bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential gene expression in non‐malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP
Authors: Harjunpää Antti , Taskinen Minna , Nykter Matti , Karjalainen‐Lindsberg Marja‐Liisa , Nyman Heidi , Monni Outi , Hemmer Samuli , Yli‐Harja Olli , Hautaniemi Sampsa , Meri Seppo , Leppä Sirpa 
Published: August 2006

SummaryRituximab in combination with chemotherapy (immunochemotherapy) is one of the most effective treatments available for follicular lymphoma (FL). This study aimed to determine whether differences in gene expression in FL tissue correlate with outcome in response to rituximab and CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) chemotherapy (R–CHOP). We divided 24 patients into long‐ [time to treatment failure (TTF) >35 months] and short‐term (TTF <23 months) responders, and analysed the gene expression profiles of lymphoma tissue using oligonucleotide microarrays. We used a supervised learning technique to identify genes correlating with outcome, and confirmed the expression of selected genes with quantitative polymerase chain reaction (qPCR) and immunohistochemistry. Among the transcripts with a high correlation between microarray and qPCR analyses, we identified EPHA1, a tyrosine kinase involved in transepithelial migration, SMAD1, a transcription factor and a mediator of bone morphogenetic protein and transforming growth factor‐β signalling, and MARCO, a scavenger receptor on macrophages. According to Kaplan–Meier estimates, high EPHA1, and low SMAD1 and MARCO expression were associated with better progression‐free survival (PFS). Immunohistochemistry showed that EphA1 was primarily localised in granulocytes. In addition, both EphA1 and Smad1 were expressed in vascular endothelia. However, no difference in vasculature was detected between long‐ and short‐term responders. In a validation set of 40 patients, a trend towards a better PFS was observed among patients with high EphA1 expression. We conclude that gene expression in non‐malignant cells contributes to clinical outcome in R–CHOP‐treated FL patients.
High D‐dimer levels at presentation in patients with venous thromboembolism is a marker of adverse clinical outcomes
Authors: Paneesha S. , Cheyne E. , French K. , Bacchu S. , Borg A. , Rose P. 
Published: August 2006

SummaryQualitative d‐dimer results, together with clinical probability scores, are well established in the diagnosis of venous thromboembolism (VTE). The predictive value of quantitative d‐dimer levels for various clinical outcomes in VTE patients is not fully understood. d‐dimer levels obtained at presentation were analysed in 699 (360 men; 339 women) VTE patients for survival and occurrence of malignancy. Patients were followed for a median of 23 months. 17·2% patients had a d‐dimer level >8000 ng FEU/mlat presentation, which was associated with decreased overall survival (OS) (P < 0·001) and event‐free survival (EFS) (P < 0·001). 25·4% patients had malignancy and 4% subsequently developed malignancy following VTE. 29·9% of patients with VTE and malignancy had a d‐dimer level >8 mg/l when compared with 13·4% of patients with VTE without malignancy (P < 0·001). 50% of patients who developed subsequent malignancy following VTE had a presentation d‐dimer >8000 ng FEU/mlas compared with 13·3% of patients with VTE with out malignancy (P = 0·009). In conclusion, d‐dimer >8000 ng FEU/ml at presentation in patients with VTE is a marker of poor OS, EFS and underlying malignancy. Consideration of screening for malignancy is recommended in patients with VTE with a presentation d‐dimer >8000 ng FEU/ml and age >60 years.
Influence of trees on soil organic matter in Mediterranean agroforestry systems: an example from the ‘Espinal’ of central Chile
Authors: Muñoz C. , Zagal E. , Ovalle C. 
Published: August 2006

SummaryThe ‘Espinal’ agroforestry system of the Mediterranean zone of central Chile, which covers an area of 2000 000 ha, is in various stages of degradation due to human activities. The objective of our study was: (i) to determine the effects of the canopy cover of Acacia caven (‘Espino’) on total soil organic carbon (SOC), soil respiration and the labile components of soil organic matter (microbial biomass, and light fraction); and (ii) to determine the influence of ecosystem degradation on total and labile components of SOC. Soils of the study area are classified as fine, mixed, active, mesic Ultic Palexeralfs, typical of the Mediterranean‐type environment. We investigated sites according to the percentage coverage of A. caven canopy: (i) well‐preserved Espinal (WPE), 80–51% cover; (ii) good Espinal (GE), 50–26% cover; (iii) degraded Espinal (DE), 25–11% cover; and (iv) very degraded Espinal (VDE), < 10% cover. In addition, a site under native forest (NF) was included to characterize the original state of the zone. Soil samples were taken under and outside the canopy of A. caven at two depths, 0–5 and 5–10 cm. We conclude that the microbial biomass carbon (Cmic), and total and labile components of SOC are influenced by the presence of the A. caven tree, with greater values under than outside its canopy. Under the tree canopy, to a depth of 10 cm, Cmic was less under all the agroforestry systems than in NF (46 and 30% less for WPE and GE, respectively, and 67 and 57% less for DE and VDE). However, there was no clear trend for less Cmic with increased ecosystem degradation, especially outside the canopy. However, the respiration of microbial communities was affected by ecosystem degradation for both soil depths under the tree canopy, e.g. soil respiration in VDE ecosystems was about 50% greater than that found in WPE ecosystems. Increasing the coverage of the A. caven tree in the semiarid ecosystems of central Chile, e.g. changing from VDE to WPE, would result in an eventual, long‐term (over several centuries) increase in soil organic C of approximately 50%.
Landscape‐scale variation in the seed banks of floodplain wetlands with contrasting hydrology in China
Authors: LIU GUI H. , LI WEI , LI EN H. , YUAN LONG Y. , DAVY ANTHONY J. 
Published: August 2006

Summary1. At a local scale, the species composition, diversity and spatial variation of wetland plant communities are determined primarily by spatial and temporal heterogeneity in their environments. Less is known about variation at a landscape‐level. The floodplain of the Changjiang (Yangtze) River in China includes hydrologically connected, subtropical wetlands with different hydrological characteristics.2. We examined seed‐bank species composition and richness in marshes of two contrasting hydrological types: permanent marshes, fed by local runoff, and lakeshore marshes more closely connected to the regulated river. Lakeshore marshes are flooded annually to depth of approximately 1 m and during flooding they support an alternate, aquatic vegetation type. The soil seed bank in March was a comparative estimator of species diversity. At the beginning of the growing season it included seeds from both phases of alternating vegetation types associated with the annual hydrological cycle.3. A regional pool of 101 species was detected in the seed banks of six wetlands associated with the river and its tributaries: 56 occurred in permanent marshes and 59 in lakeshore marshes, with only 15 common to both. Species rarefaction curves indicated that more species occurred in permanent than lakeshore marshes at equal numbers of individuals sampled. However, the more heterogeneous lakeshore seed banks were estimated (Chao 2) to have greater total species richness (81) than permanent marsh (60).4. Analysis using Sørensen's coefficient of similarity and DCA ordination revealed complex variation, with much greater differences between hydrological types than within them, irrespective of geographical distance. The types also differed significantly in the composition of four functional groups of species.5. Despite the potential for dispersal of propagules via the annually pulsing river system (hydrochory), at a regional and landscape scale, diversity is maintained largely by large‐scale temporal hydrological heterogeneity and smaller scale spatial and topographic heterogeneity.
Urban ecosystems and the North American carbon cycle
Authors: PATAKI D. E. , ALIG R. J. , FUNG A. S. , GOLUBIEWSKI N. E. , KENNEDY C. A. , MCPHERSON E. G. , NOWAK D. J. , POUYAT R. V. , ROMERO LANKAO P. 
Published: August 2006

AbstractApproximately 75–80% of the population of North America currently lives in urban areas as defined by national census bureaus, and urbanization is continuing to increase. Future trajectories of fossil fuel emissions are associated with a high degree of uncertainty; however, if the activities of urban residents and the rate of urban land conversion can be captured in urban systems models, plausible emissions scenarios from major cities may be generated. Integrated land use and transportation models that simulate energy use and traffic‐related emissions are already in place in many North American cities. To these can be added a growing dataset of carbon gains and losses in vegetation and soils following urbanization, and a number of methods of validating urban carbon balance modeling, including top down atmospheric monitoring and urban ‘metabolic’ studies of whole ecosystem mass and energy flow. Here, we review the state of our understanding of urban areas as whole ecosystems with regard to carbon balance, including both drivers of fossil fuel emissions and carbon cycling in urban plants and soils. Interdisciplinary, whole‐ecosystem studies of the socioeconomic and biophysical factors that influence urban carbon cycles in a range of cities may greatly contribute to improving scenarios of future carbon balance at both continental and global scales.
MOP3, a component of the molecular clock, regulates the development of B cells
Authors: Sun Yimin , Yang Zhihui , Niu Zeqing , Peng Jianxiao , Li Qinghuan , Xiong Wanfen , Langnas Alan N. , Ma Mark Y. , Zhao Yong 
Published: August 2006

SummaryDifferentiation and proliferation of haematopoietic progenitor cells occur in intimate contact with the bone marrow microenvironment which is composed of stromal cells and extracellular matrix proteins. MOP3 (also known as brain and muscle Arnt‐like protein‐1, BMAL1), a master regulator of circadian rhythm, plays important roles in the regulation of cell differentiation and general physical functions. In the present studies, MOP3‐deficient mice had significantly reduced levels of B cells in the peripheral blood, spleen and bone marrow compared MOP3+/– or MOP3+/+ littermates. Flow cytometry analysis showed the levels of pre‐B cells in bone marrow of MOP3–/– mice were similar as that in control mice. Adoptive transfer of MOP3–/– bone marrow cells (BMC) to lethally irradiated BALB/c Rag2–/– recipients, normal T and B cell development was observed, whereas Adoptive transfer of BALB/c BMC to lethally irradiated MOP3–/– recipients, B‐cell development was significantly impaired. These results presented herein with MOP3‐deficient mice reveal the involvement of MOP3 in the development of B cells, but not other immune cells. The effect of MOP3 on the differentiation of pre‐B cells to mature B cells might be mediated by the bone marrow microenvironment. This study also showed a connection between a master regular of circadian rhythm with B‐cell development in mice.
The effect of tapping for frankincense on sexual reproduction in Boswellia papyrifera
Authors: RIJKERS TOON , OGBAZGHI WOLDESELASSIE , WESSEL MARIUS , BONGERS FRANS 
Published: August 2006

Summary

In the Horn of Africa, frankincense (an aromatic hardened wood resin) is obtained by tapping Boswellia papyrifera. World‐wide, frankincense is of great economic and social importance as an important element of incense and perfumes. The production is declining as a result of poor natural regeneration of the Boswellia woodlands, possibly as a result of the low production of viable seeds. We hypothesize that this is because of the current intensive tapping regime, which might favour allocation of carbohydrates for synthesis of resin at the expense of allocation for generative growth.
Investigations were carried out at sites in different agro‐ecological zones with annually tapped trees and with trees that had not been tapped for several years. Seed viability and germination success were determined for 200 randomly collected seeds in each site. For three stands, the sexual reproduction (number of flowers, fruits and seeds) was determined for different sized trees subjected to three experimental tapping intensities (no, normal and heavy tapping).
At the stand level, non‐tapped trees produced three times as many healthy and filled seeds as tapped trees. Germination success was highest in stands with non‐tapped trees (> 80%) and lowest for those with tapped trees (< 16%).
At the tree level, sexual reproduction decreased with increasing tapping regime irrespective of tree size. Overall, large trees tended to produce slightly heavier seeds than small trees, and seeds from non‐tapped trees were heavier than those from tapped trees. In the stands where tapping was prohibited changes in tapping regimes had the greatest effect on sexual reproduction. Trees subjected to annual tapping always showed the lowest sexual reproduction.
Synthesis and applications. Tapping for frankincense results in limited flower and fruit production, and low production of mainly non‐viable seeds in B. papyrifera. We argue that tapping causes competition for carbohydrates between frankincense production, and fruit and seed setting. Consequently, the current tapping regimes will cause tree exhaustion and eventually a decline in vitality. Tapping may potentially reduce natural regeneration of the species. New tapping regimes are suggested that include periods of time in which tapping is prohibited in order for trees to recover and replenish their stored carbon pool, and a reduction in the number of tapping points per tree. This is important in view of the long‐term sustainability of frankincense production, an internationally highly valued resource.
Assessing the carbon sequestration potential of managed forests: a case study from temperate Australia
Authors: ROXBURGH S. H. , WOOD S. W. , MACKEY B. G. , WOLDENDORP G. , GIBBONS P. 
Published: August 2006

Summary

The concept of assessing forests for carbon sequestration is well established. Operationally, estimating a forests’ potential to sequester carbon requires comparing its current carbon state with a prediction of its carbon carrying capacity (CCC). Assessment of CCC is, however, problematic. Mathematical models can be used, although traditional modelling techniques, where parameters are estimated from empirical measurements, are usually limited by a lack of field data. For example, estimates of carbon residency times in vegetation and soil are not generally available, nor are they easily measured. Alternative methods are required.
Current carbon stocks in 17 previously logged field sites were measured by field survey. CCC for those sites was then predicted using a terrestrial carbon model, calibrated with measurements from mature, unlogged vegetation of a comparable forest type. Model parameters were estimated using ‘model–data fusion’ methods, where the model is inverted and field measurements of the carbon stocks (the model outputs) are used to calibrate the model parameters. Spatial variation was included through functions defining landscape‐scale effects on plant growth relating to topographic influences on light and soil water availability.
Current above‐ground carbon stocks (living plus litter) varied with management history, averaging 273 ± 30 tC ha−1 (mean ± SE). Model‐predicted CCC was 445 ± 13 tC ha−1, yielding a carbon sequestration potential of 172 ± 31 tC ha−1. Model simulations predicted the recovery of an average site to take 53 years to reach 75% carrying capacity, and 152 years to reach 90% carrying capacity. Extrapolation of these results to 7 Mha of comparable managed forests in the same region suggested a potential carbon sink of 680–895 Mt C.
Synthesis and applications. In this study we have demonstrated that forests recovering from prior logging have the potential to store significant amounts of carbon, with current biomass stocks estimated to be approximately 60% of their predicted carrying capacity, a value similar to those reported for northern temperate forests. Although sequestration activities often focus on the aforestation and reforestation of previously cleared land, our results suggest that, where appropriate, native forest management should also be considered when developing terrestrial carbon management options, and for terrestrial carbon accounting more generally.
Capybara (Hydrochoerus hydrochaeris) distribution in agroecosystems: a cross‐scale habitat analysis
Authors: De Barros Ferraz Katia Maria P. M. , De Barros Ferraz Silvio F. , Moreira José Roberto , Couto Hilton Thadeu Z. , Verdade Luciano M. 
Published: August 2006

AbstractAim  The aim of this study was to understand the spatial distribution of capybara (Hydrochoerus hydrochaeris) according to habitat attributes, using a multiscale approach based on fine‐ and broad‐scale variables in agroecosystems.Location  Piracicaba river basin, south‐eastern Brazil (22°00′–23°30′ S; 45°45′–48°30′ W).Methods  Potential habitats for capybara were selected in order to evaluate species presence/absence from October 2001 to December 2002. In each site, habitat attributes were sampled in the field (fine scale) and from GIS maps (broad scale) in terms of their presence or absence close to water. The variability of land cover between study sites was described by principal components analysis. Chi‐square tests were calculated for capybara presence/absence and the presence of each habitat attribute. A linear discriminant function analysis was used to describe to what extent the species’ presence could be explained by habitat attributes.Results  The species presence was predominantly related to flat open areas (slope ranging from 0% to 6%) (χ2 = 37.054, d.f. = 4, P < 0.001), covered by sugar cane or cultivated pasture (χ2 = 84.814, d.f. = 9, P < 0.001). Terrain curvature, water meadows, aquatic vegetation, forest cover and open areas resulted in the best combination of variables, explaining 69.7% of capybara occurrence in the study sites in this river basin.Main conclusions  Capybaras are widespread in the Piracicaba river basin, except in elevated areas. The spatial distribution of capybara was associated with the main types of land cover in the river basin – sugar cane plantations or pasture – both key food sources for capybara. This probably explains the species’ recent abundance in the region, since an intensive process of landscape alteration has taken place in this region owing to the expansion of agriculture in recent decades. These results may be useful in understanding the relationship between recent landscape modifications and the species’ population expansion in agroecosystems.
ORIGINAL ARTICLE: Elevational parallels of latitudinal variation in the proportion of lianas in woody floras
Authors: Jiménez‐Castillo M. , Wiser S. K. , Lusk C. H. 
Published: August 2006

AbstractAim  To determine if elevational variation in the proportion of lianas in woody floras parallels the variation observed on latitudinal gradients. This is to be expected if the poleward decrease in the importance of lianas is related to the vulnerability of their wide vessels to freeze embolism.Location  Coastal ranges of south‐central Chile (latitude 37°–40° S) and western South Island of New Zealand (41°–43° S).Methods  The presence of all woody species was recorded in plots of 2500 m2 (Chile) or 100–400 m2 (New Zealand) on four elevational gradients in temperate rain forest. Each species was classified as a tree, shrub or liana. Original data were obtained from 22 plots at two sites in Chile. In New Zealand, two surveys comprising a total of 296 plots were extracted from the National Vegetation Survey data base.Results  Liana species richness declined more or less monotonically on all four gradients, whereas richness of trees and shrubs showed more varied elevational patterns. The proportion of woody species contributed by the liana life‐form was negatively correlated with elevation on all four gradients, falling from 15 to 35% of the woody flora at c. 200 m a.s.l. to nil well below the tree line. The elevational and latitudinal limits of liana species were marginally significantly correlated in Chile, but not in New Zealand.Main conclusions  The elevational parallel of the well‐documented decline in liana representation with increasing latitude is consistent with the hypothesis that cold intolerance is a strong control on the global distribution of the liana life‐form.
Do nurses promote urinary continence in hospitalized older people?: an exploratory study
Authors: Dingwall Lindsay , Mclafferty Ella 
Published: August 2006

Aim.  The aim of this paper is to explore whether nurses working in elderly medicine and in acute medical settings promote urinary continence in older people or in reality use containment strategies.Background.  Untreated urinary incontinence in older adults can result in prolonged hospital admission and increased risk of admission to long‐term care. Urinary incontinence can also have severe psychosocial effects on older people. Most studies relating to this topic have relied on quantitative approaches to data collection with a seeming lack of qualitative investigation into how nursing staff promote urinary continence in hospitalized older people.Method.  Focus groups and one‐to‐one semi‐structured interviews were carried out in two NHS regions in Scotland. Registered and non‐Registered Nurses were invited to participate. Five focus groups (n = 17) and four single interviews (n = 4) were conducted. Data generated were analysed thematically using QSR N‐VIVO 2.Findings.  Some nurses believe that older people accept urinary incontinence as a consequence of ageing. Lack of assessment results in older people being labelled as incontinent of urine. Assessment strategies in medicine for the elderly tend to focus on product identification and management of incontinence. Although nurses from all clinical areas identify the importance of promoting continence, the problem continues to be contained rather than treated. Conflicting clinical priorities, varying staff approaches to urinary continence and deficits in education are cited among the barriers to promoting continence.Conclusions.  The results suggest that nurses continue to contain urinary incontinence rather than promoting continence in older people.Relevance to clinical practice.  Nursing staff need to be aware of the impact of untreated urinary incontinence on older people. Practitioners should promote continence rather than employing containment strategies. A validated assessment tool for older people needs to be developed. Views of older people should be sought regarding their attitudes towards urinary incontinence.