ReScape: transforming coral-reefscape images for quantitative analysis

Ever since the first image of a coral reef was captured in 1885, people worldwide have been accumulating images of coral reefscapes that document the historic conditions of reefs. However, these innumerable reefscape images suffer from perspective distortion, which reduces the apparent size of distant taxa, rendering the images unusable for quantitative analysis of reef conditions. Here we solve this century-long distortion problem by developing a novel computer-vision algorithm, ReScape, which removes the perspective distortion from reefscape images by transforming them into top-down views, making them usable for quantitative analysis of reef conditions. In doing so, we demonstrate the first-ever ecological application and extension of inverse-perspective mapping-a foundational technique used in the autonomous-driving industry. The ReScape algorithm is composed of seven functions that (1) calibrate the camera lens, (2) remove the inherent lens-induced image distortions, (3) detect the scene's horizon line, (4) remove the camera-roll angle, (5) detect the transformable reef area, (6) detect the scene's perspective geometry, and (7) apply brute-force inverse-perspective mapping. The performance of the ReScape algorithm was evaluated by transforming the perspective of 125 reefscape images. Eighty-five percent of the images had no processing errors and of those, 95% were successfully transformed into top-down views. ReScape was validated by demonstrating that same-length transects, placed increasingly further from the camera, became the same length after transformation. The mission of the ReScape algorithm is to (i) unlock historical information about coral-reef conditions from previously unquantified periods and localities, (ii) enable citizen scientists and recreational photographers to contribute reefscape images to the scientific process, and (iii) provide a new survey technique that can rigorously assess relatively large areas of coral reefs, and other marine and even terrestrial ecosystems, worldwide. To facilitate this mission, we compiled the ReScape algorithm into a free, user-friendly App that does not require any coding experience. Equipped with the ReScape App, scientists can improve the management and prediction of the future of coral reefs by uncovering historical information from reefscape-image archives and by using reefscape images as a new, rapid survey method, opening a new era of coral-reef monitoring.

Association between lifestyle habits and presenteeism

BACKGROUND

Presenteeism is affected by work-related and individual factors. Among individual factors, the effect of combining various lifestyle habits on presenteeism is unknown.

AIMS

This study aimed to determine the relationship between changes in multiple good lifestyle habits with a change in presenteeism and to examine the effect of psychological factors on this relationship.

METHODS

We performed a 1-year retrospective cohort study on employees of large Japanese companies. Data were collected from health check-ups and a self-administered questionnaire. Changes in presenteeism were measured using the Quality and Quantity method. Changes in lifestyle habits were measured using a modified form of Breslow's seven health practices. Psychological factors were measured using the Kessler 6-Item Psychological Distress Scale. Linear regression was used for statistical analysis.

RESULTS

The number of practised lifestyle habit changes was negatively correlated with a change in presenteeism. This result was consistent when adjusted for age, sex and company (B, -0.010; P < 0.05), but became non-significant when additionally adjusted for psychological distress (B, -0.006). When analysed separately, only an improvement in the body mass index (B, -0.054; P < 0.05) and a worsened sleep habit (B, 0.040; P < 0.01) influenced a change in presenteeism.

CONCLUSIONS

This study suggests that improving various practised lifestyle habits in combination, rather than improving a single lifestyle habit, is beneficial in reducing presenteeism. Our finding that psychological distress altered the relationship of practised lifestyle habit changes with presenteeism indicates the importance of organizational-level intervention in presenteeism.

High thrombotic risk is associated with higher prevalence of suboptimal stent results in patients with high bleeding risk

Funding Acknowledgements

Type of funding sources: None.

Background

Shorter duration of dual antiplatelet therapy after drug-eluting stent implantation is required in patients with high bleeding risk (HBR) irrespective of the presence of concomitant high thrombotic risk (HTR). The prevalence of post-stent suboptimal findings in patients with HBR remains unclear.

Purpose

To clarify the prevalence of post-stent suboptimal findings assessed by optical coherence tomography (OCT) in patients with HBR according to the presence of HTR.

Methods

A total of 607 consecutive patients with stable coronary disease, who underwent OCT imaging of the culprit lesion were included. HBR was defined based on the Academic Research Consortium for High Bleeding Risk (ARC-HBR). HTR was defined as lesions with diffuse long (≧60 mm), treated with more than three stents, chronic total occlusion or diffuse long lesion (≧32 mm) in patients with diabetes mellitus. Post-stent suboptimal OCT criteria was defined as minimum stent area (MSA) &lt;4.5 mm2, edge dissection and stent malapposition.

Results

The prevalence of HBR was 55.8%. The prevalence of HTR was significantly higher in patients with HBR than in those without HBR (35.0 vs. 26.6%, p=0.028) (Figure A). Among patients with HBR, the prevalence of post-stent suboptimal OCT criteria was significantly higher in patients with HTR than in those without HTR (86.2 vs. 64.7%, p&lt;0.001), mainly due to the higher prevalence of MSA &lt;4.5 mm2 (Figure B) in patients with HTR.

Conclusions

HTR was associated with a higher prevalence of post-stent suboptimal findings among patients with HBR. The present results may suggest the importance of optimal stenting in patients with HBR, particularly in those with concomitant HTR.

Thermodynamic Interpretation of the Meyer-Neldel Rule Explains Temperature Dependence of Ion Diffusion in Silicate Glass

We study the temperature-dependent diffusion of many types of metal and semimetal ions in soda-lime glass using thermal relaxation ion spectroscopy, a technique that provides an electrical readout of thermally activated diffusion of charge carriers driven by built-in concentration gradients and electric fields. We measure the temperature of the onset of the motion, relevant to the long term storage of radioactive elements. We demonstrate the unique behavior of silver in soda-lime glass, enabling a thermal battery with rapid discharge of stored energy above a threshold temperature. We show that the Meyer-Neldel rule applies when comparisons of temperature-dependent diffusion rates are made between related measurements on one sample or between the same measurements on related samples. The results support a thermodynamic interpretation of the Meyer-Neldel rule as an enthalpy-entropy correlation where the Meyer-Neldel temperature (T_{MN}) is the temperature that enables liquidlike, barrier-free motion of the ions, with an upper limit set by the melting point of the host medium. This interpretation explains the observed reduction in T_{MN} by built-in electric fields in depletion layers and why the upper limit for T_{MN} for all ions is set by the glass transition temperature.

Higher triglyceride level is associated with the higher prevalence of layered plaque in nonculprit coronary plaques

Background

The impact of the high triglyceride (TG) level on the characteristics of coronary plaque in nonculprit lesion remains to be elucidated.

Purpose

To clarify the association between the TG level and the characteristics of nonculprit coronary plaque in patients with stable coronary disease using optical coherence tomography (OCT).

Methods

A total of 531 consecutive patients who underwent OCT imaging of the nonculprit lesion were included. Patients were classified into either the higher TG group (non-fasting TG ≥150 mg/dL, n=197) or the lower TG group (non-fasting TG &lt;150 mg/dL, n=334). The morphologies of nonculprit plaque assessed by OCT were compared between the two groups.

Results

The median (interquartile range) of TG in the two groups was 193.0 (168.0–244.0) mg/dL and 95.0 (75.0–120.0) mg/dL, respectively. The prevalence of layered plaque was significantly higher in the higher TG group than the lower TG group (40.1 vs. 27.5%, p=0.004), whereas the prevalence of other plaque components was comparable between the two groups (Figure 1). The prevalence of layered plaque was significantly higher in the higher TG group than in the lower TG group among patients with diabetes mellitus (DM) (44.2 vs. 28.7%, p=0.037) although it was comparable between the two groups among patients without DM (Figure 2).

Conclusion

A higher TG level was associated with a higher prevalence of layered plaque in nonculprit plaques in patients with stable coronary disease, particularly in patients with DM. The present results may partly explain the impact of TG on the progression of coronary plaque and the increased incidence of recurrent events in patients with coronary artery disease.

Funding Acknowledgement

Type of funding sources: None.

Spatial multiomic profiling reveals the novel polarization of foamy macrophages within necrotic granulomatous lesions developed in lungs of C3HeB/FeJ mice infected with Mycobacterium tuberculosis

Infection with Mycobacterium tuberculosis leads to the development of tuberculosis (TB) with the formation of granulomatous lesions. Foamy macrophages (FM) are a hallmark of TB granulomas, because they provide the primary platform of M. tuberculosis proliferation and the main source of caseous necrosis. In this study, we applied spatial multiomic profiling to identify the signatures of FM within the necrotic granulomas developed in a mouse model resembling human TB histopathology. C3HeB/FeJ mice were infected with M. tuberculosis to induce the formation of necrotic granulomas in the lungs. Using laser microdissection, necrotic granulomas were fractionated into three distinct regions, including the central caseous necrosis, the rim containing FM, and the peripheral layer of macrophages and lymphocytes, and subjected to proteomic and transcriptomic analyses. Comparison of proteomic and transcriptomic analyses of three distinct granulomatous regions revealed that four proteins/genes are commonly enriched in the rim region. Immunohistochemistry confirmed the localization of identified signatures to the rim of necrotic granulomas. We also investigated the localization of the representative markers for M1 macrophages in granulomas because the signatures of the rim included M2 macrophage markers. The localization of both macrophage markers suggests that FM in necrotic granulomas possessed the features of M1 or M2 macrophages. Gene set enrichment analysis of transcriptomic profiling revealed the upregulation of genes related to M2 macrophage activation and mTORC1 signaling in the rim. These results will provide new insights into the process of FM biogenesis, leading to further understanding of the pathophysiology of TB granulomas.

High sensitivity C-reactive protein is associated with vulnerable characteristics in non-culprit plaques in patients with ST-segment elevation myocardial infarction

Funding Acknowledgements

Type of funding sources: None.

Background

Higher level of high sensitivity C-reactive protein (hsCRP) is associated with an increased risk of recurrent cardiovascular events in patients with ST-segment elevation myocardial infarction (STEMI). However, the association between hsCRP and the characteristics of non-culprit plaques in patients with STEMI remains to be elucidated.

Purpose

To clarify the morphological characteristics of non-culprit plaque in patients with STEMI according to the hsCRP levels using optical coherence tomography (OCT).

Methods

A total of 79 non-culprit plaques in 76 consecutive patients with STEMI, who underwent OCT imaging of the non-culprit plaques in a culprit vessel were included. The characteristics of non-culprit plaques assessed by OCT were compared between the higher hsCRP group (hsCRP ≥ 0.16 mg/dL, 38 plaques in 38 patients) and the lower hsCRP group (hsCRP &lt; 0.16 mg/dL, 41 plaques in 38 patients).

Results

The prevalence of plaque with macrophage (63.2 vs. 31.7%, p = 0.006), plaque with large lipid (maximal lipid arc &gt; 180 °) (57.9 vs. 31.7%, p = 0.018), healed plaque (50.0 vs. 26.8%, p = 0.045) and cholesterol crystal (18.4 vs. 2.4%, p = 0.045) was significantly higher in the higher hsCRP group than in the lower hsCRP group (Figure). In a multivariate analysis, the higher hsCRP was independently associated with the presence of plaque with macrophage (Odds ratio [OR], 3.031; 95% confidence interval [CI]: 1.112-8.264, p = 0.030), plaque with large lipid (OR, 2.897; 95% CI: 1.122-7.478, p = 0.026) and healed plaque (OR, 2.666; 95% CI: 1.030-6.896, p = 0.040).

Conclusions

Higher level of hsCRP is associated with a higher prevalence of vulnerable characteristics in non-culprit plaques in patients with STEMI. The present results may partly explain the pathogenesis of an increased incidence of recurrent cardiovascular events in patients with STEMI. Abstract Figure.

Viral Production in Seawater Filtered Through 0.2-μm Pore-Size Filters: A Hidden Biogeochemical Cycle in a Neglected Realm

Viral production is a key parameter for assessing virus-mediated biogeochemical cycles. One widely used method for the determination of viral production, called the virus reduction assay, reduces viral abundance, while maintaining bacterial abundance, using 0.2-μm pore-size filters. Viral production is estimated from the increase of viral abundance during incubation. We hypothesized that small-cell-sized bacterial communities can pass through 0.2-μm filters and drive viral production, representing a missing fraction of viral production that is missed by the virus reduction assay. Coastal seawater was filtered through 0.2-μm filters and diluted with virus-free seawater. Viral production in the <0.2-μm filtrate was estimated from changes in viral abundance determined through flow cytometry. We found that viruses were produced in the <0.2-μm communities, which were strongly enriched with low nucleic acid content bacteria. Estimated viral production in the <0.2-μm filtrates accounted for up to 43% of total viral production and 10% of dissolved organic carbon production mediated by viral lysis of bacterial cells. By not considering viral production in these <0.2-μm communities, the virus reduction assay may underestimate viral production. Virus–bacteria interactions in <0.2-μm communities may represent a significant and overlooked role of viruses in marine food webs and carbon fluxes.

New Algorithm by Maximizing Mutual Information for Correction of Frequency Drifts Arising from One-Dimensional NMR Spectroscopic Data Acquisition

Benchtop nuclear magnetic resonance (NMR) instruments are getting popular these days. However, the obtained spectra sometimes suffer from significant frequency drifts, which cause difficulty in accumulating the raw data. In this paper, a new algorithm for correction of frequency drifts is proposed, which operates by maximizing mutual information between the obtained spectroscopic data. The algorithm worked well for both ¹H and ¹⁹F NMR spectroscopic data, even in the case of very noisy ones. In comparison with the previously reported algorithms, the present algorithm has an advantage that NMR spectra complicated by signal overlapping and spin coupling can be handled without difficulty. This makes the present algorithm particularly advantageous for application of benchtop NMR spectrometers in organic chemistry.

Transparent Exopolymer Particles in Deep Oceans: Synthesis and Future Challenges

Transparent exopolymer particles (TEP) are a class of abundant gel-like particles that are omnipresent in seawater. While versatile roles of TEP in the regulation of carbon cycles have been studied extensively over the past three decades, investigators have only recently begun to find intriguing features of TEP distribution and processes in deep waters. The emergence of new research reflects the growing attention to ecological and biogeochemical processes in deep oceans, where large quantities of organic carbon are stored and processed. Here, we review recent research concerning the role of TEP in deep oceans. We discuss: (1) critical features in TEP distribution patterns, (2) TEP sources and sinks, and (3) contributions of TEP to the organic carbon inventory. We conclude that gaining a better understanding of TEP-mediated carbon cycling requires the effective application of gel theory and particle coagulation models for deep water settings. To achieve this goal, we need a better recognition and determination of the quantities, turnover, transport, chemical properties, and microbial processing of TEP.

Perception of mutual aid and its related factors: a study of Japanese high school students

Japan is a super-ageing country. Constructing the community-based integrated care system in local communities is urgently needed. Mutual aid in local communities is critical for this system. In order to clarify the status of perception of mutual aid in Japanese high school students and to clarify the factors related to the formation of the perception, we conducted a questionnaire study of high school students in a city in Japan (n = 8,687). The results indicate that Japanese high school students show a tendency to have perception of mutual aid for local people (70.8%) rather than the local area (38.9%). Significantly fewer male students have perception of mutual aid than female students (p < 0.01). Factors that affected the perception significantly (p < 0.05) were: i) willingness to stay in the local area for 10 more years, ii) recognition of persons in need of care in the local area, iii) memories of experiencing communication with handicapped and/or elderly people, and iv) experience of taking care of local children. It is important to create opportunities for high school students to communicate with local residents, especially handicapped and/or elderly people in order to foster students' perception of mutual aid.

Evaluation of temporal changes in longitudinal strain distribution during the systolic period to determine left ventricular activation sequence: a study using 2D speckle-tracking echocardiography

Background

Evaluation of two-dimensional (2D) speckle-tracking longitudinal strain (LS) is useful for assessing global and regional left ventricular (LV) dysfunction.

Purpose

The purpose of this study was to test the hypothesis that temporal changes in regional 2D-LS distribution, (i.e., changes in area and intensity of the negative strain), during the systolic period may reflect the LV activation sequence.

Methods

We studied 52 patients with an ejection fraction &lt;35% who were classified into four groups: complete left bundle branch block (LBBB, QRS 162±17 ms, n=17); right ventricular pacing from inferior septum (RVP, QRS 180±29 ms, n=16); left VP from lateral branch of the coronary sinus (LVP, QRS 182±21 ms, n=9); and no conduction block (Narrow QRS, QRS 100±9 ms, n=19). Longitudinal strain was evaluated in three standard apical views, and then bulls-eye distribution maps were constructed every 50 ms from the QRS onset to aortic valve closing (AVC) and at the time of the end of QRS. Segments indicating negative strain at the end of QRS were regarded as an early contraction site. Segments with intensifying negativity of strain as it got closer to the AVC were regarded as a late contraction site.

Results

In patients with LBBB, negative strain appeared initially in the septum region. Then, the contracted area enlarged including the apical region, and the basal lateral region contracted late. On the other hand, Narrow QRS showed a few regional differences in strain at the end of QRS (standard deviation in 17-segments: Narrow QRS 1.3±0.4%*, LBBB 3.3±1.1%, RVP 3.2±1.0%, LVP 3.3±1.1%, *p&lt;0.001), and contracted homogeneously during the systolic period. RVP and LVP showed negative strain at the end of QRS in septum and lateral regions respectively, with the contracted area becoming enlarged towards the opposite regions of the early contracted regions.

Conclusion

The 2D-LS distribution during the systolic period reflects the LV contraction process in patients with an altered ventricular activation sequence, and may have potential for identifying the regions of early activation site and subsequent activation propagation.

Funding Acknowledgement

Type of funding source: None

Development of a novel T cell-oriented vaccine using CTL/Th-hybrid epitope long peptide and biodegradable microparticles, against an intracellular bacterium

Antigen-specific CD8+ T-lymphocytes (cytotoxic T-lymphocytes: CTL), as well as CD4+ T-lymphocytes (helper T-lymphocytes: Th), simultaneously play an important role in the elimination of intracellular bacteria such as Mycobacterium tuberculosis and Listeria monocytogenes. Administration of T-cell epitope short peptide needs large numbers of peptides for effective vaccination due to its easily degradable nature in vivo. In this respect, biocompatible and biodegradable microparticles combined with CTL/Th-hybrid epitope long peptide (long peptide) have been used to diminish the degradation of loaded peptide. The aim of this study is to develop a novel T cell-oriented vaccine against intracellular bacteria that is composed of long peptide and poly (lactic-co-glycolic acid) (PLGA) microparticles. Mouse bone marrow-derived dendritic cells (BMDCs) were loaded with L. monocytogenes listeriolysin O (LLO)-derived or ovalbumin (OVA)-derived long peptide/PLGA or other comparative antigens. The antigen-loaded BMDCs were injected subcutaneously into the flank of mice twice, and then, the spleens were collected and lymphocyte proliferation and interferon-γ production were evaluated. The median diameter of the PLGA spheres was 1.38 μm. Both LLO- and OVA-long peptide/PLGA showed significantly more robust CTL and Th proliferations with higher interferon-γ production than the long peptide alone or CTL and Th short peptides/PLGA vaccination. Furthermore, the LLO-long peptide/PLGA vaccination showed a significantly lower bacterial burden in spleens compared with the long peptide alone or the CTL and Th short peptides/PLGA vaccination after the challenge of lethal amounts of L. monocytogenes. These results suggest that the novel vaccine taking advantages of CTL/Th-hybrid epitope long peptide and PLGA microparticle is effective for protection against intracellular bacteria.

Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study

Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase (dddD and dddP) and DMSP demethylase (dmdA) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.

Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids

The long-distance migrations by marine fishes are difficult to track by field observation. Here, we propose a new method to track such migrations using stable nitrogen isotopic composition at the base of the food web (δ¹⁵ N_Base ), which can be estimated by using compound-specific isotope analysis. δ¹⁵ N_Base exclusively reflects the δ¹⁵ N of nitrate in the ocean at a regional scale and is not affected by the trophic position of sampled organisms. In other words, δ¹⁵ N_Base allows for direct comparison of isotope ratios between proxy organisms of the isoscape and the target migratory animal. We initially constructed a δ¹⁵ N_Base isoscape in the northern North Pacific by bulk and compound-specific isotope analyses of copepods (n = 360 and 24, respectively), and then we determined retrospective δ¹⁵ N_Base values of spawning chum salmon (Oncorhynchus keta) from their vertebral centra (10 sections from each of two salmon). We then estimated the migration routes of chum salmon during their skeletal growth by using a state-space model. Our isotope tracking method successfully reproduced a known chum salmon migration route between the Okhotsk and Bering seas, and our findings suggest the presence of a new migration route to the Bering Sea Shelf during a later growth stage.

Proteomic Profiling Reveals the Architecture of Granulomatous Lesions Caused by Tuberculosis and Mycobacterium avium Complex Lung Disease

Tuberculosis (TB) and Mycobacterium avium complex lung disease (MAC-LD) are both characterized pathologically by granuloma lesions, which are typically composed of a necrotic caseum at the center surrounded by fibrotic cells and lymphocytes. Although the histological characterization of TB and MAC-LD granulomas has been well-documented, their molecular signatures have not been fully evaluated. In this research we applied mass spectrometry-based proteomics combined with laser microdissection to investigate the unique protein markers in human mycobacterial granulomatous lesions. Comparing the protein abundance between caseous and cellular sub-compartments of mycobacterial granulomas, we found distinct differences. Proteins involved in cellular metabolism in transcription and translation were abundant in cellular regions, while in caseous regions proteins related to antimicrobial response accumulated. To investigate the determinants of their heterogeneity, we compared the protein abundance in caseous regions between TB and MAC-LD granulomas. We found that several proteins were significantly abundant in the MAC-LD caseum of which proteomic profiles were different from those of the TB caseum. Immunohistochemistry demonstrated that one of these proteins, Angiogenin, specifically localized to the caseous regions of selected MAC-LD granulomas. We also detected peptides derived from mycobacterial proteins in the granulomas of both diseases. This study provides new insights into the architecture of granulomatous lesions in TB and MAC-LD.