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1.  Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data 
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
PMCID: PMC3964625  PMID: 24723752
Cybertaxonomy; gene sequence data; micro-CT; data integration; molecular systematics; caves; Croatia; biospeleology
5.  An Asian Elephant Imitates Human Speech 
Current Biology  2012;22(22):2144-2148.
Vocal imitation has convergently evolved in many species, allowing learning and cultural transmission of complex, conspecific sounds, as in birdsong [1, 2]. Scattered instances also exist of vocal imitation across species, including mockingbirds imitating other species or parrots and mynahs producing human speech [3, 4]. Here, we document a male Asian elephant (Elephas maximus) that imitates human speech, matching Korean formants and fundamental frequency in such detail that Korean native speakers can readily understand and transcribe the imitations. To create these very accurate imitations of speech formant frequencies, this elephant (named Koshik) places his trunk inside his mouth, modulating the shape of the vocal tract during controlled phonation. This represents a wholly novel method of vocal production and formant control in this or any other species. One hypothesized role for vocal imitation is to facilitate vocal recognition by heightening the similarity between related or socially affiliated individuals [1, 2]. The social circumstances under which Koshik’s speech imitations developed suggest that one function of vocal learning might be to cement social bonds and, in unusual cases, social bonds across species.
► A male Asian elephant imitates human speech, accurately matching Korean formants ► The elephant makes the speech imitations by inserting his trunk into his mouth
PMCID: PMC3548412  PMID: 23122846
7.  Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information 
ZooKeys  2011;127-149.
The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.
PMCID: PMC3234435  PMID: 22207810
Creative Commons; Open Access; Open Content; Licensing; Non-profit; Open Educational Resources; Data Sharing; Software Licenses; Europeana
8.  Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID 
ZooKeys  2011;1-12.
Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.
PMCID: PMC3084489  PMID: 21594104
9.  Effectively incorporating selected multimedia content into medical publications 
BMC Medicine  2011;9:17.
Until fairly recently, medical publications have been handicapped by being restricted to non-electronic formats, effectively preventing the dissemination of complex audiovisual and three-dimensional data. However, authors and readers could significantly profit from advances in electronic publishing that permit the inclusion of multimedia content directly into an article. For the first time, the de facto gold standard for scientific publishing, the portable document format (PDF), is used here as a platform to embed a video and an audio sequence of patient data into a publication. Fully interactive three-dimensional models of a face and a schematic representation of a human brain are also part of this publication. We discuss the potential of this approach and its impact on the communication of scientific medical data, particularly with regard to electronic and open access publications. Finally, we emphasise how medical teaching can benefit from this new tool and comment on the future of medical publishing.
PMCID: PMC3040697  PMID: 21329532
10.  Computational Morphometry for Detecting Changes in Brain Structure Due to Development, Aging, Learning, Disease and Evolution 
The brain, like any living tissue, is constantly changing in response to genetic and environmental cues and their interaction, leading to changes in brain function and structure, many of which are now in reach of neuroimaging techniques. Computational morphometry on the basis of Magnetic Resonance (MR) images has become the method of choice for studying macroscopic changes of brain structure across time scales. Thanks to computational advances and sophisticated study designs, both the minimal extent of change necessary for detection and, consequently, the minimal periods over which such changes can be detected have been reduced considerably during the last few years. On the other hand, the growing availability of MR images of more and more diverse brain populations also allows more detailed inferences about brain changes that occur over larger time scales, way beyond the duration of an average research project. On this basis, a whole range of issues concerning the structures and functions of the brain are now becoming addressable, thereby providing ample challenges and opportunities for further contributions from neuroinformatics to our understanding of the brain and how it changes over a lifetime and in the course of evolution.
PMCID: PMC2729663  PMID: 19707517
brain morphometry; MRI; development; aging; learning; brain disease; evolution; gyrification
11.  In Vivo Assessment of Cold Adaptation in Insect Larvae by Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy 
PLoS ONE  2008;3(12):e3826.
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.
Given that non-destructive techniques like 1H Magnetic Resonance (MR) imaging and spectroscopy 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–the freeze-avoiding gall moth Epiblema scudderiana and the freeze-tolerant gall fly Eurosta solidaginis.
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.
These findings suggest that high resolution MR techniques provide for interesting methodological options in comparative cryobiological investigations, especially in vivo.
PMCID: PMC2586655  PMID: 19057644
12.  Cortex reorganization of Xenopus laevis eggs in strong static magnetic fields 
Observations of magnetic field effects on biological systems have often been contradictory. For amphibian eggs, a review of the available literature suggests that part of the discrepancies might be resolved by considering a previously neglected parameter for morphological alterations induced by magnetic fields – the jelly layers that normally surround the egg and are often removed in laboratory studies for easier cell handling. To experimentally test this hypothesis, we observed the morphology of fertilizable Xenopus laevis eggs with and without jelly coat that were subjected to static magnetic fields of up to 9.4 T for different periods of time. A complex reorganization of cortical pigmentation was found in dejellied eggs as a function of the magnetic field and the field exposure time. Initial pigment rearrangements could be observed at about 0.5 T, and less than 3 T are required for the effects to fully develop within two hours. No effect was observed when the jelly layers of the eggs were left intact. These results suggest that the action of magnetic fields might involve cortical pigments or associated cytoskeletal structures normally held in place by the jelly layers and that the presence of the jelly layer should indeed be included in further studies of magnetic field effects in this system.
PMCID: PMC1326199  PMID: 16351729
13.  Peer Review—The Newcomers' Perspective 
PLoS Biology  2005;3(9):e326.
The World Academy of Young Scientists argue that double blind peer-review will generate a better perception of fairness and equality in global scientific funding and publishing
PMCID: PMC1201308  PMID: 16149851

Results 1-13 (13)