Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications

As program behavior becomes complex, it’s increasingly important to analyze their behavior statistically. The article describes two separate but synergistic tools for statistically analyzing large Lisp programs. The first tool, called CLIP (Common Lisp Instrumentation Package), allows the researcher to define and run experiments, including experimental conditions (parameter values of the planner or simulator) and data to be collected. The data are written out to data files that can be analyzed by statistics software. The second tool, called CLASP (Common Lisp Analytical Statistics Package), allows the researcher to analyze data from experiments by using graphics, statistical tests, and various kinds of data manipulation. CLASP has a graphical user interface (using CLIM, the Common Lisp Interface Manager) and also allows data to be directly processed by Lisp functions. Finally, the paper describes a number of other data-analysis modules that have been added to work with CLIP and CLASP.

Fecal hormone analysis has become a powerful noninvasive tool for the study of animal endocrine status and stress physiology (Graham and Brown 1997; Wasser et al. 1997a; Whitten et al. 1998; Goymann et al. 1999; Mostl et al. 1999; Foley et al. 2001; Creel et al. 2002; Lynch et al. 2002; Morrow et al. 2002). Variation in field and storage conditions makes it essential to know whether fecal steroid concentrations change with the method and duration of sample storage. Lyophilization (freeze-drying) with subsequent storage at or below 20 C is generally regarded as the most reliable method of long-term fecal hormone preservation (e.g., Wasser et al. 1988; Terio et al. 2002). However, lyophilizers are not widely available, and therefore investigators have turned to a variety of other fecal storage methods, including freezing at 20 C, preservation in ethanol, and/or drying the feces with silica, ovens, solar radiation, fires, or other drying methods (Wasser et al. 1988; Whitten et al. 1998; Foley et al. 2001; Tecot 2001). Yet, some of these preservation methods may result in significant changes in immunoreactive hormone concentrations, varying with the preservation method, species, and hormone. In this article, we report effects of several commonly used fecal preservation methods on immunoreactive glucocorticoid concentrations in feces of two species, African elephant (Loxodonta africana) and grizzly bear (Ursus arctos horribilis), over a 2-yr period. Five different preservation methods were chosen for comparison: no preservative, oven-drying at 45 C, silicadrying, 90% ethanol, and lyophilization, each with subsequent storage either at room temperature or in a 20 C freezer. Con-

Recently Published Dissertations on Community and Junior Colleges

Understanding and utilizing the ability of stem cells to expand and differentiate into tissues and organs is a major goal of biomedical science. Ascidians are basal chordates (Tunicata) which offer unique opportunities to investigate the biology of stem cells. These marine organisms begin their life as a larva with a typical chordate body plan, including a notochord, dorsal hollow nerve tube and a striated musculature. After a swimming phase, the larvae settles and undergoes an extensive metamorphosis during which most of the chordate characteristics are resorbed, leaving a filter feeding sessile invertebrate adult. Due to its small size (in many species a larva consists of ca. 2,500 cells) and rapid development (a fertilized egg can complete development in less that 24 h in Ciona species), the study of ascidian larvae has a long history and continues to be an outstanding model for studying specification and differentiation events which occur during chordate embryogenesis. In comparison, the adult body plan is relatively unstudied at a molecular level, but several examples of extensive regeneration following surgical ablation of different tissues have been described. In addition, within this chordate subphylum two distinct adult body plans exist: solitary and colonial. Following larval metamorphosis, solitary species grow into an adult that can range from several millimeters to tens of centimeters in length. In addition, colonial species grow not by increasing in size, but by asexually propagating, eventually creating a colony of genetically identical individuals that can cover areas of several square meters. 1 Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA 2 Biology Department, Center for Developmental Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA 3 Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA 4 Department of Biological Sciences, Stanford University, Hopkins Marine Station, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA * Author for correspondence Tel.: 831 655 6206, Fax: 831 3750793 E-mail: tdet@stanford.edu T.C.G. Bosch (ed.), Stem Cells: From Hydra to Man, 95 © Springer Science + Business Media B.V. 2008

Michael Dickinson

There are many freely available molecular visualization programs used by scientists to view macromolecules. Each application has advantages. However, each of these applications also has its own scripting language. For scientists to utilize multiple molecular visualization applications, they must learn each of those scripting languages. To unite these applications, it is necessary to create tools to interconvert these scripts according to the conventions of each program. We have created a plugin that can read scripts from RasMol and execute the equivalent commands in PyMOL. Challenges have included different sets of commands and object‐oriented vs. simple text formats. It is the goal of the Structural Biology Extensible Visualization Scripting Language project to create an interface that will enable use of scripts from one molecular visualization application in a variety of other applications. This will enable users to run multiple programs while only needing to develop expertise in the scripting language for one of those programs. The project is funded in part by NIGMS grant #1R15GM078077.

A new era in science at Washington University, St. Louis: Viktor Hamburger's zoology department in the 1940's

*Department of Zoology, Oregon State University, Corvallis, OR 97331, U.S.A., email blaustea@ava.bcc.orst.edu†Institute for International Studies, Stanford University, Stanford, CA 94305, U.S.A.‡Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, PA 16802, U.S.A.§Department of Zoology, University of Washington, Seattle, WA 98195, U.S.A.**Pacific Northwest Research Station, U.S. Forest Service, Corvallis, OR 97331, U.S.A.††Redpath Museum, McGill University, 859 Sherbrooke Street W., Montreal, Quebec H3A 2K6, Canada

Molecular evidence for recent divergence of Lake Tanganyika endemic crabs (Decapoda: Platythelphusidae)

Stanley Fields*, Becky Drees, Tony R. Hazbun, Chandra Tucker, Amy Hin Yan Tong, Marie Evangelista, Charles Boone, Giuliano Nardelli, Luisa Castagnoli, Adriana Zucconi, Gianni Cesareni, Gary Bader, and Chris Hogue Departments of Genome Sciences and Medicine, Howard Hughes Medical Institute, University of Washington, Box 357730, Seattle, WA 98195; Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6; Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy;. Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, Canada, M5G 1X5 *fields@u.washington.edu

Journal of Experimental ZoologyVolume 149, Issue 2 p. 103-115 Article The functional differentiation of the small intestine. X. Duodenal succinic dehydrogenase in chick embryos and hatched chicks† David A. Nunnally, David A. Nunnally Department of Biology, Vanderbilt University, Nashville, TennesseeSearch for more papers by this author David A. Nunnally, David A. Nunnally Department of Biology, Vanderbilt University, Nashville, TennesseeSearch for more papers by this author First published: March 1962 https://doi.org/10.1002/jez.1401490203Citations: 5 † This study was supported in part by U. S. Public Health Service grant RG-3937 to Dr. Florence Moog, Department of Zoology, Washington University, St. Louis, Missouri. ‡ This work was carried out in the laboratories of the Department of Zoology, Washington University, under the tenure of a National Science Foundation Pre-Doctoral Fellowship. AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume149, Issue2March 1962Pages 103-115 RelatedInformation

A new species of Dicranostyles, D. costanensis, is described from the Costal Cordillera and lowland forests of Apure State, Venezuela. The collections of this species extend the known range of the genus northwest of the llanos. At the Instituto Botanico in 1967 we discussed collections of a new species of Dicranostyles from the cloud forests of the Venezuelan Coastal Cordillera. Because the junior author had been studying that genus and the related genera Lysiostyles and Maripa, it was decided that we would publish the new Venezuelan species together. The collections of D. costanensis are the first made from northern and northwestern Venezuela and extend the range of the genus north of the South American llanos. Dicranostyles costanensis Steyermark & Austin, sp. nov. A D. scandenti affinis et cum ea ovario glabro, sed thyrsis longioribus, tomento densiore et magis cinnamomeo vel castaneo, floribus densioribus, foliis basis obtusis vel subrotundatis, corollis et stylis longioribus, et distributis in et circa montibus costanensis Venezuelis differt. Etiam similibus a D. ampla var. ampla, sed ovario pubescenti et regna Amazona habitat distincta est. Lianas; stems gray-red to reddish-brown, smooth, with white lenticels. Leaves with petioles 12-20 mm long; blades oblong, elliptic-oblong to ovate, 4-9 (-12) cm long and 3-5 cm wide, the base subrotund to obtuse, the apex acuminate, thinly coriaceous, the secondaries 8-13 pairs; glabrescent on both sides. Inflorescences axillary, aphyllothyrsiform, 4-18 cm long, densely cinnamon-brown pubescent; bracts 1-2 mm long, oblong, acute, pubescent. Flowers with pedicels ca. 1 mm long; sepals deltoid-suborbiculate, obtuse, 1.5 mm long and 1.9-2 mm wide, pubescent without, glabrous within, margins ciliolate with non-glandular trichomes; corolla subrotate, white, ca. 5 mm long and ca. 5 mm wide, the tube short, ca. 1.2 mm long, ca. 2 mm wide at summit, ca. 1.5 mm wide at base, glabrous without, the lobes elliptic-oblong, thickened and subinflexed at the acute apex, ca. 3.5 mm long and ca. 1.8-1.9 mm wide, pubescent without, glabrous within; stamens excluded, the filaments ca. 3 mm long, inserted ca. 1 mm above corolla base, basally glandular pubescent, the anthers ca. 1 mm long, oblong, basally sagittate; ovary conic-oblong, ca. 1 mm long and ca. 0.5 mm in diameter, glabrous, the styles 2, free for 0.5-1.5 mm, mostly united in basal 0.3-0.7 mm, total length ca. 2 mm, glabrous, the stigmas capitate to ? complanate and irregularly lobed. Fruits ellipsoid, 22-25 mm long and 17-19 mm in diameter, striae 1Instituto Botanico, Ministerio de Agricultura, Caracas, Venezuela. 2Missouri Botanical Garden and Department of Biology, Washington University, St. Louis, 63130. Present address: Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida 33432. ANN. MISSOURI BOT. GARD. 57: 155-157. 1970. This content downloaded from 207.46.13.71 on Wed, 27 Apr 2016 05:29:46 UTC All use subject to http://about.jstor.org/terms [VOL. 5 7 156 ANNALS OF THE MISSOURI BOTANICAL GARDEN FIGURE 1. Dicranostyles costanensis-A. Habit.-B. Flower.-C. Bud before complete anthesis.-D. Detail of stamens and attachment.-E. Detail of gynoecium.-F. Detail of immature gynoecium dissected from bud. [After Steyermark et al. 100263 (VEN).] This content downloaded from 207.46.13.71 on Wed, 27 Apr 2016 05:29:46 UTC All use subject to http://about.jstor.org/terms

In some regions of the world, the regular use of more than one language within a single geographical area is commonplace in everyday life. This is true from the hills and valleys of the American Southwest, where English and Spanish can be heard in everyday conversations in restaurants, shopping areas, and other public places, to the campus of Gallaudet University in Washington, DC, where American Sign Language (ASL), English, and other signed and spoken languages pepper the auditory and visual landscape of that historical institution. Evidence of language contact can be found in everyday conversations (e.g., with bits of one language surfacing in the other) and also in various linguistic features of languages that have been in sustained contact over a period of time (e.g., fully integrated words that originated in another language). One can find features of an ambient spoken or written language within a signed language just as one can find words, sounds, and grammatical constructions from one spoken language within another. Language contact is part of the evolutionary history of languages in the world, and in this chapter we focus on various aspects of contact that surface when considering communities of language users that are bilingual and bimodal (i.e., they use languages that are perceived either visually, auditorally, or both).

Poor blood glucose regulation has been linked to various long‐term metabolic disruptions in adults, such as tissue damage in the eye. Yet, little is known about the effects of embryonic hyperglycemia on retinal development. To address this question, our lab has established a protocol for inducing hyperglycemia in zebrafish embryos by submerging zebrafish embryos in fish water containing 50mM glucose +/− 10μM dexamethasone from 10 hours post fertilization (hpf) until 120 hpf. Following treatment, larval heads were either fixed for sectioning or used for RNA extraction and the remaining body was used to quantify glucose concentration. The fixed heads were processed for sectioning and immunohistochemistry to label and quantify cell types in the retina. Treatment with 50mM glucose + 10μM dexamethasone reliably produced hyperglycemic larvae, with at least 2.5‐fold increased whole‐body glucose concentration compared to control‐treated larvae. Our results show that hyperglycemic larvae had a significant reduction in rod and cone photoreceptors with abnormal morphology, and significant increase in reactive oxygen species (ROS) production in the retina. In addition, Müller glia cells showed abnormal morphology, but an increase in number. Finally, genes related to the pentose phosphate pathway were also up‐regulated in hyperglycemic eyes. Our results suggest that embryonic hyperglycemia results in abnormal photoreceptor development via ROS production, which is accompanied by an elevation in pentose phosphate pathway activity. As the population of women with uncontrolled diabetes during pregnancy continues to grow, it is imperative to pinpoint the effects of embryonic hyperglycemia. The similarities between humans and zebrafish will allow us to study these effects, which will aid in the development of therapeutic strategies.Support or Funding InformationGertrude F. Ribble Mini Grant, Department of Biology, University of Kentucky Diabetes Research Center, Washington University, Grant No. 5P30 DK020579

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