In situ x-ray photoelectron spectroscopy of model catalysts: at the edge of the gap

We present high-pressure x-ray photoelectron spectroscopy (HP-XPS) and first-principles kinetic Monte Carlo study addressing the nature of the active surface in CO oxidation over Pd(100). Simultaneously measuring the chemical composition at the surface and in the near-surface gas phase, we reveal both O-covered pristine Pd(100) and a surface oxide as stable, highly active phases in the near-ambient regime accessible to HP-XPS. Surprisingly, no adsorbed CO can be detected during high CO(2) production rates, which can be explained by a combination of a remarkably short residence time of the CO molecule on the surface and mass-transfer limitations in the present setup.

A practical framework for data management processes and their evaluation in population-based medical registries

INTRODUCTION

We present a framework for data management processes in population-based medical registries. Existing guidelines lack the concreteness we deem necessary for them to be of practical use, especially concerning the establishment of new registries. Therefore, we propose adjustments and concretisations with regard to data quality, data privacy, data security and registry purposes.

MATERIALS AND METHODS

First, we separately elaborate on the issues to be included into the framework and present proposals for their improvements. Thereafter, we provide a framework for medical registries based on quasi-standard-operation procedures.

RESULTS

The main result is a concise and scientifically based framework that tries to be both broad and concrete. Within that framework, we distinguish between data acquisition, data storage and data presentation as sub-headings. We use the framework to categorise and evaluate the data management processes of a German cancer registry.

DISCUSSION

The standardisation of data management processes in medical registries is important to guarantee high quality of the registered data, to enhance the realisation of purposes, to increase efficiency and to enable comparisons between registries. Our framework is destined to show how one central impediment for such standardisations - lack of practicality - can be addressed on scientific grounds.

Abstract P2-10-37: Long-term prognosis of early breast cancer in a population-based cohort with a known BRCA1/2 mutation status

Background: The impact of germline BRCA1/2 mutations on breast cancer prognosis and treatment is currently not clear. We investigate how different factors, including BRCA1/2 mutation status, correlate with long-term outcome in early breast cancer in a population-based cohort.

Methods: As previously reported, all women in the Southern Health Care Region in Sweden with breast cancer diagnosed before age 41 years between 1990 and 1995 (n = 262) were contacted in 1996 and offered mutation analysis of the BRCA1 and BRCA2 genes. Mutation analysis was performed on 234 of them, the others were excluded from further studies. 23 pathogenic mutations were found; 18 in BRCA1 and 5 in BRCA2. We will now present data on tumor and patient characteristics, treatment and long-term follow-up for the patients from this population-based cohort. Three patients have declined further study follow-up and were therefore excluded. Six patients had metastatic breast cancer at the time diagnosis (one of them a BRCA2 mutation carrier) and are also excluded, leaving 225 in the present analysis.

Results: Among the 225 cases estrogen receptor (ER) status is known for 191 (49% ER+, 51% ER−); histologic grade for 169 (24% grade I; 33% grade II; 43% grade III); stage for 225 (36% stage I, 44% stage II, 20% stage III); type of surgery, adjuvant systemic treatment and postoperative radiotherapy for 225. In the cohort, 46% received adjuvant or neoadjuvant chemotherapy, whereas 15% were given adjuvant endocrine therapy. There is complete follow-up > 10 years for 205 and present vital status for 224.

Of the 225 women, 128 (57%) have had a local, regional or distant recurrence of breast cancer (contralateral breast cancer not included) at the date of last follow-up. One hundred and six patients (47%) have died, 98 of whom from breast cancer and 2 from presumably radiation-induced malignancies caused by postoperative radiotherapy. Thirteen of the 22 BRCA1/2 mutation carriers (59 %) have died, all from breast cancer. Of the 9 mutation carriers that are alive today, 3 have had an in-breast tumor recurrence and 3 have had a contralateral breast cancer; the 3 women that have had neither have all performed bilateral prophylactic mastectomy as well as prophylactic salpingo-ooforectomy.

Data on how the long-term prognosis of early breast cancer is correlated to BRCA1/2 mutation status, adjuvant treatment, stage at diagnosis, histologic grade and ER status of the tumor will be presented.

Conclusion: Women with early breast cancer in this cohort from the early 90ies had a poor long-term prognosis. The prognosis for women diagnosed with early breast cancer today is likely to be better, thanks to more modern chemotherapy regimens, endocrine and targeted treatments. The prognostic significance of BRCA1/2 mutation status will be further analyzed.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-10-37.

Bagging, bumping, multiview, and active learning for record linkage with empirical results on patient identity data

Record linkage or deduplication deals with the detection and deletion of duplicates in and across files. For this task, this paper introduces and evaluates two new machine-learning methods (bumping and multiview) together with bagging, a tree-based ensemble-approach. Whereas bumping represents a tree-based approach as well, multiview is based on the combination of different methods and the semi-supervised learning principle. After providing a theoretical background of the methods, initial empirical results on patient identity data are given. In the empirical evaluation, we calibrate the methods on three different kinds of training data. The results show that the smallest training data set, which is obtained by a simple active learning strategy, leads to the best results. Multiview can outperform the other methods only when all are calibrated on a randomly sampled training set; in all other cases, it performs worse. The results of bumping do not differ significantly from the overall best performing method bagging. We cautiously conclude that tree-based record linkage methods are likely to produce similar results because of the low-dimensionality (p≪n) and straightforwardness of the underlying problem. Multiview is possibly rather suitable for problems that are more sophisticated.

P3-06-08: SCAN-B: An Accelerated Translational Pipeline from Profile to Prognosis and Prediction for Individual Breast Cancer Patients

The South Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative is a multidisciplinary network of clinical providers of breast cancer (BC) treatment and pre-clinical scientists whose multiyear purpose is to 1) prospectively collect and analyze the “-omes” of a very large, consecutive, and population-based sample of BCs for translational research; 2) utilize this genomic data to develop new clinically-relevant biomarker assays; and 3) to build the infrastructure for future real-time clinical implementation of resultant biomarkers for individualized treatment. Patient enrollment began in the Fall of 2010 at the seven BC surgical units of the South Sweden Healthcare Region, where approximately 1500 new breast cancer diagnoses are treated yearly following the guidelines of the South Sweden Breast Cancer Group. Currently, tumor and blood samples are being collected at the rate of 80–100 patients per month, which represents approximately 75% of the catchment population. SCAN-B will initially focus on tumor transcriptome analysis using mRNA-sequencing on Illumina HiSeq 2000 instruments, and in the future multimodal data generated from other genomic platforms will also be integrated. Here we present initial experiences from this multidisciplinary collaboration including descriptions of the clinical routines, specimen handling, laboratory processing, mRNA-seq data quality control, short- and long-term projects and future directions. We believe large initiatives like SCAN-B could significantly reduce the time to discovery, validation, and clinical implementation of more powerful diagnostic, prognostic, and treatment-predictive tests for breast cancer.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-08.

Missing values in deduplication of electronic patient data

INTRODUCTION

Systematic approaches to dealing with missing values in record linkage are still lacking. This article compares the ad-hoc treatment of unknown comparison values as 'unequal' with other and more sophisticated approaches. An empirical evaluation was conducted of the methods on real-world data as well as on simulated data based on them.

MATERIAL AND METHODS

Cancer registry data and artificial data with increased numbers of missing values in a relevant variable are used for empirical comparisons. As a classification method, classification and regression trees were used. On the resulting binary comparison patterns, the following strategies for dealing with missingness are considered: imputation with unique values, sample-based imputation, reduced-model classification and complete-case induction. These approaches are evaluated according to the number of training data needed for induction and the F-scores achieved.

RESULTS

The evaluations reveal that unique value imputation leads to the best results. Imputation with zero is preferred to imputation with 0.5, although the latter shows the highest median F-scores. Imputation with zero needs considerably less training data, it shows only slightly worse results and simplifies the computation by maintaining the binary structure of the data.

CONCLUSIONS

The results support the ad-hoc solution for missing values 'replace NA by the value of inequality'. This conclusion is based on a limited amount of data and on a specific deduplication method. Nevertheless, the authors are confident that their results should be confirmed by other empirical analyses and applications.

Adsorption of methylamine on Ni 3 Al(111) and NiAl(110)--a high resolution photoelectron spectroscopy and density functional theory study

Methylamine adsorption on the ordered Ni(3)Al(111) and NiAl(110) surfaces has been investigated by high resolution photoelectron spectroscopy and density functional theory calculations. Methylamine adsorbs molecularly at both surfaces at low temperature (90 K). The experiments show that methylamine interacts with the surface aluminium atoms on both surfaces, resulting in a positive binding energy shift relative to the Al 2p bulk contributions. A shift towards lower binding energy is also observed on NiAl(110) attributed to first and second layer surface Al atoms not bonded to methylamine. According to total energy calculations methylamine binds through its N atom to Al on-top sites on NiAl(110) while the Ni on-top site is found to be slightly preferred over the Al on-top site on Ni(3)Al(111). Calculated adsorbate induced shifts are, however, in good agreement with the experimental values only when methylamine is situated in the Al on-top site on both surfaces. In both cases, a lone pair bonding mechanism is found.

Evaluation of record linkage methods for iterative insertions

OBJECTIVES

There have been many developments and applications of mathematical methods in the context of record linkage as one area of interdisciplinary research efforts. However, comparative evaluations of record linkage methods are still underrepresented. In this paper improvements of the Fellegi-Sunter model are compared with other elaborated classification methods in order to direct further research endeavors to the most promising methodologies.

METHODS

The task of linking records can be viewed as a special form of object identification. We consider several non-stochastic methods and procedures for the record linkage task in addition to the Fellegi-Sunter model and perform an empirical evaluation on artificial and real data in the context of iterative insertions. This evaluation provides a deeper insight into empirical similarities and differences between different modelling frames of the record linkage problem. In addition, the effects of using string comparators on the performance of different matching algorithms are evaluated.

RESULTS

Our central results show that stochastic record linkage based on the principle of the EM algorithm exhibits best classification results when calibrating data are structurally different to validation data. Bagging, boosting together with support vector machines are best classification methods when calibrating and validation data have no major structural differences.

CONCLUSIONS

The most promising methodologies for record linkage in environments similar to the one considered in this paper seem to be stochastic ones.

CHEK2*1100delC is not an important high-risk gene in families with hereditary prostate cancer in southern Sweden

OBJECTIVE

CHEK2*1100delC is a frame-shifting germ-line mutation which abolishes the function of cell-cycle-checkpoint kinase 2 (chk2) and hence impairs the cells' response to DNA damage. This variant occurs in 1% of the general Western population but has been reported to be more common among patients with breast and prostate cancer. The aim of this study was to investigate the significance of CHEK2*1100delC as a possible high-risk gene for hereditary prostate cancer in the population of southern Sweden.

MATERIAL AND METHODS

We screened for the CHEK2*1100delC variant in 419 men diagnosed with prostate cancer in southern Sweden, 145 of whom were sporadic cases that were divided into two subgroups depending on whether they were diagnosed before (n=64) or after (n=81) the age of 55 years. A further 126 men were classified as familial prostate cancer cases and 148 as hereditary prostate cancer cases. The control group consisted of 305 military conscripts aged 18 years (range 18-21 years).

RESULTS

The CHEK2*1100delC variant was found in 1.2% of the cases (sporadic: 0.7%; familial: 1.6%; hereditary: 1.4%) and in 1.0% of the controls.

CONCLUSION

The CHEK2 1100delC mutation is not a clinically important high-risk gene for hereditary prostate cancer susceptibility in the population of southern Sweden.

The fabrication and characterization of PbTiO3 nanomesas realized on nanostructured SrRuO3/SrTiO3 templates

We report the fabrication of PbTiO(3) nanomesas down to 30 nm lateral size and 4 nm high on nanostructured SrRuO(3)/SrTiO(3) templates by off-axis radio frequency magnetron sputtering. The templates were prepared using a top-down lithography approach based on scanning tunneling microscopy. The growth rate of the PbTiO(3) nanomesas was found to decrease with increasing growth temperature as well as with shrinking template size. Piezoresponse force microscopy measurements for the PbTiO(3) nanomesas showed a strong increase in response with decreasing lateral size. A decrease of the coercive voltage was also observed for the same lateral size range. This laterally size-dependent behavior is attributed to reduction of in-plane strain, when shrinking the nanomesa lateral dimensions.

The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions

Multiple genetic loci confer susceptibility to breast and ovarian cancers. We have previously developed a model (BOADICEA) under which susceptibility to breast cancer is explained by mutations in BRCA1 and BRCA2, as well as by the joint multiplicative effects of many genes (polygenic component). We have now updated BOADICEA using additional family data from two UK population-based studies of breast cancer and family data from BRCA1 and BRCA2 carriers identified by 22 population-based studies of breast or ovarian cancer. The combined data set includes 2785 families (301 BRCA1 positive and 236 BRCA2 positive). Incidences were smoothed using locally weighted regression techniques to avoid large variations between adjacent intervals. A birth cohort effect on the cancer risks was implemented, whereby each individual was assumed to develop cancer according to calendar period-specific incidences. The fitted model predicts that the average breast cancer risks in carriers increase in more recent birth cohorts. For example, the average cumulative breast cancer risk to age 70 years among BRCA1 carriers is 50% for women born in 1920-1929 and 58% among women born after 1950. The model was further extended to take into account the risks of male breast, prostate and pancreatic cancer, and to allow for the risk of multiple cancers. BOADICEA can be used to predict carrier probabilities and cancer risks to individuals with any family history, and has been implemented in a user-friendly Web-based program (http://www.srl.cam.ac.uk/genepi/boadicea/boadicea_home.html).

Tiling resolution array CGH of dic(7;9)(p11∼13;p11∼13) in B-cell precursor acute lymphoblastic leukemia reveals clustered breakpoints at 7p11.2∼12.1 and 9p13.1

The dic(7;9)(p11 approximately 13;p11 approximately 13) is a recurrent chromosomal abnormality in acute lymphoblastic leukemia (ALL), mainly of B-lineage. Although more than 20 dic(7;9)-positive ALLs have been reported to date, the molecular genetic consequences of this aberration are unknown. We performed tiling resolution (32K) genome-wide array-based comparative genomic hybridization (array CGH) analysis of three cases with dic(7;9) in order to characterize the breakpoints on 7p and 9p. The analysis showed a clustering of breakpoints within 9p13.1 in all three cases and within 7p11.2 in two cases; the array CGH revealed two different breakpoints - 7p12.1 and 7p14.1 - in the remaining case. Based on these findings the abnormality should hence be designated dic(7;9)(p11.2 approximately 12.1;p13.1). Locus-specific fluorescence in situhybridization analysis of one of the cases narrowed down the 7p11.2 breakpoint to a <500-kb segment in this sub-band, a region containing three known genes. Unfortunately, lack of material precluded further molecular genetic studies, and it thus remains unknown whether the pathogenetically important outcome of the dic(7;9) is formation of a chimeric gene or loss of 7p and/or 9p material.