SIPP Topical Module Categories and Uses of SIPP Category Topical Module Health, Disability, & Physical WellBeing Adult Well-Being; Extended Measures of Well-Being; Children’s Well-Being; Functional Limitations and Disability (Child and Adult); Health Status and Utilization of Health Care Services; Long-Term Care; Medical Expenses, Work Disability; Work Disability History. Financial Annual Income and Retirement Accounts; Assets and Liabilities; Real Estate Property and Vehicles; Recipiency History; Retirement Expectations and Pension Plan Coverage; School Enrollment and Financing; Wealth and Eligibility, Selected Financial Assets; Shelter Costs and Energy Usage; Support for Non-household Members; Taxes. Child Care & Financial Support Child Care Child Support Agreements; Child Support Paid; Support for Non-household Members. Education & Employment Education and Training History; Employment History; School Enrollment and Financing; Work-Related Expenses; Work Schedule. Family Characteristics & Living Conditions Household Extended Measures of Well-Being; Fertility History; Household Relationships; Marital History. Personal History Education and Training History; Employment History; Fertility History; Marital History; Migration History; Recipiency History; Work Disability History. Welfare Reform Eligibility for and Recipiency of Public Assistance; Job Search and Training Assistance; Job Subsidies; Transportation Assistance; Health Care; Food Assistance. • Program Participation - One of the most important reasons for conducting SIPP is to gather detailed information on participation in income transfer programs. - How have changes in eligibility rules or benefit levels affected recipients? - How do wealth and income patterns differ for various age, gender, and racial groups? • Longitudinal Survey - What factors affect change in household and family structure and living arrangements? - What are the interactions between changes in the structure of households and families and the distribution of income? - What effects do changes in household composition have on economic status and program eligibility? - What are the primary determinants of turnover in programs such as Food Stamps? Source: (U.S. Census Bureau, 2008; http://www.census.gov/content/dam/Census/programssurveys/sipp/methodology/SIPP_USERS_Guide_Chapter3_2008.pdf) 4
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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.
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Course Outline • Introduction to logic synthesis – • High level synthesis, basics – • Retiming; integrating synthesis, retiming and mapping (ABC) Satisfiability (SAT) – • Graph based, standard cell mapping (ASICs) Cut-based (FPGAs) Sequential optimization – • Kernel-based algebraic decomposition (SIS) AIG-based optimization (ABC) Technology mapping – – • Asenhurst-Curtis method BDD based decomposition, bi-decomposition Multi-level logic synthesis (technology independent) – – • Exact logic minimization (Quine) Heuristic logic optimization (Espresso) Functional decomposition – – • Sum of products, factored form representations Canonical representations, BDDs, BMDs, others Two-level logic optimization – – • Scheduling, resoource allocation, binding Boolean functions and their representations – – • VLSI design flow, target technologies Application to synthesis and verification Formal verification – – – Equivalence checking, property checking Sequential verification, FSM reachability Verification of arithmetic circuits, symbolic algebra 2 ECE 667 Synthesis & Verification - Design Flow
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Supplemental packet page 49 Atomic Number: 11 Name: • Symbol: 23 Na 11 mass # 23 #p ______ 11 #n ______ 12 #e Physical Properties: ••• •• •• • ••• sodium-23 soft metal, conducts eChemical Properties: reacts w/ H2O Electronic Configuration: 1s 2s 2 2 2p 6 3s 1 Atomic Number: 12 24 Mg 12 mass # 24 ______ 12 #n 12 ______ #e 12 ______ Electronic Configuration: Na• Physical Properties: Name:magnesium-24 #p •• Name: chlorine-35 •• • 35 Symbol: •• •• • • Cl 17 • •• • mass # 35 •• #p ______ Atomic Number: 17 #n Lewis Dot: ______ 11 Symbol: Atomic Structure ••• •• •• •• ••• ductile metal, conducts e- 1s 2s 2 2p 6 Configuration: Properties: burns in O2 3s 2 • Mg • 1s2 2s2 2p6 •• • • • •• • 16 O 8 mass # 16 #p ______ 8 #n ______ 8 #e 8 ______ Properties: reacts w/ Na(s) Physical Properties: oxygen-16 Symbol: Chemical • •• •Cl• 3s2 3p5 • • Atomic Number: 8 Name: yellow gas, nonconductor Lewis Dot: Electronic Chemical Lewis Dot: 2 #e 17 ______ 18 ______ 17 Physical Properties: Electronic Configuration: colorless gas, nonconductor Chemical Properties: supports combustion Lewis Dot: 1s 2s 2 2 2p 4 •• • O• ••
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Supplemental packet page 50 Atomic Number: 11 sodium-23 ion Name: • Symbol: 23 1+ Na 11 mass # 23 #p ______ 11 #n ______ 12 #e ••• •• •• ••• More protons than electrons ______ 10 Electronic Configuration: 1s2 2s2 2p6 3s0 Atomic Number: 12 magnesium-24 ion Name: Symbol: 24 Mg 12 mass # 24 #p ______ 12 #n 12 ______ #e 10 ______ 2+ Electronic Configuration: Ionic Structure Physical Properties: Atomic Number: 17 metal cation positive ion 1+ charge Chemical Name: Properties: mass # 35 combines w/ anions Lewis Dot: [Na]1+ Physical Properties: ••• •• •• ••• More protons than electrons 1s2 2s2 2p6 3s0 metal cation positive ion 2+ charge Symbol: Chemical #p ______ #n ______ #e ______ combines w/ anions Lewis Dot: [Mg]2+ Properties: Lewis Dot: Electronic Configuration: Atomic Number: 8 Physical Properties: Name: Symbol: Chemical Properties: Physical Properties: Chemical mass # 16 #p ______ #n ______ #e ______ Electronic Configuration: Properties: Lewis Dot:
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Supplemental packet page 50 Atomic Number: 11 sodium-23 ion Name: • Symbol: 23 1+ Na 11 mass # 23 #p ______ 11 #n ______ 12 #e ••• •• •• ••• More protons than electrons ______ 10 Electronic Configuration: 1s2 2s2 2p6 3s0 Atomic Number: 12 magnesium-24 ion Name: Symbol: 24 2+ 12Mg mass # 24 #p ______ 12 #n 12 ______ #e 10 ______ Electronic Configuration: ••• •• •• ••• More protons than electrons 1s2 2s2 2p6 3s2 Ionic Structure Physical Properties: metal cation positive ion 1+ charge Chemical Properties: combines w/ anions Lewis Dot: [Na] 1+ •• chloride-35 ion Name: ••• 35 1Symbol: •• • 17Cl •• •• • • •• mass # 35 •• #p ______ 17 Atomic Number: 17 #n ______ 18 #e ______ 18 Electronic Configuration: Physical Properties: metal cation positive ion 2+ charge Properties: combines w/ anions Lewis Dot: 2+ 1s2 2s2 2p6 3s2 3p6 Atomic Number: 8 Symbol: 16 8 O mass # 16 #p ______ 8 #n 8 ______ #e 10 ______ Electronic Configuration: 2- nonmetal anion negative ion 1- charge Chemical Properties: combines w/ cations Lewis Dot: •• •Cl• •• •• [ ]1Physical Properties: Name: oxygen-16 Chemical [Mg] More electrons than protons Physical Properties: ion ••• •• •• ••• More electrons than protons 1s2 2s2 2p6 3s0 nonmetal anion negative ion 2- charge Chemical Properties: combines w/ cations Lewis Dot: •• •O• •• •• [ ]2-
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Print slide Atomic Number: 11 Atomic Structure Physical Properties: Name: Atomic Number: 17 Name: • Symbol: Symbol: Chemical mass # 23 #p ______ #n ______ #e ______ Properties: Lewis Dot: Chemical mass # 35 #p ______ #n ______ #e ______ Electronic Electronic Configuration: Configuration: Atomic Number: 12 Physical Properties: Atomic Number: 8 Name: Name: Symbol: Symbol: Chemical mass # 24 Physical Properties: Properties: Lewis Dot: Physical Properties: Chemical mass # 16 #p ______ #p ______ #n ______ #n ______ #e ______ #e ______ Lewis Dot: Properties: Electronic Electronic Configuration: Configuration: Properties: Lewis Dot:
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Record into your notes Atomic Number: 11 Name: • Symbol: 23 Na 11 mass # 23 ______ 11 #n ______ 12 #e Physical Properties: ••• •• •• • ••• sodium-23 #p Atomic Structure soft metal, conducts eChemical Properties: reacts w/ H2O #n Lewis Dot: ______ 11 Electronic Configuration: 1s 2s 2 2 2p 6 3s 1 Atomic Number: 12 24 Mg 12 mass # 24 #p ______ 12 #n 12 ______ #e 12 ______ Electronic Configuration: Na• Physical Properties: Name:magnesium-24 Symbol: •• Name: chlorine-35 •• • 35 Symbol: •• •• • • Cl 17 • •• • mass # 35 •• #p ______ Atomic Number: 17 ••• •• •• •• ••• ductile metal, conducts e- 1s 2s 2 2p 6 Configuration: Properties: burns in O2 3s 2 • Mg • 1s2 2s2 2p6 •• • • • •• • 16 O 8 mass # 16 #p ______ 8 #n ______ 8 #e 8 ______ Properties: reacts w/ Na(s) Physical Properties: oxygen-16 Symbol: Chemical • •• •Cl• 3s2 3p5 • • Atomic Number: 8 Name: yellow gas, nonconductor Lewis Dot: Electronic Chemical Lewis Dot: 2 #e 17 ______ 18 ______ 17 Physical Properties: Electronic Configuration: colorless gas, nonconductor Chemical Properties: supports combustion Lewis Dot: 1s 2s 2 2 2p 4 •• • O• ••
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Section 5.2 - Octet Rule & Ions Print Slide Atomic Number: 11 Ionic Structure Physical Properties: Name: Atomic Number: 17 Name: • Symbol: Symbol: Chemical mass # 23 #p ______ #n ______ #e ______ Properties: Lewis Dot: Chemical mass # 35 #p ______ #n ______ #e ______ Electronic Electronic Configuration: Configuration: Atomic Number: 12 Physical Properties: Atomic Number: 8 Name: Name: Symbol: Symbol: Chemical mass # 24 Physical Properties: Properties: Lewis Dot: Physical Properties: Chemical mass # 16 #p ______ #p ______ #n ______ #n ______ #e ______ #e ______ Lewis Dot: Properties: Electronic Electronic Configuration: Configuration: Properties: Lewis Dot:
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Record into your notes Atomic Number: 11 sodium-23 ion Name: • Symbol: 23 1+ Na 11 mass # 23 #p ______ 11 #n ______ 12 #e ••• •• •• ••• More protons than electrons ______ 10 Electronic Configuration: 1s2 2s2 2p6 3s0 Atomic Number: 12 magnesium-24 ion Name: Symbol: 24 Mg 12 mass # 24 #p ______ 12 #n 12 ______ #e 10 ______ 2+ Electronic Configuration: Ionic Structure Physical Properties: Atomic Number: 17 metal cation positive ion 1+ charge Chemical Name: Properties: mass # 35 combines w/ anions Lewis Dot: [Na]1+ Physical Properties: ••• •• •• ••• More protons than electrons 1s2 2s2 2p6 3s0 metal cation positive ion 2+ charge Symbol: Chemical #p ______ #n ______ #e ______ combines w/ anions Lewis Dot: [Mg]2+ Properties: Lewis Dot: Electronic Configuration: Atomic Number: 8 Physical Properties: Name: Symbol: Chemical Properties: Physical Properties: Chemical mass # 16 #p ______ #n ______ #e ______ Electronic Configuration: Properties: Lewis Dot:
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Record into your notes Atomic Number: 11 sodium-23 ion Name: • Symbol: 23 1+ Na 11 mass # 23 #p ______ 11 #n ______ 12 #e ••• •• •• ••• More protons than electrons ______ 10 Electronic Configuration: 1s2 2s2 2p6 3s0 Atomic Number: 12 magnesium-24 ion Name: Symbol: 24 2+ 12Mg mass # 24 #p ______ 12 #n 12 ______ #e 10 ______ Electronic Configuration: ••• •• •• ••• More protons than electrons 1s2 2s2 2p6 3s2 Ionic Structure Physical Properties: metal cation positive ion 1+ charge Chemical Properties: combines w/ anions Lewis Dot: [Na] 1+ •• chloride-35 ion Name: ••• 35 1Symbol: •• • 17Cl •• •• • • •• mass # 35 •• #p ______ 17 Atomic Number: 17 #n ______ 18 #e ______ 18 Electronic Configuration: Physical Properties: metal cation positive ion 2+ charge Properties: combines w/ anions Lewis Dot: 2+ 1s2 2s2 2p6 3s2 3p6 Atomic Number: 8 Symbol: 16 8 O mass # 16 #p ______ 8 #n 8 ______ #e 10 ______ Electronic Configuration: 2- nonmetal anion negative ion 1- charge Chemical Properties: combines w/ cations Lewis Dot: •• •Cl• •• •• [ ]1Physical Properties: Name: oxygen-16 Chemical [Mg] More electrons than protons Physical Properties: ion ••• •• •• ••• More electrons than protons 1s2 2s2 2p6 3s0 nonmetal anion negative ion 2- charge Chemical Properties: combines w/ cations Lewis Dot: •• •O• •• •• [ ]2-
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Supplemental packet page 49 Atomic Number: 11 Name: • Symbol: 23 Na 11 mass # 23 #p ______ 11 #n ______ 12 #e Physical Properties: ••• •• •• • ••• sodium-23 soft metal, conducts eChemical Properties: reacts w/ H2O Electronic Configuration: 1s 2s 2 2 2p 6 3s 1 Atomic Number: 12 24 Mg 12 mass # 24 ______ 12 #n 12 ______ #e 12 ______ Electronic Configuration: Na• Physical Properties: Name:magnesium-24 #p •• Name: chlorine-35 •• • 35 Symbol: •• •• • • Cl 17 • •• • mass # 35 •• #p ______ Atomic Number: 17 #n Lewis Dot: ______ 11 Symbol: Atomic Structure ••• •• •• •• ••• ductile metal, conducts e- 1s 2s 2 2p 6 Configuration: Properties: burns in O2 3s 2 • Mg • 1s2 2s2 2p6 •• • • • •• • 16 O 8 mass # 16 #p ______ 8 #n ______ 8 #e 8 ______ Properties: reacts w/ Na(s) Physical Properties: oxygen-16 Symbol: Chemical • •• •Cl• 3s2 3p5 • • Atomic Number: 8 Name: yellow gas, nonconductor Lewis Dot: Electronic Chemical Lewis Dot: 2 #e 17 ______ 18 ______ 17 Physical Properties: Electronic Configuration: colorless gas, nonconductor Chemical Properties: supports combustion Lewis Dot: 1s 2s 2 2 2p 4 •• • O• ••
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