Incidence of bone metastases in breast cancer patients in the United Kingdom: Results of a multi-database linkage study using the general practice research database

BackgroundBone is a frequent site for metastases among women with breast cancer. We conducted a study using the General Practice Research Database (GPRD), with linkage to the National Cancer Registry (NCR) and Hospital Episode Statistics (HES), to estimate the incidence of bone metastases in women with breast cancer in the United Kingdom.MethodsWe identified all women in the GPRD aged 20–99 with a first-time diagnosis of breast cancer between 2000 and 2006. To address potential underreporting, we developed and validated an algorithm to serve as a proxy for bone metastases. Bone metastases were defined as (1) a bone cancer diagnosis code on the same day or following breast cancer diagnosis date, or (2) another metastasis code plus codes consistent with bone metastases diagnosis or treatment using the algorithm. We sent questionnaires to a sample of general practitioners to validate these definitions.ResultsWe included 13,207 breast cancer patients (median age at diagnosis of 61 years) who contributed 70,885 person-years of follow-up. The majority of patients had stage 1 or 2 breast cancer (90.4%), and 2.6% had metastatic breast cancer at diagnosis. We identified 788 women (6.0%) with bone metastases after a median follow-up of 5.4 years. Questionnaire results validated the diagnosis of bone metastases in 88% of patients with a bone cancer code and for 70% identified with the algorithm.ConclusionThis is the first time the GPRD has been linked to HES and NCR to study the epidemiology of bone metastases, adding important information on the burden of bone metastasis.     

A novel virus detected in papillomas and carcinomas of the endangered western barred bandicoot (Perameles bougainville) exhibits genomic features of both the Papillomaviridae and Polyomaviridae

Conservation efforts to prevent the extinction of the endangered western barred bandicoot (Perameles bougainville) are currently hindered by a progressively debilitating cutaneous and mucocutaneous papillomatosis and carcinomatosis syndrome observed in captive and wild populations. In this study, we detected a novel virus, designated the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), in lesional tissue from affected western barred bandicoots using multiply primed rolling-circle amplification and PCR with the cutaneotropic papillomavirus primer pairs FAP59/FAP64 and AR-L1F8/AR-L1R9. Sequencing of the BPCV1 genome revealed a novel prototype virus exhibiting genomic properties of both the Papillomaviridae and the Polyomaviridae. Papillomaviral properties included a large genome size ( approximately 7.3 kb) and the presence of open reading frames (ORFs) encoding canonical L1 and L2 structural proteins. The genomic organization in which structural and nonstructural proteins were encoded on different strands of the double-stranded genome and the presence of ORFs encoding the nonstructural proteins large T and small t antigens were, on the other hand, typical polyomaviral features. BPCV1 may represent the first member of a novel virus family, descended from a common ancestor of the papillomaviruses and polyomaviruses recognized today. Alternatively, it may represent the product of ancient recombination between members of these two virus families. The discovery of this virus could have implications for the current taxonomic classification of Papillomaviridae and Polyomaviridae and can provide further insight into the evolution of these ancient virus families.     

Thermodynamics of Ni2+, Cu2+, and Zn2+ binding to the urease metallochaperone UreE

The two Ni2+ ions in the urease active site are delivered by the metallochaperone UreE, whose metal binding properties are central to the assembly of this metallocenter. Isothermal titration calorimetry (ITC) has been used to quantify the stoichiometry, affinity, and thermodynamics of Ni2+, Cu2+, and Zn2+ binding to the well-studied C-terminal truncated H144*UreE from Klebsiella aerogenes, Ni2+ binding to the wild-type K. aerogenes UreE protein, and Ni2+ and Zn2+ binding to the wild-type UreE protein from Bacillus pasteurii. The stoichiometries and affinities obtained by ITC are in good agreement with previous equilibrium dialysis results, after differences in pH and buffer competition are considered, but the concentration of H144*UreE was found to have a significant effect on metal binding stoichiometry. While two metal ions bind to the H144*UreE dimer at concentrations <10 microM, three Ni2+ or Cu2+ ions bind to 25 microM dimeric protein with ITC data indicating sequential formation of Ni/Cu(H144*UreE)4 and then (Ni/Cu)2(H144*UreE)4, or Ni/Cu(H144*UreE)2, followed by the binding of four additional metal ions per tetramer, or two per dimer. The thermodynamics indicate that the latter two metal ions bind at sites corresponding to the two binding sites observed at lower protein concentrations. Ni2+ binding to UreE from K. aerogenes is an enthalpically favored process but an entropically driven process for the B. pasteurii protein, indicating chemically different Ni2+ coordination to the two proteins. A relatively small negative value of DeltaCp is associated with Ni2+ and Cu2+ binding to H144*UreE at low protein concentrations, consistent with binding to surface sites and small changes in the protein structure.     

Roles of vasoconstrictor prostaglandins, COX-1 and -2, and AT1, AT2, and TP receptors in a rat model of early 2K,1C hypertension

Angiotensin (ANG) II activating type 1 receptors (AT(1)Rs) enhances superoxide anion (O(2)*(-)) and arachidonate (AA) formation. AA is metabolized by cyclooxygenases (COXs) to PGH(2), which is metabolized by thromboxane (Tx)A(2) synthase to TxA(2) or oxidized to 8-isoprostane PGF(2alpha) (8-Iso) by O(2)*(-). PGH(2), TxA(2), and 8-Iso activate thromboxane-prostanoid receptors (TPRs). We investigated whether blood pressure in a rat model of early (3 wk) two-kidney, one-clip (2K,1C) Goldblatt hypertension is maintained by AT(1)Rs or AT(2)Rs, driving COX-1 or -2-dependent products that activate TPRs. Compared with sham-operated rats, 2K,1C Goldblatt rats had increased mean arterial pressure (MAP; 120 +/- 4 vs. 155 +/- 3 mmHg; P < 0.001), plasma renin activity (PRA; 22 +/- 7 vs. 48 +/- 5 ng x ml(-1) x h(-1); P < 0.01), plasma malondialdehyde (1.07 +/- 0.05 vs. 1.58 +/- 0.16 nmol/l; P < 0.01), and TxB(2) excretion (26 +/- 4 vs. 51 +/- 7 ng/24 h; P < 0.01). Acute graded intravenous doses of benazeprilat (angiotensin-converting enzyme inhibitor) reduced MAP at 20 min (-36 +/- 5 mmHg; P < 0.001) and excretion of TxA(2) metabolites. Indomethacin (nonselective COX antagonist) or SC-560 (COX-1 antagonist) reduced MAP at 20 min (-25 +/- 5 and -28 +/- 7 mmHg; P < 0.001), whereas valdecoxib (COX-2 antagonist) was ineffective (-9 +/- 5 mmHg; not significant). Losartan (AT(1)R antagonist) or SQ-29548 (TPR antagonist) reduced MAP at 150 min (-24 +/- 6 and -22 +/- 3 mmHg; P < 0.001), whereas PD-123319 (AT(2)R antagonist) was ineffective. Acute blockade of TPRs, COX-1, or COX-2 did not change PRA, but TxB(2) generation by the clipped kidney was reduced by blockade of COX-1 and increased by blockade of COX-2. 2K,1C hypertension in rats activates renin, O(2)*(-), and vasoconstrictor PGs. Hypertension is maintained by AT(1)Rs and by COX-1, but not COX-2, products that activate TPRs.     

Hydrogen peroxide mediates a transient vasorelaxation with tempol during oxidative stress

Tempol catalyzes the formation of H(2)O(2) from superoxide and relaxes blood vessels. We tested the hypothesis that the generation of H(2)O(2) by tempol in vascular smooth muscle cells during oxidative stress contributes to the vasorelaxation. Tempol and nitroblue tetrazolium (NBT) both metabolize superoxide in vascular smooth muscle cells, but only tempol generates H(2)O(2). Rat pressurized mesenteric arteries were exposed for 20 min to the thromboxane-prostanoid receptor agonist, U-46619, or norepinephrine. During U-46619, tempol caused a transient dilation (22 +/- 2%), whereas NBT was ineffective (2 +/- 1%), and neither dilated vessels constricted with norepinephrine, which does not cause vascular oxidative stress. Neither endothelium removal nor blockade of K(+) channels with 40 mM KCl affected the tempol-induced dilation, but catalase blunted the tempol dilation by 53 +/- 7%. Tempol, but not NBT, increased H(2)O(2) in rat mesenteric vessels detected with dichlorofluorescein. To test physiological relevance in vivo, topical application of tempol caused a transient dilation (184 +/- 20%) of mouse cremaster arterioles exposed to angiotensin II for 30 min, which was not seen with NBT (9 +/- 4%). The vasodilation to tempol was reduced by 68 +/- 6% by catalase. We conclude that the transient relaxation of blood vessels by tempol after prolonged exposure to U-46619 or angiotensin II is mediated in part via production of H(2)O(2) and is largely independent of the endothelium and potassium channels.     

How patch configuration affects the impact of disturbances on metapopulation persistence

Disturbances affect metapopulations directly through reductions in population size and indirectly through habitat modification. We consider how metapopulation persistence is affected by different disturbance regimes and the way in which disturbances spread, when metapopulations are compact or elongated, using a stochastic spatially explicit model which includes metapopulation and habitat dynamics. We discover that the risk of population extinction is larger for spatially aggregated disturbances than for spatially random disturbances. By changing the spatial configuration of the patches in the system--leading to different proportions of edge and interior patches--we demonstrate that the probability of metapopulation extinction is smaller when the metapopulation is more compact. Both of these results become more pronounced when colonization connectivity decreases. Our results have important management implication as edge patches, which are invariably considered to be less important, may play an important role as disturbance refugia.     

Assessment of factors influencing finite element vertebral model predictions

This study aimed to establish model construction and configuration procedures for future vertebral finite element analysis by studying convergence, sensitivity, and accuracy behaviors of semiautomatically generated models and comparing the results with manually generated models. During a previous study, six porcine vertebral bodies were imaged using a microcomputed tomography scanner and tested in axial compression to establish their stiffness and failure strength. Finite element models were built using a manual meshing method. In this study, the experimental agreement of those models was compared with that of semiautomatically generated models of the same six vertebrae. Both manually and semiautomatically generated models were assigned gray-scale-based, element-specific material properties. The convergence of the semiautomatically generated models was analyzed for the complete models along with material property and architecture control cases. A sensitivity study was also undertaken to test the reaction of the models to changes in material property values, architecture, and boundary conditions. In control cases, the element-specific material properties reduce the convergence of the models in comparison to homogeneous models. However, the full vertebral models showed strong convergence characteristics. The sensitivity study revealed a significant reaction to changes in architecture, boundary conditions, and load position, while the sensitivity to changes in material property values was proportional. The semiautomatically generated models produced stiffness and strength predictions of similar accuracy to the manually generated models with much shorter image segmentation and meshing times. Semiautomatic methods can provide a more rapid alternative to manual mesh generation techniques and produce vertebral models of similar accuracy. The representation of the boundary conditions, load position, and surrounding environment is crucial to the accurate prediction of the vertebral response. At present, an element size of 2x2x2 mm(3) appears sufficient since the error at this size is dominated by factors, such as the load position, which will not be improved by increasing the mesh resolution. Higher resolution meshes may be appropriate in the future as models are made more sophisticated and computational processing time is reduced.     

Bird demographic responses to predator removal programs

Invasive predators pose a significant risk to bird populations worldwide. Humans have a long history of removing predators from ecosystems; current island restoration actions typically focus on the removal of invasive predators, such as non-native rodents, from seabird breeding islands. While not overly abundant, the results of predator removal studies provide valuable information on the demographic response of birds, and can assist conservation practitioners with prioritizing invasive predator removal projects. We review such studies focusing on observed demographic responses of bird populations to predator removal campaigns and whether ecological factors are useful in predicting those responses. From the 800+ predator removal programs indentified, a small fraction (n = 112) reported demographic responses of bird populations. Change in productivity was the most commonly reported response, which on average increased by 25.3% (2.5 SE) with predator removal. The best supported model for predicting the change in productivity from predator removal incorporated bird body mass, egg mass, predator type, nest type and an interaction term for body mass and nest type (AIC_c weight = 0.457). The predicted percent increase in productivity resulting from hypothetical predator removal ranged from 16.9 to 63.0% (mean = 45.0, 5.6 SE), and was lowest for large, surface nesting birds such as albatrosses. The predicted increase in productivity resulting from predator removal alone was insufficient to reverse the predicted population decline for 30–67% of bird species considered, suggesting that in many cases, removal of predators must be performed in combination with other conservation actions in order to ensure a stable or increasing population.     

Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes

Background  

Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi.