User:Daniel Mietchen/Notebook/Open Science/Wiki journal

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This page is a test page related to a demo of a wiki-based journal article.


It hosts a demo version of how a typical research article could be condensed if all the previously known parts were available in a contextualized fashion. Similar ideas have been tossed around under the name of a Wikipedia Journal ( http://www.wittylama.com/2009/09/wikipedia-journal/ ), so I will stick to this label for the time being. Also relevant is RNA Biology's initiative to require, for a subset of their articles, that authors submit the draft of a Wikipedia page along with their maunscript ( http://www.landesbioscience.com/journals/rnabiology/guidelines/ ).

I started by pasting the HTML source of a PLoS ONE (and thus CC-licensed) paper of mine into an Etherpad and reworked it (see Time Slider) such that the information was reduced to the bare essentials, while all of the background knowledge was shifted to "encyclopedic" articles on the respective subjects.


HTML source of http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003826 , simplified to display only the article contents and none of the journal's general markup.


Now let's simplify: Suppose we are going to put up a research project with this topic into a wiki, the natural thing to do is starting a new page with just that title, perhaps as a subpage in our user space: Mietchen/Notebook/Open Science/Wiki journal In Vivo Assessment of Cold Adaptation in Insect Larvae by Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy

Authors of a wiki entry will be recognizable from the article history page if it has been drafted entirely on that page. Some wikis - e.g. http://www.wikigenes.org/ - also display which word was entered by which author. For our purposes, it should be sufficient to link to the authors' user pages (supposing they all have one on that wiki), which could be made unambiguous by using some sort of AuthorID system:

Authors: Daniel Mietchen, Bertram Manz, Frank Volke, Kenneth Storey

Affiliations would be listed on the authors' user pages and can thus be deleted here.

An abstract is a nice thing to have for any research project, so we will keep this in:


Contents

Abstract

Background

Let us link to the core concepts as they appear in the abstract. For those who wonder: OpenWetWare does not offer encyclopedic entries but in principle, wikis based on the same platform (e.g. MediaWiki) can be configured such that they link to other wikis almost as if they were on the same server (e.g. on the English Wikiversity, you can get to a page on the German one by prefixing it with :de), and in this way, the research wiki (where notes had been collected throughout the research project) could indeed very simlpy be linked to encyclopedic background knowledge. I will ignore this point now and later paste this code into a wiki where context exists, e.g. Wikipedia or Citizendium.

Temperatures below the freezing point of water and the ensuing ice crystal formation pose serious challenges to cell structure and function. Consequently, species living in seasonally cold environments have evolved a multitude of strategies to reorganize their cellular architecture and metabolism, and the underlying mechanisms are crucial to our understanding of life. In multicellular organisms, and poikilotherm animals in particular, our knowledge about these processes is almost exclusively due to invasive studies, thereby limiting the range of conclusions that can be drawn about intact living systems.


Methodology

Given that non-destructive techniques like 1H MR imaging and spectroscopy exhibit an enormous signal loss upon freezing and a corresponding signal increase upon thawing and have proven useful for in vivo investigations of a wide range of biological systems, we aimed at evaluating their potential to observe cold adaptations in living insect larvae. Specifically, we chose two cold-hardy insect species that frequently serve as cryobiological model systems and share the same habitat (stem galls on goldenrod plants, genus Solidago) but use different overwintering strategies–the freeze-avoiding gall moth Epiblema scudderiana and the freeze-tolerant gall fly Eurosta solidaginis.

CHESS imaging has previously been used to investigate insect larval development in a non-cryobiological context, and technological developments in the MR field have recently seen in vivo spatial resolution in non-frozen samples reach the size range relevant for entomological and subcellular investigations. The present study combined these two fields of investigation by demonstrating the feasibility of high-resolution MR imaging of insect larvae in a cryobiological context.


Results

In vivo MR images were acquired from autumn-collected larvae at temperatures between 0°C and about −70°C and at spatial resolutions down to 27 µm. These images revealed three-dimensional (3D) larval anatomy at a level of detail currently not in reach of other in vivo techniques. Furthermore, they allowed visualization of the 3D distribution of the remaining liquid water and of the endogenous cryoprotectants at subzero temperatures, and temperature-weighted images of these distributions could be derived. Finally, individual fat body cells and their nuclei could be identified in intact frozen Eurosta larvae.


Conclusions

These findings suggest that high resolution MR techniques provide for interesting methodological options in comparative cryobiological investigations, especially in vivo.

Citation information could be generated automatically, e.g. by means of templates for authors and title, but let's leave that in for now.

Citation: Mietchen D, Manz B, Volke F, Storey K (2008) In Vivo Assessment of Cold Adaptation in Insect Larvae by Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy. PLoS ONE 3(12): e3826. doi:10.1371/journal.pone.0003826 Editor: Brent Sinclair

Funding: The study was supported by an IBMT-internal grant. Competing interests: The authors have declared that no competing interests exist.


Introduction

Merged into abstract.

Methods

This section could certainly be simplified too, e.g. by referring to pages hosting standard protocols, or to copies describing variations thereof.

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