Rebuttal to Irons

[email protected]

Intelligent Design Will Survive: Kitzmiller v. Dover

Intelligent Design Will Surviv

Intelligent Design Will Survive: Kitzmiller v. Dover

Intelligent Design Will Surviv

Validation of S. Pombe sequence assembly by microarray hybridization

We describe a method to make physical maps of genomes using correlative hybridization patterns of probes to random pools of BACs. We derive thereby an estimated distance between probes, and then use this estimated distance to order probes. To test the method, we used BAC libraries from Schizzosaccharomyces pombe. We compared our data to the known sequence assembly, in order to assess accuracy. We demonstrate a small number of significant discrepancies between our method and the map derived by sequence assembly. Some of these discrepancies may arise because genome order within a population is not stable; imposing a linear order on a population may not be biologically meaningful

Go Forth and Multiply: Revisiting Religion and Fertility in the United States, 1984-2008

Many studies on the fertility differential by religion have considered both Catholics and Protestants to be equally homogenous groups. Contrary to these studies, we contend that Protestant fertility must be studied in the context of heterogeneous groups. Specifically, conservative Protestantism, with its beliefs about artificial birth control mirroring Catholic teaching, should be examined separately from other Protestant traditions. Using data from the General Social Survey we find that conservative Protestants and Catholics had about the same level of fertility, while mainline Protestants have a fertility rate that is significantly lower than that of Catholics. We also examine the changes in these differences over time

Object-oriented modeling of the communications networks of the MAGTF

The Marine Air-Ground Task Force (MAGTF) is supported by a communications system comprised of heterogenous links and widely shared network resources. In this work, we describe our approach to modeling the MAGTF communications network. This model employs a new concept of workload modeling which we have developed. We provide a mathematical development of our measures of effectiveness and show how our model will be used to seek improvement in MAGTF communications performanceWarfighting Center—Studies and Analysis MCCDC, Quantico, VAhttp://archive.org/details/objectorientedmo00bailM9545091WRR1AK2NAApproved for public release; distribution is unlimited

Tumor-immune metaphenotypes orchestrate an evolutionary bottleneck that promotes metabolic transformation

Introduction: Metabolism plays a complex role in the evolution of cancerous tumors, including inducing a multifaceted effect on the immune system to aid immune escape. Immune escape is, by definition, a collective phenomenon by requiring the presence of two cell types interacting in close proximity: tumor and immune. The microenvironmental context of these interactions is influenced by the dynamic process of blood vessel growth and remodelling, creating heterogeneous patches of well-vascularized tumor or acidic niches. Methods: Here, we present a multiscale mathematical model that captures the phenotypic, vascular, microenvironmental, and spatial heterogeneity which shapes acid-mediated invasion and immune escape over a biologically-realistic time scale. The model explores several immune escape mechanisms such as i) acid inactivation of immune cells, ii) competition for glucose, and iii) inhibitory immune checkpoint receptor expression (PD-L1). We also explore the efficacy of anti-PD-L1 and sodium bicarbonate buffer agents for treatment. To aid in understanding immune escape as a collective cellular phenomenon, we define immune escape in the context of six collective phenotypes (termed “meta-phenotypes”): Self-Acidify, Mooch Acid, PD-L1 Attack, Mooch PD-L1, Proliferate Fast, and Starve Glucose. Results: Fomenting a stronger immune response leads to initial benefits (additional cytotoxicity), but this advantage is offset by increased cell turnover that leads to accelerated evolution and the emergence of aggressive phenotypes. This creates a bimodal therapy landscape: either the immune system should be maximized for complete cure, or kept in check to avoid rapid evolution of invasive cells. These constraints are dependent on heterogeneity in vascular context, microenvironmental acidification, and the strength of immune response. Discussion: This model helps to untangle the key constraints on evolutionary costs and benefits of three key phenotypic axes on tumor invasion and treatment: acid-resistance, glycolysis, and PD-L1 expression. The benefits of concomitant anti-PD-L1 and buffer treatments is a promising treatment strategy to limit the adverse effects of immune escape

Exile Vol. LII No. 2

Title Page 2 Epigraph by Ezra Pound 3 Table of Contents 4 Editor\u27s Note 6 Contributors\u27 Notes 45 Editorial Board 46 ART Wallace Monument by Casey Flax 9 Blind Man by Abbe Wright 18 Untitled by Adrienne Hunter 20 Sentinel by Eric Ahnmark 28 Untitled by Abbe Wright 32 Under Charles by Medha Jaishankar 43 FICTION The Great Lego Wall by Dawson West 12-16 Gods by Nick Wright 21-24 Some Days Hit like Mack Trucks by Sarah Broderick 33-42 POETRY The Liberation from Jack Kerouac by Katie Berta 7-8 Fragmented Grief by Jen Humbert 10 Rauschenberg Painting Iris Clért by Jeremy Heartberg 11 Outgrowing by Sarah Rogers 17 Garden of Eden by Jen Humbert 19 She whispered to the moon by Dave Murrin-von Ebers 25 A Joke by Jeremy Heartberg 26 Retrospective by Casey Flax 27 Ketchup Fetish by Dawson West 29 Winter Raspberries by Jennifer Luebbers 30-31 Knot by Sarah Rogers 44 Editor\u27s Note The process by which Exile comes into being each semester is by no means a quick or simple one, and was further confounded in this instance by having me at its core. I do not necessarily mean to discredit myself ad nauseam as some editors would, but they will all tell you that transitional periods are the toughest on a publication. The collaborative effort of Jeremy Heartberg and Jennifer Humbert over the past several semesters, not to mention the competent and eager editorial staff they have recruited, has seen to it that the transition made in these past few months has not been bulky or awkward, but rather quite seamless. It is appropriate then, that the two of them are both prominently featured in the edition of Exile on which you presently fix your gaze. In recent years, you have benefited from Jeremy\u27s and Jen\u27s dedication to Exile as a whole; this year, enjoy their dedication to the flexibility and nuance of language, to the manipulation of form, to poetry. Jeremy, Jen, Sarah, and Emily, thank you, you will be missed. / April 2006 -6 Front Cover Art by Chris Davis: Reflections / Back Cover Art by Eric Ahnmark: Trucks Only -46 All submissions are reviewed on an anonymous basis, and all editorial decisions are shared equally among the members of the editorial board. -4

Pancreas-derived mesenchymal stromal cells share immune response-modulating and angiogenic potential with bone marrow mesenchymal stromal cells and can be grown to therapeutic scale under GMP conditions

Background aims: Mesenchymal stromal cells (MSCs) isolated from various tissues are under investigation as cellular therapeutics in a wide range of diseases. It is appreciated that the basic biological functions of MSCs vary depending on tissue source. However, in-depth comparative analyses between MSCs isolated from different tissue sources under Good Manufacturing Practice (GMP) conditions are lacking. Human clinical-grade low-purity islet (LPI) fractions are generated as a byproduct of islet isolation for transplantation. MSC isolates were derived from LPI fractions with the aim of performing a systematic, standardized comparative analysis of these cells with clinically relevant bone marrow-derived MSCs (BM MSCs). Methods: MSC isolates were derived from LPI fractions and expanded in platelet lysate-supplemented medium or in commercially available xenogeneic-free medium. Doubling rate, phenotype, differentiation potential, gene expression, protein production and immunomodulatory capacity of LPIs were compared with those of BM MSCs. Results: MSCs can be readily derived in vitro from non-transplanted fractions resulting from islet cell processing (i.e., LPI MSCs). LPI MSCs grow stably in serum-free or platelet lysate-supplemented media and demonstrate in vitro self-renewal, as measured by colony-forming unit assay. LPI MSCs express patterns of chemokines and pro-regenerative factors similar to those of BM MSCs and, importantly, are equally able to attract immune cells in vitro and in vivo and suppress T-cell proliferation in vitro. Additionally, LPI MSCs can be expanded to therapeutically relevant doses at low passage under GMP conditions. Conclusions: LPI MSCs represent an alternative source of GMP MSCs with functions comparable to BM MSCs