An in situ instrument for planar O2 optode measurements at benthic interfaces

A new in situ instrument for two‐dimensional mapping of oxygen in coastal sediments is presented. The measuring principle is described, and potential mechanical disturbances, solute and particle smearing associated with the measurements, and calibration routines are evaluated. The first in situ measurements obtained in two different benthic communities are presented. In a shallow photosynthetic sediment (1 m of water depth), an extensive horizontal and temporal variation in the O2 distribution caused by benthic photosynthesis and irrigating fauna was resolved. Repetitive planar optode measurements performed along a transect in central Øresund, Denmark (17 m of water depth) revealed a positive correlation between the apparent O2 penetration depths (OP) measured with a lateral distance <5.0 mm, whereas OP measured with a larger horizontal distance (up to 50 m) were not correlated. Consequently, the OP varied in patches with a characteristic size of 5.0 mm. The instrument described is a powerful new tool for in situ characterization of spatiotemporal variations in O2 distributions within benthic communities. The instrument can be adapted for use at full ocean depths, e.g., on deep‐sea landers or remote operating vehicles

The Settlement of Industrial Disputes in Great Britain

The external phosphorus (P) loading has been halved, but the P content in the water column and the area of anoxic bottoms in Baltic proper has increased during the last 30 years. This can be explained by a temporary internal source of dissolved inorganic phosphorus (DIP) that is turned on when the water above the bottom sediment becomes anoxic. A load-response model, explaining the evolution from 1980 to 2005, suggests that the average specific DIP flux from anoxic bottoms in the Baltic proper is about 2.3 g P m(-2) year(-1). This is commensurable with fluxes estimated in situ from anoxic bottoms in the open Baltic proper and from hydrographic data in the deep part of Bornholm Basin. Oxygenation of anoxic bottoms, natural or manmade, may quickly turn off the internal P source from anoxic bottoms. This new P-paradigm should have far-reaching implications for abatement of eutrophication in the Baltic proper.Funding Agencies|Swedish EPA [NV 08/302 F-255-08]</p

A computer vision system for appearance-based descriptive sensory evaluation of meals

This paper presents a complete machine vision system for automatic descriptive sensory evaluation of meals. A human sensory panel first developed a set of 72 sensory attributes describing the appearance of a prototypical meal, and then evaluated the intensities of those attributes on a data set of 58 images of example meals. This data was then used both to train and validate the performance of the artificial system. This system covers all stages of image analysis from pre-processing to pattern recognition, including novel techniques for enhancing the segmentation of meal components and extracting image features that mimic the attributes developed by the panel. Artificial neural networks were used to learn the mapping from image features to attribute intensity values. The results showed that the new system was extremely good in learning and reproducing the opinion of the human sensory experts, achieving almost the same performance as the panel members themselves

ESS Control System Data Lab - Executive Summary

Driven by the idea to use alarm data to explore machine learning across Industry 4.0 applications, the goal of this pilot study was to explore how to collect, store, manage and share data from the ESS Control System. Generally, we seek to make any control system data available for research and innovation but started with alarms as a feasible domain in which to explore machine learning. The goals were threefold, each explored in a work package:1. How to govern a data ecosystem, and which tools are needed to support it?2. How can alarm data be interpreted across industrial contexts, i.e., which meta dataand reference models are needed?3. How can data sharing be practically and legally handled at ESS?In summary, we identify a set of potential alleys for continued work to foster industrial innovation and collaboration in a control system data ecosystem with ESS as a catalyst

Correlation test to assess low-level processing of high-density oligonucleotide microarray data

BACKGROUND: There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data. RESULTS: We analyzed coregulation between genes in order to detect insufficient normalization between arrays, where coregulation is measured in terms of statistical correlation. In a large collection of genes, a random pair of genes should have on average zero correlation, hence allowing a correlation test. For all data sets that we evaluated, and the three most commonly used low-level processing procedures including MAS5, RMA and MBEI, the housekeeping-gene normalization failed the test. For a real clinical data set, RMA and MBEI showed significant correlation for absent genes. We also found that a second round of normalization on the probe set level improved normalization significantly throughout. CONCLUSION: Previous evaluation of low-level processing in the literature has been limited to artificial spike-in and mixture data sets. In the absence of a known gold-standard, the correlation criterion allows us to assess the appropriateness of low-level processing of a specific data set and the success of normalization for subsets of genes

Predictors for discontinuation of adjuvant hormone therapy in breast cancer patients

PURPOSE: To identify predictors of discontinuation of adjuvant hormone therapy in patients with breast cancer. PATIENTS AND METHODS: We conducted a record-linkage study based on data from Stockholm-Gotland Breast Cancer Register, Swedish Prescribed Drug Register, and self-reported questionnaire. Women diagnosed with breast cancer between 2005 and 2008 in Stockholm, Sweden, were prospectively followed for 5 years until 2013, starting from their first prescription of tamoxifen or aromatase inhibitors (N = 3,395). RESULTS: Family history of ovarian cancer (hazard ratio [HR], 1.55; 95% CI, 1.19 to 2.02); younger (< 40 years; HR, 1.39; 95% CI, 1.08 to 1.78) and older (>/= 65 years; HR, 1.15; 95% CI, 1.03 to 1.28) age; higher Charlson comorbidity index (>/= 2 v 0; HR, 1.35; 95% CI, 1.03 to 1.76); and use of analgesics (HR, 1.33; 95% CI, 1.16 to 1.52), hypnotics/sedatives (HR, 1.24; 95% CI, 1.07 to 1.43), GI drugs (HR, 1.25; 95% CI, 1.08 to 1.43), and hormone replacement therapy (HR, 1.27; 95% CI, 1.08 to 1.49) were identified as baseline predictors for hormonal treatment discontinuation. Use of analgesics (HR, 1.22; 95% CI, 1.08 to 1.37), hypnotics/sedatives (HR, 1.21; 95% CI, 1.07 to 1.37), antidepressants (HR, 1.22; 95% CI, 1.06 to 1.40), or GI drugs (HR, 1.27; 95% CI, 1.13 to 1.43), and switching therapy between tamoxifen and aromatase inhibitors (HR, 1.50; 95% CI, 1.23 to 1.83) during the first year of hormonal treatment were associated with increased risk of discontinuation during the next 4 years. CONCLUSION: Predictors identified in our study can be used in developing targeted intervention to prevent adjuvant hormone therapy discontinuation and subsequently to improve breast cancer outcomes.Swedish Research CouncilSwedish Cancer SocietyFORTESwedish Society of Medical Research (SSMF)Accepte

Interval breast cancer is associated with other types of tumors

Contributions: F.G. and K.C. conceived and designed the project; K.C. acted as the principal investigator; P.H., M.E, M.G., Women’s Health Initiative organized patient recruitment and sample collection; F.G. and W.H. analyzed the data; W.H., M.G., P.H., K.C. contributed to data interpretation; F.G. and K.C. wrote the manuscript with input from all authors. All authors approved of the final manuscript. Acknowledgements: This work was financed by the Swedish Research Council (Grant 2018-02547), the Swedish Cancer Society (grants CAN 2016/684 and 2013/469), the Cancer Society in Stockholm (Grant 141092), the Stockholm County Council (Grant No. LS 1211–1594), and the Karolinska Institutet’s Research Foundation (Grant 2018-02146). The KARMA study is supported by the Märit and Hans Rausing Initiative Against Breast Cancer and the Cancer and Risk Prediction Center (CRisP), a Linnaeus center (grant 70867902) financed by the Swedish Research Council. F.G. was a Leopoldina Postdoctoral Fellow (Grant No. LPDS 2018-06) funded by the Academy of Sciences Leopoldina. W.H. was supported by the Swedish Research Council for Health, Working Life and Welfare (FORTE, 2018-00877). We thank Dr. Johanna Holm for her valuable contribution to the manuscript. Genotyping of the OncoArray was principally funded by three sources: the PERSPECTIVE project, funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the Ministère de l’Économie, de la Science et de l’Innovation du Québec through Genome Québec, and the Quebec Breast Cancer Foundation; the National Cancer Institute Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) projects (National Institutes of Health [NIH] grants U19 CA148065 and X01HG007492); and Cancer Research UK (C1287/A10118 and C1287/A16563). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175); Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the “CIHR Team in Familial Risks of Breast Cancer” program; and the Ministry of Economic Development, Innovation and Export Trade of Quebec (grant PSR-SIIRI-701). Combination of the GWAS data was supported in part by NIH Cancer Post-Cancer GWAS initiative grant U19 CA148065 (DRIVE, part of the GAME-ON initiative). All studies and funders are listed in ref. 60. The WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, US Department of Health and Human Services through contracts N01WH22110, 24152, 32100–2, 32105–6, 32108–9, 32111–13, 32115, 32118–32119, 32122, 42107–26, 42129–32, and 44221. This manuscript was not prepared in collaboration with investigators of the WHI, has not been reviewed, and/or approved by the WHI, and does not necessarily reflect the opinions of the WHI investigators or the NHLBI. The study sponsors had no role in the design of the study, the collection, analysis, or interpretation of the data, the writing of the manuscript, or the decision to submit the manuscript for publication. Open access funding provided by Karolinska InstitutePeer reviewedPublisher PD

Mammographic features are associated with cardiometabolic disease risk and mortality

Open Access via the OUP Open Access Agreement Acknowledgements: The authors thank all the participants in the KARMA study and personnel for their devoted work during data collection. They also would like to acknowledge Jose ́ Tapia for helping in data management. Funding: This work was supported by “Ma ̈rit and Hans Rausing’s Initiative Against Breast Cancer” and was financed by the Swedish Research Council (Grant 2018-02547 to K.C.), the Swedish Cancer Society (Grant 19 0266 and 19 0267 to K.C.), FORTE (Grant 2016-00081 to K.C.), and the Karolinska Institutet’s Research Foundation (Grant 2018-02146 to F.G.). F.G. was a Leopoldina Postdoctoral Fellow (Grant No. LPDS 2018-06) funded by the Academy of Sciences Leopoldina. H.Y. was supported by Start-up Fund for high-level talents of Fujian Medical University (Grant .No. XRCZX2020007) and Start-up Fund for Scientific Research, Fujian Medical University (Grant No. 2019QH1002). The funding agency had no role in the study design, data collection, analyses, and data interoperation, in writing the manuscript, or in the decision to submit the manuscript for publication.Peer reviewedPublisher PD

Exome sequencing of contralateral breast cancer identifies metastatic disease

Women with contralateral breast cancer (CBC) have significantly worse prognosis compared to women with unilateral cancer. A possible explanation of the poor prognosis of patients with CBC is that in a subset of patients, the second cancer is not a new primary tumor but a metastasis of the first cancer that has potentially obtained aggressive characteristics through selection of treatment. Exome and whole-genome sequencing of solid tumors has previously been used to investigate the clonal relationship between primary tumors and metastases in several diseases. In order to assess the relationship between the first and the second cancer, we performed exome sequencing to identify somatic mutations in both first and second cancers, and compared paired normal tissue of 25 patients with metachronous CBC. For three patients, we identified shared somatic mutations indicating a common clonal origin thereby demonstrating that the second tumor is a metastasis of the first cancer, rather than a new primary cancer. Accordingly, these patients all developed distant metastasis within 3 years of the second diagnosis, compared with 7 out of 22 patients with non-shared somatic profiles. Genomic profiling of both tumors help the clinicians distinguish between true CBCs and subsequent metastasesVetenskapsrådetForteAccepte