91,695 research outputs found
Michael Rodriguez interviews historian and author Keith Widder
No full textHistorian and author Keith Widder talks about his move to Michigan from Wisconsin, his career as Curator of History for the Mackinac Island State Park Commission, his research interests, his book "Michigan Agricultural College", and his current projects. Widder is interviewed by Michigan State University Librarian Michael Rodriguez for the MSU Libraries' Michigan Writers Series. Held in the MSU Main Library
Paleogenomic and ancient DNA
No full textIntroduction The DNA is a nucleic acid that contains the genetic information necessary for RNA and protein biosynthesis. DNA extracted from past samples (teeth, bones, faeces, etc.) is defined ancient DNA (aDNA) and needs, to preserve, low level of oxygen, fast decrease in water content and, above all, according to the Arrhenius equation, low temperature. From 1985 (first aDNA extracted from a mummy) with the introduction of the Polymerase Chain Reaction (PCR) several studies of paleogenomic were born, but it is essential to identify some possible errors such as fragmentations, contaminations and post-mortal mutations [1]. The applications of the paleogenomic are: evolutionary biology, population studies, studies of the pathogens and microorganism. Materials and methods We report 3 cases studied by the Division of Paleopathology of Pisa: a) Ferrante I, king of Naples (1431-1494). The natural mummy showed round white formations of the pelvis infiltrating the abdominal wall ( 1a-b). b) Maria of Aragon (1503-1568). The well-preserved artificial mummy had a small peduncolate arborescence neoformation in the right inguinal region. c) Andean female mummy (so-called ‘Fi9’) dated 10th–11th century A.D by radiocarbonium analyses. The natural young mummy presented a marked megavisceral syndrome characterized by megacolon, megaoesophagus and cardiomegaly. It was possible to perform complete autopsies and collect tissue samples utilized for histological analyses and DNA extraction. Results a) Histology performed on the round formations confirmed the diagnosis of colorectal adenocarcinoma. Amplification of aDNA highlighted a point mutation of the codon 12 in K-Ras oncogene responsible for the cancer [2] (fig. 1c). b) Macroscopic and histological aspects seemed peculiar of condyloma acuminatum, a papillomavirus-induced squamous lesion also called “venereal wart”. Molecular study revealed the presence of HPV 18, a virus with high oncogenic potential. Automated sequencing of several clones revealed 100% similarity sequences of both HPV 18 and JC9813 DNA, a putative novel HPV with low oncogenic potential [3] (fig. 2c) c) Analysis of the gut microbiome (paleofeces, descending, transverse and ascending colon) underlined the massive presence of Clostridiceae. Sequences homologous to HPVs in the mummified gut (descending colon) was particularly surprising. It was detected also the Tripanosoma cruzi; by comparing a partial sequence homologous to the large ribosomal subunit alpha of the presumptive ancient T. cruzi with modern strains, we suggest that this pathogen may have a more remote origin than previously expected. We also found sequences associated with putative beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters [4] (fig. 3c). Conclusion a) The alimentary “environment” of the Neapolitan court of the XV century, with its abundance of natural alimentary alkylating agents (red smoked meat), well explains the acquired mutation of K-Ras. b) This represented the first molecular diagnosis of HPV in mummies. HPV is a very old virus that evolved together with man. c) Streptococcus, Staphylococcus, Bacillus and Pseudomonas sequences were identified in the mummified gut, opening the opportunity to investigate possible mechanisms by which these bacteria are preserved. The detection of sequences homologous to those of pathogens such as T. cruzi and HPV indicate their presence in the Americas prior to European colonization. The presence of antibiotic-resistance genes in an 11th century pre-Columbian Andean mummy is intriguing as antibiotics were introduced recently. The presence of beta-lactam antibiotic resistance is certainly not unexpected in any culture, as would be in the case of resistance to any natural rather than a semi- or completely synthetic antibiotic as a result of exposure to natural antibiotic-producing microbiota originating from the environment (e.g. soil); however, vancomycin, particularly, was discovered more than 50 years ago, and vancomycin-resistance genes have been mainly implicated with the increased use of this antibiotic. The presence of antibiotic-resistance genes in the ancient human gut microbiome clearly indicates that these genes pre-date therapeutical use of these compounds and that they are not necessarily associated to a selective pressure of antibiotics use. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses. References Willerslev E, Cooper A. Review paper. Ancient Dna. Proceedings of the Royal Society of London B: Biological Sciences. 2005; 272(1558):3– 16. Marchetti A, Pellegrini S, Bevilacqua G, Fornaciari G. K-RAS mutation in the tumour of Ferrante I of Aragon, King of Naples. The Lancet; 1996, May 4;347(9010):1272. Fornaciari G, Zavaglia K, Ciranni R. Human papillomavirus in a 16th century mummy. The Lancet; 2003, Oct 3, vol 362. Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Gut Microbiome of an 11th Century A.D. PreColumbian Andean Mummy. PLoS One, 2015 Sep 30;10(9)
Agustin Martin G. Rodriguez, Governing the Other: Exploring the Discourse of Democracy
No full textAgustin Martin G. Rodriguez, Governing the Other: Exploring the Discourse of Democrac
Smoothing and local refinement techniques for improving tetrahedral mesh quality
No full textThe improvement in the mesh quality without changing its connectivity is bounded. This bound is associated with the topology of the mesh and with the constraints imposed by the boundary of the domain. To solve this problem, we propose in this work to combine the tetrahedral mesh optimisation technique introduced in [Montenegro R, Montero G, Escobar JM, Rodriguez E, Gonzalez-Yuste JM. Tetrahedral mesh generation for environmental problems over complex terrains. Lect Notes Comput Sci 2002;2329:335-44; Escobar JM, Rodriguez E, Montenegro R, Montero G, Gonzalez-Yuste JM. Simultaneous untangling and smoothing of tetrahedral meshes. Comput Methods Appl Mech Eng 2003; 192:2775-87] with the local mesh refinement algorithm presented in [Gonzalez-Yuste JM, Montenegro R, Escobar JM, Montero G, Rodriguez E. An object oriented method for tetrahedral mesh refinement. In: Proceedings of the 3rd international conference on engineering computational technology, Praga 2002; 1-18]. The main idea consists in increasing the node number, and thus, the degrees of freedom, in the neighbourhood of the regions where the elements have poor quality. Then, we refine all the elements whose quality are below to a certain threshold. Once it is done, we initiate another stage of optimisation until the quality of the mesh reaches a limit.243024230,632Q2SCI
Numerical behaviour of the Keplerian Integrals methods for initial orbit determination
No full textWe investigate the behaviour of two recent methods for the computation of preliminary orbits. These methods are based on the conservation laws of Kepler’s problem, and enable the linkage of very short arcs of optical observations even when they are separated in time by a few years. Our analysis is performed using both synthetic and real data of 822 main belt asteroids. The differences between computed and true orbital elements have been analysed for the true linkages, as well as the occurrence of alternative solutions. Some metrics have been introduced to quantify the results, with the aim of discarding as many of the false linkages as possible and keeping the vast majority of true ones. These numerical experiments provide thresholds for the metrics which take advantage of the knowledge of the ground truth: the values of these thresholds can be used in normal operation mode, when we do not know the correct values of the orbital elements and whether the linkages are true or false
Histological and paleogenetic analyses of a pre-Columbian mummy: Gut microbiome and antibiotic-resistence genes
No full textThe seriation problem in the presence of a double Fiedler value
No full textSeriation is a problem consisting of seeking the best enumeration order of a set of units whose interrelationship is described by a bipartite graph, that is, a graph whose nodes are partitioned in two sets and arcs only connect nodes in different groups. An algorithm for spectral seriation based on the use of the Fiedler vector of the Laplacian matrix associated to the problem was developed by Atkins et al., under the assumption that the Fiedler value is simple. In this paper, we analyze the case in which the Fiedler value of the Laplacian is not simple, discuss its effect on the set of the admissible solutions, and study possible approaches to actually perform the computation. Examples and numerical experiments illustrate the effectiveness of the proposed methods.sponsorship: Anna Concas, Caterina Fenu, and Giuseppe Rodriguez were partially supported by Regione Autonoma della Sardegna research project "Algorithms and Models for Imaging Science (AMIS)"(RASSR57257, intervento finanziato con risorse FSC 2014-2020 - Patto per lo Sviluppo della RegioneSardegna) and by the INdAM-GNCS research project "Tecniche numeriche per l'analisi delle reti com-plesse e lo studio dei problemi inversi." Caterina Fenu also gratefully acknowledges Regione Autonomadella Sardegna for the financial support provided under the Operational Programme P.O.R. Sardegna F.S.E.(European Social Fund 2014-2020 - Axis III Education and Formation, Objective 10.5, Line of Activity10.5.12). The research of Raf Vandebril was partially supported by the Research Council KU Leuven,project C16/21/002 (Manifactor: Factor Analysis for Maps into Manifolds). (Regione Autonoma della Sardegna research project "Algorithms and Models for Imaging Science (AMIS)", INdAM-GNCS research project "Tecniche numeriche per l'analisi delle reti com-plesse e lo studio dei problemi inversi."|RASSR57257, Regione Autonomadella Sardegna, Research Council KU Leuven, C16/21/002)status: Published onlin
Michigan State University Music Librarian Mary Black Junttonen talks about classical conductor and pianist R. Nathaniel Dett
No full textMichigan State University Music Librarian Mary Black Junttonen talks about R. Nathaniel Dett, Michigan resident and world renowned classical conductor and pianist. Junttonen relates how Dett, of African-Canadian and African-American decent, attended Oberlin College in Ohio, toured the world teaching and composing and eventually settled in Battle Creek, Michigan. Junttonen plays selections of Dett's compositions and explains his influence on American music. She also describes Dett materials held in the MSU Archives and other collections. She answers questions from the audience. Junttonen is introduced by MSU librarian Michael Rodriguez. Part of the Michigan State University Libraries' Colloquia series. Held at the Michigan State University Main Library
Phase transitions in tumor growth VI: Epithelial–Mesenchymal transition
No full textHerewith we discuss a network model of the epithelial–mesenchymal transition (EMT) based on our previous proposed framework. The EMT appears as a “first order” phase transition process, analogous to the transitions observed in the chemical–physical field. Chiefly, EMT should be considered a transition characterized by a supercritical Andronov–Hopf bifurcation, with the emergence of limit cycle and, consequently, a cascade of saddle-foci Shilnikov's bifurcations. We eventually show that the entropy production rate is an EMT-dependent function and, as such, its formalism reminds the van der Waals equation.Fil: Guerra, A.. Universidad de La Habana; CubaFil: Rodriguez, D. J.. Universidad de La Habana; CubaFil: Montero, S.. Medical Sciences University Of Havana; CubaFil: Betancourt Mar, J. A.. Universidad de La Habana; CubaFil: Martín Pardo, Reinaldo Román. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Investigaciones en Tecnología Química. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Instituto de Investigaciones en Tecnología Química; Argentina. Mexican Institute Of Complex Systems. Tamaulipas; MéxicoFil: Silva Lamar, Eduardo. Universidad de La Habana; CubaFil: Bizzarri, María Julia. Universidad de La Habana; CubaFil: Cocho, G.. Universidad Nacional Autónoma de México; MéxicoFil: Mansilla, R.. Universidad Nacional Autónoma de México; MéxicoFil: Nieto Villar, José Manuel. Universidad de La Habana; Cub
The dialogue between the author and the hero in the “Notes” of G. R. Derzhavin
No full textВ центре внимания автора статьи «Записки» Г. Р. Державина, представляющие по своей сути его автобиографию. Труд этот был создан на закате жизни, он включает все важнейшие события жизни Г. Р. Державина, поэта и государственного деятеля. Рассказ ведется от третьего лица, что придает особую атмосферу повествованию, выстраивается своеобразный диалог между автором и героем, все это и является предметом исследования автора статьи.The focus of the author of the article “Notes” G. R. Derzhavin, representing in essence his autobiography. This work was created at the end of his life; it includes all the most important events in the life of G. R. Derzhavin, poet and statesman. The story is told in a third person, which gives a special atmosphere to the story, a certain dialogue emerges between the author and the hero, all this is the subject of the author's research
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