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1.  Infant Weight Gain and School-age Blood Pressure and Cognition in Former Preterm Infants 
Pediatrics  2010;125(6):e1419-e1426.
OBJECTIVES
More rapid infant weight gain may be associated with better neurodevelopment but also with higher blood pressure (BP). The objective of this study was to determine the extent to which infant weight gain is associated with systolic BP (SBP) and IQ at school age in former preterm, low birth weight infants.
METHODS
We studied 911 participants in the Infant Health and Development Program, an 8-center longitudinal study of children born at ≤37 weeks' gestation and ≤2500 g. Study staff weighed participants at term and at 4 and 12 months' corrected ages; measured BP 3 times at 6.5 years; and administered the Wechsler Intelligence Scale for Children, Third Edition (WISC-III), an IQ test, at 8 years. In linear regression, we modeled our exposure “infant weight gain” as the 12-month weight z score adjusted for the term weight z score.
RESULTS
Median (interquartile range) weight z score was −0.7 (−1.5 to −0.0) at 12 months. Mean ± SD SBP at 6.5 years was 104.2 ± 8.4 mm Hg, and mean ± SD WISC-III total score at 8 years was 91 ± 18. Adjusting for child gender, age, and race and maternal education, income, age, IQ, and smoking, for each z score additional weight gain from term to 12 months, SBP was 0.7 mm Hg higher and WISC-III total score was 1.9 points higher.
CONCLUSIONS
In preterm infants, there seem to be modest neurodevelopmental advantages of more rapid weight gain in the first year of life and only small BP-related effects.
doi:10.1542/peds.2009-2746
PMCID: PMC4138041  PMID: 20478940
preterm infant; infant; blood pressure; cognition; fetal programming; growth and development; postnatal growth; small for gestational age
2.  Preterm Infant Swallowing of Thin and Nectar-Thick Liquids: Changes in Lingual–Palatal Coordination and Relation to Bolus Transit 
Dysphagia  2013;28(2):234-244.
Tongue–soft palate coordination and bolus head pharyngeal transit were studied by means of postacquisition kinematic analysis of videofluoroscopic swallowing images of ten preterm infants referred from hospital NICUs due to poor oral feeding and suspicion of aspiration. Sequences of coordinated tongue–soft palate movements and bolus transits during swallows of thin-consistency and nectar-thick-consistency barium were digitized, and time series data were used to calculate continuous relative phase, a measure of coordination. During swallows of nectar-thick compared to thin barium, tongue–soft palate coordination was more likely to be antiphase, bolus head pharyngeal transit time was longer, and coordination was significantly correlated with bolus head pharyngeal transit. Analysis of successive swallows indicated that tongue–soft palate coordination variability decreased with nectar-thick but not with thin-consistency barium. Together, the results suggest that slower-moving bolus transits may promote greater opportunity for available sensory information to be used to modulate timing of tongue–soft palate movements so that they are more effective for pumping liquids.
doi:10.1007/s00455-012-9440-y
PMCID: PMC3638056  PMID: 23274694
Infant; Swallowing; Coordination; Liquid properties
3.  Linking multiple biodiversity informatics platforms with Darwin Core Archives 
We describe an implementation of the Darwin Core Archive (DwC-A) standard that allows for the exchange of biodiversity information contained within the Scratchpads virtual research environment with external collaborators. Using this single archive file Scratchpad users can expose taxonomies, specimen records, species descriptions and a range of other data to a variety of third-party aggregators and tools (currently Encyclopedia of Life, eMonocot Portal, CartoDB, and the Common Data Model) for secondary use. This paper describes our technical approach to dynamically building and validating Darwin Core Archives for the 600+ Scratchpad user communities, which can be used to serve the diverse data needs of all of our content partners.
doi:10.3897/BDJ.2.e1039
PMCID: PMC3964728  PMID: 24723785
Darwin Core; Darwin Core Archive; Scratchpads; biodiversity informatics; virtual research environment; taxonomy; biodiversity
4.  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.
doi:10.3897/BDJ.1.e1013
PMCID: PMC3964625  PMID: 24723752
Cybertaxonomy; gene sequence data; micro-CT; data integration; molecular systematics; caves; Croatia; biospeleology
5.  Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description 
GigaScience  2013;2:14.
With the publication of the first eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data, GigaScience and Pensoft demonstrate how classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. This 'holistic’ approach in taxonomic description of a new species of cave-dwelling centipede is published in the Biodiversity Data Journal (BDJ), with coordinated data release in the GigaScience GigaDB database.
doi:10.1186/2047-217X-2-14
PMCID: PMC4076509  PMID: 24229463
7.  1-tert-Butyl 2-ethyl 5-chloro-3-(2-furo­yl)-1H-indole-1,2-dicarboxyl­ate 
In the title compound, C21H20ClNO6, the furan moiety is located above the mean plane of the indole ring and displays rotational disorder (i.e. rotation through 180°); the site occupancy of the major component is 0.809 (6). In the crystal, C—H⋯O inter­actions link the mol­ecules into chains which run parallel to the b axis.
doi:10.1107/S1600536813005059
PMCID: PMC3588483  PMID: 23476614
8.  1-tert-Butyl 2-ethyl 5-bromo-3-(thio­phen-2-ylcarbon­yl)-1H-indole-1,2-dicarboxyl­ate 
In the title compound, C21H20BrNO5S, the thio­phene group is located above the mean plane of the indole ring and displays rotational disorder (i.e. rotation through 180°). The site occupancy of the major component is 0.902 (2), while that of the minor component is 0.098 (2). In the crystal, pairs of weak C—H⋯O inter­actions link the mol­ecules into centrosymmetric dimers.
doi:10.1107/S1600536813000809
PMCID: PMC3569770  PMID: 23424516
9.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry 
Bentley, David R. | Balasubramanian, Shankar | Swerdlow, Harold P. | Smith, Geoffrey P. | Milton, John | Brown, Clive G. | Hall, Kevin P. | Evers, Dirk J. | Barnes, Colin L. | Bignell, Helen R. | Boutell, Jonathan M. | Bryant, Jason | Carter, Richard J. | Cheetham, R. Keira | Cox, Anthony J. | Ellis, Darren J. | Flatbush, Michael R. | Gormley, Niall A. | Humphray, Sean J. | Irving, Leslie J. | Karbelashvili, Mirian S. | Kirk, Scott M. | Li, Heng | Liu, Xiaohai | Maisinger, Klaus S. | Murray, Lisa J. | Obradovic, Bojan | Ost, Tobias | Parkinson, Michael L. | Pratt, Mark R. | Rasolonjatovo, Isabelle M. J. | Reed, Mark T. | Rigatti, Roberto | Rodighiero, Chiara | Ross, Mark T. | Sabot, Andrea | Sankar, Subramanian V. | Scally, Aylwyn | Schroth, Gary P. | Smith, Mark E. | Smith, Vincent P. | Spiridou, Anastassia | Torrance, Peta E. | Tzonev, Svilen S. | Vermaas, Eric H. | Walter, Klaudia | Wu, Xiaolin | Zhang, Lu | Alam, Mohammed D. | Anastasi, Carole | Aniebo, Ify C. | Bailey, David M. D. | Bancarz, Iain R. | Banerjee, Saibal | Barbour, Selena G. | Baybayan, Primo A. | Benoit, Vincent A. | Benson, Kevin F. | Bevis, Claire | Black, Phillip J. | Boodhun, Asha | Brennan, Joe S. | Bridgham, John A. | Brown, Rob C. | Brown, Andrew A. | Buermann, Dale H. | Bundu, Abass A. | Burrows, James C. | Carter, Nigel P. | Castillo, Nestor | Catenazzi, Maria Chiara E. | Chang, Simon | Cooley, R. Neil | Crake, Natasha R. | Dada, Olubunmi O. | Diakoumakos, Konstantinos D. | Dominguez-Fernandez, Belen | Earnshaw, David J. | Egbujor, Ugonna C. | Elmore, David W. | Etchin, Sergey S. | Ewan, Mark R. | Fedurco, Milan | Fraser, Louise J. | Fajardo, Karin V. Fuentes | Furey, W. Scott | George, David | Gietzen, Kimberley J. | Goddard, Colin P. | Golda, George S. | Granieri, Philip A. | Green, David E. | Gustafson, David L. | Hansen, Nancy F. | Harnish, Kevin | Haudenschild, Christian D. | Heyer, Narinder I. | Hims, Matthew M. | Ho, Johnny T. | Horgan, Adrian M. | Hoschler, Katya | Hurwitz, Steve | Ivanov, Denis V. | Johnson, Maria Q. | James, Terena | Jones, T. A. Huw | Kang, Gyoung-Dong | Kerelska, Tzvetana H. | Kersey, Alan D. | Khrebtukova, Irina | Kindwall, Alex P. | Kingsbury, Zoya | Kokko-Gonzales, Paula I. | Kumar, Anil | Laurent, Marc A. | Lawley, Cynthia T. | Lee, Sarah E. | Lee, Xavier | Liao, Arnold K. | Loch, Jennifer A. | Lok, Mitch | Luo, Shujun | Mammen, Radhika M. | Martin, John W. | McCauley, Patrick G. | McNitt, Paul | Mehta, Parul | Moon, Keith W. | Mullens, Joe W. | Newington, Taksina | Ning, Zemin | Ng, Bee Ling | Novo, Sonia M. | O'Neill, Michael J. | Osborne, Mark A. | Osnowski, Andrew | Ostadan, Omead | Paraschos, Lambros L. | Pickering, Lea | Pike, Andrew C. | Pike, Alger C. | Pinkard, D. Chris | Pliskin, Daniel P. | Podhasky, Joe | Quijano, Victor J. | Raczy, Come | Rae, Vicki H. | Rawlings, Stephen R. | Rodriguez, Ana Chiva | Roe, Phyllida M. | Rogers, John | Rogert Bacigalupo, Maria C. | Romanov, Nikolai | Romieu, Anthony | Roth, Rithy K. | Rourke, Natalie J. | Ruediger, Silke T. | Rusman, Eli | Sanches-Kuiper, Raquel M. | Schenker, Martin R. | Seoane, Josefina M. | Shaw, Richard J. | Shiver, Mitch K. | Short, Steven W. | Sizto, Ning L. | Sluis, Johannes P. | Smith, Melanie A. | Sohna, Jean Ernest Sohna | Spence, Eric J. | Stevens, Kim | Sutton, Neil | Szajkowski, Lukasz | Tregidgo, Carolyn L. | Turcatti, Gerardo | vandeVondele, Stephanie | Verhovsky, Yuli | Virk, Selene M. | Wakelin, Suzanne | Walcott, Gregory C. | Wang, Jingwen | Worsley, Graham J. | Yan, Juying | Yau, Ling | Zuerlein, Mike | Rogers, Jane | Mullikin, James C. | Hurles, Matthew E. | McCooke, Nick J. | West, John S. | Oaks, Frank L. | Lundberg, Peter L. | Klenerman, David | Durbin, Richard | Smith, Anthony J.
Nature  2008;456(7218):53-59.
doi:10.1038/nature07517
PMCID: PMC2581791  PMID: 18987734
10.  1-[(1-Methyl-1H-imidazol-5-yl)meth­yl]-1H-indole-5-carbonitrile 
In the title compound, C14H12N4, the dihedral angle between the indole ring system (r.m.s. deviation = 0.010 Å) and the imidazole ring is 77.70 (6)°. In the crystal, mol­ecules are linked by C—H⋯N hydrogen bonds. One set of hydrogen bonds forms an undulating chain running parallel to the b-axis direction, while the other undulating chain is parallel to the c-axis direction. In combination, (100) sheets result.
doi:10.1107/S1600536812048404
PMCID: PMC3589058  PMID: 23476294
11.  5-Chloro-1-(4-methyl­phenyl­sulfon­yl)-1H-indole 
In the title compound, C15H12ClNO2S, the indole ring is essentially planar (r.m.s. deviation = 0.0107 Å) and makes a dihedral angle of 85.01 (6)° with the benzene ring. In the crystal, three C—H⋯O hydrogen bonds result in a hydrogen-bonded spiral running parallel to the c axis.
doi:10.1107/S1600536812046466
PMCID: PMC3588956  PMID: 23476192
12.  N-(4-Amino­pyrimidin-5-yl)-4-methyl-N-(4-methyl­phenyl­sulfon­yl)benzene­sulfonamide 
In the title compound, C18H18N4O4S2, the mean planes passing through the tosyl benzene rings form dihedral angles of 48.42 (9) and 15.1 (1)° with the amino­pyrimidine ring. In the crystal, mol­ecules associate via N—H⋯N and N—H⋯O hydrogen bonds, forming extended hydrogen-bonded sheets that lie parallel to the bc plane. The N—H⋯N hydrogen bonds propagate along the b-axis direction, while the N—H⋯O hydrogen bonds propagate along the c-axis direction.
doi:10.1107/S1600536812046442
PMCID: PMC3588960  PMID: 23476196
13.  Multiple lineages of lice pass through the K–Pg boundary 
Biology Letters  2011;7(5):782-785.
For modern lineages of birds and mammals, few fossils have been found that predate the Cretaceous–Palaeogene (K–Pg) boundary. However, molecular studies using fossil calibrations have shown that many of these lineages existed at that time. Both birds and mammals are parasitized by obligate ectoparasitic lice (Insecta: Phthiraptera), which have shared a long coevolutionary history with their hosts. Evaluating whether many lineages of lice passed through the K–Pg boundary would provide insight into the radiation of their hosts. Using molecular dating techniques, we demonstrate that the major louse suborders began to radiate before the K–Pg boundary. These data lend support to a Cretaceous diversification of many modern bird and mammal lineages.
doi:10.1098/rsbl.2011.0105
PMCID: PMC3169043  PMID: 21471047
Phthiraptera; evolution; cospeciation; dating
14.  Bringing collections out of the dark 
ZooKeys  2012;1-6.
doi:10.3897/zookeys.209.3699
PMCID: PMC3406462  PMID: 22859874
15.  No specimen left behind: industrial scale digitization of natural history collections 
ZooKeys  2012;133-146.
Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.
doi:10.3897/zookeys.209.3178
PMCID: PMC3406472  PMID: 22859884
Digitization; imaging; specimen metadata; natural history collections; biodiversity informatics
16.  Repeated adaptive divergence of microhabitat specialization in avian feather lice 
BMC Biology  2012;10:52.
Background
Repeated adaptive radiations are evident when phenotypic divergence occurs within lineages, but this divergence into different forms is convergent when compared across lineages. Classic examples of such repeated adaptive divergence occur in island (for example, Caribbean Anolis lizards) and lake systems (for example, African cichlids). Host-parasite systems in many respects are analogous to island systems, where host species represent isolated islands for parasites whose life cycle is highly tied to that of their hosts. Thus, host-parasite systems might exhibit interesting cases of repeated adaptive divergence as seen in island and lake systems.
The feather lice of birds spend their entire life cycle on the body of the host and occupy distinct microhabitats on the host: head, wing, body and generalist. These microhabitat specialists show pronounced morphological differences corresponding to how they escape from host preening. We tested whether these different microhabitat specialists were a case of repeated adaptive divergence by constructing both morphological and molecular phylogenies for a diversity of avian feather lice, including many examples of head, wing, body and generalist forms.
Results
Morphological and molecular based phylogenies were highly incongruent, which could be explained by rampant convergence in morphology related to microhabitat specialization on the host. In many cases lice from different microhabitat specializations, but from the same group of birds, were sister taxa.
Conclusions
This pattern indicates a process of repeated adaptive divergence of these parasites within host group, but convergence when comparing parasites across host groups. These results suggest that host-parasite systems might be another case in which repeated adaptive radiations could be relatively common, but potentially overlooked, because morphological convergence can obscure evolutionary relationships.
doi:10.1186/1741-7007-10-52
PMCID: PMC3391173  PMID: 22717002
adaptive radiation; convergence; Phthiraptera; ectoparasites; phylogenetics
17.  N-(2-Amino­pyridin-3-yl)-4-methyl-N-(4-methyl­phenyl­sulfon­yl)benzene­sulfonamide 
The title compound, C19H19N3O4S2, was prepared by the reaction of 2,3-diamino­pyridine with tosyl chloride in a mixture of dichloro­methane–pyridine as solvent. In the crystal, mol­ecules associate via pairs of N—H⋯N hydrogen bonds, forming a centrosymmetric eight-membered {⋯HNCN}2 synthon. The dihedral angles between the amino­pyridine ring and the tosyl benzene rings are 50.01 (6) and 32.01 (4)°.
doi:10.1107/S1600536812010872
PMCID: PMC3344082  PMID: 22606085
18.  Collaborative electronic infrastructures to accelerate taxonomic research 
ZooKeys  2011;1-3.
doi:10.3897/zookeys.150.2458
PMCID: PMC3234428  PMID: 22207803
19.  Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science 
ZooKeys  2011;53-70.
The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project’s operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.
doi:10.3897/zookeys.150.2193
PMCID: PMC3234431  PMID: 22207806
Taxonomy; database; Virtual Research Environment; Biodiversity; e-infrastructure
20.  Who learns from whom? Supporting users and developers of a major biodiversity e-infrastructure 
ZooKeys  2011;177-192.
Support systems play an important role for the communication between users and developers of software. We studied two support systems, an issues tracker and an email service available for Scratchpads, a Web 2.0 social networking tool that enables communities to build, share, manage and publish biodiversity information on the Web. Our aim was to identify co-learning opportunities between users and developers of the Scratchpad system by asking which support system was used by whom and for what type of questions. Our results show that issues tracker and emails cater to different user mentalities as well as different kind of questions and suggest ways to improve the support system as part of the development under the EU funded ViBRANT programme.
doi:10.3897/zookeys.150.2191
PMCID: PMC3234438  PMID: 22207813
Shared knowledge; computer-supported cooperative work; issue tracking; software engineering; e-infrastructures
21.  A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites 
Background
Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of possible events including host switching and host independent speciation. However, in recently diverged lineages stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and evolutionary informative components of genealogic data in these recently diverged organisms.
Results
Mitochondrial DNA sequences were obtained for four species of Galápagos mockingbirds and three sympatric species of ectoparasites - two louse and one mite species. These data were complemented with nuclear EF1α sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds. Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the nuclear data and the geological history of the islands.
Conclusions
The gene genealogies of Galápagos mockingbirds and two of their ectoparasites show strong phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism. A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation and taxonomy of Galápagos mockingbirds and their parasites.
doi:10.1186/1471-2148-11-284
PMCID: PMC3209464  PMID: 21966954
22.  Premature Infant Swallowing: Patterns of Tongue-Soft Palate Coordination Based Upon Videofluoroscopy 
Infant behavior & development  2010;33(2):209-218.
Coordination between movements of individual tongue points, and between soft palate elevation and tongue movements, were examined in 12 prematurely born infants referred from hospital NICUs for videofluoroscopic swallow study (VFSS) due to poor oral feeding and suspicion of aspiration. Detailed post-evaluation kinematic analysis was conducted by digitizing images of a lateral view of digitally superimposed points on the tongue and soft palate. The primary measure of coordination was continuous relative phase of the time series created by movements of points on the tongue and soft palate over successive frames. Three points on the tongue (anterior, medial, and posterior) were organized around a stable in-phase pattern, with a phase lag that implied an anterior to posterior direction of motion. Coordination between a tongue point and a point on the soft palate during lowering and elevation was close to anti-phase at initiation of the pharyngeal swallow. These findings suggest that anti-phase coordination between tongue and soft palate may reflect the process by which the tongue is timed to pump liquid by moving it into an enclosed space, compressing it, and allowing it to leave by a specific route through the pharynx.
doi:10.1016/j.infbeh.2009.10.001
PMCID: PMC2844905  PMID: 20181397
Infant; coordination; swallowing; videofluoroscopy; dysphagia; tongue; soft palate
23.  Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura) 
Background
Sucking lice (Phthiraptera: Anoplura) are obligate, permanent ectoparasites of eutherian mammals, parasitizing members of 12 of the 29 recognized mammalian orders and approximately 20% of all mammalian species. These host specific, blood-sucking insects are morphologically adapted for life on mammals: they are wingless, dorso-ventrally flattened, possess tibio-tarsal claws for clinging to host hair, and have piercing mouthparts for feeding. Although there are more than 540 described species of Anoplura and despite the potential economical and medical implications of sucking louse infestations, this study represents the first attempt to examine higher-level anopluran relationships using molecular data. In this study, we use molecular data to reconstruct the evolutionary history of 65 sucking louse taxa with phylogenetic analyses and compare the results to findings based on morphological data. We also estimate divergence times among anopluran taxa and compare our results to host (mammal) relationships.
Results
This study represents the first phylogenetic hypothesis of sucking louse relationships using molecular data and we find significant conflict between phylogenies constructed using molecular and morphological data. We also find that multiple families and genera of sucking lice are not monophyletic and that extensive taxonomic revision will be necessary for this group. Based on our divergence dating analyses, sucking lice diversified in the late Cretaceous, approximately 77 Ma, and soon after the Cretaceous-Paleogene boundary (ca. 65 Ma) these lice proliferated rapidly to parasitize multiple mammalian orders and families.
Conclusions
The diversification time of sucking lice approximately 77 Ma is in agreement with mammalian evolutionary history: all modern mammal orders are hypothesized to have diverged by 75 Ma thus providing suitable habitat for the colonization and radiation of sucking lice. Despite the concordant timing of diversification events early in the association between anoplurans and mammals, there is substantial conflict between the host and parasite phylogenies. This conflict is likely the result of a complex history of host switching and extinction events that occurred throughout the evolutionary association between sucking lice and their mammalian hosts. It is unlikely that there are any ectoparasite groups (including lice) that tracked the early and rapid radiation of eutherian mammals.
doi:10.1186/1471-2148-10-292
PMCID: PMC2949877  PMID: 20860811
24.  Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys 
ZooKeys  2010;17-28.
We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue.
doi:10.3897/zookeys.50.539
PMCID: PMC3088019  PMID: 21594114
Online publishing; taxonomy; nomenclature; ICZN; ICBN
25.  Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples 
ZooKeys  2010;1-16.
The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.
doi:10.3897/zookeys.50.538
PMCID: PMC3088020  PMID: 21594113
Semantic tagging; semantic enhancements; systematics; taxonomy

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