (not)? • How and what did you do to handle negative emotions arising from doing this subject? How could these feelings be minimized? • Did you try to find out if your feelings were different from your peers? Why? What did you do to help your peers? • Did you reflect on your learning altitude? How was it? Is there room for improvement? How? Why (not)? • What did you learn about your relationship with your peers/supervisors? What did you learn about working with others? Ideas for Reflective Journaling Writing Contributor(s): Dr. Michael Ying and Dr. Pauline Cho
A Graph Kernel Method for DNA-Binding Site Prediction Changhui Yan* and Yingfeng Wang CS, Utah State U, Logan, UT ABSTRACT: This paper presents a graph kernel method for predicting DNA-binding sites on protein structures. Surface patches are represented using labeled graphs. Then, the graph kernel method is used to calculate the similarities between graphs. A new surface patch is predicted to be interface or non-interface patch based on its similarities to known DNA-binding patches and non-DNA-binding patches. The proposed method achieves 88.7% accuracy, 89.7% specificity, and 87.7% sensitivity when tested on a representative set of 146 protein-DNA complexes using leave-one-out cross-validation. Then, the method is applied to identify DNA-binding sties on 13 unbound structures of DNA-binding proteins. In each of the unbound structure, the top 1 patch predicted by the proposed method precisely indicates the location of the DNA-binding site. Comparisons with other methods confirm the effectiveness of the method. Introduction Structural genomics projects are yielding an increasingly large number of protein structures with unknown function. As a result, computational methods for predicting functional sites on these structures are in urgent demand. There has been significant interest in developing computational methods for identifying amino acid residues that participate in protein-DNA interactions based on combinations of sequence, structure, evolutionary information, and chemical or physical properties. For example, Jones et al. (2003) analyzed residue patches on the surface of DNA-binding proteins and used electrostatic potentials of residues to predict DNA-binding sites. Later, they extended that method by including DNA-binding structural motifs (Shanahan, et al., 2004). In related studies, Tsuchiya et al. (2004) used a structure-based method to identify protein-DNA binding sites based on electrostatic potentials and surface shape, and Keil et al. (2004) trained a neural network classifier to identify patches likely to be DNA-binding sites based on physical and chemical properties of the patches. Neural network classifiers have also been used to identify protein-DNA interface residues based on a combination of sequence and structure information (Ahmad, et al., 2004). Recently, Tjong and Zhou (2007) developed a neural network method for predicting whether a surface residue is in the DNA-binding sites based on the sequence profile of that residue and its structural neighbors. On another track, several methods have been developed for predicting DNA-binding sites using only protein sequence-derived information as input (Ahmad and Sarai, 2005; Wang and Brown, 2006; Yan, et al., 2006). To date, the methods that take the advantage of structure-derived information achieve better results than those using only sequence-derived information. One common limitation of the above-mentioned methods is that the sequence and structural properties of a surface patch are input to machinelearning methods in the form of vectors. When the properties of a surface patch are encoded as a vector, the information of how these properties distribute over the surface is lost. For example, if a surface patch includes five amino acid residues, the above-mentioned methods will encode the amino acid identities of this surface patch as five independent values in a vector. In this representation, the spatial arrangement of these five residues on the surface patch is not encoded. Unfortunately, the spatial arrangement of properties on a surface patch plays a crucial role in determining the function of the surface patch. To overcome this limitation, this paper presents a graphical approach for DNA-binding site prediction. In this study, graphs are used to represent surface patches, such that the spatial arrangement of various properties on the surface is explicitly encoded. The similarities between surface patches are then computed using a graph kernel method. A voting strategy is then used to classify surface patches into DNA-binding sites versus non-binding sites. The proposed method achieves 88.7% accuracy, 89.7% specificity, and 87.7% sensitivity in leave-one-out crossvalidation. When applied to set of unbound structures of DNA-binding proteins, the proposed method can precisely identify the locations of DNA-binding sites.
Question: you gave me five different equations for electric flux. Which one do I need to use? Answer: use the simplest (easiest!) one that works. E EA Flat surface, E A, E constant over surface. Easy! E EA cos Flat surface, E not A, E constant over surface. E E A E E dA E E dA Flat surface, E not A, E constant over surface. Surface not flat, E not uniform. Avoid, if This is the definition of electric flux, so it is on your equation sheet. possible. Closed surface. The circle on the integral just reminds you to integrate over a closed surface. If the surface is closed, you may be able to “break it up” into simple segments and still use E=E·A for each segment.
Important Legal Information for Adolescents and Parents According to Iowa law, a minor (an individual younger than 18 years) may seek medical care for the following without the permission or knowledge of his parents: • Substance abuse treatment; • Sexually Transmitted Infection(STI) testing and treatment; • HIV testing – if test is positive, Iowa law requires parent notification; • Contraceptive care and counseling, including emergency contraception; and Even though teenagers young • Blood donation if 17and years of age or adults can receive these treatments older. without their parent’s knowledge, it is important to remember parents are a key part of all aspects of your life. We encourage parents and teens to be open and honest with each other when it comes to health care decisions. It is important for teens to know that if they are covered by their parents’ medical insurance and want it to cover their treatment, they will need to consent to their medical records being shared – possibly even with parents. A minor may also consent for evaluation and treatment in a medical emergency or following a sexual assault. However, treatment information can not be kept confidential from parents. Bill of Rights for Teens and Young Adults • The things you tell us in confidence will be kept private. • We will speak and write respectfully about your teen and family. • We will honor your privacy. YOU HAVE THE RIGHT TO: Emotional Support • Care that respects your teen’s growth and development. • We will consider all of your teen’s interests and needs, not just those related to illness or disability. Respect and Personal Dignity • You are important. We want to get to know you. • We will tell you who we are, and we will call you by your name. We will take time to listen to you. • We will honor your privacy. Care that Supports You and Your Family • All teens are different. We want to learn what is important to you and your family. Information You Can Understand • We will explain things to you. We will speak in ways you can understand. You can ask about what is happening to you and why. Care that Respects Your Need to Grow and Learn • We will consider all your interests and needs, not just those related to your illness or disability. Make Choices and Decisions • Your ideas and feelings about how you want to be cared for are important. • You can tell us how we can help you feel more comfortable. • You can tell us how you want to take part in your care. • You can make choices whenever possible like when and where you YOU HAVE THE RIGHT TO: receive your treatments. Bill of Rights for Parents Respect and Personal Dignity • You and your teen will be treated with courtesy and respect. Make Decisions About Your Teen’s Care • We will work in partnership with you and your teen to make decisions about his care. • You can ask for a second opinion from another healthcare provider. Family Responsibilities YOU HAVE THE RESPONSIBILITY TO: Provide Information • You have important information about your teen’s health. We need to know about symptoms, treatments, medicines, and other illnesses. • You should tell us what you want for your child. It is important for you to tell us how you want to take part in your teen’s care. • You should tell us if you don’t understand something about your teen’s care. • If you are not satisfied with your teen’s care, please tell us. Provide Appropriate Care • You and the other members of the health care team work together to plan your teen’s care. • You are responsible for doing the things you agreed to do in this plan
