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Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
1 Federal Register Notice DEPARTMENT of JUSTICE
This document is scheduled to be published in the Federal Register on 015/ 14/2014 and available online at http://federalregister.gov/a/2014-11056, and on FDsys.gov Federal Register Notice DEPARTMENT OF JUSTICE Antitrust Division United States v. Ebay Inc. Proposed Final Judgment and Competitive Impact Statement Notice is hereby given pursuant to the Antitrust Procedures and Penalties Act, 15 U.S.C. 16(b)-(h), that a proposed Final Judgment, Stipulation and Competitive Impact Statement have been filed with the United States District Court for the Northern District of California in United States of America v. eBay Inc., Civil Action No. 12-5869. On November 16, 2012, the United States filed a Complaint alleging that eBay Inc. entered into an agreement with Intuit, Inc., that restrained the recruiting and hiring of high technology workers, in violation of Section 1 of the Sherman Act, 15 U.S.C. 1. The proposed Final Judgment prevents eBay from maintaining or entering into similar agreements. Copies of the Complaint, as amended, Stipulation, proposed Final Judgment and Competitive Impact Statement are available for inspection at the Department of Justice, Antitrust Division, Antitrust Documents Group, 450 Fifth Street, NW, Suite 1010, Washington, DC 20530 (telephone: 202-514-2481), on the Department of Justice’s Web site at http://www.usdoj.gov/atr, and at the Office of the Clerk of the United States District Court for the Northern District of California. Copies of these materials may be obtained from the Antitrust Division upon request and payment of the copying fee set by Department of Justice regulations. -
ACOX3 Antibody
Product Datasheet ACOX3 antibody Catalog No: #22136 Orders: [email protected] Description Support: [email protected] Product Name ACOX3 antibody Host Species Rabbit Clonality Polyclonal Purification Purified by antigen-affinity chromatography. Applications WB IHC Species Reactivity Hu Immunogen Type Recombinant protein Immunogen Description Recombinant protein fragment contain a sequence corresponding to a region within amino acids 408 and 613 of ACOX3 Target Name ACOX3 Accession No. Swiss-Prot:O15254Gene ID:8310 Concentration 1mg/ml Formulation Supplied in 0.1M Tris-buffered saline with 20% Glycerol (pH7.0). 0.01% Thimerosal was added as a preservative. Storage Store at -20°C for long term preservation (recommended). Store at 4°C for short term use. Application Details Predicted MW: 70kd Western blotting: 1:500-1:3000 Immunohistochemistry: 1:100-1:500 Images Sample (30 ug of whole cell lysate) A: A549 7.5% SDS PAGE Primary antibody diluted at 1: 1000 Address: 8400 Baltimore Ave., Suite 302, College Park, MD 20740, USA http://www.sabbiotech.com 1 Immunohistochemical analysis of paraffin-embedded H441 xenograft, using ACOX3 antibody at 1: 500 dilution. Background Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. -
Earth-717: Avengers Vol 1 Chapter 10: Suicide Mission “My, My, My! to Have So Many of Our Friends Together in the Same Place!
Earth-717: Avengers Vol 1 Chapter 10: Suicide Mission “My, my, my! To have so many of our friends together in the same place! I know that it is under quite distressing circumstances, but still, it's wonderful to have such a congregation!” Steve, Tasha, Thor, Bruce, Carol, Reed, Susan, Johnny, Ben and Herbie were all in one of the hangars on board the Valiant. The Rogue One had been moved from the Senatorium to the Valiant earlier that day, and Tasha had finished installing her new upgrade to the ship. Hundreds of other Nova pilots and officers were moving around the hangar, preparing for the battle ahead. Herbie bounced up and down as he looked around at the group. “To see the Fantastic Four ready to go into battle alongside such brave and noble heroes like yourselves! It is truly remarkable, is it not, Doctor Richards?” “It sure is,” said Reed. “You've got quite a team.” “Put it together at the last minute,” said Tasha. “Since somebody decided that they wanted an interstellar vacation at the worst possible time.” “Hey!” said Johnny. “Wasn't my fault! Blame these guys! I just went along for the ride!” Ben gave Johnny a light smack on the back of the head. “Nobody asked you, junior.” Johnny grumbled as he tried to fix his hair. Reed laughed before looking back Steve. “Don't suppose you'd like to tell me how I'm standing across from Captain America?” “I guess that a man of science like yourself would be interested in that sort of thing,” said Steve. -
Evolution Confers Morality
Evolution Confers Morality Matt Young Department of Physics Colorado School of Mines Golden, Colorado 80401 www.mines.edu/~mmyoung [Paper presented Darwin Week, February 9, 2011, in Old Main at the University of Colorado. A shorter paper was presented to third Colorado Skepticamp, May 9, 2009, at the Tivoli Student Union in Denver. Based in part on Chapter 17 of Young and Strode, 2009. All figures are mine, in the public domain, or used with permission. Copyright 2011 by Matt Young.] [Paul Cézanne] IANA IANAB IANAL Ф from modification Descends with [Rembrandt van Rijn] IANAB But Some of my best friends are biologists I am coeditor of Why Intelligent Design Fails I am coauthor of Why Evolution Works (And Creationism Fails) So I am at least a fellow traveler Define morality same way as same morality Define Mass Pornography Time Length Definition [Official portrait] Francis Collins – Human Genome Project Morality is uniquely human Debatable Altruism is uniquely human propositions Inductive leap Morality must have been conferred by God Rejects arguments based on ] H disparate ethical codes I N [ Rejects sociobiological argument that morality could be evolved trait IANAФ But Serious philosophical problems with idea that God conferred morality Suppose that God said murder was moral Would it be so? No Moral code would take precedence over God God would be a pipeline We look elsewhere for the origin of morality Collins refers to a Moral Law So is there a moral law? I will Analogous to assume Law of gravity not Laws of logic or mathematics If I am wrong, title of talk is How our sense of morality evolved Evidence that morality is somehow built in Incest taboo Brother and sister Over 21, consenting adults, and all that Agree to sleep together Just once To see what it is like Is that wrong? Take special Why? precautions to avoid pregnancy Will never tell anyone Always wrong Almost always Further evidence Sometimes Gay marriage Never wrong Adultery Stem-cell research Authoritative God Abortion Benevolent G od P.M. -
COVID-19 Vaccine Weekly Update
Ramona Whittington From: Roxana Cruz Sent: Tuesday, February 23, 2021 10:02 PM To: [email protected]; [email protected]; Myrta Garcia; Lindsay Lanagan; catherine.threatt; [email protected]; Medical Directors; Dental Directors; [email protected]; [email protected] Cc: ClinicalTeam; Cassandra Caravello; Jana Eubank; Daniel Diaz; Shelby Tracy; Nancy Gilliam; Ramona Whittington Subject: COVID-19 Vaccine Weekly Update: Week 11 (02/22/2021) Attachments: COVIDVaccineAllocation-Week11_final.pdf; americanlungassociation_vaccineeducationtoolkit.pdf; ACP_Addressing Mistrust About COVID-19 Vaccines.pdf; COVIDVaccineAllocation-Week10.pdf Dear Fellow CMOs and Vaccine Coordinators, We hope you are well and that your communities have recovered since last week’s winter storm. As I am sure you know by now, COVID vaccine distribution was put on hold last week 2/15‐ 2/19 (Week 10) due to the inclement weather. Per the weekly DSHS Call today, the following updates were provided: • 100K of 1st dose vaccine not shipped/distributed • 300K of 2nd dose vaccine not shipped/distributed • 1 million vaccine doses will be distributed this week, to include last and this week’s allotments. • 600k 1st doses will go to 563 providers in 230 counties • Mass vaccination clinics this week: Dallas, Tarrant, Harris Counties COVID‐19 Vaccine Weekly Update: Week 11 (02/22/2021) During week 11, there were 61 health center sites that received allocations that total 18,550 doses this week. Vaccine Allocations for Week 11 (02/22/2021) attached w/orange highlighted health center sites. Vaccine Allocations for Week 10 (02/15/2022) although previously sent out, we have attached this list again for your reference. -
Jessica Pierce and Marc Bekoff
Soc Just Res (2012) 25:122–139 DOI 10.1007/s11211-012-0154-y Wild Justice Redux: What We Know About Social Justice in Animals and Why It Matters Jessica Pierce • Marc Bekoff Published online: 17 May 2012 Ó Springer Science+Business Media, LLC 2012 Abstract Social justice in animals is beginning to attract interest in a broad range of academic disciplines. Justice is an important area of study because it may help explain social dynamics among individuals living in tightly-knit groups, as well as social interactions among individuals who only occasionally meet. In this paper, we provide an overview of what is currently known about social justice in animals and offer an agenda for further research. We provide working definitions of key terms, outline some central research questions, and explore some of the challenges of studying social justice in animals, as well as the promise of the work we’re pro- posing. Finally, we suggest why continued research into animal cognition and social behavior has significant ethical implications for our treatment of nonhuman animals. Keywords Social justice Á Animals Á Wild justice Á Play Á Prosocial, captive Á Fairness Á Inequity aversion Á Ethics Á Empathy Á Cooperation Á Morality Á Primates Á Canids Á Cognitive ethology In our 2009 book Wild Justice, we argued that animals have the capacity for moral behavior, and not merely the early traces of what was to evolve into morality in humans but full-fledged moral behaviors in their own right. We defined morality as J. Pierce Center for Bioethics and Humanities, University of Colorado Health Sciences, Denver, CO 80540, USA J. -
ACOX3 Human Shrna Plasmid Kit (Locus ID 8310) Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TL314988 ACOX3 Human shRNA Plasmid Kit (Locus ID 8310) Product data: Product Type: shRNA Plasmids Product Name: ACOX3 Human shRNA Plasmid Kit (Locus ID 8310) Locus ID: 8310 Vector: pGFP-C-shLenti (TR30023) Format: Lentiviral plasmids Components: ACOX3 - Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 8310). 5µg purified plasmid DNA per construct Non-effective 29-mer scrambled shRNA cassette in pGFP-C-shLenti Vector, TR30021, included for free. RefSeq: NM_001101667, NM_003501, NM_003501.1, NM_003501.2, NM_001101667.1, BC017053, NM_003501.3, NM_001101667.2 Summary: Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. [provided by RefSeq, Jul 2008] shRNA Design: These shRNA constructs were designed against multiple splice variants at this gene locus. To be certain that your variant of interest is targeted, please contact [email protected]. -
Coalition Communication: Healthcare
Updated 1/15/2021 Coalition Communication: Healthcare COVID-19 UPDATES We need your help in sharing information about the COVID-19 vaccine. KEY STATS Vaccine.coronavirus.ohio.gov is an online resource for Ohioans to learn which providers received a COVID-19 vaccine allotment and how to contact them. Data as of 1/14/2021 Tentative dates to start vaccinating these Phase 1B populations are: • Jan. 19, 2021—Ohioans 80 years of age and older. PUBLIC HEALTH • Jan. 25, 2021—Ohioans 75 years of age and older; those with severe ADVISORY SYSTEM congenital or developmental disorders. • Feb. 1, 2021—Ohioans 70 years of age and older; employees of K-12 schools that wish to remain or return to in-person or hybrid learning. • Feb. 8, 2021—Ohioans 65 years of age and older. When a new age group begins, vaccinations may not be complete for the previous age group. It will take a number of weeks to distribute all of the vaccines given the limited doses available. If you are older than 65, please connect with an Area Agencies on Aging about questions or if you need transportation assistance. For more information, visit aginig.ohio.gov or call 1-866-243-5678. More information can be found at coronavirus.ohio.gov. 21-DAY TRENDS INDUSTRY INFORMATION Case Average 7,316 ■ The Ad Council and the COVID Collaborative have released a series of Death Average 73 videos, available in a YouTube playlist, feature an introduction from Dr. Anthony Fauci and include experts leading healthcare organizations. Hospitalization 293 Average ■ BlackDoctor.org’s Making It Plain: What Black America Needs to Know ICU Admission 29 About COVID-19 and Vaccines aired on January 7 and is now available on- Average demand on YouTube. -
Club Add 2 Page Designoct07.Pub
H M. ADVS. HULK V. 1 collects #1-4, $7 H M. ADVS FF V. 7 SILVER SURFER collects #25-28, $7 H IRR. ANT-MAN V. 2 DIGEST collects #7-12,, $10 H POWERS DEF. HC V. 2 H ULT FF V. 9 SILVER SURFER collects #12-24, $30 collects #42-46, $14 H C RIMINAL V. 2 LAWLESS H ULTIMATE VISON TP collects #6-10, $15 collects #0-5, $15 H SPIDEY FAMILY UNTOLD TALES H UNCLE X-MEN EXTREMISTS collects Spidey Family $5 collects #487-491, $14 Cut (Original Graphic Novel) H AVENGERS BIZARRE ADVS H X-MEN MARAUDERS TP The latest addition to the Dark Horse horror line is this chilling OGN from writer and collects Marvel Advs. Avengers, $5 collects #200-204, $15 Mike Richardson (The Secret). 20-something Meagan Walters regains consciousness H H NEW X-MEN v5 and finds herself locked in an empty room of an old house. She's bleeding from the IRON MAN HULK back of her head, and has no memory of where the wound came from-she'd been at a collects Marvel Advs.. Hulk & Tony , $5 collects #37-43, $18 club with some friends . left angrily . was she abducted? H SPIDEY BLACK COSTUME H NEW EXCALIBUR V. 3 ETERNITY collects Back in Black $5 collects #16-24, $25 (on-going) H The End League H X-MEN 1ST CLASS TOMORROW NOVA V. 1 ANNIHILATION A thematic merging of The Lord of the Rings and Watchmen, The End League follows collects #1-8, $5 collects #1-7, $18 a cast of the last remaining supermen and women as they embark on a desperate and H SPIDEY POWER PACK H HEROES FOR HIRE V. -
Mathematics Without Borders - Winter 2020 Group 1
MATHEMATICS WITHOUT BORDERS - WINTER 2020 GROUP 1 Age № Full name of the participant Country City Award group 1 Abboskhodjaeva Mohasalkhon Uzbekistan Tashkent 1 Certificate 2 Abdel Karim Alya Maria Romania Bucharest 1 Certificate 3 Abdraimov Alan Kazakhstan Nur-Sultan 1 Certificate 4 Abdraimova Adiya Kazakhstan Nur-Sultan 1 Certificate 5 Abdujabborova Alizoda Uzbekistan Tashkent 1 Bronze 6 Abdullaev Amirbek Uzbekistan Tashkent 1 Certificate 7 Abdullaeva Dinara Uzbekistan Namangan 1 Silver 8 Abdullaeva Samiya Uzbekistan Tashkent 1 Certificate 9 Abdullah Balogun Nigeria Lagos 1 Certificate 10 Abdullayev Azam Uzbekistan Tashkent 1 Certificate 11 Abdullayev Mirolim Uzbekistan Tashkent 1 Silver 12 Abdullayev Saidumar Uzbekistan Tashkent 1 Certificate 13 Abdullayeva Diyora Uzbekistan Tashkent 1 Silver 14 Abdurahimov Abduhakim Uzbekistan Tashkent 1 Certificate 15 Abduvosidov Abbosbek Uzbekistan Namangan 1 Certificate 16 Abidov Islombek Uzbekistan Tashkent 1 Certificate 17 Abiyev Alan Kazakhstan Almaty 1 Certificate 18 Abriol, Willary A. Philippines Naga City 1 Silver 19 Abrolova Laylokhon Uzbekistan Tashkent 1 Silver 20 Abrorova Afruza Uzbekistan Tashkent 1 Certificate 21 Abulkhairova Amina Kazakhstan Atyrau 1 Certificate 22 Ada Arif Vasvi Bulgaria Isperih 1 Certificate 23 Ada Selim Selim Bulgaria Razgrad 1 Bronze 24 Adel Dzheyn Brand Bulgaria Bansko 1 Certificate 25 Adelina Dobrinova Angelova Bulgaria Varna 1 Bronze 26 Adelina Georgieva Ivanova Bulgaria Svishtov 1 Silver 27 Adelina Svetoslav Yordanova Bulgaria Kyustendil 1 Bronze 28 Adina Zaharieva -
Chapter 18: Heart Disease and Diabetes
CHAPTER 18 HEART DISEASE AND DIABETES Elizabeth Barrett-Connor, MD, Deborah Wingard, PhD, Nathan Wong, PhD, and Ron Goldberg, MD Dr. Elizabeth Barrett-Connor is Distinguished Professor, Division of Epidemiology, Department of Family Medicine and Public Health at the University of California, San Diego, La Jolla, CA. Dr. Deborah Wingard is Professor, Division of Epidemiology, Department of Family Medicine and Public Health at the University of California, San Diego, La Jolla, CA. Dr. Nathan Wong is Professor and Director of the Heart Disease Prevention Program, Division of Cardiology, University of California, Irvine, Irvine, CA. Dr. Ron Goldberg is Professor of Medicine and Biochemistry and Molecular Biology, Division of Endocrinology, Diabetes and Metabolism, Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL. SUMMARY Heart disease remains a major cause of morbidity and mortality in type 2 diabetes and is estimated to account for 10%–11% of all vascular deaths. Surveys of the U.S. population have demonstrated an age-standardized differential for heart disease in adults with mostly type 2 diabetes that varies from 1.9 to 2.5. The age-standardized prevalence is about 50% higher in men than women overall and for most categories of heart disease, except congestive heart failure. Although rates of diabetes are higher in nonwhites than in non-Hispanic whites, it should be noted that non-Hispanic whites with diabetes generally report heart disease rates about 50% higher than Hispanic subjects with diabetes, with an intermediate prevalence in non-Hispanic blacks. Despite an approximate doubling in type 2 diabetes prevalence from the 1980s to the 2010s, the prevalence of heart disease in diabetes has remained stable.