bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wetland degradation leads to homogenization of the biota at local and landscape scales
Authors: LOUGHEED VANESSA L. , MCINTOSH MOLLIE D. , PARKER CHRISTIAN A. , STEVENSON R. JAN 
Published: July 2008

Summary1. We examined whether the anthropogenic degradation of wetlands leads to homogenization of the biota at local and/or landscape scales and, if so, what specific factors account for such an effect. We compared 16 isolated wetlands (Michigan, U.S.A.) that varied in surrounding land use: half had developed, and half undeveloped, riparian zones. Samples of macrophytes, epiphytic diatoms, zooplankton, macroinvertebrates and water chemistry were collected along three transects in each wetland.2. Developed wetlands were more nutrient‐rich with higher Cl concentrations. The plant community at developed sites was dominated by Lemnaceae (duckweed), while undeveloped wetlands were dominated by rooted, floating‐leaved vegetation and sensitive plant species. Undeveloped wetlands contained heterogeneous and species‐rich plant communities, greater species richness of zooplankton and diatoms, and heterogeneous zooplankton distributions as compared to developed sites.3. A comparison among wetlands showed that diatom and zooplankton assemblages in developed wetlands were nested subsets of richer biota found in less developed wetlands. Conversely, plant communities were more heterogeneously distributed among developed wetlands at the landscape level. This may be attributable to patchy invasions by exotic species, which were a feature of the degraded wetlands within developed landscapes.4. Our results indicate that several taxonomic groups showed similar, probably inter‐dependent, responses to wetland degradation and habitat homogenization at both the local and landscape scales. This change in community structure from a species‐rich and heterogeneous community dominated by floating‐leaved plants in undeveloped wetlands, to nutrient‐rich wetlands dominated by duckweed may represent a shift to an alternate stable state.
Impact of past and present land‐management on the C‐balance of a grassland in the Swiss Alps
Authors: ROGIERS NELE , CONEN FRANZ , FURGER MARKUS , STÖCKLI RETO , EUGSTER WERNER 
Published: July 2008

AbstractGrasslands cover about 40% of the ice‐free global terrestrial surface, but their quantitative importance in global carbon exchange with the atmosphere is still highly uncertain, and thus their potential for carbon sequestration remains speculative. Here, we report on CO2 exchange of an extensively used mountain hay meadow and pasture in the Swiss pre‐Alps on high‐organic soils (7–45% C by mass) over a 3‐year period (18 May 2002–20 September 2005), including the European summer 2003 heat‐wave period. During all 3 years, the ecosystem was a net source of CO2 (116–256 g C m−2 yr−1). Harvests and grazing cows (mostly via C export in milk) further increased these C losses, which were estimated at 355 g C m−2 yr−1 during 2003 (95% confidence interval 257–454 g C m−2 yr−1). Although annual carbon losses varied considerably among years, the CO2 budget during summer 2003 was not very different from the other two summers. However, and much more importantly, the winter that followed the warm summer of 2003 observed a significantly higher carbon loss when there was snow (133±6 g C m−2) than under comparable conditions during the other two winters (73±5 and 70±4 g C m−2, respectively). The continued annual C losses can most likely be attributed to the long‐term effects of drainage and peat exploitation that began 119 years ago, with the last significant drainage activities during the Second World War around 1940. The most realistic estimate based on depth profiles of ash content after combustion suggests that there is an 500–910 g C m−2 yr−1 loss associated with the decomposition of organic matter. Our results clearly suggest that putting efforts into preserving still existing carbon stocks may be more successful than attempts to increase sequestration rates in such high‐organic mountain grassland soils.
Interannual variation in soil CO2 efflux and the response of root respiration to climate and canopy gas exchange in mature ponderosa pine
Authors: IRVINE J. , LAW B. E. , MARTIN J. G. , VICKERS D. 
Published: July 2008

AbstractWe examined a 6‐year record of automated chamber‐based soil CO2 efflux (Fs) and the underlying processes in relation to climate and canopy gas exchange at an AmeriFlux site in a seasonally drought‐stressed pine forest. Interannual variability of Fs was large (CV=17%) with a range of 427 g C m−2 yr−1 around a mean annual Fs of 811 g C m−2 yr−1. On average, 76% of the variation of daily mean Fs could be quantified using an empirical model with year‐specific basal respiration rate that was a linear function of tree basal area increment (BAI) and modulated by a common response to soil temperature and moisture. Interannual variability in Fs could be attributed almost equally to interannual variability in BAI (a proxy for above‐ground productivity) and interannual variability in soil climate. Seasonal total Fs was twice as sensitive to soil moisture variability during the summer months compared with temperature variability during the same period and almost insensitive to the natural range of interannual variability in spring temperatures. A strong seasonality in both root respiration (Rr) and heterotrophic respiration (Rh) was observed with the fraction attributed to Rr steadily increasing from 18% in mid‐March to 50% in early June through early July before dropping rapidly to 10% of Fs by mid‐August. The seasonal pattern in Rr (10‐day averages) was strongly linearly correlated with tree transpiration (r2=0.90, P<0.01) as measured using sap flux techniques and gross ecosystem productivity (GEP, r2=0.83, P<0.01) measured by the eddy‐covariance approach. Rr increased by 0.43 g C m−2 day−1 for every 1 g C m−2 day−1 increase in GEP. The strong linear correlation of Rr to seasonal changes in GEP and transpiration combined with longer‐term interannual variability in the base rate of Fs, as a linear function of BAI (r2=0.64, P=0.06), provides compelling justification for including canopy processes in future models of Fs.
Effects of tractor wheeling on root morphology and yield of lucerne (Medicago sativa L.)
Authors: Głąb T. 
Published: July 2008

SummaryThe purpose of this study was to determine the effect of soil compaction on the herbage yield and root growth of lucerne (Medicago sativa L.). A field experiment was conducted on a silty loam Mollic Fluvisols soil in 2003–2006. Herbage yield and root morphology, in terms of root length density, mean root diameter, specific root length and distribution of dry matter (DM) in roots, were measured. Four compaction treatments were applied three times annually by tractor using the following number of passes: control without experimental traffic, two passes, four passes and six passes. The tractor traffic changed the physical properties of the soil by increasing bulk density and penetration resistance. Soil compaction also improved its water retention properties. These changes were associated with changes in root morphology and distribution of the DM in roots. Soil compaction resulted in higher proportions of the DM in roots, especially in the upper, 0–10 cm, soil horizon. Decreases in the root length density were observed in a root diameter range of 0·1–1·0 mm. It was also found that roots in a more compacted soil were significantly thicker. An effect of the root system of lucerne on soil compaction was observed. The root system of lucerne decreased the effects of soil compaction that had been recorded in the first and the second year of the experiment. An increase in the number of passes resulted in a decrease in the DM yield of herbage in the second and third harvests each year.
Enhanced secretion of interferon‐γ by bovine γδ T cells induced by coculture with Mycobacterium bovis‐infected dendritic cells: evidence for reciprocal activating signals
Authors: Price Sally J. , Hope Jayne C. 
Published: July 2008

SummaryEvidence suggests that γδ T cells form part of the innate immune response to Mycobacterium bovis infection. Dendritic cells (DCs) are capable of secreting high levels of interleukin‐12 (IL‐12) following infection with mycobacteria and can induce interferon‐γ (IFN‐γ) secretion by natural killer and γδ T cells We investigated the innate interactions occurring between WC1+γδ T cells and M. bovis‐infected DCs. Following coculture with M. bovis‐infected DCs, secretion of IFN‐γ and expression of CD25 and major histocompatibility complex class II on WC1+γδ T cells were significantly enhanced. Reciprocal enhancement of IL‐12 secretion by the DCs was also observed and this interaction was found to be contact dependent. We hypothesize that there is an early, transient signal between the WC1+γδ T cells and the DCs, which promotes the synthesis of biologically active IL‐12, and which is dependent upon cell–cell contact. Reciprocal signals including IL‐12 are then delivered to WC1+γδ cells, which leads to the enhanced secretion of IFN‐γ, and the up‐regulation of activation markers and antigen presentation molecules by the WC1+γδ T cells. These interactions are likely to form a critical part of the T helper type 1‐conditioning response of DCs to M. bovis.
Differential expression of CD26 on virus‐specific CD8+ T cells during active, latent and resolved infection
Authors: Ibegbu Chris C. , Xu Yong‐Xian , Fillos Dimitri , Radziewicz Henry , Grakoui Arash , Kourtis Athena P. 
Published: July 2008

SummaryThe hallmark of effective establishment of immune memory is the long‐term memory cell that persists in the absence of antigen. To explore its characteristics, we investigated the differences between a resolved successful immune response, such as after influenza (flu) vaccination, and the state of chronic infection with persistent antigen, such as with cytomegalovirus (CMV), Epstein–Barr virus (EBV) or human immunodeficiency virus (HIV), which leads to defective T‐cell memory. Immunophenotypic analyses using multi‐parameter flow cytometry and tetramer technology identified a unique pattern of CD26high expression among influenza‐specific CD8+ T cells, but not among CD8+ T cells specific for CMV, EBV (three different epitopes) or HIV. The median percentage of CD8+ T cells expressing CD26 was 95·5% for influenza, but for cells specific for CMV, EBV and HIV it was 10·5%, 12%–19%, and 13·2%, respectively. These findings suggest that expression of CD26high may be a characteristic of a memory cell. CD26high expression correlates with expression of CD127, a marker of memory cells. Furthermore, CD26high cells can produce interleukin‐2. These findings offer insight into the dynamics of T‐cell differentiation, and they may offer a specific marker of a successfully developed memory CD8+ T cell, that of CD26high. This marker has the potential to be useful in studies of immune responses to infectious agents, and to new vaccine candidates.
Endogenous DNA damage and testicular germ cell tumors
Authors: Cook M. B. , Sigurdson A. J. , Jones I. M. , Thomas C. B. , Graubard B. I. , Korde L. , Greene M. H. , McGlynn K. A. 
Published: July 2008

SummaryTesticular germ cell tumors are comprised of two histologic groups, seminomas and non‐seminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable levels of net endogenous DNA damage. To test our hypothesis, we conducted a case–case analysis of 51 seminoma and 61 non‐seminoma patients using data and specimens from the Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort. A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modelled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with non‐seminoma compared with seminoma (OR50th percentile = 3.31, 95% CI: 1.00, 10.98; OR75th percentile = 3.71, 95% CI: 1.04, 13.20; p for trend = 0.039). OTM exhibited similar, albeit statistically non‐significant, risk estimates (OR50th percentile = 2.27, 95% CI: 0.75, 6.87; OR75th percentile = 2.40, 95% CI: 0.75, 7.71; p for trend = 0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that net endogenous levels are higher in patients who develop non‐seminoma compared with seminoma. This may partly explain the more aggressive biology and younger age‐of‐onset of this histologic subgroup compared with the relatively less aggressive, later‐onset seminoma.
Hidden phylogeographic complexity in the Sierra Madre Oriental: the case of the Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae)
Authors: Sosa Victoria , Ruiz‐Sanchez Eduardo , Rodriguez‐Gomez Flor C. 
Published: July 2008

AbstractAim  A phylogeographic study of the endemic Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae) was conducted to determine: (1) the historical processes that influenced its geographical pattern of genetic variation; (2) whether isolation by distance was one of the main factors that caused genetic divergence in populations of this species; and (3) whether genetic flow still exists between populations from northern arid zones (Chihuahuan Desert and Sierra Madre Oriental) and those from southern arid zones (Tehuacán‐Cuicatlán Valley) – populations that are separated by the Transvolcanic Belt.Location  Xerophytic vegetation in Mexico.Methods  Chloroplast DNA (cpDNA) sequences of three regions, trnH‐psbA, rpl32‐trnL(UAG) and ndhF‐rpl32, were obtained for 85 individuals from 17 populations sampled in the field, covering the entire range of H. fumariifolia. The evolutionary history of these populations was investigated using a nested clade phylogeographic analysis and also by conducting various population genetic analyses.Results  In total, 17 haplotypes were detected, 14 of which were found in the Sierra Madre Oriental. Differentiation among populations based on cpDNA variation (GST = 0.787, SE 0.0614) indicated population structure in H. fumariifolia, corroborated by a fixation index (FST) of 0.907. Results from analysis of molecular variance found that most of the total variation (90.71%, P < 0.001) was explained by differences among populations. Three regions were determined based on geological correspondence – the Chihuahuan Desert, Sierra Madre Oriental and Tehuacán‐Cuicatlán Valley – and the variation between them was significant (43.39%, P < 0.001). Results of a Mantel test showed a significant correlation between genetic and geographic distances (r = 0.511; P = 0.0001), suggesting a pattern of isolation by distance, which was corroborated by nested clade phylogeographic analysis. Mismatch distribution analysis indicated a sudden demographic expansion.Main conclusions  Our study found that isolation by distance influenced genetic divergence in populations of H. fumariifolia. The finding that allopatric fragmentation influenced genetic divergence in populations in the Sierra Madre Oriental may be a reflection of the complex geology of the area. Our results suggest that the areas located in the north of the Sierra Madre Oriental acted as post‐glacial refugia for some populations.
Nurses’ experiences of and opinions about using standardised care plans in electronic health records – a questionnaire study
Authors: Dahm Marie Fogelberg , Wadensten Barbro 
Published: July 2008

Aim.  The aim of the present study was to investigate nurses’ opinions about using standardised care plans in electronic health record and quality standards for clinical practice.Background.  Following introduction of an electronic health record, use of standardised care plans and quality standards has increased among nurses at two hospitals in Sweden. Understanding nurses’ opinions is important to continued development in this area. There are few previous studies on nurses’ opinions about standardised care plans.Design.  Survey.Method.  The study was quantitative, descriptive and based on a questionnaire. The questionnaire included items on nurses’ knowledge of and opinions about standardised care plans and quality standards.Results.  The majority of the nurses were of the opinion that standardised care plans increase their ability to provide the same high‐quality basic care for all patients. They also thought that a common standardised care plan across several professions would improve conditions for provision of high‐quality care. The majority of the nurses also felt that the quality standards are a prerequisite of maintaining standardised care plans of high quality. There was no consensus on whether standardised care plans increase the risk of failing to notice patients’ individual problems. Most agreed that standardised care plans decrease documentation time as well as redundant documentation. The study showed that training is needed to teach nurses how to use standardised care plans in care provision.Conclusions.  The nurses in the study had positive attitudes towards use of standardised care plans and felt that they could facilitate nursing practice.Relevance to clinical practice.  Use of standardised care plans can improve nursing documentation and facilitate work for nurses. Moreover, it can support nurses in their use of evidence‐based nursing methods. The present study shows that nurses have positive attitudes, which could facilitate continued use of standardised care plans.
Strong genetic population structure in the boring giant clam, Tridacna crocea, across the Indo‐Malay Archipelago: implications related to evolutionary processes and connectivity
Authors: KOCHZIUS MARC , NURYANTO AGUS 
Published: July 2008

AbstractEven though the Indo‐Malay Archipelago hosts the world's greatest diversity of marine species, studies on the genetic population structure and gene flow of marine organisms within this area are rather rare. Consequently, not much is known about connectivity of marine populations in the Indo‐Malay Archipelago, despite the fact that such information is important to understand evolutionary and ecological processes in the centre of marine biodiversity. This study aims to investigate the genetic population structure of the boring giant clam, Tridacna crocea. The analysis is based on a 456‐bp fragment of the cytochrome oxidase I gene from 300 individuals collected from 15 localities across the Indo‐Malay Archipelago. Tridacna crocea shows a very strong genetic population structure and isolation by distance, indicating restricted gene flow between almost all sample sites. The observed ΦST‐value of 0.28 is very high compared to other studies on giant clams. According to the pronounced genetic differences, the sample sites can be divided into four groups from West to East: (i) Eastern Indian Ocean, (ii) Java Sea, (iii) South China Sea, Indonesian throughflow, as well as seas in the East of Sulawesi, and (iv) Western Pacific. This complex genetic population structure and pattern of connectivity, characterised by restricted gene flow between some sites and panmixing between others can be attributed to the geological history and prevailing current regimes in the Indo‐Malay Archipelago.
Phylogeography of the invasive weed Hypochaeris radicata (Asteraceae): from Moroccan origin to worldwide introduced populations
Authors: ORTIZ M. Á. , TREMETSBERGER K. , TERRAB A. , STUESSY T. F. , GARCÍA‐CASTAÑO J. L. , URTUBEY E. , BAEZA C. M. , RUAS C. F. , GIBBS P. E. , TALAVERA S. 
Published: July 2008

AbstractIn an attempt to delineate the area of origin and migratory expansion of the highly successful invasive weedy species Hypochaeris radicata, we analysed amplified fragment length polymorphisms from samples taken from 44 populations. Population sampling focused on the central and western Mediterranean area, but also included sites from Northern Spain, Western and Central Europe, Southeast Asia and South America. The six primer combinations applied to 213 individuals generated a total of 517 fragments of which 513 (99.2%) were polymorphic. The neighbour‐joining tree presented five clusters and these divisions were supported by the results of Bayesian analyses: plants in the Moroccan, Betic Sierras (Southern Spain), and central Mediterranean clusters are all heterocarpic. The north and central Spanish, southwestern Sierra Morena, and Central European, Asian and South American cluster contain both heterocarpic (southwestern Sierra Morena) and homocarpic populations (all other populations). The Doñana cluster includes two homocarpic populations. Analyses of fragment parameters indicate that the oldest populations of H. radicata are located in Morocco and that the species expanded from this area in the Late Quaternary via at least three migratory routes, the earliest of which seems to have been to the southwestern Iberian Peninsula, with subsequent colonizations to the central Mediterranean area and the Betic Sierras. Homocarpic populations originated in the southwestern Iberian Peninsula and subsequently spread across north and central Spain, Central Europe and worldwide, where they became a highly successful weed.
Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce
Authors: NAMROUD MARIE‐CLAIRE , BEAULIEU JEAN , JUGE NICOLAS , LAROCHE JÉRÔME , BOUSQUET JEAN 
Published: July 2008

AbstractConifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome‐wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce (Picea glauca) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations (FST) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates (HE = 0.270 andFST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers withFSTat the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes’ putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels.