bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of retinal pigment epithelium properties in ciliary margin progenitor cells
Authors: Vossmerbaeumer Urs , Kuehl Sandra , Kern Susanne , Kluter Harald , Jonas Jost B , Bieback Karen 
Published: July 2008

AbstractPurpose:  Degenerative processes in the retinal pigment epithelium (RPE) are known to play a pivotal role in the development of age‐related maculopathy. Substitute RPE analogue cells could be used to preserve visual function. In this paper we investigate methods for the isolation, cultivation and RPE differentiation of undifferentiated cells from the ciliary marginal zone (CMZ) of rat eyes.Methods:  The CMZ was isolated from enucleated rat eyes, cell spheres formed in serum‐free suspension culture, Bromodeoxyuridine (BrdU) incorporation indicated mitotic activity. Following baseline differentiation status assessment, directional differentiation was induced by cultivating cells in RPE‐conditioned medium and vasoactive intestinal peptide (VIP). The differentiation status was analysed by immunocytochemistry. Fluorescein isothiocyanate (FITC)‐labelled latex beads were used for functional evaluation.Results:  CMZ‐derived cells were expanded for 6–12 months. Formation of spherical cellular conglomerates, subsphere formation and expression of nestin indicated progenitor cells. Baseline levels of markers MAP‐2 for neuronal and GFAP for glial properties and baseline levels of bestrophin, cytokeratins 8 and 18 and RPE 65 for RPE properties were induced by serum culture, respectively. Culture in conditioned medium with addition of VIP significantly increased RPE marker expression and reduced neuronal features, uptake of latex beads indicated phagocytosis.Conclusions:  We succeeded in isolating and cultivating cells from rodent CMZ with progenitor cell characteristics. Subsequently, these cells tested positive for neuronal, glial and RPE markers. Appropriate conditions significantly increased RPE marker expression. Unidirectional induction of differentiation makes the CMZ eligible as a source of regenerative ocular tissue for RPE‐reconditioning therapy.
Postoperative Mycobacterium abscessus nodular conjunctivitis
Authors: Merani Rohan , Orekondy Sid , Gottlieb Thomas , Janarthanan Perumal , McCarthy Stanley , Karim Rooshdiya , Booth Frances 
Published: July 2008

AbstractNon‐tuberculous or ‘atypical’ mycobacteria are unusual causes of ocular or periocular infection. We report a case of postoperative Mycobacterium abscessus infection of the conjunctiva. A 71‐year‐old gentleman developed nodular conjunctival injection and irritation 6 weeks after cataract surgery. After failure of topical therapy with antibiotics, steroids and lubricants, a biopsy was taken. Histological examination revealed non‐caseating granulomas within which were clusters of acid‐fast bacilli, subsequently identified as M. abscessus. The patient received a total of 16 weeks of oral antimycobacterial treatment and the conjunctivitis completely resolved. A suspected recurrence was successfully treated with topical ciprofloxacin and at final follow up 15 months later there was no evidence of infection. To the best of our knowledge this is the first report of non‐tuberculous mycobacterial infection of the conjunctiva occuring after cataract surgery.
Former patients' experience of psychiatric care: A qualitative investigation
Authors: Lilja Lars , Hellzén Ove 
Published: July 2008

ABSTRACT:  In this study, 10 former patients' experiences of hospitalization are described using a qualitative approach. The informant group consisted of three men and seven women with different diagnoses and each with his or her individual experience of life as an inpatient. The aim of this study was to extend our understanding of former psychiatric inpatients' experience their time of admission to a psychiatric inpatients unit.Data were collected and analysed using a content analysis approach. From the former patients' descriptions, the following five themes emerged: being seen as a disease, striving for a sense of control in an alienating and frightening context, succumbing to repressive care, meeting an omniscient master, and care as a light in the darkness. In conclusion, the experience of psychiatric inpatient care could be interpreted and understood from former patients' narratives as a struggle for dignity in the face of discrimination and rejection.
Commentary on Holmes et al. (2007): resolving the debate on when extinction risk is predictable
Authors: Ellner Stephen P. , Holmes Elizabeth E. 
Published: July 2008

AbstractWe reconcile the findings of Holmes et al. (Ecology Letters, 10, 2007, 1182) that 95% confidence intervals for quasi‐extinction risk were narrow for many vertebrates of conservation concern, with previous theory predicting wide confidence intervals. We extend previous theory, concerning the precision of quasi‐extinction estimates as a function of population dynamic parameters, prediction intervals and quasi‐extinction thresholds, and provide an approximation that specifies the prediction interval and threshold combinations where quasi‐extinction estimates are precise (vs. imprecise). This allows PVA practitioners to define the prediction interval and threshold regions of safety (low risk with high confidence), danger (high risk with high confidence), and uncertainty.
Plant species traits are the predominant control on litter decomposition rates within biomes worldwide
Authors: Cornwell William K. , Cornelissen Johannes H. C. , Amatangelo Kathryn , Dorrepaal Ellen , Eviner Valerie T. , Godoy Oscar , Hobbie Sarah E. , Hoorens Bart , Kurokawa Hiroko , Pérez‐Harguindeguy Natalia , Quested Helen M. , Santiago Louis S. , Wardle David A. , Wright Ian J. , Aerts Rien , Allison Steven D. , Van Bodegom Peter , Brovkin Victor , Chatain Alex , Callaghan Terry V. , Díaz Sandra , Garnier Eric , Gurvich Diego E. , Kazakou Elena , Klein Julia A. , Read Jenny , Reich Peter B. , Soudzilovskaia Nadejda A. , Vaieretti M. Victoria , Westoby Mark 
Published: July 2008

AbstractWorldwide decomposition rates depend both on climate and the legacy of plant functional traits as litter quality. To quantify the degree to which functional differentiation among species affects their litter decomposition rates, we brought together leaf trait and litter mass loss data for 818 species from 66 decomposition experiments on six continents. We show that: (i) the magnitude of species‐driven differences is much larger than previously thought and greater than climate‐driven variation; (ii) the decomposability of a species’ litter is consistently correlated with that species’ ecological strategy within different ecosystems globally, representing a new connection between whole plant carbon strategy and biogeochemical cycling. This connection between plant strategies and decomposability is crucial for both understanding vegetation–soil feedbacks, and for improving forecasts of the global carbon cycle.
The complete genome sequence ofMoorella thermoacetica(f.Clostridium thermoaceticum)
Authors: Pierce Elizabeth , Xie Gary , Barabote Ravi D. , Saunders Elizabeth , Han Cliff S. , Detter John C. , Richardson Paul , Brettin Thomas S. , Das Amaresh , Ljungdahl Lars G. , Ragsdale Stephen W. 
Published: July 2008

SummaryThis paper describes the genome sequence ofMoorella thermoacetica(f.Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood–Ljungdahl pathway of CO and CO2fixation. This pathway, which is also known as the reductive acetyl‐CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into 3 mol of acetate and to grow autotrophically using H2and CO as electron donors and CO2as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO2. Acetogenic bacteria also couple the Wood–Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols and aromatic compounds) and electron acceptors (CO2, nitrate, nitrite, thiosulfate, dimethylsulfoxide and aromatic carboxyl groups). The genome consists of a single circular 2 628 784 bp chromosome encoding 2615 open reading frames (ORFs), which includes 2523 predicted protein‐encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. A total of 2384 (91.17%) of the ORFs in theM. thermoaceticagenome can be grouped in orthologue clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the coreacsgene cluster of the Wood–Ljungdahl pathway.
Enrichment of a dioxin‐dehalogenating Dehalococcoides species in two‐liquid phase cultures
Authors: Bunge Michael , Wagner Anke , Fischer Marco , Andreesen Jan R. , Lechner Ute 
Published: July 2008

SummaryEnrichment cultures capable of reductively dechlorinating 1,2,4‐trichlorodibenzo‐p‐dioxin (1,2,4‐TrCDD) were shown to dechlorinate 1,2,3‐trichlorobenzene (1,2,3‐TrCB) to 1,3‐dichlorobenzene. To test if this activity can be used to enrich for dioxin‐dechlorinating bacteria, a two‐liquid phase cultivation with 200 mM 1,2,3‐TrCB dissolved in hexadecane was established. During the dechlorination of 1,2,3‐TrCB, the number of 1,2,4‐TrCDD‐dechlorinating bacteria increased by four orders of magnitude, eventually accounting for 11% of the total cell number. Characterization of the bacterial communities of the initial dioxin‐dechlorinating culture and of the trichlorobenzene enrichments by restriction fragment length polymorphism (RFLP) analysis of cloned 16S rRNA genes revealed a proportional increase of nine different sequence types, one representing a Dehalococcoides strain. Inhibition of methanogens further enhanced the rate of chlorobenzene dehalogenation and also resulted in a rapid dechlorination of 1,2,3,4‐tetrachlorodibenzo‐p‐dioxin that was applied via a hexadecane phase. The further enrichment was monitored by terminal RFLP, quantitative real‐time PCR and microscopy, and aimed at the reduction of the accompanying non‐dehalogenating populations by using different combinations of electron donors and the application of antibiotics. Hydrogen as the sole electron donor proved to be less efficient due to the co‐enrichment of acetogens. The novel Dehalococcoides strain DCMB5 was enriched up to 50% by the cultivation with organic acids, hydrogen and vancomycin, and was finally purified by conventional isolation techniques.
Enriching plant microbiota for a metagenomic library construction
Authors: Wang Hao‐Xin , Geng Zhao‐Liang , Zeng Ying , Shen Yue‐Mao 
Published: July 2008

SummaryPlant microbiota (the microorganisms that live in any associations with plant tissues) represents a rather unexplored area of metagenomic research compared with soils and oceans. Constructing a metagenomic library for plant microbiota is technically challenging. Using all the biomass without pre‐enrichment could lead to vast proportions of the host plant DNA in the metagenomic library, doubtless obliterating the microbial contribution. Therefore, the first and essential step is to enrich for the constituent microorganisms from plant tissues. Here, a strong enrichment for plant microbiota was achieved by coupling SDS (sodium dodecyl sulfate) with NaCl, creating a predominantly microbial metagenomic library that contains 88% bacterial inserts. 16S rDNA sequence analysis revealed that the metagenomic DNA of enrichments originates from very diverse microorganisms. At least 74 distinct ribotypes (at a 97% threshold) from seven different bacterial phyla were identified and mainly distributed among Actinobacteria and Proteobacteria. Additionally, a simplified version of Amplified Ribosomal DNA Restriction Analysis (ARDRA) was developed for a quick and efficient assessment of the enriching procedures. This work opens further insight into the great biotechnical potential of plant microbiota, holding more potential for drug discovery through a metagenomic strategy, and paving the way for recovery and biochemical characterization of functional gene repertoire from plant microbiota.
Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton
Authors: Quaiser Achim , López‐García Purificación , Zivanovic Yvan , Henn Matthew R. , Rodriguez‐Valera Francisco , Moreira David 
Published: July 2008

Summary Acidobacteria constitute a still poorly studied phylum that is well represented in soils. Recent studies suggest that members of this phylum may be also abundant in deep‐sea plankton, but their relative abundance and ecological role in this ecosystem are completely unknown. A recent screening of three metagenomic deep‐sea libraries of bathypelagic plankton from the South Atlantic (1000 m depth), the Adriatic (1000 m depth) and the Ionian (3000 m depth) seas in the Mediterranean revealed an unexpected relative proportion of acidobacterial fosmids, which affiliated to the Solibacterales (Group 3), to the Group 11 and, most frequently, to the Group 6 of this diverse phylum. Here, we present the comparative analysis of 11 acidobacterial genome fragments containing the rrn operon from these Mediterranean libraries. A highly conserved syntenic region spanning up to 30 kb and containing up to 25 open reading frames was shared by Group 6 Acidobacteria. Synteny was also partially conserved in distantly related acidobacterial genome fragments derived from a metagenomic soil library, indicating a remarkable conservation of this genomic region within these Acidobacteria. A search for Acidobacteria‐specific hits in directly comparable, available fosmid‐end sequences from soil and marine metagenomic libraries showed a significant increase of their relative proportion in plankton libraries as a function of increasing depth reaching, at high depth, levels nearly comparable to those of soil. Thus, our results suggest that Acidobacteria are abundant and represent a significant proportion of the microbial community in the deep‐sea ecosystem.
Soil salinity determines the relative abundance of C3/C4 species in Argentinean grasslands
Authors: Feldman S. R. , Bisaro V. , Biani N. B. , Prado D. E. 
Published: July 2008

ABSTRACTAim  The C4 and crassulacean acid metabolism (CAM) pathways are adaptations to compensate for high rates of photorespiration and water and carbon deficiency. This is the first attempt to compare the relative abundance of C3 vs. C4 + CAM species in temperate and subtropical grasslands across a latitudinal gradient in central Argentina. We predict that under the same rainfall regime, C4 + CAM plants will have larger soil coverage in highly saline soils than in neighbouring non‐saline ones.Location  Data were taken from three phytogeographical provinces in the Santa Fe province of Argentina: Chaquenian, Pampean and Espinal.Methods  The salinity of the soil was estimated through aqueous solution conductivity. The proportions of species belonging to C3/C4 + CAM photosynthetic pathways were compared among halophyte and non‐halophyte communities with a χ2 homogeneity test. The sum of cover percentages corresponding to the C3 and C4 + CAM photosynthetic pathways were calculated and compared using analysis of variance (ANOVA).Results  The soil conductivity values were higher in the halophyte than in the non‐halophyte communities for the same phytogeographical area. The C4 + CAM plants had much higher soil coverage values in halophyte than in non‐halophyte communities in the Pampean and Espinal phytogeographical provinces. The differences were not statistically significant in the Chaquenian province.Main conclusions  Soil drought provoked by soil salinity results in a much higher soil cover by C4 + CAM plants in regions with positive to neutral water balance (i.e. Pampean and Espinal). This differential abundance pattern in C4 + CAM functional group is not observed in areas where a pronounced water deficit exists per se (Chaquenian region), and therefore C4 + CAM plants predominate in all environments regardless of soil salinity. Our results suggest that one of the main environmental forces driving the upsurge of C4 species in Argentinean grasslands might have been the strong local soil salinity gradient.
Contrasting alien and native plant species–area relationships: the importance of spatial grain and extent
Authors: Hulme Philip E. 
Published: July 2008

ABSTRACTAim  The proportion of alien plant species in floras is increasingly being used to indicate the threat of invasions to native species and/or the homogenization of biodiversity. However, this indicator is only valuable if it is independent of the spatial extent and grain of observation. This study tested the equivalence of native and alien species–area relationships (SARs) in order to assess the support for scale invariance in the proportion of alien species in floras.Location  England, UK.Methods  Nested SARs were generated by assessing the richness of native and alien plant species drawn from the New atlas of the British and Irish flora for six areas comprising 100, 400, 900, 1600, 2500 and 3600 km2 with each larger area containing all smaller areas. Five replicate sets of nested areas encompassing northern, southern, eastern, western and central regions were chosen. For each set of nested areas, the log‐transformed species richness was regressed on log‐transformed area to fit a power function to the SAR.Results  Native and alien plant SARs reveal consistent differences in slope, highlighting that the proportion of alien species is a function of spatial grain. Aliens are more rare than natives and have higher spatial turnover leading to faster accumulation of species as area increases. However, equivalent samples drawn from a larger spatial extent reveal similar alien and native SARs.Main conclusions  The significant differential scale dependence in native and alien species richness observed in this study reflects dissimilar influences of regional drivers such as habitat, but potentially also propagule pressure and introduction history, that leads to the relative rarity and high spatial turnover of alien species. Maps of invasion hotspots that identify areas where the proportion of the alien flora is particularly high should therefore be treated with considerable caution since patterns across most grains used for species monitoring will be scale dependent.
Optimal foraging constrains macroecological patterns: body size and dietary niche breadth in lizards
Authors: Costa Gabriel C. , Vitt Laurie J. , Pianka Eric R. , Mesquita Daniel O. , Colli Guarino R. 
Published: July 2008

ABSTRACTAim To explore and identify probable mechanisms contributing to the relationships among body size, dietary niche breadth and mean, minimum, maximum and range of prey size in predaceous lizards.Location Our data set includes species from tropical rainforests, semi‐arid regions of Brazil, and from deserts of the south‐western United States, Australia and the Kalahari of Africa.Methods We calculated phylogenetic and non‐phylogenetic regressions among predator body size, dietary breath and various prey size measures.Results We found a negative association between body size and dietary niche breadth in 159 lizard species sampled across most evolutionary lineages of squamate reptiles and across major continents and habitats. We also show that mean, minimum, maximum and range of prey size were positively associated with body size.Main conclusions Our results suggest not only that larger lizards tend to eat larger prey, but in doing so offset their use of smaller prey. Reduction of dietary niche breadth with increased body size in these lizards suggests that large predators target large and more profitable prey. Consequently, the negative association between body size and niche breadth in predators most likely results from optimal foraging. Though this result may appear paradoxical and runs counter to previous studies, resources for predators may be predictably more limited than resources for herbivores, thus driving selection for more profitable prey.
Continental‐scale tree population response to rapid climate change, competition and disturbance
Authors: Peros Matthew C. , Gajewski K. , Viau André E. 
Published: July 2008

ABSTRACTAim  Using a new approach to analyse fossil pollen data, we investigate temporal and spatial patterns in Populus (poplar, cottonwood, aspen) from the Late Glacial to the present at regional to continental scales.Location  North America.Methods  We extracted data on the timing and magnitude of the maximum value of Populus pollen from each pollen diagram in the North American Pollen Database (NAPD). The information was plotted in histograms of 150‐year bins to identify times when Populus was abundant on the landscape. We also mapped the maximum values to identify spatial patterns and their causes.Results  Our analyses show that there have been several periods since the Late Glacial when Populus was abundant on the landscape: (1) from 12.35 to 12.65 kyr bp, in eastern North America, largely in response to the opening of the forest following the onset of the Younger Dryas; (2) from 10.85 to 11.75 kyr bp, following the termination of the Younger Dryas; and (3) during the last 150 years, as land was cleared for agricultural use, especially in the midwestern United States.Main conclusion  Since the Late Glacial, changes in the abundance of Populus were caused more by the effects of abrupt climate change on its major competitors, rather than the direct effects of climate on Populus itself.
Market Orientation, Generative Learning, Innovation Strategy and Business Performance Inter‐Relationships in Bioscience Firms
Authors: Morgan Robert E. , Berthon Pierre 
Published: July 2008

abstractWe propose conceptual arguments to establish relationships between market orientation and generative learning and their respective impact on exploitative innovation strategy and explorative innovation strategy. We then consider the ambidextrous association between both forms of innovation strategy and business performance. This model is subject to an empirical test using data generated from 160 bioscience firms. Using structural equation modelling, two mutually exclusive paths are specified where market orientation leads to exploitative innovation strategy, while generative learning leads to explorative innovation strategy. We then find that the ambidexterity exhibited by firms in the form of exploitative innovation strategy and explorative innovation strategy significantly explains improvements in firms’ business performance. Discussion is given to these findings and managerial implications are presented along with avenues for further research.