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

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

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

Benthic fluxes of oxygen and inorganic nutrients in the archipelago of Gulf of Finland, Baltic Sea – Effects of sediment resuspension measured in situ

Abstract Benthic fluxes of oxygen and dissolved inorganic nutrients; phosphate (DIP), ammonium (NH4), nitrate + nitrite (NOx), and silicate (DSi); and the effects of resuspension on these were studied in situ with the Göteborg benthic landers in the Gulf of Finland archipelago, Baltic Sea. The benthic fluxes were examined at two shallow stations at depths of 7 m and 20 m in May and August 2014. Resuspension altered benthic fluxes of oxygen and nutrients in most of the experiments in August, but not in May, which was mainly due to weaker resuspension treatments in spring. Additionally, the benthic nutrient regeneration rates were higher and redox conditions lower in August when the water was warmer. In August, resuspension increased the benthic oxygen uptake by 33–35%, which was, in addition to stronger resuspension treatment, attributed to higher amounts of dissolved reduced substances in the sediment pore water in comparison to conditions in May. Adsorption onto newly formed iron oxyhydroxides could explain the uptake of DIP by the sediment at the 20 m station and the lowering of the DSi efflux by 31% at the 7 m station during resuspension in August. In addition, resuspension promoted nitrification, as indicated by increased NOx fluxes at both stations (by 30% and 27% at the 7 m and 20 m station, respectively) and a lowered NH4 flux (by 48%) at the 7 m station. Predicted increases in the magnitude and frequency of resuspension will thus markedly affect the transport of phosphorus and silicon and the cycling of nitrogen in the shallow areas of the Gulf of Finland.Peer reviewe

Sulfide oxidation in deep Baltic Sea sediments upon oxygenation and colonization by macrofauna

Coastal and shelf sediments affected by transient or long-term bottom water anoxia and sulfidic conditions undergo drastic changes in macrofauna communities and abundances. This study investigates how early colonization by two macrofaunal functional traits (epifauna vs. infauna) affects oxygen, sulfide, and pH dynamics in anoxic sediment upon recent bottom water oxygenation. Large mesocosms (area 900 cm 2) with 150-m-deep Baltic Sea soft sediments were exposed to three treatments: (1) no animals; (2) addition of 170 polychaetes (Marenzelleria arctia); (3) addition of 181 amphipods (Monoporeia affinis). Porewater chemistry was investigated repeatedly by microsensor profiling over a period of 65 days. Colonization by macrofauna did not significantly deepen penetration of oxygen compared to the animal-free sediment. Bioturbation by M. affinis increased the volume of the oxidized, sulfide-free sediment by 66% compared to the animal-free control already after 13 days of incubation. By the end of the experiment M. affinis and M. arctia increased the oxidized sediment volume by 87 and 35%, respectively. Higher efficiency of epifaunal amphipods in removing hydrogen sulfide than deep-burrowing polychaetes is likely due to more substantial re-oxidation of manganese and/or nitrogen compounds associated with amphipod mixing activity. Our results thus indicate that early colonization of different functional groups might have important implications for the later colonization by benthic macrofauna, meiofauna and microbial communities that benefit from oxidized and sulfide-free sediments

A new approach to model oxygen dependent benthic phosphate fluxes in the Baltic Sea

Highlights • A new description of sediment phosphorus dynamics was implemented in a 3D-model. • Oxygen consumption affects oxygen penetration in coastal sediments. • Low oxygen concentrations determine the oxygen penetration in deeper water sediments. • More than 80% of the phosphorus loads (1980–2008) are retained in the Baltic Sea. • Phosphorus is released from anoxic sediments and retained in oxic sediments. Abstract The new approach to model the oxygen dependent phosphate release by implementing formulations of the oxygen penetration depths (OPD) and mineral bound inorganic phosphorus pools to the Swedish Coastal and Ocean Biogeochemical model (SCOBI) is described. The phosphorus dynamics and the oxygen concentrations in the Baltic proper sediment are studied during the period 1980–2008 using SCOBI coupled to the 3D-Rossby Centre Ocean model. Model data are compared to observations from monitoring stations and experiments. The impact from oxygen consumption on the determination of the OPD is found to be largest in the coastal zones where also the largest OPD are found. In the deep water the low oxygen concentrations mainly determine the OPD. Highest modelled release rate of phosphate from the sediment is about 59 × 103 t P year− 1 and is found on anoxic sediment at depths between 60–150 m, corresponding to 17% of the Baltic proper total area. The deposition of organic and inorganic phosphorus on sediments with oxic bottom water is larger than the release of phosphorus, about 43 × 103 t P year− 1. For anoxic bottoms the release of total phosphorus during the investigated period is larger than the deposition, about 19 × 103 t P year− 1. In total the net Baltic proper sediment sink is about 23.7 × 103 t P year− 1. The estimated phosphorus sink efficiency of the entire Baltic Sea is on average about 83% during the period