Ellenberg-type indicator values for European vascular plant species

Aims: Ellenberg-type indicator values are expert-based rankings of plant species according to their ecological optima on main environmental gradients. Here we extend the indicator-value system proposed by Heinz Ellenberg and co-authors for Central Europe by incorporating other systems of Ellenberg-type indicator values (i.e., those using scales compatible with Ellenberg values) developed for other European regions. Our aim is to create a harmonized data set of Ellenberg-type indicator values applicable at the European scale. Methods: We collected European data sets of indicator values for vascular plants and selected 13 data sets that used the nine-, ten- or twelve-degree scales defined by Ellenberg for light, temperature, moisture, reaction, nutrients and salinity. We compared these values with the original Ellenberg values and used those that showed consistent trends in regression slope and coefficient of determination. We calculated the average value for each combination of species and indicator values from these data sets. Based on species’ co-occurrences in European vegetation plots, we also calculated new values for species that were not assigned an indicator value. Results: We provide a new data set of Ellenberg-type indicator values for 8908 European vascular plant species (8168 for light, 7400 for temperature, 8030 for moisture, 7282 for reaction, 7193 for nutrients, and 7507 for salinity), of which 398 species have been newly assigned to at least one indicator value. Conclusions: The newly introduced indicator values are compatible with the original Ellenberg values. They can be used for large-scale studies of the European flora and vegetation or for gap-filling in regional data sets. The European indicator values and the original and taxonomically harmonized regional data sets of Ellenberg-type indicator values are available in the Supporting Information and the Zenodo repository

CYP17 genetic polymorphism, breast cancer, and breast cancer risk factors: Australian Breast Cancer Family Study

INTRODUCTION: Because CYP17 can influence the degree of exposure of breast tissues to oestrogen, the interaction between polymorphisms in this gene and hormonal risk factors is of particular interest. We attempted to replicate the findings of studies assessing such interactions with the -34T→C polymorphism. METHODS: Risk factor and CYP17 genotyping data were derived from a large Australian population-based case-control-family study of 1,284 breast cancer cases and 679 controls. Crude and adjusted odds ratio (OR) estimates and 95% confidence intervals (CIs) were calculated by unconditional logistic regression analyses. RESULTS: We found no associations between the CYP17 genotype and breast cancer overall. Premenopausal controls with A(2)/A(2 )genotype had a later age at menarche (P < 0.01). The only associations near statistical significance were that postmenopausal women with A(1)/A(1 )(wild-type) genotype had an increased risk of breast cancer if they had ever used hormone replacement therapy (OR 2.40, 95% CI 1.0 to 5.7; P = 0.05) and if they had menopause after age 47 years (OR 2.59, 95% CI 1.0 to 7.0; P = 0.06). We found no associations in common with any other studies, and no evidence for interactions. CONCLUSION: We observed no evidence of effect modification of reproductive risk factors by CYP17 genotype, although the experiment did not have sufficient statistical power to detect small main effects and modest effects in subgroups. Associations found only in subgroup analyses based on relatively small numbers require cautious interpretation without confirmation by other studies. This emphasizes the need for replication in multiple and large population-based studies to provide convincing evidence for gene–environment interactions

Interactions between genes involved in the antioxidant defence system and breast cancer risk

The aim of the study is to examine the association between multilocus genotypes across 10 genes encoding proteins in the antioxidant defence system and breast cancer. The 10 genes are SOD1, SOD2, GPX1, GPX4, GSR, CAT, TXN, TXN2, TXNRD1 and TXNRD2. In all, 2271 cases and 2280 controls were used to examine gene–gene interactions between 52 single nucleotide polymorphisms (SNPs) that are hypothesised to tag all common variants in the 10 genes. The statistical analysis is based on three methods: unconditional logistic regression, multifactor dimensionality reduction and hierarchical cluster analysis. We examined all two- and three-way combinations with unconditional logistic regression and multifactor dimensionality reduction, and used a global approach with all SNPs in the hierarchical cluster analysis. Single-locus studies of an association of genetic variants in the antioxidant defence genes and breast cancer have been contradictory and inconclusive. It is the first time, to our knowledge, the association between multilocus genotypes across genes coding for antioxidant defence enzymes and breast cancer is investigated. We found no evidence of an association with breast cancer with our multilocus approach. The search for two-way interactions gave experiment-wise significance levels of P=0.24 (TXN [t2715c] and TXNRD2 [g23524a]) and P=0.58 (GSR [c39396t] and TXNRD2 [a442g]), for the unconditional logistic regression and multifactor dimensionality reduction, respectively. The experiment-wise significance levels for the three-way interactions were P=0.94 (GPX4 [t2572c], TXN [t2715c] and TXNRD2 [g23524a]) and P=0.29 (GSR [c39396t], TXN [t2715c] and TXNRD2 [a442g]) for the unconditional logistic regression and multifactor dimensionality reduction, respectively. In the hierarchical cluster analysis neither the average across four rounds with replacement of missing values at random (P=0.12) nor a fifth round with more balanced proportion of missing values between cases and controls (P=0.17) was significant

The Short-Term Effect of Weight Loss Surgery on Volumetric Breast Density and Fibroglandular Volume

Purpose: Obesity and breast density are both associated with an increased risk of breast cancer and are potentially modifiable. Weight loss surgery (WLS) causes a significant reduction in the amount of body fat and a decrease in breast cancer risk. The effect of WLS on breast density and its components has not been documented. Here, we analyze the impact of WLS on volumetric breast density (VBD) and on each of its components (fibroglandular volume and breast volume) by using three-dimensional methods. Materials and Methods: Fibroglandular volume, breast volume, and their ratio, the VBD, were calculated from mammograms before and after WLS by using Volpara™ automated software. Results: For the 80 women included, average body mass index decreased from 46.0 ± 7.22 to 33.7 ± 7.06 kg/m2. Mammograms were performed on average 11.6 ± 9.4 months before and 10.1 ± 7 months after WLS. There was a significant reduction in average breast volume (39.4 % decrease) and average fibroglandular volume (15.5 % decrease), and thus, the average VBD increased from 5.15 to 7.87 % (p < 1 × 10−9) after WLS. When stratified by menopausal status and diabetic status, VBD increased significantly in all groups but only perimenopausal and postmenopausal women and non-diabetics experienced a significant reduction in fibroglandular volume. Conclusions: Breast volume and fibroglandular volume decreased, and VBD increased following WLS, with the most significant change observed in postmenopausal women and non-diabetics. Further studies are warranted to determine how physical and biological alterations in breast density components after WLS may impact breast cancer risk.ECU Open Access Publishing Support Fun

Evaluation of variation in the phosphoinositide-3-kinase catalytic subunit alpha oncogene and breast cancer risk

Background: Somatic mutations in phosphoinositide-3-kinase catalytic subunit alpha (PIK3CA) are frequent in breast tumours and have been associated with oestrogen receptor (ER) expression, human epidermal growth factor receptor-2 overexpression, lymph node metastasis and poor survival. The goal of this study was to evaluate the association between inherited variation in this oncogene and risk of breast cancer. Methods: A single-nucleotide polymorphism from the PIK3CA locus that was associated with breast cancer in a study of Caucasian breast cancer cases and controls from the Mayo Clinic (MCBCS) was genotyped in 5436 cases and 5280 controls from the Cancer Genetic Markers of Susceptibility (CGEMS) study and in 30 949 cases and 29 788 controls from the Breast Cancer Association Consortium (BCAC). Results: Rs1607237 was significantly associated with a decreased risk of breast cancer in MCBCS, CGEMS and all studies of white Europeans combined (odds ratio (OR)=0.97, 95% confidence interval (CI) 0.95–0.99, P=4.6 × $10^{−3}$), but did not reach significance in the BCAC replication study alone (OR=0.98, 95% CI 0.96–1.01, P=0.139). Conclusion: Common germline variation in PIK3CA does not have a strong influence on the risk of breast cancer

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Effect of esomeprazole triple therapy on eradication rates of Helicobacter pylori, gastric ulcer healing and prevention of relapse in gastric ulcer patients

OBJECTIVES: To compare esomeprazole-based triple therapy with esomeprazole alone for the eradication of Helicobacter pylori (H. pylori), healing of ulcer and prevention of relapse in H. pylori-related gastric ulcer (GU) diseases. METHODS: In this double-blind study, 401 H. pylori-positive patients with more than or equal to two GUs were randomized to: esomeprazole (20 mg) twice daily (bid) and amoxicillin (1000 mg) bid and clarithromycin (500 mg) bid (EAC) for 1 week, followed by placebo for 3 weeks (EAC and placebo); EAC for 1 week, followed by esomeprazole (20 mg) once daily (E20) for 3 weeks (EAC and E20); or esomeprazole (20 mg) bid and placebo antimicrobials for 1 week, followed by E20 for 3 weeks (E20 bid and E20). Patients with unhealed GUs at 4 weeks received E20 for an additional 4 weeks. Healed patients were followed up for 12 months. RESULTS: Eradication rates at 4 weeks or 8 weeks were 82% for EAC and E20, 77% for EAC and placebo and 9.5% for E20 bid and E20 (intention-to-treat analysis). Significantly more patients receiving EAC than those receiving esomeprazole alone remained free of GUs during follow-up [EAC and E20, 90%; EAC and placebo, 87%; P=0.0005 for combined group vs. esomeprazole alone [E20 bid and E20 (74%)]. All treatments were well tolerated. CONCLUSION: Esomeprazole-based triple therapy is effective for the eradication of H. pylori, healing of GU and prevention of relapse. Esomeprazole monotherapy for 3 weeks after triple therapy may be beneficial in terms of healing. © 2008 Lippincott Williams & Wilkins, Inc.link_to_subscribed_fulltex

Evaluation of variation in the phosphoinositide-3-kinase catalytic subunit alpha oncogene and breast cancer risk.

BACKGROUND: Somatic mutations in phosphoinositide-3-kinase catalytic subunit alpha (PIK3CA) are frequent in breast tumours and have been associated with oestrogen receptor (ER) expression, human epidermal growth factor receptor-2 overexpression, lymph node metastasis and poor survival. The goal of this study was to evaluate the association between inherited variation in this oncogene and risk of breast cancer. METHODS: A single-nucleotide polymorphism from the PIK3CA locus that was associated with breast cancer in a study of Caucasian breast cancer cases and controls from the Mayo Clinic (MCBCS) was genotyped in 5436 cases and 5280 controls from the Cancer Genetic Markers of Susceptibility (CGEMS) study and in 30 949 cases and 29 788 controls from the Breast Cancer Association Consortium (BCAC). RESULTS: Rs1607237 was significantly associated with a decreased risk of breast cancer in MCBCS, CGEMS and all studies of white Europeans combined (odds ratio (OR)=0.97, 95% confidence interval (CI) 0.95-0.99, P=4.6 × 10(-3)), but did not reach significance in the BCAC replication study alone (OR=0.98, 95% CI 0.96-1.01, P=0.139). CONCLUSION: Common germline variation in PIK3CA does not have a strong influence on the risk of breast cancer

Rising temperature modulates pH niches of fen species

Rising temperatures may endanger fragile ecosystems because their character and key species show different habitat affinities under different climates. This assumption has only been tested in limited geographical scales. In fens, one of the most endangered ecosystems in Europe, broader pH niches have been reported from cold areas and are expected for colder past periods. We used the largest European-scale vegetation database from fens to test the hypothesis that pH interacts with macroclimate temperature in forming realized niches of fen moss and vascular plant species. We calibrated the data set (29,885 plots after heterogeneity-constrained resampling) with temperature, using two macroclimate variables, and with the adjusted pH, a variable combining pH and calcium richness. We modelled temperature, pH and water level niches for one hundred species best characterizing European fens using generalized additive models and tested the interaction between pH and temperature. Fifty-five fen species showed a statistically significant interaction between pH and temperature (adj p&nbsp;˂.01). Forty-six of them (84%) showed a positive interaction manifested by a shift or restriction of their niche to higher pH in warmer locations. Nine vascular plants and no moss showed the opposite interaction. Mosses showed significantly greater interaction. We conclude that climate significantly modulates edaphic niches of fen plants, especially bryophytes. This result explains previously reported regional changes in realized pH niches, a current habitat-dependent decline of endangered taxa, and distribution changes in the past. A warmer climate makes growing seasons longer and warmer, increases productivity, and may lower the water level. These effects prolong the duration and intensity of interspecific competition, support highly competitive Sphagnum mosses, and, as such, force niches of specialized fen species towards narrower high-pH ranges. Recent anthropogenic landscape changes pose a severe threat to many fen species and call for mitigation measures to lower competition pressure in their refugia