bluuebunny/crossref_metadata_2025_split huggingface dataset:
BHL, The Biodiversity Heritage Library: An Expanding International Collaboration
Authors: Rinaldo Constance , Norton Catherine 
Published: August 2009

Abstract
*Background/Question/Methods*
The Biodiversity Heritage Library (BHL; "http://www.biodiversitylibrary.org/":http://www.biodiversitylibrary.org/), one of the cornerstones of the Encyclopedia of Life (eol.org), now contains nearly 13 million digitized pages of 12,000 titles comprised of 32,000 volumes of the published literature of biodiversity held in the collections of major natural history libraries. The BHL has made this literature available for open access and responsible use as a part of a global “biodiversity commons.” The BHL partnership is working with the global taxonomic community, publishers, organizations such as JSTOR and BIOONE, and the Internet Archive, to ensure that the biodiversity literature is available to all, from students to scientists with diverse interests.This poster will describe the BHL with particular focus on the taxonomic tools available and the development of international partnerships and expanded collaborations with scientists. BHL-Europe has now formed and participation by other countries and projects will augment the available literature and provide redundant repositories and mirror sites. New tools such as the PDF-generator, article repository, updated search interface and social networking tools will be reviewed.

Results/Conclusions
The BHL Portal is a transformative research environment for scientific inquiry. The tools and information in the BHL have accelerated research in life sciences. Users reach the BHL through a free, service-based portal formed by coupling existing databases with digitized, searchable images and OCR text. The array of tools for taxonomically intelligent services has expanded. These tools are designed to overcome the problem of common name versus scientific name and changes of names over time and provide easy access to the available literature on a particular organism. This scientific reference system for investigating literature offers a model that reflects, and also amplifies, scientists' use of the natural history literature. In 2008, name finding statistics showed that 30 million name string occurrences were extracted from the BHL with 4.4 million of these being unique. Of these, 23.7 million have been verified by NameBank. Enhancement of OCR tools or manual text correction is crucial to the further development of data mining. Social networking tools may be utilized to expand OCR text correction to users and for tagging maps and illustrations. Scientists are providing bibliographies for taxonomic groups that can be incorporated into the selection process. Organizations have offered already digitized articles for deposit to the BHL. Hence, an article repository has been developed together with tools to extract pages of text, from BHL content (PDF-generator).
The National Vegetation Classification Standard: Implementation and outreach for the state of Oklahoma
Authors: Fagin Todd , Hoagland Bruce , Lowther David 
Published: August 2009

AbstractEfficient stewardship of the nation’s biological resources requires a systematic inventory and classification of the systems which support these resources. However, until recently, a single classification system utilized across jurisdictional boundaries and throughout multiple collecting agencies was non-existent. Rather, conservation priorities were focused primarily at the local and regional scales, with inventory and mapping standards varying from one area to the next. Inconsistent standards of inventories and classifications compounded the difficulties inherent in management of biological resources, namely the ability to present multi-scale, synoptic views of vegetation resources. In order to address these problems, the Federal Geographic Data Committee (FGDC) Vegetation Subcommittee was formed to develop a single vegetation classification and mapping standard for the United States. This effort resulted in the U.S. National Vegetation Classification Standard ((NVCS), accepted by the FGDC in 1997 (version 2 endorsed by the FGDC in 2008). Under Executive Order 12906, federal agencies collecting or producing geospatial data, either directly or indirectly, are mandated to collect data in a manner that adheres to all relevant standards adopted through the FGDC process. However, unless otherwise mandated through contract or agreement, FGDC standards are voluntary for non-federal agencies. In the state of Oklahoma, many individuals involved in vegetation collection and reporting are not mandated to adhere to the NVCS. In order to encourage wider acceptance of the NVCS among these individuals, we developed educational and other training materials and engaged in direct to promote the Standard.
Ontology for Biomedical Investigations
Authors: Peters Bjoern , OBI Consortium The 
Published: August 2009

AbstractThe goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives, experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological reality. The use of OBI by the scientific community to represent or annotate their investigations within electronic data resources will facilitate interdisciplinary data synthesis, enable access to their data on the semantic web and improve third-party understanding of information related to life-science and clinical investigations.
Impact of selenite and selenate on differentially expressed genes in rat liver examined by microarray analysis
Authors: Bosse Astrid C. , Pallauf Josef , Hommel Bettina , Sturm Mariana , Fischer Susanne , Wolf Nicole M. , Mueller Andreas S. 
Published: August 2009

Sodium selenite and sodium selenate are approved inorganic Se (selenium) compounds in human and animal nutrition serving as precursors for selenoprotein synthesis. In recent years, numerous additional biological effects over and above their functions in selenoproteins have been reported. For greater insight into these effects, our present study examined the influence of selenite and selenate on the differential expression of genes encoding non-selenoproteins in the rat liver using microarray technology. Five groups of nine growing male rats were fed with an Se-deficient diet or diets supplemented with 0.20 or 1.0 mg of Se/kg as sodium selenite or sodium selenate for 8 weeks. Genes that were more than 2.5-fold up- or down-regulated by selenite or selenate compared with Se deficiency were selected. GPx1 (glutathione peroxidase 1) was up-regulated 5.5-fold by both Se compounds, whereas GPx4 was up-regulated by only 1.4-fold. Selenite and selenate down-regulated three phase II enzymes. Despite the regulation of many other genes in an analogous manner, frequently only selenate changed the expression of these genes significantly. In particular, genes involved in the regulation of the cell cycle, apoptosis, intermediary metabolism and those involved in Se-deficiency disorders were more strongly influenced by selenate. The comparison of selenite- and selenate-regulated genes revealed that selenate may have additional functions in the protection of the liver, and that it may be more active in metabolic regulation. In our opinion the more pronounced influence of selenate compared with selenite on differential gene expression results from fundamental differences in the metabolism of these two Se compounds.
‘Parisomania’? Jack Hylton and the French Connection
Authors: Mawer Deborah 
Published: August 2009

AbstractLike many figures in popular music, the British dance bandleader and entrepreneur Jack Hylton (1892–1965) has been largely forgotten. Through concert tours of France and nostalgic recordings with Chevalier, Hylton forged a connection which peaked at the Paris Opéra. Despite his large French-related repertory, which included ‘jazz’ arrangements of Stravinsky's Mavra, Ravel's Boléro and chansons, his American-influenced style was ultimately international. If his obsession justified the quip of ‘Parisomania’, there was reason in his madness.
Operational limits during high power long pulses with radiofrequency heating in Tore Supra
Authors: Ekedahl A. , Bucalossi J. , Basiuk V. , Brémond S. , Colas L. , Corre Y. , Delchambre E. , Douai D. , Dumont R. , Dunand G. , Giruzzi G. , Goniche M. , Hong S. , Imbeaux F. , Kazarian F. , Lombard G. , Manenc L. , Meyer O. , Millon L. , Mitteau R. , Monier-Garbet P. , Moreau P. , Pégourié B. , Rimini F.G. , Saint-Laurent F. , Samaille F. , Schwob J.L. , Tsitrone E. 
Published: August 2009

Issues related to the limitations and optimization of long pulse operation at high radiofrequency (RF) power levels in the Tore Supra tokamak are presented. An increasing operational limitation was encountered during the experimental campaigns in 2006–2007, affecting the high power and long pulse performance. This limitation was characterized by the sudden appearance of a multifaceted asymmetric radiation from the edge (MARFE), often followed by a disruption. The analyses revealed that the limitation could be linked to over-heating and flaking of the carbon re-deposition layers on the main plasma facing components (PFCs). The carbon deposits on all PFCs were therefore completely removed during the winter shutdown 2007–2008. Following this, a remarkable improvement in the injected power capability was observed, resulting in almost 12 MW of injected power during 10 s, without any of the previous signs of limitation (MARFE, disruption).
Furthermore, the RF antennas are subject to localized heat loads due to RF sheath effects and interaction by fast particles, effects which need to be minimized in particular for long pulse operation. Experimental results concerning the heat load on the antennas, caused by fast ion losses in the presence of magnetic ripple, are presented in this paper.
A retrospective analysis to explore the applicability of fish biomarkers and sediment bioassays along contaminated salinity transects
Authors: Schipper Cor A. , Lahr Joost , van den Brink Paul J. , George Steve G. , Hansen Peter-Diedrich , da Silva de Assis Helena C. , van der Oost Ron , Thain John E. , Livingstone Dave , Mitchelmore Carys , van Schooten Frederik-Jan , Ariese Freek , Murk Albertinka J. , Grinwis Guy C. M. , Klamer Hans , Kater Belinda J. , Postma Jaap F. , van der Werf Bert , Vethaak A. Dick 
Published: August 2009

AbstractSchipper, C. A., Lahr, J., van den Brink, P. J., George, S. G., Hansen, P-D., da Silva de Assis, H. C., van der Oost, R., Thain, J. E., Livingstone, D., Mitchelmore, C., van Schooten, F-J., Ariese, F., Murk, A. J., Grinwis, G. C. M., Klamer, H., Kater, B. J., Postma, J. F., van der Werf, B., and Vethaak, A. D. 2009. A retrospective analysis to explore the applicability of fish biomarkers and sediment bioassays along contaminated salinity transects. – ICES Journal of Marine Science, 66: 2089–2105. Biological-effects monitoring in estuarine environments is complex as a result of strong gradients and fluctuations in salinity and other environmental conditions, which may influence contaminant bioavailability and the physiology and metabolism of the organisms. To select the most robust and reliable biological-effect methods for monitoring and assessment programmes, a large-scale field study was conducted in two estuarine transects in the Netherlands. The locations ranged from heavily polluted harbour areas (the ports of Rotterdam and Amsterdam) to cleaner coastal and freshwater sites. Assessment methods used included a variety of biomarkers in flounder (Platichthys flesus) and a range of in vitro (sediment extracts) and in vivo bioassays. Multivariate statistical analysis was applied to investigate correlations and relationships between various biological effects and contaminant levels in flounder liver or sediments. Several biological methods seemed to be too much affected by salinity differences for routine use in estuaries. The most discriminative biomarkers in the study were hepatic metallothionein content and biliary 1-OH pyrene in fish. Mechanism-based in vitro assays DR-CALUX and ER-CALUX applied to sediment extracts for screening of potential toxicity were much more responsive than in vivo bioassays with macro-invertebrates using survival as an endpoint.
Progress in modelling herring populations: an individual-based model of growth
Authors: Russo Tommaso , Mariani Stefano , Baldi Paolo , Parisi Antonio , Magnifico Giuseppe , Clausen Lotte Worsøe , Cataudella Stefano 
Published: August 2009

Abstract
Russo, T., Mariani, S., Baldi, P., Parisi, A., Magnifico, G., Clausen, L. W., and Cataudella, S. 2009. Progress in modelling herring populations: an individual-based model of growth. – ICES Journal of Marine Science, 66: 1718–1725. Stock assessment may gain from taking into account individual variations in growth, because size is a key predictor of survival and reproduction. In trying to understand patterns in empirical observations, a major challenge is to model the changes in the size distribution of a cohort with age. We introduce an individual-based growth model that is founded on the use of a stochastic class of processes called subordinators. This modelling approach has several desirable features, because it (i) can take account of both individual and environmental sources of random variations, (ii) has the property of letting size increase monotonically, and (iii) ensures that the mean size-at-age follows the widely accepted von Bertalanffy equation. The parameterization of the model is tested on two Atlantic herring (Clupea harengus) datasets collected from the stocks of North Sea autumn spawners (ICES Divisions IVa, IVb, and IVc) and western Baltic spring spawners (ICES Subarea III). The size distributions obtained from the subordinator model largely match the observed size distributions, suggesting that this approach might be successfully implemented to support the assessment of commercial fish stocks, such as when modelling of size variability is required.
Expression of Pyrococcus furiosus Superoxide Reductase in Arabidopsis Enhances Heat Tolerance
Authors: Im Yang Ju , Ji Mikyoung , Lee Alice , Killens Rushyannah , Grunden Amy M. , Boss Wendy F. 
Published: August 2009

Abstract
Plants produce reactive oxygen species (ROS) in response to environmental stresses sending signaling cues, which, if uncontrolled, result in cell death. Like other aerobic organisms, plants have ROS-scavenging enzymes, such as superoxide dismutase (SOD), which removes superoxide anion radical (O2 −) and prevents the production and buildup of toxic free radicals. However, increasing the expression of cytosolic SODs is complex, and increasing their production in vivo has proven to be challenging. To avoid problems with endogenous regulation of gene expression, we expressed a gene from the archaeal hyperthermophile Pyrococcus furiosus that reduces O2 −. P. furiosus uses superoxide reductase (SOR) rather than SOD to remove superoxide. SOR is a thermostable enzyme that reduces O2 − in a one-electron reduction without producing oxygen. We show that P. furiosus SOR can be produced as a functional enzyme in planta and that plants producing SOR have enhanced tolerance to heat, light, and chemically induced ROS. Stress tolerance in the SOR-producing plants correlates positively with a delayed increase in ROS-sensitive transcripts and a decrease in ascorbate peroxidase activity. The SOR plants provide a good model system to study the impact of cytosolic ROS on downstream signaling in plant growth and development. Furthermore, this work demonstrates that this synthetic approach for reducing cytosolic ROS holds promise as a means for improving stress tolerance in crop plants.
MATE Transporters Facilitate Vacuolar Uptake of Epicatechin 3′-O-Glucoside for Proanthocyanidin Biosynthesis inMedicago truncatulaandArabidopsis
Authors: Zhao Jian , Dixon Richard A. 
Published: August 2009

AbstractExpression of the Arabidopsis thaliana MYB transcription factor TRANSPARENT TESTA 2 (TT2) in Medicago trunculata hairy roots induces both proanthocyanidin accumulation and the ATP-dependent vacuolar/vesicular uptake of epicatechin 3′-O-glucoside; neither process is active in control roots that do, however, possess anthocyanidin 3-O-glucoside vacuolar uptake activity. A vacuolar membrane-localized multidrug and toxic compound extrusion (MATE) transporter, Medicago MATE1, was identified at the molecular level and shown to preferentially transport epicatechin 3′-O-glucoside. Genetic evidence has implicated TT12, a tonoplastic MATE transporter from Arabidopsis, in the transport of precursors for proanthocyanidin biosynthesis in the seed coat. However, although Arabidopsis TT12 facilitates the transport of cyanidin 3-O-glucoside into membrane vesicles when expressed in yeast, there is no evidence that cyanidin 3-O-glucoside is converted to proanthocyanidins after transport into the vacuole. Here, we show that Arabidopsis TT12, like Medicago MATE1, functions to transport epicatechin 3′-O-glucoside as a precursor for proanthocyanidin biosynthesis, and Medicago MATE1 complements the seed proanthocyanidin phenotype of the Arabidopsis tt12 mutant both quantitatively and qualitatively. On the basis of biochemical properties, tissue-specific expression pattern, and genetic loss-of-function analysis, we conclude that MATE1 is an essential membrane transporter for proanthocyanidin biosynthesis in the Medicago seed coat. Implications of these findings for the assembly of oligomeric proanthocyanidins are discussed.
The effects of low summer flow on wild salmon (Salmo salar), trout (Salmo trutta) and grayling (Thymallus thymallus) in a small stream
Authors: RILEY W. D. , MAXWELL D. L. , PAWSON M. G. , IVES M. J. 
Published: August 2009

Summary1. The effects of an experimentally imposed low summer flow on habitat use, displacement and survival of wild populations of juvenile salmon (Salmo salar), trout (Salmo trutta) and grayling (Thymallus thymallus) were investigated in a chalk stream. The habitat use and mobility of the fish in response to reduced flow was determined using passive integrated transponder‐tag detector systems.2. Habitat use was compared to that available under different flow regimes. These consisted of an initial control phase of normal summer flow, an abrupt step change to 21 days of low flow, followed by a second control phase when normal summer flow was reinstated. First year (0+) salmon showed little change in their preferred substratum during low flow, whilst 1+ salmon increased their use of gravel and reduced that of mud during the day. Both 0+ and 1+ salmon were found in relatively deep water by day under low flow, whilst 1+ salmon preferred relatively shallow water at night. First year trout increased their use of gravel and reduced their use of mud and submerged tree roots under low flow, using relatively deep and fast flowing water by day. Older trout increased their use of gravel and occupied relatively deep, slow flowing water by day and relatively fast and shallow water at night. Grayling showed little change in their preferred substratum, but occupied relatively shallow water following the introduction of low flow.3. The range of movement of juvenile salmon increased at night under low flow, and was greater by day under normal flow. There was also an initial increase in the range of movement of 0+ trout following the introduction of low flow. Older trout initially moved less under low flow. With reduced flow, the range of movement by grayling increased significantly during the day.4. There was no net downstream displacement of any species with reduced flow, but the mortality rate in 0+ salmon, trout and grayling increased. This may be related to their small size and increased vulnerability to predation under low flow, and due to the reduction in depth and loss of the stream margins that are normally the preferred habitat of 0+ trout and grayling.5. The findings of this field study have implications for the management of braided, and highly regulated, chalk stream systems. In particular, they underline the importance of the stream margins as juvenile salmonid habitat, and suggest that a flow management strategy is required to mitigate for drought conditions. Such a strategy might include pre‐emptive controls on abstraction and the maintenance of river flow via a prioritised route, predetermined using fish or habitat surveys, to minimise the effects of drought conditions on the more vulnerable or valued fish groups.
Invasion, genetic variation and species identity of the calanoid copepod Sinodiaptomus valkanovi
Authors: MAKINO WATARU , KNOX MATTHEW A. , DUGGAN IAN C. 
Published: August 2009

Summary1. Although Sinodiaptomus valkanovi [sensu Ueda & Ohtsuka (Hydrobiologia, 379, 1998, 159)] is one of the most common freshwater calanoid copepods in Japan, it was originally described from specimens collected in Sofia, Bulgaria, as a subspecies of S. sarsi. This original description raises two issues requiring further investigation. One is whether or not S. valkanovi should be differentiated from S. sarsi at a species level, and the other is whether or not records of S. valkanovi from outside of Japan are the result of biological invasions.2. We examined the gene flow between S. valkanovi and S. sarsi in Japan, using nuclear DNA (the ribosomal internal transcribed spacers 1 and 2 plus the intervening 5.8S ribosomal DNA subunit) sequence to clarify if these two taxa are separable at a species level. We also investigated the population genetic structure of S. valkanovi in Japan, using the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene, and subsequently of two recently discovered New Zealand populations, to elucidate the origin and colonisation/invasion history of this taxon.3. In total, 43 and three Japanese populations of S. valkanovi and S. sarsi, respectively, were analysed. These two taxa did not occur together in any of the localities. Nuclear DNA analysis did not provide any evidence of gene flow between them, and the inter‐taxon variability of mtCOI was high, corroborating the conclusion of Ueda & Ohtsuka based on morphological characteristics that S. valkanovi and S. sarsi should be differentiated at the species level.4. In Japan S. valkanovi populations are segregated into two areas, around the Seto Inland Sea (SIS) and northeastern (NE) area. A distinct contrast in the genetic diversity was observed between the areas; five mtCOI haplotypes were recovered from the NE area while 38 were observed in the SIS area, despite a similar geographical range and number of individuals analysed in both areas. Furthermore, S. valkanovi in the SIS area possessed a mixture of both ancestral and derived haplotypes, while those in the NE area mostly consisted of derived haplotypes. These results suggest that the NE populations were founded recently by a limited numbers of individuals from SIS populations.5. All specimens of S. valkanovi from New Zealand possessed one specific mtCOI haplotype. In Japan, this haplotype was found only in the NE area, suggesting the origin of New Zealand S. valkanovi. It is likely that this copepod has on several occasions invaded areas outside of Japan, one of which was associated with the original description of this taxon in Bulgaria.