Cluster Entropy: Active Domain Adaptation in Pathological Image Segmentation

The domain shift in pathological segmentation is an important problem, where a network trained by a source domain (collected at a specific hospital) does not work well in the target domain (from different hospitals) due to the different image features. Due to the problems of class imbalance and different class prior of pathology, typical unsupervised domain adaptation methods do not work well by aligning the distribution of source domain and target domain. In this paper, we propose a cluster entropy for selecting an effective whole slide image (WSI) that is used for semi-supervised domain adaptation. This approach can measure how the image features of the WSI cover the entire distribution of the target domain by calculating the entropy of each cluster and can significantly improve the performance of domain adaptation. Our approach achieved competitive results against the prior arts on datasets collected from two hospitals.Comment: Accepted by IEEE ISBI'2

Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis

Upcycling wastes into valuable products by mixed microbial communities has recently received considerable attention. Sustainable production of high-value substances from one-carbon (C1) compounds, e.g., methanol supplemented as an external electron donor in bioreactors for wastewater treatment, is a promising application of upcycling. This study undertook a gene-centric approach to screen valuable production potentials from mixed culture biomass, removing organic carbon and nitrogen from landfill leachate. To this end, the microbial community of the activated sludge from a landfill leachate treatment plant and its metabolic potential for the production of seven valuable products were investigated. The DNA extracted from the activated sludge was subjected to shotgun metagenome sequencing to analyze the microbial taxonomy and functions associated with producing the seven products. The functional analysis confirmed that the activated sludge could produce six of the valuable products, ectoine, polyhydroxybutyrate (PHB), zeaxanthin, astaxanthin, acetoin, and 2,3-butanediol. Quantification of the detected functional gene hit numbers for these valuable products as a primary trial identified a potential rate-limiting metabolic pathway, e.g., conversion of L-2,4-diaminobutyrate into N-γ-acetyl-L2,4,-diaminobutyrate during the ectoine biosynthesis. Overall, this study demonstrated that primary screening by the proposed gene-centric approach can be used to evaluate the potential for the production of valuable products using mixed culture or single microbe in engineered systems. The proposed approach can be expanded to sites where water purification is highly required, but resource recovery, or upcycling has not been implemented

Validation Study of the International Association for the Study of Lung Cancer Histologic Grading System of Invasive Lung Adenocarcinoma

[Introduction] A histologic grading system for invasive lung adenocarcinoma (ADC) has been proposed by the International Association for the Study of Lung Cancer (IASLC) Pathology Committee in June 2020. This study evaluated the prognostic value of the IASLC histologic grading system (the IASLC system) in a large Japanese cohort. [Methods] We performed comprehensive histologic subtyping using the semiquantitative estimation of five major patterns and complex glandular patterns in patients with a completely resected lung ADC and determined the histologic grade using the IASLC system. Concordance index and receiver-operating characteristic curves were used to evaluate the clinical utility of the IASLC system for recurrence and death; the comparison was performed with the architectural-pattern system (the Arch system) and the grading system on the basis of the two most predominant patterns (the Sica’s system). [Results] Of 1002 patients with invasive ADC, 235 had recurrent disease and 166 died of lung cancer. The concordance index and area under the curve of the IASLC system were 0.777 and 0.807 for recurrence and 0.767 and 0.776 for death, respectively. These were similar to those of the Arch system (0.763 and 0.796 for recurrence, 0.743 and 0.755 for death) and the Sica’s system (0.786 and 0.814 for recurrence, 0.762 and 0.773 for death). [Conclusions] We reported that the IASLC system for invasive lung ADC has prognostic significance by evaluating a large Japanese cohort. We believe that the IASLC grading system will provide physicians with better information for postsurgery treatment

Responses of soil nitrite-oxidizers to global environmental changes

Background/Question/Methods
There is increasing evidence that global change can alter the structure of plant
communities with large impacts on the functioning of terrestrial ecosystems. However, little is known about the impact of global change on soil microbial communities. In particular, the response of soil nitrite-oxidizers microorganisms that mediate the second step of nitrification, a key process of the nitrogen cycle, has never been investigated.
Here, we examined the effects of four main global environmental changes on the activity, the abundance and the diversity of soil nitrite-oxidizers in an annual grassland ecosystem as part of the Jasper Ridge Global Change Experiment (CA, USA). This experiment includes four treatments - CO2, temperature, precipitation and nitrogen - with two levels per treatment (ambient and elevated, with elevated treatment based on prediction for the end of the century), and all of their factorial combinations. We measured potential nitrite oxidation, the abundance of soil Nitrobacter- and Nitrospiralike nitrite-oxidizers (using quantitative PCR targeting nxrA and 16S rRNA gene, respectively) and the diversity of soil Nitrobacter-like nitrite-oxidizers (using cloning sequencing targeting the nxrA gene) in each treatment combination at the end of the 7th and 8th growing seasons under treatments. Furthermore, we analyzed to what extent changes in the activity of the soil nitrite-oxidizers result from changes in their abundance or diversity.

Results/Conclusions
Simulated global environmental changes significantly altered the activity, as well as the abundance and the diversity of soil nitrite-oxidizers. Potential nitrite oxidation decreased with increased precipitation and increased with elevated CO2 when combined with added nitrogen or precipitation. The abundance of soil Nitrobacter-like nitrite-oxidizers also decreased with increased precipitation and increased with elevated levels of CO2 and nitrogen. In contrast, the abundance of soil Nitrospira-like nitrite-oxidizers increased with enhanced precipitation and decreased with elevated levels of CO2 and temperature. Finally, the structure of the soil Nitrobacter-like nitrite-oxidizers was significantly altered by the treatments. Consistent with results reported by Attard et al. (2010) for agroecosystems, we found that changes in potential rates of nitrite oxidation in response to treatments were partly explained by changes in the abundance of soil Nitrobacter-like nitrite-oxidizers, but not by changes in the abundance of soil Nitrospiralike nitrite-oxidizers, suggesting that Nitrobacter-like nitrite-oxidizers were the main functional players of the soil nitrite-oxidizing microbial community.
Our study provides evidence that global change could alter the abundance and diversity of soil nitrite-oxidizers, with potential impacts for soil nitrogen cycling.

*The audio track for talks in this symposium may be obtained at the following web address:*

*https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content

Association between markers of arterial stiffness and atrial fibrillation in the Circulatory Risk in Communities Study (CIRCS).

Background and aims:Limited evidence is available on the association between markers of arterial stiffness and the prevalence of atrial fibrillation among Asian populations. Therefore, we examined those associations in the Japanese population.Methods:We conducted a cross-sectional population-based study of 4264 men and women aged 40-79 years. The augmentation index (AI), a marker of arterial stiffness, was calculated as the ratio of central pulse pressure/brachial pulse pressure, where the AI and central aortic pressure were measured by an automated tonometer: the HEM-9000AI device (Omron Healthcare co., Kyoto, Japan). Atrial fibrillation was estimated by the Minnesota codes using resting electrocardiograph (ECG).Results:The prevalence of atrial fibrillation and total arrhythmia were higher with larger AI values. These associations did not change after adjustment for known cardiovascular risk factors. The multivariable odd ratios (95% confidence intervals) in the highest versus lowest tertiles of AI were 3.4 (1.4-8.6, p for trend = 0.008) for atrial fibrillation and 1.8 (1.2-2.7, p for trend = 0.004) for total arrhythmia. There was no association of central or brachial pulse pressure levels with the prevalence of atrial fibrillation or total arrhythmia.ConclusionAI values, but not brachial or central pulse pressures, were positively associated with the prevalence of atrial fibrillation and total arrhythmia, independent of cardiovascular risk factors