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To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes and nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms, by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25°C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91% to 95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing; after genome alignment, only 0.2% to 0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line that was prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between Mayo Clinic vs TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes.
High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.
The Journal of Surrealism and the Americas: Vol. 1 No. 1 (2007) - Table of Contents
"Introduction to the Journal" by Samantha Kavky, Claudia Mesch, and Amy H. Winter, p. i-iii.
"Anti-Surrealist Cross-Word Puzzles: Breton, Dalí and Print in Wartime America" by Julia Pine, p. 1-29.
"William Carlos Williams’ A Novelette: an American Counterproposal to French Surrealism" by Céline Mansanti, p. 30-43
"The Vernacular as Vanguard: Alfred Barr, Salvador Dalí, and the U.S. Reception of Surrealism in the 1930s" by Sandra Zalman, p. 44-67
"Ben Cobb, Anarchy and Alchemy: The Films of Alejandro Jodorowsky" by David Church, p. 68-71
"Tamayo: A Modern Icon Reinterpreted" by Marta Julia Clapp, p. 72-76
"Robert Desnos, Surrealism, and 'Poetic Politics'" by Terri J. Gordon, p. 77-80
"Dali and the Specter of Cinema" by Frédérique Camille Joseph-Lowery, p. 81-84
"Julia Kelly's Art, Ethnography and the Life of Objects: Paris, c. 1925-1935" by Susan Power, p. 85-90
"The Janus-faced Legacy of Joseph Beuys" by Tatjana Myoko von Prittwitz, p. 91-93
"A.J. Meek, Clarence John Laughlin: Prophet Without Honor" by Jeffrey Ian Ross, p. 94-98
The Journal of Surrealism and the Americas: Vol. 2 No. 1 (2008) - Table of Contents
“Surrealism and Ethnography: Introduction” by Amy H. Winter, p. i-vi.
“Totemic Landscapes and Vanishing Cultures Through the Eyes of Wolfgang Paalen and Kurt Seligmann” by Marie Mauzé, p. 1-24.
“Surrealist Visions of Pre-Columbian Mesoamerica and the Legacy of Colonialism: the Good, the (Revalued) Bad, and the Ugly” by Keith Jordan, p. 25-63.
“Surrealism and Inuit Art: The Fascination of the Far North” by Florence Duchemin-Pelletier, p. 64-94.
“Bound Objects and Blurry Boundaries: Surrealist Display and (Anti)Nationalism” by Susan Power, p. 95-113.
“Man Ray’s Lost and Found Photographs: Arts of the Americas in Context” by Wendy Grossman, p. 114-139.
“T.J. Demos, The Exiles of Marcel Duchamp” by Bradley Bailey, p. 140-144.
“The Dalí Renaissance: New Perspectives on His Life and Art after 1940 and Danser Gala: L’Art Bouffe de Salvador Dalí” by Mary Ann Caws, p. 145-146.
“Review of ‘The Art of Lee Miller’: Victoria and Albert Museum, 2007” by Peter Barberie, p. 147-151.
“Frida Kahlo in Philadelphia: Life and Death” by Samantha Kavky, p. 152-156.
“Thinking the ‘Post-Indian’: Remix: New Modernities in a Post-Indian World” by Claudia Mesch, p. 157-161.
The Journal of Surrealism and the Americas: Vol. 10 No. 1 (2019) - Table of Contents
“Introduction to the Special Issue on Max Ernst” by Samantha Kavky, p. 1-6.
“Napoleon in the Wilderness: The Transmogrification of a Picture by Max Ernst” by Martin Schieder, p. 7-23.
“Seeing Through an (American) Temperament: Max Ernst’s Microbes, 1946-1953” by Danielle M. Johnson, p. 24-45.
“Max Ernst and the Aesthetic of Commercial Tourism: Max Among Some of His Favorite Dolls” by Carolyn Butler Palmer, p, 46-68.
“Arizona Dream: Maxime Rossi Meets Max Ernst” by Julia Drost, p. 69-83.
“Glowing Like Phosphorus: Dorothea Tanning and the Sedona Western” by Catriona McAra, p. 84-105.
“Conference Review: ‘SURREALISMS: the Inaugural Conference of the International Society for the Study of Surrealism’” by Kristen Strange, p. 106-110.
“Exhibition Review of ‘A Home for Surrealism: Fantastic Painting in Midcentury Chicago’” by Jennifer R. Cohen, p. 111-114.
“Exhibition Review: ‘Native American Art at Documenta 14 and the Issue of Democracy’” by Claudia Mesch, p. 115-120.
The Journal of Surrealism and the Americas: Vol. 7 No. 1 (2013) - Table of Contents
“Introduction to the Issue and Special Section on Native American Surrealisms” by Claudia Mesch, p. i-iv.
“George Morrison’s Surrealism” by W. Jackson Rushing III, p. 1-18.
“César Moro’s Transnational Surrealism” by Michele Greet, p. 19-51.
“A Modernist Moment: Native Art and Surrealism at the University of Oklahoma” by Mark A. White, p. 52-70.
“The Opposite of Snake: Surrealism and the Art of Jimmie Durham” by Mary Modeen, p. 71-95.
“‘My World is Surreal,’ or ‘The Northwest Coast’ is Surreal” by Charlotte Townsend-Gault, p. 96-107.
“Complexity and Contradiction in Native American Surrealism” by Robert Silberman, p. 108-130.
“Review of ‘Double Solitaire: The Surreal Worlds of Kay Sage and Yves Tanguy’ & Kay Sage, ‘The Biographical Chronology and Four Surrealist One Act Plays’” by Larry List, p. 131-134.
The Journal of Surrealism and the Americas: Vol. 6 No. 1 (2012) - Table of Contents
“Notes for a Historiography of Surrealism in America, or the Reinterpretation of the Repressed” by Samantha Kavky, p. i-ix.
“What Makes a Collection Surrealist?: Twentieth-Century Cabinets of Curiosities in Paris and Houston” by Katharine Conley, p. 1-23.
“Dalí, Magritte, and Surrealism’s Legacy, New York c. 1965” by Sandra Zalman, p. 24-38.
“‘What Makes Indians Laugh’: Surrealism, Ritual, and Return in Steven Yazzie and Joseph Beuys” by Claudia Mesch, p. 39-60.
“Cracking up an Alligator: Ethnography, Juan Downey’s Videos, and Irony” by Hjorleifur Jonsson, p. 61-86.
“Review of Effie Rentzou, ‘Littérature Malgré Elle: Le Surréalisme et la Transformation du Littéraire’” by Pierre Taminiaux, p. 87-90.
“In Wonderland: the Surrealist Adventures of Women Artists in Mexico and the United States” by Susan L. Aberth, p. 91-94.