Twenty five year follow-up for breast cancer incidence and mortality of the Canadian national breast screening study: randomised screening trial

Annual mammography in women aged 40-59 does not reduce mortality from breast cancer beyond that of physical examination or usual care when adjuvant therapy for breast cancer is freely available. Abstract Objective: To compare breast cancer incidence and mortality up to 25 years in women aged 40-59 who did or did not undergo mammography screening. Design: Follow-up of randomised screening trial by centre coordinators, the study’s central office, and linkage to cancer registries and vital statistics databases. Setting: 15 screening centres in six Canadian provinces,1980-85 (Nova Scotia, Quebec, Ontario, Manitoba, Alberta, and British Columbia). Participants: 89 835 women, aged 40-59, randomly assigned to mammography (five annual mammography screens) or control (no mammography). Interventions: Women aged 40-49 in the mammography arm and all women aged 50-59 in both arms received annual physical breast examinations. Women aged 40-49 in the control arm received a single examination followed by usual care in the community. Main outcome measure: Deaths from breast cancer. Results: During the five year screening period, 666 invasive breast cancers were diagnosed in the mammography arm (n=44 925 participants) and 524 in the controls (n=44 910), and of these, 180 women in the mammography arm and 171 women in the control arm died of breast cancer during the 25 year follow-up period. The overall hazard ratio for death from breast cancer diagnosed during the screening period associated with mammography was 1.05 (95% confidence interval 0.85 to 1.30). The findings for women aged 40-49 and 50-59 were almost identical. During the entire study period, 3250 women in the mammography arm and 3133 in the control arm had a diagnosis of breast cancer, and 500 and 505, respectively, died of breast cancer. Thus the cumulative mortality from breast cancer was similar between women in the mammography arm and in the control arm (hazard ratio 0.99, 95% confidence interval 0.88 to 1.12). After 15 years of follow-up a residual excess of 106 cancers was observed in the mammography arm, attributable to over-diagnosis. Conclusion: Annual mammography in women aged 40-59 does not reduce mortality from breast cancer beyond that of physical examination or usual care when adjuvant therapy for breast cancer is freely available. Overall, 22% (106/484) of screen detected invasive breast cancers were over-diagnosed, representing one over-diagnosed breast cancer for every 424 women who received mammography screening in the trial

RnaseIII and T4 Polynucleotide Kinase Sequence Biases and Solutions During RNA-Seq Library Construction

Background: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. Results: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5' and 3' end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. Conclusions: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data.National Institute on Alcohol Abuse and Alcoholism (NIAAA) AA12404, AA019382, AA020926, AA016648National Institutes of Health (NIH) R01 GM088344Waggoner Center for Alcohol and Addiction Researc

Nonaffine rubber elasticity for stiff polymer networks

We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces (``stretching''). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic characterization of the deformation field in terms of ``floppy modes'' -- low-energy bending excitations that retain a high degree of non-affinity. The length-scale characterizing the emergent non-affinity is given by the ``fiber length'' $l_f$, defined as the scale over which the polymers remain straight. The calculated scaling properties for the shear modulus are in excellent agreement with the results of recent simulations obtained in two-dimensional model networks. Furthermore, our theory can be applied to rationalize bulk rheological data in reconstituted actin networks.Comment: 12 pages, 10 figures, revised Section II

A Paleolithic diet lowers resistant starch intake but does not affect serum trimethylamine-N-oxide concentrations in healthy women

The Paleolithic diet excludes two major sources of fibre, grains and legumes. However, it is not known whether this results in changes to resistant starch (RS) consumption. Serum trimethylamine-N-oxide (TMAO) is produced mainly from colonic fermentation and hepatic conversion of animal protein and is implicated in CVD, but changes in RS intake may alter concentrations. We aimed to determine whether intake of RS and serum concentrations of TMAO varied in response to either the Paleolithic or the Australian Guide to Healthy Eating (AGHE) diets and whether this was related to changes in food group consumption. A total of thirty-nine women (mean age 47 (sd 13) years, BMI 27 (sd 4) kg/m2) were randomised to AGHE (n 17) or Paleolithic diets (n 22) for 4 weeks. Serum TMAO concentrations were measured using liquid chromatography-MS; food groups, fibre and RS intake were estimated from weighed food records. The change in TMAO concentrations between groups (Paleolithic 3·39 μm v. AGHE 1·19 μm, P = 0·654) did not reach significance despite greater red meat and egg consumption in the Paleolithic group (0·65 serves/d; 95 % CI 0·2, 1·1;

A Paleolithic diet lowers resistant starch intake but does not affect serum trimethylamine-N-oxide concentrations in healthy women

The Paleolithic diet excludes two major sources of fibre, grains and legumes. However, it is not known whether this results in changes to resistant starch (RS) consumption. Serum trimethylamine-N-oxide (TMAO) is produced mainly from colonic fermentation and hepatic conversion of animal protein and is implicated in CVD, but changes in RS intake may alter concentrations. We aimed to determine whether intake of RS and serum concentrations of TMAO varied in response to either the Paleolithic or the Australian Guide to Healthy Eating (AGHE) diets and whether this was related to changes in food group consumption. A total of thirty-nine women (mean age 47 (sd 13) years, BMI 27 (sd 4) kg/m2) were randomised to AGHE (n 17) or Paleolithic diets (n 22) for 4 weeks. Serum TMAO concentrations were measured using liquid chromatography–MS; food groups, fibre and RS intake were estimated from weighed food records. The change in TMAO concentrations between groups (Paleolithic 3·39 μmv. AGHE 1·19 μm, P = 0·654) did not reach significance despite greater red meat and egg consumption in the Paleolithic group (0·65 serves/d; 95 % CI 0·2, 1·1; P <0·01, and 0·22 serves/d; 95 % CI 0·1, 0·4, P <0·05, respectively). RS intake was significantly lower on the Paleolithic diet (P <0·01) and was not associated with TMAO concentrations. However, the limited data for RS and the small sample size may have influenced these findings. While there were no significant changes in TMAO concentrations, increased meat consumption and reduced RS intake warrant further research to examine the markers of gastrointestinal health of Paleolithic diet followers and to update Australian food databases to include additional fibre components

Associations between incident breast cancer and ambient concentrations of nitrogen dioxide from a national land use regression model in the Canadian National Breast Screening Study

Background: Air pollution has been classified as a human carcinogen based largely on epidemiological studies of lung cancer. Recent research suggests that exposure to ambient air pollution increases the risk of female breast cancer especially in premenopausal women. Methods: Our objective was to determine the association between residential exposure to ambient nitrogen dioxide (NO2) and newly diagnosed cases of invasive breast cancer in a cohort of 89,247 women enrolled in the Canadian National Breast Screening Study between 1980 and 1985.

Airborne dust and high temperatures are risk factors for invasive bacterial disease

Background The Sahel region of West Africa has the highest bacterial meningitis attack and case fatality rate in the world. The effect of climatic factors on patterns of invasive respiratory bacterial disease is not well documented. Objective We aimed to assess the link between climatic factors and occurrence of invasive respiratory bacterial disease in a Sahel region of Niger. Methods We conducted daily disease surveillance and climatic monitoring over an 8-year period between January 1, 2003, and December 31, 2010, in Niamey, Niger, to determine risk factors for bacterial meningitis and invasive bacterial disease. We investigated the mechanistic effects of these factors on Streptococcus pneumoniae infection in mice. Results High temperatures and low visibility (resulting from high concentrations of airborne dust) were identified as significant risk factors for bacterial meningitis. Dust inhalation or exposure to high temperatures promoted progression of stable asymptomatic pneumococcal nasopharyngeal carriage to pneumonia and invasive disease. Dust exposure significantly reduced phagocyte-mediated bacterial killing, and exposure to high temperatures increased release of the key pneumococcal toxin pneumolysin through increased bacterial autolysis. Conclusion Our findings show that climatic factors can have a substantial influence on infectious disease patterns, altering density of pneumococcal nasopharyngeal carriage, reducing phagocytic killing, and resulting in increased inflammation and tissue damage and consequent invasiveness. Climatic surveillance should be used to forecast invasive bacterial disease epidemics, and simple control measures to reduce particulate inhalation might reduce the incidence of invasive bacterial disease in regions of the world exposed to high temperatures and increased airborne dust

Lympho-vascular invasion in BRCA related breast cancer compared to sporadic controls

<p>Abstract</p> <p>Background</p> <p>Germline mutations in the BRCA1 gene predispose to the development of breast cancer, exhibiting a specific histological phenotype. Identification of possible hallmarks of these tumors is important for selecting patients for genetic screening and provides inside in carcinogenetic pathways.</p> <p>Since BRCA1-associated breast cancers have pushing borders that prevent them from easily reaching vessels and are often of the medullary (like) type that is known to have a low rate of lympho-vascular invasion (LVI), we hypothesized that absence of LVI could characterize BRCA1 related breast cancer.</p> <p>Methods</p> <p>A population of 68 BRCA1 related invasive breast cancers was evaluated for LVI by an experienced breast pathologist blinded to mutation status, and compared to a control group matched for age, grade and tumor type.</p> <p>Results</p> <p>LVI was present in 25.0% of BRCA1 related cases, compared to 20.6% of controls (P = 0.54, OR = 1.29, CI 0.58-2.78).</p> <p>Conclusion</p> <p>LVI is frequent in BRCA1 germline mutation related breast cancers, but seems to occur as often in sporadic controls matched for age, grade and tumor type. Apparently, these hereditary cancers find their way to the blood and lymph vessels despite their well demarcation and often medullary differentiation.</p

Detecting Clusters of Mutations

Positive selection for protein function can lead to multiple mutations within a small stretch of DNA, i.e., to a cluster of mutations. Recently, Wagner proposed a method to detect such mutation clusters. His method, however, did not take into account that residues with high solvent accessibility are inherently more variable than residues with low solvent accessibility. Here, we propose a new algorithm to detect clustered evolution. Our algorithm controls for different substitution probabilities at buried and exposed sites in the tertiary protein structure, and uses random permutations to calculate accurate P values for inferred clusters. We apply the algorithm to genomes of bacteria, fly, and mammals, and find several clusters of mutations in functionally important regions of proteins. Surprisingly, clustered evolution is a relatively rare phenomenon. Only between 2% and 10% of the genes we analyze contain a statistically significant mutation cluster. We also find that not controlling for solvent accessibility leads to an excess of clusters in terminal and solvent-exposed regions of proteins. Our algorithm provides a novel method to identify functionally relevant divergence between groups of species. Moreover, it could also be useful to detect artifacts in automatically assembled genomes