1 Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Department of Microbiology and Research Institute of Life Science, Gyeongsang ...National University, Jinju 660-701, Republic of Korea
3 Jeju Hi-Tech Industry Development Institute, 4-8 Ara-1 dong, Jeju 690-121, Republic of Korea
Correspondence Che Ok Jeon cojeon{at}gnu.ac.kr
A Gram-negative bacterium, designated strain EMB117 T , was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 2530 °C and pH 7.08.0. Strain EMB117 T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C 15 : 0 , iso-C 17 : 0 3-OH, iso-C 15 : 0 3-OH and summed feature 3 (C 16 : 1 7 c and/or iso-C 15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117 T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425 T (97.8 % sequence similarity). The DNADNA relatedness between strain EMB117 T and F. johnsoniae ATCC 17061 T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117 T represents a novel species within the genus Flavobacterium , for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117 T (=KCTC 12612 T =DSM 17963 T ).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB117 T is DQ372986 .
A transmission electron micrograph of cells of strain EMB117 T is available as a supplementary figure in IJSEM Online.
Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
Correspondence Che Ok Jeon cojeon{at}gnu.ac.kr
A Gram-negative bacterium, ...designated strain EMB71 T , was isolated from activated sludge used for enhanced biological phosphorus removal in a sequencing batch reactor. The cells of the isolate were facultatively aerobic, motile rods with single polar flagella. Growth was observed to occur at 1535 °C (optimally at 30 °C) and at pH 6.09.0 (optimally at pH 7.08.0). The predominant fatty acids of strain EMB71 T were C 16 : 0 and summed feature 3 (C 16 : 1 7 c and/or iso-C 15 : 0 2-OH), and the polar lipids comprised a large amount of phosphatidylethanolamine and a small amount of diphosphatidylglycerol. The G+C content of the genomic DNA was 61.6 mol % and the major quinone was Q-8. Comparative 16S rRNA gene sequence analyses showed that strain EMB71 T formed a phyletic lineage with the genus Hydrogenophaga within the family Comamonadaceae . The levels of 16S rRNA gene sequence similarity with respect to the type strains of Hydrogenophaga species ranged from 95.1 to 96.9 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB71 T represents a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga caeni sp. nov. is proposed. The type strain is EMB71 T (=KCTC 12613 T =DSM 17962 T ).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB71 T is DQ372983 .
Figures showing the morphology of negatively stained cells of strain EMB71 T and phylogenetic trees generated using maximum-likelihood and maximum-parsimony and a table detailing the cellular fatty acid compositions of strain EMB71 T and related species are available as supplementary material in IJSEM Online.
Background
Deep learning models require large‐scale training to perform confidently, but obtaining annotated datasets in medical imaging is challenging. Weak annotation has emerged as a way to save ...time and effort.
Purpose
To develop a deep learning model for 3D breast cancer segmentation in dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) using weak annotation with reliable performance.
Study Type
Retrospective.
Population
Seven hundred and thirty‐six women with breast cancer from a single institution, divided into the development (N = 544) and test dataset (N = 192).
Field Strength/Sequence
3.0‐T, 3D fat‐saturated gradient‐echo axial T1‐weighted flash 3D volumetric interpolated brain examination (VIBE) sequences.
Assessment
Two radiologists performed a weak annotation of the ground truth using bounding boxes. Based on this, the ground truth annotation was completed through autonomic and manual correction. The deep learning model using 3D U‐Net transformer (UNETR) was trained with this annotated dataset. The segmentation results of the test set were analyzed by quantitative and qualitative methods, and the regions were divided into whole breast and region of interest (ROI) within the bounding box.
Statistical Tests
As a quantitative method, we used the Dice similarity coefficient to evaluate the segmentation result. The volume correlation with the ground truth was evaluated with the Spearman correlation coefficient. Qualitatively, three readers independently evaluated the visual score in four scales. A P‐value <0.05 was considered statistically significant.
Results
The deep learning model we developed achieved a median Dice similarity score of 0.75 and 0.89 for the whole breast and ROI, respectively. The volume correlation coefficient with respect to the ground truth volume was 0.82 and 0.86 for the whole breast and ROI, respectively. The mean visual score, as evaluated by three readers, was 3.4.
Data Conclusion
The proposed deep learning model with weak annotation may show good performance for 3D segmentations of breast cancer using DCE‐MRI.
Level of Evidence
3
Technical Efficacy
Stage 2
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Item response tree (IRTree) models are recently introduced as an approach to modeling response data from Likert-type rating scales. IRTree models are particularly useful to capture a variety of ...individuals’ behaviors involving in item responding. This study employed IRTree models to investigate response styles, which are individuals’ tendencies to prefer or avoid certain response categories in a rating scale. Specifically, we introduced two types of IRTree models, descriptive and explanatory models, perceived under a larger modeling framework, called explanatory item response models, proposed by De Boeck and Wilson. This extends the typical application of IRTree models for studying response styles. As a demonstration, we applied the descriptive and explanatory IRTree models to examine acquiescence and extreme response styles in Rosenberg’s Self-Esteem Scale. Our findings suggested the presence of two distinct extreme response styles and acquiescence response style in the scale.
Full text
Available for:
NUK, OILJ, SAZU, UKNU, UL, UM, UPUK, VSZLJ
School interventions to address sexual orientation discrimination can be important tools for fostering inclusive school climate, and improving student wellbeing. In this study, we empirically ...evaluated a film-based intervention, Out in Schools, designed to reduce sexual orientation prejudice and foster inclusive school attitudes. Our evaluation mapped data about Out in Schools presentations onto student data from the random cluster-stratified, province-wide 2013 British Columbia Adolescent Health Survey (BCAHS) as well as potential confounding variables of Gay-Straight Alliance clubs (GSAs) and inclusive school policies. Outcome measures included past year sexual orientation discrimination, bullying, suicidal ideation, and school connectedness among lesbian, gay, and bisexual (LGB) and heterosexual (HET) students in grades 8 through 12 (ages 13 to 18; unweighted
= 21,075, weighted/scaled
= 184,821). Analyses used complex samples logistic regression, adjusted for sample design, conducted separately by gender and orientation. We found Out in Schools presentations were associated with reduced odds of LGB students experiencing discrimination, and both LGB and HET girl students being bullied or considering suicide, and increased levels of school connectedness, even after controlling for GSAs and policies. Out in Schools appears to have an additive contribution to reducing orientation prejudice and improving LGB and heterosexual student wellbeing within schools.
1 Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Division of Environmental Science and Ecological Engineering, Korea University, ...Seoul 136-701, Republic of Korea
Correspondence Che Ok Jeon cojeon{at}gnu.ac.kr
A Gram-negative bacterium, designated strain EMB34 T , was isolated from a wastewater treatment plant in Korea. Growth was observed between 10 and 40 °C (optimum, 25–35 °C) and between pH 6.0 and 9.5 (optimum, pH 7.5–8.0). The cells were non-motile rods, linked with extracellular fibrils. The predominant fatty acids of strain EMB34 T were iso-C 15 : 0 , C 15 : 0 , iso-C 15 : 1 G, iso-C 16 : 0 3-OH and iso-C 15 : 0 3-OH and the strain contained phosphatidylethanolamine and phosphatidylinositol as the polar lipids. The G+C content of the genomic DNA was 34.2 mol% and the major quinone was menaquinone-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB34 T formed a distinct phyletic line within the genus Flavobacterium . The levels of 16S rRNA gene sequence similarity with other Flavobacterium species were less than 94.5 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB34 T represents a novel species within the genus Flavobacterium , for which the name Flavobacterium filum sp. nov. is proposed. The type strain is EMB34 T (=KCTC 12610 T =DSM 17961 T ).
Abbreviations: ML, maximum-likelihood; MP, maximum-parsimony; NJ, neighbour-joining
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB34 T is DQ372981 .
A transmission electron micrograph showing cells of strain EMB34 T linked by extracellular fibrils is available as a supplementary figure with the online version of this paper.
1 Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Jeju Hi-Tech industry Development Institute, 4-8 Ara-1 dong, Jeju 690-121, ...Republic of Korea
Correspondence Che Ok Jeon cojeon{at}gnu.ac.kr
A Gram-negative, rod-like, stalk-producing bacterium, designated strain EMB102 T , was isolated from activated sludge that performed enhanced biological phosphorus removal in a sequencing batch reactor. Cells without stalks were motile with single polar flagella, but cells that did produce stalks were non-motile and lacked polar flagella. Growth of strain EMB102 T was observed at temperatures between 15 and 35 °C (optimum, 30 °C) and between pH 6.0 and 9.0 (optimum, pH 7.58.5). The predominant fatty acids of strain EMB102 T were C 18 : 1 7c , C 16 : 0 and C 15 : 0 . The predominant polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 64.1 mol% and the major quinone was Q-10. Comparative 16S rRNA gene sequence analyses showed that strain EMB102 T formed a distinct phyletic lineage within the genus Brevundimonas . The levels of 16S rRNA gene sequence similarity between the type strains of Brevundimonas species ranged from 95.8 to 97.5 %. DNADNA relatedness levels between the EMB102 T and closely related Brevundimonas species were below 15.0 %. On the basis of chemotaxonomic data and molecular properties, strain EMB102 T represents a novel species within the genus Brevundimonas , for which the name Brevundimonas aveniformis sp. nov. is proposed. The type strain is EMB102 T (=KCTC 12609 T =DSM 17977 T ).
Abbreviations: EBPR, enhanced biological phosphorus removal
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB102 T is DQ372984 .
The cellular fatty acid compositions and substrate-assimilation data for strain EMB102 T and some related Brevundimonas species are available in supplementary tables available with the online version of this paper.
1 Division of Applied Life Science (BK21 Program), EB-NCRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Department of Animal Science & Technology, Sunchon National University, ...Sunchon 540-742, Republic of Korea
3 Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
Correspondence Che Ok Jeon cojeon{at}cau.ac.kr
A Gram-negative, non-spore-forming bacterium, designated strain BD-d46 T , was isolated from a playground soil sample in Jinju, South Korea. Cells were straight or curved rods and showed catalase- and oxidase-positive reactions. Growth of strain BD-d46 T was observed between 15 and 35 °C (optimum 25–30 °C) and between pH 6.5 and 8.0 (optimum pH 7.0–7.5). The predominant fatty acids were summed feature 3 (C 16 : 1 7 c and/or iso-C 15 : 0 2-OH), C 12 : 0 3-OH and C 16 : 0 . Strain BD-d46 T contained phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Isoprenoid quinones were Q-8 (75 %) and MK-7 (25 %). The G+C content of the genomic DNA was 49.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BD-d46 T formed a distinct lineage with Rheinheimera chironomi K19414 T within the genus Rheinheimera . Levels of 16S rRNA gene sequence similarity between strain BD-d46 T and the type strains of recognized Rheinheimera species ranged from 94.4 to 96.9 %. On the basis of chemotaxonomic data and molecular properties, strain BD-d46 T is considered to represent a novel species of the genus Rheinheimera , for which the name Rheinheimera soli sp. nov. is proposed. The type strain is BD-d46 T (=KCTC 22077 T =DSM 19413 T ).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain BD-d46 T is EF575565 .
A transmission electron micrograph of a negatively stained cell and a table detailing the cellular fatty acid composition of strain BD-d46 T and TLC of polar lipids of strain BD-d46 T and R. chironomi K19414 T are available as supplementary material with the online version of this paper.
Background
An international panel achieved consensus on 9 need-based and 2 time-based major referral criteria to identify patients appropriate for outpatient palliative care referral. To better ...understand the operational characteristics of these criteria, we examined the proportion and timing of patients who met these referral criteria at our Supportive Care Clinic.
Methods
We retrieved data on consecutive patients with advanced cancer who were referred to our Supportive Care Clinic between January 1, 2016, and February 18, 2016. We examined the proportion of patients who met each major criteria and its timing.
Results
Among 200 patients (mean age 60, 53% female), the median overall survival from outpatient palliative care referral was 14 (95% confidence interval 9.2, 17.5) months. A majority (
n
= 170, 85%) of patients met at least 1 major criteria; specifically, 28%, 30%, 20%, and 8% met 1, 2, 3, and ≥ 4 criteria, respectively. The most commonly met need-based criteria were severe physical symptoms (
n
= 140, 70%), emotional symptoms (
n
= 36, 18%), decision-making needs (
n
= 26, 13%), and brain/leptomeningeal metastases (
n
= 25, 13%). For time-based criteria, 54 (27%) were referred within 3 months of diagnosis of advanced cancer and 63 (32%) after progression from ≥ 2 lines of palliative systemic therapy. The median duration from patient first meeting any criterion to palliative care referral was 2.4 (interquartile range 0.1, 8.6) months.
Conclusions
Patients were referred early to our palliative care clinic and a vast majority (85%) of them met at least one major criteria. Standardized referral based on these criteria may facilitate even earlier referral.
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