What do I learn while at GDC? • Data structures, data structures, data structures, shading, data structures, data structures, data structures, physics, data structures, data structures, graphics, data structures, data structures, data structures, memory management, data structures, data structures, & data structures
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Specific Aim 2: Develop new graph kernel methods for binding site prediction. The Co-PI will use the machine-learning approach to develop predictors for binding sites. The procedure includes (1) collect structures of complexes; (2) extract binding sites from the structures; (3) generate surface patches and graphs; (4) develop graph kernel methods for binding site prediction; and (5) evaluate the methods. Datasets collection Crystal structures of protein-protein complexes and protein-nucleic acid complexes will be collected from the PDB57. To ensure the quality of the dataset, we will discard structures with resolution value greater than 2.5 or R factor greater than 0.3. Many groups have tackled the problem of distinguishing biologically important contacts from crystal compact. Their results are deposited in databases like PQS58, PISA59, and PiQSi60. We will remove crystal contacts in the structures using these databases. The apo-state (unbounded) structures of the involving proteins will also be collected from the PDB if they are available. Extract binding sites Two types of definitions for binding-site residues have been widely used to extra binding sites from complex structures. One is based on the reduction of solvent accessible surface upon the formation of complex61. A residue is defined to be a binding-site residue if its solvent accessible surface is reduced by at least a certain amount during the formation of the complex. The second definition is based on the atom distance62. A residue is defined as a binding-site residue if its distance to the interacting partner is less than a certain distance. We will explore both types of definitions. Another issue in extracting binding site from PDB structure is that a protein may involve in multiple interactions, but a PDB structure may only shows one of them. Furthermore, some PDB structures only show a partial binding site due to incomplete structures63. Previously we have developed a tool, named TCBRP63 (http://bioweb.cs.ndsu.nodak.edu/Server/PPBindingprediction.html), for automatic extraction of complete binding sites from PDB complexes. We will use TCBRP for this step. Generate surface patches and graphs We will divide the protein surfaces into overlapping patches and represent them using the graph models developed in Specific Aim 1. For each residue on the protein surface, we will generate a patch that includes it and its contacting neighbors. In the training stage, a patch is assigned to either positive class (i.e., binding sites) or negative class (i.e., non-binding sites) depending on whether the center residue is a binding-site residue. In the prediction stage, the predicted class of a graph is assigned to its center residue.
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WHY? ANNOTATE TO KNOW WHY. TITLE Why GOES HERE TITLE GOES Why HERE Why was this first, that second, and the other last? Why did this event trigger that event and if not for one would the other occur? TITLE Why GOES HERE TITLE Why GOES HERE Why are these connected and why would they fail without each other? Why is this key and that is key and the other is not? TITLE GOES HERE Why did that need to happen? TITLE GOES HERE
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differ from vs. differ with  differ  The last tutorial greatly differed from this one.  differ  from – to be different from with – to disagree I differed with my father over the value of his old Ford Fairlane.
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Why Why Do Do Structures Structures Differ? Differ?
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Why Why Do Do Structures Structures Differ? Differ?
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Why Why Do Do Structures Structures Differ? Differ? –– Strategy Strategy
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Why Why Do Do Structures Structures Differ? Differ? –– Technology Technology Characteristics Characteristicsof ofroutineness routineness(standardized (standardizedor or customized) customized)ininactivities: activities: • •Routine Routinetechnologies technologiesare areassociated associatedwith withtall, tall, departmentalized departmentalizedstructures structuresand andformalization formalizationinin organizations. organizations. • •Routine Routinetechnologies technologieslead leadto tocentralization centralizationwhen when formalization formalizationisislow. low. • •Nonroutine Nonroutinetechnologies technologiesare areassociated associatedwith withdelegated delegated decision decisionauthority. authority.
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Why Why Do Do Structures Structures Differ? Differ? –– Environment Environment Key KeyDimensions: Dimensions: • • Capacity: Capacity:the thedegree degreeto to which whichan anenvironment environment can cansupport supportgrowth. growth. • • Volatility: Volatility:the thedegree degreeof of instability instabilityininthe the environment. environment. • • Complexity: Complexity:the thedegree degree of ofheterogeneity heterogeneityand and concentration concentrationamong among environmental environmental elements. elements.
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Mineral Groups • Joining silicate structures • Single tetrahedra are linked together to form various structures including: – Isolated tetrahedra – Ring structures – Single- and double-chain structures – Sheet or layered structures – Complex three-dimensional structures © 2011 Pearson Education, Inc.
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Place Slide Title 11 Text Here Dashboard Chapter Learning 1. Organizing as a Management Function 1. What is organization structure? 2. Formal structures 3. Informal structures 2. Traditional Organization Structures 1. Functional structures 2. Divisional structures 3. Matrix structures ©2013 John Wiley & Sons, Inc. All rights reserved. 11-3
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  QUESTION EVERYTHING: WHY, WHY, WHY? Why  Why  Why  Why  Why  Why  that that that that that that person? gender, race, age, or class? pose, in those clothes? magazine or that show? music? setting? 3
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Why Discriminative Subgraphs? Sample database (a) (b) (c) • All graphs contain structures: C, C-C, C-C-C • Why bother indexing these redundant frequent structures? – Only index structures that provide more information than existing structures 3/19/19 16
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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
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Fact Finding  Who, (Cont.) What, Where, When, How, and Why? ◦ Who performs each of the procedures within the system? Why? Are the correct people performing the activity? Could other people perform the tasks more effectively? ◦ What is being done? What procedures are being followed? Why is that process necessary? Often, procedures are followed for many years and no one knows why. You should question why a procedure is being followed at all ◦ Where are operations being performed? Why? Where could they be performed? Could they be performed more efficiently elsewhere? ◦ When is a procedure performed? Why is it being performed at this time? Is this the best time? ◦ How is a procedure performed? Why is it performed in that manner? Could it be performed better, more efficiently, or less expensively in some other manner? 36
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The Two-Chord Power Theorem. What Given:is given? (1) Statement 1 (2) Statement 2 (3) Statement 3 (4) Statement 4 (5) Statement 5 (6) Statement 6 (7) Statement 7 (8) Statement 8 QED Prove: What will we prove? Reason 1. Why? Reason 2. Why? Reason 3. Why? Reason 4. Why? Reason 5. Why? Reason 6. Why? Reason 7. Why? Reason 8. Why? DRAWING 30
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If the two pairs of corresponding sides are proportional, and the included angles are congruent, then the triangles are similar. we prove? Given: is AB/DE =AC/DF, A=D What What given? Prove:will ∆ABC ~ ∆DEF Construction Why? (1) AE’ = DE, AF’ = DF SAS Why? (2) ∆AE’F’ ≌ ∆DEF Given & substitution (1) Why? (3) AB/AE’ = AC/AF’ Basic Proportion Thm Why? (4) E’F’∥ BC (5) B =  AE’F’ Corresponding angles Why? (6) A =  A Reflexive Why? AA Why? (7) ∆ABC ≈ ∆AE’F’ Substitute Why? 2 & 7 (8) ∆ABC ≈ ∆DEF A D QED E’ B F’ E C F 26
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