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Ancient Metaproteomics: a Novel Approach for Understanding Disease And
Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ............................................................................................................................... -
Old Japan Redux 3
Old Japan Redux 3 Edited by X. Jie YANG February 2017 The cover painting is a section from 弱竹物語, National Diet Library. Old Japan Redux 3 Edited by X. Jie YANG, February 2017 Content Poem and Stories The Origins of Japan ……………………………………………… April Grace Petrascu 2 Journal of an Unnamed Samurai ………………………………… Myles Kristalovich 5 Holdout at Yoshino ……………………………………………………… Zachary Adrian 8 Memoirs of Ieyasu ……………………………………………………………… Selena Yu 12 Sword Tales ………………………………………………………………… Adam Cohen 15 Comics Creation of Japan …………………………………………………………… Karla Montilla 19 Yoshitsune & Benkei ………………………………………………………… Alicia Phan 34 The Story of Ashikaga Couple, others …………………… Qianhua Chen, Rui Yan 44 This is a collection of poem, stories and manga comics from the final reports submitted to Japanese Civilization, fall 2016. Please enjoy the young creativity and imagination! P a g e | 2 The Origins of Japan The Mythical History April Grace Petrascu At the beginning Izanagi and Izanami descended The universe was chaos Upon these islands The heavens and earth And began to wander them Just existed side by side Separately, the first time Like a yolk inside an egg When they met again, When heaven rose up Izanami called to him: The kami began to form “How lovely to see Four pairs of beings A man such as yourself here!” After two of genesis The first-time speech was ever used. Creating the shape of earth The male god, upset Izanagi, male That the first use of the tongue Izanami, the female Was used carelessly, Kami divided He once again circled the land By their gender, the only In an attempt to cool down Kami pair to be split so Once they met again, Both of these two gods Izanagi called to her: Emerged from heaven wanting “How lovely to see To build their own thing A woman like yourself here!” Upon the surface of earth The first time their love was matched. -
Military Retirement Fund Audited Financial Report
Fiscal Year 2020 Military Retirement Fund Audited Financial Report November 9, 2020 Table of Contents Management’s Discussion and Analysis ..............................................................................................................1 REPORTING ENTITY ....................................................................................................................................... 1 THE FUND ......................................................................................................................................................... 2 General Benefit Information ........................................................................................................................... 2 Non-Disability Retirement from Active Service ............................................................................................ 3 Disability Retirement ...................................................................................................................................... 5 Reserve Retirement ......................................................................................................................................... 6 Survivor Benefits ............................................................................................................................................ 7 Temporary Early Retirement Authority (TERA) ............................................................................................ 9 Cost-of-Living Increase ................................................................................................................................. -
The Importance of Land Warfare: This Kind of War Redux
No. 117 JANUARY 2018 The Importance of Land Warfare: This Kind of War Redux David E. Johnson The Importance of Land Warfare: This Kind of War Redux by David E. Johnson The Institute of Land Warfare ASSOCIATION OF THE UNITED STATES ARMY AN INSTITUTE OF LAND WARFARE PAPER The purpose of the Institute of Land Warfare is to extend the educational work of AUSA by sponsoring scholarly publications, to include books, monographs and essays on key defense issues, as well as workshops and symposia. A work selected for publication as a Land Warfare Paper represents research by the author which, in the opinion of the Institute’s editorial board, will contribute to a better understanding of a particular defense or national security issue. Publication as an Institute of Land Warfare Paper does not indicate that the Association of the United States Army agrees with everything in the paper but does suggest that the Association believes the paper will stimulate the thinking of AUSA members and others concerned about important defense issues. LAND WARFARE PAPER No. 117, January 2018 The Importance of Land Warfare: This Kind of War Redux by David E. Johnson David Johnson is a principal researcher at the RAND Corporation. His work focuses on strategy, military doctrine, history, innovation, civil-military relations and professional military education. From June 2012 to July 2014 he established and led the Chief of Staff of the Army Strategic Studies Group for General Raymond Odierno. He is an adjunct professor at Georgetown University and an adjunct scholar at the Modern War Institute at West Point. -
(CCAC) Guide to the Care and Use of Experimental Animals Volume
Canadian Council on Animal Care Conseil canadien de protection des animaux Guide to the Care and Use of Experimental Animals Volume 1, 2nd Edition Sections of this document that have been revised are replaced by links to the relevant documents. The remaining sections are undergoing revision; however, they will continue to be used for CCAC assessments until revised guidelines are published. Editors Dr E.D. Olfert Dr B.M. Cross Mrs A.A. McWilliam Director Asssistant Director Information Officer Animal Resources Centre Animal Resources Centre Canadian Council on Animal Care University of Saskatchewan University of Saskatchewan 1000-151 Slater Street Saskatoon, Saskatchewan Saskatoon, Saskatchewan Ottawa, Ontario K1P 5H3 S7N 0W0 S7N 0W0 In keeping with the CCAC policy of revising statements and guidelines as needed, users of this Guide are encouraged to forward any comments to the Secretariat. Citing certain devices or manufacturers is not to be perceived as the endorsement of the Canadian Council on Animal Care (CCAC) of one particular product over another. Publication Date: 1993 Revision Date: April 2020 © Canadian Council on Animal Care, 1993 ISBN: 0-919087-18-3 Canadian Council on Animal Care 190 O’Connor St., Suite 800 Ottawa, Ontario, K2P 2R3 http://www.ccac.ca Table of Contents TABLE OF CONTENTS DEDICATION ...................................................................................................................1 PREFACE.........................................................................................................................2 -
Decelerated Genome Evolution in Modern Vertebrates Revealed by Analysis of Multiple Lancelet Genomes
ARTICLE Received 20 May 2014 | Accepted 18 Nov 2014 | Published 19 Dec 2014 DOI: 10.1038/ncomms6896 OPEN Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes Shengfeng Huang1, Zelin Chen1, Xinyu Yan1, Ting Yu1, Guangrui Huang1, Qingyu Yan1, Pierre Antoine Pontarotti2, Hongchen Zhao1, Jie Li1, Ping Yang1, Ruihua Wang1, Rui Li1, Xin Tao1, Ting Deng1, Yiquan Wang3,4, Guang Li3,4, Qiujin Zhang5, Sisi Zhou1, Leiming You1, Shaochun Yuan1, Yonggui Fu1, Fenfang Wu1, Meiling Dong1, Shangwu Chen1 & Anlong Xu1,6 Vertebrates diverged from other chordates B500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. 1 State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. 2 Evolution Biologique et Mode´lisation UMR 7353 Aix Marseille Universite´/CNRS, 3 Place Victor Hugo, 13331 Marseille, France. -
CHALLENGING ETHNIC PROFILING in EUROPE a Guide for Campaigners and Organizers
CHALLENGING ETHNIC PROFILING IN EUROPE A Guide for Campaigners and Organizers — 1 ACKNOWLEDGMENTS This guide was written by Zsolt Bobis, Rebekah Delsol, Maryam H’madoun, Lanna Hollo, A tremendous appreciation is also expressed for the countless and often invisible yet critical Susheela Math, and Rachel Neild of the Fair and Effective Policing team at the Open Society efforts and contributions of other OSF colleagues and the many local actors involved in Justice Initiative (OSJI). Open Society Foundations Communications Officer Brooke Havlik litigation, mobilizing and organizing, and advocacy and campaigning against ethnic profiling made significant contributions, and further assistance was provided by OSF Aryeh Neier in different EU countries. The work described here would not have been possible without Fellow Michèle Eken. them, and reflects the collective efforts of all. Examples and case studies were included from key organizations tackling ethnic profiling and The report was reviewed and edited by David Berry, Erika Dailey, James A. Goldston, and police abuse in Europe and the US, including StopWatch, Controle Alt Delete, Amnesty Robert O. Varenik. International Netherlands, the French platform En finir avec les contrôles au faciès, Eclore, Maison Communautaire pour un Développement Solidaire (MCDS, Paris 12), WeSignIt, Plataforma por la Gestión Policial de la Diversidad, Rights International Spain, SOS Racisme Catalunya, Hungarian Helsinki Committee, Hungarian Civil Liberties Union (HCLU), the Belgian platform Stop Ethnic Profiling, -
Proteomic Strategies for Cultural Heritage: from Bones to Paintings☆
Microchemical Journal 126 (2016) 341–348 Contents lists available at ScienceDirect Microchemical Journal journal homepage: www.elsevier.com/locate/microc Proteomic strategies for cultural heritage: From bones to paintings☆ Roberto Vinciguerra a, Addolorata De Chiaro a, Piero Pucci a, Gennaro Marino b, Leila Birolo a,⁎ a Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S.Angelo, Via Cinthia, Napoli, Italy b Università degli Studi ‘Suor Orsola Benincasa’, 80132 Napoli, Italy article info abstract Article history: In recent years, proteomics procedures have become increasingly popular for the characterization of proteina- Received 30 July 2015 ceous materials in ancient samples of several cultural heritage objects. The knowledge of the materials used in Received in revised form 18 December 2015 a work of art is crucial, not only to give an insight in the historical context of objects and artists, but also to analyse Accepted 18 December 2015 degradation processes taking place in aged objects and to develop appropriate conservation and/or restoration Available online 29 December 2015 treatments. However, protocols routinely applied for typical modern samples still need to be fully adapted to Keywords: take into account the low amount of proteinaceous material, the heterogeneity and the unusual physical state Proteomics of the samples, as well as the high levels of damage found in ancient samples. This paper deals with some exam- Ancient proteins ples of the adaptation of classical proteomic strategies in the analysis of ancient samples to meet the different LC-MS/MS aims in the cultural heritage field. © 2015 Elsevier B.V. All rights reserved. -
Analysis of 5000 Year-Old Human Teeth Using Optimized Large-Scale And
Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet-Schiltz, et al. To cite this version: Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, et al.. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. Journal of Proteomics, Elsevier, 2020, 211, pp.103548. 10.1016/j.jprot.2019.103548. hal-02322441 HAL Id: hal-02322441 https://hal.archives-ouvertes.fr/hal-02322441 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal Pre-proof Analysis of 5000year-old human teeth using optimized large- scale and targeted proteomics approaches for detection of sex- specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet- Schiltz, Catherine Mollereau PII: S1874-3919(19)30320-3 DOI: https://doi.org/10.1016/j.jprot.2019.103548 Reference: JPROT 103548 To appear in: Journal of Proteomics Received date: 24 January 2019 Revised date: 30 August 2019 Accepted date: 7 October 2019 Please cite this article as: C. -
The President and Immigration Law Redux Abstract
C.104.COX-RODRIGUEZ.225.DOCX (DO NOT DELETE) 10/23/15 3:47 PM Adam b. cox & Cristina M. Rodríguez The President and Immigration Law Redux abstract. In November 2014, President Obama announced his intention to dramatically reshape immigration law through administrative channels. Together with relief policies announced in 2012, his initiatives would shield nearly half the population of unauthorized immigrants from removal and enable them to work in the United States. These events have drawn renewed attention to the President’s power to shape immigration law. They also have reignited a longstanding controversy about whether constitutional limits exist on a central source of executive authority: the power to enforce the law. In using the Obama relief policies to explore these dynamics, we make two central claims. First, it is futile to try to constrain the enforcement power by tying it to a search for congressional enforcement priorities. Congress has no discernible priorities when it comes to a very wide swath of enforcement activity—a reality especially true for immigration law today. The immigration code has evolved over time into a highly reticulated statute through the work of numerous Congresses and political coalitions. The modern structure of immigration law also effectively delegates vast screening authority to the President. Interlocking historical, political, and legislative developments have opened a tremendous gap between the law on the books and the law on the ground. Under these conditions, there can be no meaningful search for congressionally preferred screening criteria. Far from reflecting a faithful-agent framework, then, immigration enforcement more closely resembles a two-principals model of policymaking—one in which the Executive can and should help construct the domain of regulation through its independent judgments about how and when to enforce the law. -
1 Title: Yellow Peril Redux: How the COVID-19
Title: Yellow Peril Redux: How the COVID-19 Pandemic is Fostering Racial Discrimination Toward Asian Americans Name: Nobuko Adachi Affiliation: Illinois State University In the Mid-March, April, and May 2020, I was in Ocala Florida, Franklin, Tennessee, and Normal Illinois, and noticed several local Chinese restaurants had closed down soon after some states enacted a stay-at home order. It turned out that not several, but numerous, Chinese restaurants, including many of which being mainly take-out even in a normal period, were closing completely, putting up signs like “Due to the coronavirus outbreak we are temporally closed. We will open again when we can.” On the other hand, other restaurants, such as Mexican and Italian establishments were providing food for their customers by adopting, at first, take-out and, later, new ad hoc ways (like curbside service). I wondered at that time why Chinese restaurants were completely closed instead of staying opening for business with take-out or home delivery, which had been their specialty prior to the epidemic. Was it only in the Midwest, or other places? Was it only Chinese restaurants, other Asian restaurants as well? What about restaurants of other ethnic groups whose ancestors’ homelands were severely suffering with Covid-19? In April, 2020, a team of several people and I started calling various Asian restaurants— such as Indian, Chinese, Korean, and Japanese—and Italian and Mexican restaurants all over the United States to find out who was open and who was closed. It looked like no matter what the state or size of town—for example, small towns like Springfield, South Carolina; Hamilton, Montana; and Brunswick, Maine; or large cities like New York, Chicago, and Los Angles— small family-run restaurants were more frequently closed than those run by big chain restaurants. -
SYSTEMS BIOLOGY Ancient Protein Complexes Revealed
RESEARCH HIGHLIGHTS SYSTEMS BIOLOGY Ancient protein complexes revealed A systematic analysis of protein-complex history, they applied the approach to eight some interesting conclusions. For example, composition across a billion years of evo- species—mouse, frog, fly, worm, sea urchin, despite the fact that the majority of human lution reveals a spectrum of conservation. sea anemone, amoeba and yeast—spanning proteins arose in animals, they found that by Comparative analyses of protein-protein a billion years of evolution. and large, most stable human protein com- interaction networks from Escherichia coli to With this massive set of experiments, the plexes were likely inherited from a unicellular humans have shown that such networks are researchers identified and quantified 13,386 ancestor. Membership in such ancient com- conserved and relatively slow-evolving. Yet protein orthologues. They developed a plexes was either conserved or mixed with open questions remain about whether physi- machine learning–classification method to animal-specific components, and these com- cal interactions are preserved between evolu- pull out interactions that were conserved plexes tended to be abundant, ubiquitously tionarily distinct species, what these protein between human proteins and their worm, expressed and functionally associated with complexes are and what they do. fly, mouse and sea urchin orthologues (the core cellular processes. The relatively rare These are some of the questions that data from the other four species were used complexes consisting solely of proteins that Andrew Emili of the University of Toronto, to benchmark the approach). Their final net- arose in animals, in contrast, tended to have Edward Marcotte of the University of Texas at work contained 16,655 human co-complex functions strongly linked to multicellularity.