bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of matrix metalloproteinases and their tissue inhibitors in ductal in situ carcinomas of the breast
Authors: Gonzalez L O , Corte M D , Vazquez J , Junquera S , Sanchez R , Viña A , Rodriguez J C , Lamelas M L , Vizoso F 
Published: September 2008

Aims:  To analyse the expression of metalloproteinases (MMPs) and their inhibitors (TIMPs) in ductal carcinoma in situ of the breast (DCIS).Methods and results:  An immunohistochemical study was performed in 56 patients with pure DCIS, in 39 with DCIS adjacent to invasive carcinoma (IDC) and 63 patients with T1 IDC, using tissue microarrays and specific antibodies against MMPs and TIMPs. Immunohistochemical results were categorized using a specific software program. The data were analysed by unsupervised hierarchical cluster analysis by each cellular type. IDC showed a higher expression rate of MMP‐7 and TIMP‐1 than pure DCIS, as well as a higher expression rate of MMP‐9 and TIMP‐3 than the DCIS component of mixed cases, whereas pure DCIS showed a higher rate of expression of MMP‐9 and ‐11 and TIMP‐3 than in the DCIS component of mixed cases. Pure DCIS with a periductal inflammatory infiltrate showed significantly higher MMP‐2, ‐14 and TIMP‐1. Dendograms identified two cluster groups with distinct MMP/TIMP expression profiles in neoplastic cells and fibroblastic or mononuclear inflammatory cells surrounding the neoplastic ducts of pure DCIS.Conclusions:  The results indicate the distinct variability in MMP/TIMP expression by DCIS, which may be of potential biological and clinical interest in breast cancer.
Activation of the NF‐κB signalling pathway in diffuse large B‐cell lymphoma: clinical implications
Authors: Espinosa I , Briones J , Bordes R , Brunet S , Martino R , Sureda A , Sierra J , Prat J 
Published: September 2008

Aim:  To characterize the activation of the nuclear factor (NF)‐κB pathway in diffuse large B‐cell lymphoma (DLBCL) by immunohistochemistry.Methods and results:  Sixty‐six DLBCLs treated with anthracycline‐containing chemotherapy were evaluated with antibodies against phosphorylated p65 (P‐p65), p65, p50, p52, IKKα, and phosphorylated IκB (P‐IκB). NF‐κB activation was based on the expression of P‐p65, P‐IκB, and nuclear expression of p65 or p52 in the tumour cells. P‐p65 and P‐IκB were expressed in 13 (20%) and 17 cases (26%), respectively. p65, p52 and IKKα were found in the cytoplasm. A correlation was found between expression of P‐p65 and P‐IκB (P < 0.0001), but not between the two subtypes of DLBCL [germinal centre B cell and non‐germinal centre (GC)]. P‐p65+ tumours showed a better response to chemotherapy (P = 0.025) and a trend to increased event‐free survival (P = 0.08). However, P‐IκB expression was not associated with either clinical response or survival. Bcl‐2 was not preferentially expressed on DLBCL tumours with NF‐κB activation, as determined by expression of P‐p65 and P‐IκB proteins.Conclusions:  NF‐κB activation in DLBCL is preferentially mediated through the classical pathway and a novel mechanism involving phosphorylation of p65. Activation of NF‐κB by P‐p65 is associated with good prognosis. NF‐κB activation is not confined to non‐GC DLBCL exclusively.
Individual and combined responses of stream ecosystems to multiple stressors
Authors: Townsend Colin R. , Uhlmann S. Sebastian , Matthaei Christoph D. 
Published: September 2008

Summary

Managers must understand the effects of stressors on ecosystems in order to identify thresholds of harm but, to be meaningful, thresholds will usually need to be defined for situations where multiple stressors are operating.
We investigated the individual and combined effects of the principal stressors (nutrient concentration and streambed fine sediment cover) operating in native grassland streams converted to pasture in New Zealand, using two different approaches: a survey of 32 small streams and an experiment involving nine streams where the stressors were manipulated in a factorial design. We investigated the consequences for populations of benthic invertebrates and for the structure of communities, including taxon richness and the representation of species traits.
Up to half the taxa and most community metrics responded to at least one stressor. Our results suggest that in these streams, an increase in fine sediment loading from anthropogenic causes had more widespread effects than augmented nutrient concentrations. Of most significance is our finding, both from the survey and, in particular, the experiment, of a variety of complex interactions among the stressors.
Synthesis and applications. The development of indices of stream health that distinguish the effects of sediment from those of nutrients should help prioritize catchment management actions. Of more general importance is our finding that the consequences of stressors are often unpredictable on the basis of knowledge of single effects; if managers only consider the effects of individual stressors, their assessment of risk may be higher or lower than reality.
Impacts of massive landscape change on a carnivorous marsupial in south‐eastern Australia: inferences from landscape genetics analysis
Authors: Lada Hania , Thomson James R. , Mac Nally Ralph , Taylor Andrea C. 
Published: September 2008

Summary

In much of the world, fauna has been adversely affected by human actions, including conversion of forests to farmland, logging and regulation of river flows. Landscape genetics data can provide information about dispersal and gene flow across the landscape, identifying barriers and facilitators of gene flow. Landscapes of central Victoria, Australia, have been altered extensively in the last 160 years. Much vegetation has been cleared or degraded, and only forest patches of mainly re‐growth remain, yet some forest‐dependent species like the yellow‐footed antechinus Antechinus flavipes persist. The antechinus has good dispersal capabilities and is the only native, small, carnivorous mammal on most floodplains. We use antechinus as a model to understand species persistence in fragmented landscapes.
We analysed variation at 11 microsatellite loci and the control region of mitochondrial DNA to infer past and contemporary gene flow among A. flavipes populations. To explore genetic connectivity, we used least‐cost path methods, which assign different ‘friction’ costs to vegetation, cleared land, roads and rivers.
Populations from 11 forests formed six distinct genetic groups, and with few exceptions, animals from nearby forests clustered together despite the intervening Murray River or farmland with only narrow vegetation corridors between them.
Genetic connectivity was aided by corridors of vegetation and inhibited by cleared land.
Synthesis and applications. Our approach, capitalizing on inferences on both historic and contemporary gene flow, provides management agencies with key information on metapopulation dynamics in landscapes. Rather than merely maintaining existing vegetation upon which this (and many other) species depend, the genetic information also informs where future plantings should be prioritized to facilitate demographic and genetic exchange among sub‐populations of species. Moreover, the decline in condition (‘health’) of riparian trees in this region must be reversed by provision of flooding flows; otherwise, metapopulation dynamics will become even more disarticulated than at present.
Response of broadleaved evergreen Mediterranean forest vegetation to fire disturbance during the Holocene: insights from the peri‐Adriatic region
Authors: Colombaroli Daniele , Tinner Willy , Van Leeuwen Jacqueline , Noti Roland , Vescovi Elisa , Vannière Boris , Magny Michel , Schmidt Roland , Bugmann Harald 
Published: September 2008

AbstractAim  To test whether fire contributed to the expansion and compositional change of evergreen forests in the Mediterranean region during the Holocene.Location  The peri‐Adriatic region, encompassing the Italian peninsula, Sicily and the western and southern Balkans between latitudes 46° and 37° N.Methods  New high‐resolution pollen and microscopic charcoal data from Lago dell’Accesa (Tuscany, Italy) were used to estimate the response of the evergreen oak, Quercus ilex L., to fire during its expansion phase at 8500 cal. yr bp. The data were compared with the pollen and charcoal series from other Mediterranean sites (Lago di Massaciuccoli in Tuscany, Malo Jezero in Croatia, Biviere di Gela in Sicily) and analysed using numerical techniques (redundancy analysis, detrended canonical correspondence analysis) to identify long‐term fire–vegetation linkages and the degree of compositional change.Results  Microscopic charcoal and pollen of evergreen oaks were negatively correlated during the period of quasi‐natural fire regime (Mesolithic, 10,000–8000 cal. yr bp). In addition, there was no such positive correlation during periods when the fire regime was potentially more influenced by people (Neolithic–Bronze Age, 8000–3000 cal. yr bp). Compared with inland sites, coastal sites that are currently located at a distinct ecotone showed more compositional change.Main conclusions  The analyses suggest that climatic change, without an additional effect of fire regimes, favoured the expansion and compositional change of evergreen forests across the peri‐Adriatic region. Strikingly different patterns occurred along a north–south gradient. In the north (Tuscany and Croatia, meso‐Mediterranean belt), Q. ilex replaced deciduous forests when conditions became drier; in the south (Sicily, thermo‐Mediterranean belt) the species replaced maquis or steppe vegetation when climatic conditions became moister. We conclude that the projected increase in fire activity may lead to the loss of most of the remaining relict forests of Q. ilex in southern Europe.
Y‐chromosome analysis confirms highly sex‐biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus)
Authors: ERIKSSON JONAS , SIEDEL HEIKE , LUKAS DIETER , KAYSER MANFRED , ERLER AXEL , HASHIMOTO CHIE , HOHMANN GOTTFRIED , BOESCH CHRISTOPHE , VIGILANT LINDA 
Published: September 2008

AbstractDispersal is a rare event that is difficult to observe in slowly maturing, long‐lived wild animal species such as the bonobo. In this study we used sex‐linked (mitochondrial DNA sequence and Y‐chromosome microsatellite) markers from the same set of individuals to estimate the magnitude of difference in effective dispersal between the sexes and to investigate the long‐term demographic history of bonobos. We sampled 34 males from four distinct geographical areas across the bonobo distribution range. As predicted for a female‐dispersing species, we found much higher levels of differentiation among local bonobo populations based upon Y‐chromosomal than mtDNA genetic variation. Specifically, almost all of the Y‐chromosomal variation distinguished populations, while nearly all of the mtDNA variation was shared between populations. Furthermore, genetic distance correlated with geographical distance for mtDNA but not for the Y chromosome. Female bonobos have a much higher migration rate and/or effective population size as compared to males, and the estimate for the mitochondrial TMRCA (time to most recent common ancestor) was approximately 10 times greater than the estimate for the Y chromosome (410 000 vs. 40 000–45 000). For humans the difference is merely a factor of two, suggesting a more stable demographic history in bonobos in comparison to humans.
Fitness of hybrids between rapeseed (Brassica napus) and wild Brassica rapa in natural habitats
Authors: ALLAINGUILLAUME J. , ALEXANDER M. , BULLOCK J. M. , SAUNDERS M. , ALLENDER C. J. , KING G. , FORD C. S. , WILKINSON M. J. 
Published: September 2008

AbstractFitness of hybrids between genetically modified (GM) crops and wild relatives influences the likelihood of ecological harm. We measured fitness components in spontaneous (non‐GM) rapeseed × Brassica rapa hybrids in natural populations. The F1 hybrids yielded 46.9% seed output of B. rapa, were 16.9% as effective as males on B. rapa and exhibited increased self‐pollination. Assuming 100% GM rapeseed cultivation, we conservatively predict < 7000 second‐generation transgenic hybrids annually in the United Kingdom (i.e. ∼20% of F1 hybrids). Conversely, whilst reduced hybrid fitness improves feasibility of bio‐containment, stage projection matrices suggests broad scope for some transgenes to offset this effect by enhancing fitness.
History vs. current demography: explaining the genetic population structure of the common frog (Rana temporaria)
Authors: JOHANSSON MARKUS , PRIMMER CRAIG R. , MERILÄ JUHA 
Published: September 2008

AbstractThe amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208–885 km apart), three subregions within regions and nine populations (5–20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker‐based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species’ range.
The enigmatic invasiveSpartina densiflora: A history of hybridizations in a polyploidy context
Authors: FORTUNE P. M. , SCHIERENBECK K. , AYRES D. , BORTOLUS A. , CATRICE O. , BROWN S. , AINOUCHE M. L. 
Published: September 2008

AbstractThe aim of this study was to explore the origin of the invasiveSpartina densifloraby analysing samples from the native region (South America) and from a recently colonized area (California). A combination of various molecular data (chloroplast and nuclear sequences, molecular fingerprint) and ploidy level estimations was used to answer the question whether the reticulate phylogenetic pattern previously detected inS. densiflorawas restricted to California, or alternatively, whether a more ancient hybrid origin preceded formation of this species in its native area. We found that this species is heptaploid in both its native and introduced range. Identification of nuclear homeologous sequences indicate that this species has a reticulate origin in its native range, involving a lineage related to the hexaploid clade formed byS. alterniflora,S. foliosa, andS. maritima, and another lineage related to the sub‐Antarctic endemicS. arundinaceathat provided the chloroplast genome. The samples from California displayed similar multilocus patterns to the samples from Chile, supporting the hypothesis that this species originated on the southeast American coast (Argentina), from where it eventually spread to the west coast of South America (Chile) first and to the Northern Hemisphere (California) later.
Interdependence of two NarK domains in a fused nitrate/nitrite transporter
Authors: Goddard Alan D. , Moir James W. B. , Richardson David J. , Ferguson Stuart J. 
Published: September 2008

SummaryNitrate uptake is essential for various bacterial processes and combines with nitrite export to form the usual initial steps of denitrification, a process that reduces nitrate to dinitrogen gas. Although many bacterial species contain NarK‐like transporters that are proposed to function as either nitrate/proton symporters or nitrate/nitrite antiporters based on sequence homology, these transporters remain, in general, poorly characterized. Several bacteria appear to contain a transporter that is a fusion of two NarK‐like proteins, although the significance of this arrangement remains elusive. We demonstrate that NarK fromParacoccus denitrificansis expressed as a fusion of two NarK‐like transporters. NarK1 and NarK2 are separately capable of supporting anaerobic denitrifying growth but with growth defects that are partially mitigated by coexpression of the two domains. NarK1 appears to be a nitrate/proton symporter with high affinity for nitrate and NarK2 a nitrate/nitrite antiporter with lower affinity for nitrate. Each transporter requires two conserved arginine residues for activity. A transporter consisting of inactivated NarK1 fused to active NarK2 has a dramatically increased affinity for nitrate compared with NarK2 alone, implying a functional interaction between the two domains. A potential model for nitrate and nitrite transport inP. denitrificansis proposed.
CD8+CD60+ T Cells, Cells Expressing Epsilon Specific mRNA and Th1/Th2 Cytokines in Cord Blood and at 7 Months of Age
Authors: Smith‐Norowitz T. A. , Norowitz K. B. , Silverberg J. I. , Chice S. , Shah V. , Stanek A. , Walker D. , Brennan J. P. , Durkin H. G. , Bluth M. H. 
Published: September 2008

AbstractIgE levels in cord blood have been investigated as predictors of atopy, but no definitive findings have been made. Other factors, including cells and/or cytokines may serve as predictors of this disease. Cord blood and peripheral blood was obtained at birth and at 7 months of age, respectively, from children (n = 2) with a family history of allergy. Cells in cord blood and peripheral blood were phenotyped and levels of serum immunoglobulins (IgM, IgG, IgA and IgE) were determined. In addition, placentas from these pregnancies were obtained and stained for IgE+ cells and CD8+CD60+ T cells. We found immunoglobulin levels were within normal ranges although IgE levels were negligible in cord blood and at 7 months of age. Similar numbers of CD8+ T cells and CD19+ B cells were detected in cord blood and at 7 months of age. However, CD4+ T cells increased (twofold) and CD16+/CD56+ natural killer precursor cells decreased (twofold) at 7 months of age. CD8+ T cells in their cord blood and at 7 months of age comprised of >50% CD8+CD60+ T cells. Cord blood cells expressed epsilon‐specific mRNA and mRNA for interleukin‐2 (IL‐2), IL‐4, IL‐10 and interferon‐γ (IFN‐γ) but not IL‐6. At 7 months of age, peripheral blood mononuclear cells expressed epsilon‐specific mRNA and mRNA for all cytokines. In the placental membrane, we detected IgE+ cells, while CD8+CD60+ T cells were detected in the chorionic villi. CD8+CD60+ T cells, cells expressing epsilon‐specific and IL‐6‐specific mRNA may contribute to the pathobiology and provide important prognostic indicators of atopy.
Differential Invasion of Trypanosoma brucei brucei and Lymphocytes into the Brain of C57BL/6 and 129Sv/Ev Mice
Authors: Masocha W. , Amin D. N. , Kristensson K. , Rottenberg M. E. 
Published: September 2008

Abstract Trypanosoma brucei subspecies invade the brain parenchyma at late stages of human and experimental rodent infections. In this study, we compared the outcome of infection with T. b. brucei in MHC‐matched (H‐2b) C57BL/6 (B6) and 129Sv/Ev (Sv‐129). Sv‐129 showed higher parasitaemia and lower specific IgM (but not IgG) antibody levels than B6 mice. The number of trypanosomes, CD4+ and CD8+ T cells in the brain parenchyma was higher in B6 mice. B6 mice lost weight and showed higher cumulative mortality when compared with Sv‐129 mice. Higher levels of IL‐1β, IL‐6, IL‐10, TNF‐α, IFN‐γ, ICAM‐1 and E‐selectin, but low levels of TGF‐β mRNA were present in brains of B6 when compared with Sv‐129‐infected mice. Thus, host genetics differentially determine the invasion of T. b. brucei into the brain parenchyma, which is paralleled by the severity of inflammation in the brain and course of the disease, but not by parasitaemia nor by antibody titres.
Effect of Neonatal Sublingual Vaccination with Native or Denatured Ovalbumin and Adjuvant CpG or Cholera Toxin on Systemic and Mucosal Immunity in Mice
Authors: Huang C.‐F. , Wu T.‐C. , Chu Y.‐H. , Hwang K.‐S. , Wang C.‐C. , Peng H.‐J. 
Published: September 2008

AbstractSublingual immunotherapy has been applied for allergic diseases, but whether sublingual immunization in neonates can prevent sensitization has not been studied. In this study, we evaluate the effect of neonatal sublingual vaccination with native or denatured allergens alone or plus adjuvant on allergy prevention. Newborn BALB/c mice were sublingually vaccinated daily for the first 3 days with native or denatured ovalbumin (OVA) only, or combined adjuvant CpG or cholera toxin (CT). They were sensitized with OVA adsorbed onto alum 7 weeks after the last vaccination. Specific secretory IgA antibody responses were readily induced by neonatal vaccination with antigen plus CpG or CT, but not with antigen alone. Whereas vaccination with denatured OVA plus CpG markedly enhanced T helper 1 (Th1) responses and inhibited IgE production, vaccination with denatured OVA plus CT increased cervical lymph node cell production of interleukin‐4 (IL‐4), IL‐5, IL‐6, and serum IgG1 responses. These data demonstrate that neonatal sublingual vaccination with denatured OVA and CpG not only preferentially induces systemic Th1 responses and mucosal immunity, but also simultaneously abrogates IgE production. Neonatal sublingual vaccines may play a role for the strategy of allergy prevention.