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Understanding the factors influencing the variability in the composition of fish assemblages is essential for bolstering the resilience of coral reef ecosystems, effective coral reef management and maintaining sustainable fisheries. The benthic composition and reef fish assemblages at eight sites at the poorly studied St. Brandon, also known as a bank fisheries area in the Indian Ocean, were assessed to discern distribution patterns, including differences between channel (Passe Grand Capitaine, Passe Ile Longue-Canal Coco and Passe La Cayane) and non-channel (Chaloupe, Anchor Points 1 and 2, Bain des Dames, Pearl Island) sites and fisheries sustainability. The benthic composition exhibited clusters, revealing the distinct separation of Chaloupe which predominantly featured sand (75.26%) interspersed with sporadic coral patches characterized by live and dead corals and rubble. The three channel sites composed a cluster. Coral species across eight families were identified, with significant variability (p < 0.05) observed in their benthic cover, particularly live coral cover (LCC). Fish density and diversity analyses unveiled 58 fish species from 12 families, with no statistically significant disparity in density among sites. Total fish biomass (TFB) and target fish biomass (TB) ranged from 138.02 ± 65.04 to 4110.16 ± 3048.70 kg/ha and from 28.31 ± 24.52 to 3851.27 ± 2753.18 kg/ha, respectively. TFB and TB differed significantly (p < 0.05) among sites irrespective of channel and non-channel sites, with Pearl Island recording the highest biomass. TFB and TB recorded at five out of the eight surveyed sites exceeded the mean biomass benchmark (B0) for the Western Indian Ocean, set at 1150.00 and 560.00 kg/ha for TFB and TB, respectively. Functional group analysis unveiled six discrete groups influencing TFB, with scrapers being the most dominant. This study presents the first report on fish biomass surveys in St. Brandon, highlighting a case for sustainable fisheries in the waters of the Republic of Mauritius.

IntroductionSeveral fluorescent proteins (FPs) and chromoproteins (CPs) are present in anthozoans and play possible roles in photoprotection. Coral tissues in massive corals often display discoloration accompanied by inflammation. Incidences of the pink pigmentation response (PPR) in massive Porites, described as inflammatory pink lesions of different shapes and sizes, has recently increased worldwide. FPs are reported to be present in PPR lesions, wherein a red fluorescent protein (RFP) appears to play a role in reducing reactive oxygen species. However, to date, the biochemical characterization and possible roles of the pigments involved are poorly understood. The present study aimed to identify and characterize the proteins responsible for pink discoloration in massive Porites colonies displaying PPRs, as well as to assess the differential distribution of pigments and the antioxidant properties of pigmented areas.MethodCPs were extracted from PPR lesions using gel-filtration chromatography and identified via genetic analysis using liquid chromatography-tandem mass spectrometry. The coexistence of CPs and RFP in coral tissues was assessed using microscopic observation. Photosynthetic antivity and hydrogen peroxide-scavenging activitiy were measured to assess coral stress conditions.ResultsThe present study revealed that the same CP (plut2.m8.16902.m1) isolated from massive Porites was present in both the pink spot and patch morphologies of the PPR. CPs were also found to coexist with RFP in coral tissues that manifested a PPR, with a differential distribution (coenosarc or tip of polyps’ tentacles). High hydrogen peroxide-scavenging rates were found in tissues affected by PPR.Discussion and ConclusionThe coexistence of CPs and RFP suggests their possible differential role in coral immunity. CPs, which are specifically expressed in PPR lesions, may serve as an antioxidant in the affected coral tissue. Overall, this study provides new knowledge to our understanding of the role of CPs in coral immunity.

Coral diseases represent a prominent menace to coral reefs and to the associated ecological services they provide to the surrounding coastal communities. Studies on diseases and compromised health conditions (CHCs) on hard corals in the Southwest Indian Ocean (SWIO) are scarce, and their consequences are often overlooked. This study aimed to establish the baseline prevalence of diseases and CHC of hard corals around Rodrigues Island. Coral disease and CHC prevalence were visually assessed using 2 m × 50 m belt transects at eight sites around the island. This is the first report of four coral diseases, namely White Plague (WP), White Syndrome (WS), Black Band (BB), and Growth Anomalies (GA), and two CHCs, two forms of Pink Pigmentation Responses (PPR)—Pink Patches (PP) and Pink Line Syndrome (PLS)—observed on six genera of hard corals from the island of Rodrigues. PP on Fungia (15.92 ± 5.65%), followed by the WS on Montipora (4.67 ± 3.72%) and GA on Gardineroseris (4.16 ± 4.16%), so far unreported from the SWIO, were the most prevalent around the island. The least prevalent disease was BB on Montipora (0.13 ± 0.13%). Although the overall disease and CHC prevalence for Rodrigues Island (0.98 ± 0.30%) were much lower than the surrounding islands in the SWIO, the observations of these diseases and CHCs on hard corals and relevant environmental parameters warrant further in-depth characterization to better inform coral reefs management and conservation actions.

Bayesian optimization (BO) is commonly used to optimize the hyperparameters of transfer learning models to improve the model’s performance significantly. In BO, the acquisition functions direct the hyperparameter space exploration during the optimization. However, the computational cost of evaluating the acquisition function and updating the surrogate model can become prohibitively expensive due to increasing dimensionality, making it more challenging to achieve the global optimum, particularly in image classification tasks. Therefore, this study investigates and analyses the effect of incorporating metaheuristic methods into BO to improve the performance of acquisition functions in transfer learning. By incorporating four different metaheuristic methods, namely Particle Swarm Optimization (PSO), Artificial Bee Colony (ABC) Optimization, Harris Hawks Optimization, and Sailfish Optimization (SFO), the performance of acquisition function, Expected Improvement (EI), was observed in the VGGNet models for visual field defect multi-class classification. Other than EI, comparative observations were also conducted using different acquisition functions, such as Probability Improvement (PI), Upper Confidence Bound (UCB), and Lower Confidence Bound (LCB). The analysis demonstrates that SFO significantly enhanced BO optimization by increasing mean accuracy by 9.6% for VGG-16 and 27.54% for VGG-19. As a result, the best validation accuracy obtained for VGG-16 and VGG-19 is 98.6% and 98.34%, respectively.

TGF-β signaling is one of important function during palatal fusion. Three types of TGF-β receptor (TβR1, TβR2, and TβR3) have been identified, and play essential roles in mechanisms leading to palatal fusion. However, the balance between Smad-dependent/-independent signaling during palatal fusion with inhibited TβR1/2 functions is not fully understood. The objective of this study was to investigate palatal fusion via TGF-β signaling when TβR1 and TβR2, but not TβR3, were inhibited. In addition, the present study examined the functional balance between Smad-dependent/-independent signaling and related gene expression. Palatal organ cultures were treated with TβR1/2 inhibitor in vitro. Control palates were cultured without inhibitor. We observed histological phenotype of palatal fusion, and evaluation of expression pattern by Western blot or real time RT-PCR. Palatal organ cultures treated with the inhibitor did not fuse and the medial edge epithelium remained at embryonic 13 day +72 h in culture. The inhibitor decreased TβR1 and TβR2 expression by approximately 90%, but did not affect TβR3 expression. The expression of p-Smad2 and p-Smad3 was significantly decreased in treated palates compared with controls. The expression of p-Smad4 was slightly decreased in treated palates compared with controls. Smad-independent signaling was also affected by the inhibitor; p-ERK, p-JNK, and p-p38 expressions was significantly reduced in treated palates compared with controls. The expression of transcription factors (Runx1 and Msx1) and extracellular matrix proteins (MMP2/13) was also significantly decreased by inhibitor exposure. Treatment with TβR1/2 inhibitor altered the patterns of the Smad-dependent and -independent signaling pathways during palatal fusion.

Abstract Innate immune factors exert widespread effects on cytokine secretion, cell survival, autophagy, and apoptosis. Nucleotide-binding and oligomerization domain-like receptors (NLRs) are members of the innate immune system in the cytosol that sense pathogens, endogenous danger molecules such as uric acid, and pollutants. Nucleotide-binding oligomerization domain-containing protein 1 and 2 (NOD1 and NOD2) are components of NLR family, and ligands of these factors are γ-d-glutamyl-meso-diaminopimelic acid (iE-DAP) and muramyl dipeptide (MDP), respectively. Upon recognition of ligands, NOD1 and NOD2 induce the production of inflammatory cytokines and transcription factors including interleukin-6 (IL-6) and nuclear factor-κB (NF-κB). We examined the function of NOD1 and NOD2 in innate immunity, with a focus on their differing roles in disease pathogenesis between Japanese and Caucasian populations. Susceptibility to several immune-related diseases, including Crohn’s disease, colorectal and breast cancers, and graft-versus-host-disease (GVHD) showed a correlation with genetic variants of NOD2 in Caucasian, but not in Japanese, populations. This difference may be primarily due to the fact that three major NOD2 SNPs (R702W, G908R, L1007insC) prevalent in Caucasians are rare or absent in Japanese populations. Because NLR has diverse effects on immune function, it is possible that many as yet uncharacterized immune-related diseases will also show different susceptibilities between races due to the different ratio of genetic variants in innate immune genes.

Paraphrase identification has been one of the major topics in Natural Language Processing (NLP). However, how to interpret a diversity of contexts such as lexical and semantic information within a sentence as relevant features is still an open problem. This paper addresses the problem and presents an approach for leveraging contextual features with a neural-based learning model. Our Lexical, Syntactic, and Sentential Encodings (LSSE) learning model incorporates Relational Graph Convolutional Networks (R-GCNs) to make use of different features from local contexts, i.e., word encoding, position encoding, and full dependency structures. By utilizing the hidden states obtained by the R-GCNs as well as lexical and sentential encodings by Bidirectional Encoder Representations from Transformers (BERT), our model learns the contextual similarity between sentences effectively. The experimental results by using the two benchmark datasets, Microsoft Research Paraphrase Corpus (MRPC) and Quora Question Pairs (QQP) show that the improvement compared with the baseline, BERT sentential encodings model, was 1.7% F1-score on MRPC and 1.0% F1-score on QQP. Moreover, we verified that the combination of position encoding and syntactic features contributes to performance improvement.

Propionibacterium acnes is thought to be a causative agent of sarcoidosis. Patients with sarcoidosis have circulating immune complexes. We attempted to detect P. acnes-derived immune complexes in sarcoid lesions.We evaluated formalin-fixed and paraffin-embedded lymph node samples from 38 sarcoidosis patients and 90 non-sarcoidosis patients (27 patients with necrotizing lymphadenitis, 28 patients with reactive lymphadenitis, 16 patients with colon cancer, 19 patients with gastric cancer) by immunohistochemistry using anti-human immunoglobulins (IgG, IgA, and IgM) and complement (C1q and C3c) antibodies, and a P. acnes-specific monoclonal antibody (PAB antibody) that reacts with the membrane-bound lipoteichoic acid of P. acnes.Small round bodies (SRBs) bound to IgA, IgM, or IgG were detected in sinus macrophages, in 32 (84%), 32 (84%), or 11 (29%) sarcoid samples, respectively, and in 19 (21%), 26 (29%), or no (0%) control samples, respectively. Some of these insoluble immune complexes (IICs) also bound to C1q and C3c. We developed a microwave treatment followed by brief trypsin digestion (MT treatment) to detect PAB-reactive SRBs bound to immunoglobulins (IIC-forming P. acnes). MT treatment revealed abundant IIC-forming P. acnes in most (89%) of the sarcoid samples and sparse distribution in some (20%) of the control samples with lymphadenitis, but no IIC-forming P. acnes was detected in control samples without inflammation. IIC-forming P. acnes were mostly bound to both IgA and IgM. The PAB-reactive antigen and immunoglobulins were both located at the peripheral rim of the IIC-forming P. acnes. Conventional electron microscopy identified many SRBs (0.5-2.0 μm diameter) in sinus macrophages of sarcoid lymph nodes with many IIC-forming P. acnes, some of which were in phagolysosomes with a degraded and lamellar appearance.P. acnes-derived IICs in sinus macrophages were frequent and abundant in sarcoid lymph nodes, suggesting a potential etiologic link between sarcoidosis and this commensal bacterium.

Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the ‘coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N2 fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with 13C and 15N tracers to measure primary production and N2 fixation in coral tissues and endoliths. Assimilation of the 13C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N2 fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.

Propionibacterium acnes has recently been implicated as a cause of chronic prostatitis and this commensal bacterium may be linked to prostate carcinogenesis. The occurrence of intracellular P. acnes infection in prostate glands and the higher frequency of P. acnes-positive glands in radical prostatectomy specimens from patients with prostate cancer (PCa) than in those from patients without PCa led us to examine whether the P. acnes-positive gland frequency can be used to assess the risk for PCa in patients whose first prostate biopsy, performed due to an increased prostate-specific antigen (PSA) titer, was negative.We retrospectively collected the first and last prostate biopsy samples from 44 patients that were diagnosed PCa within 4 years after the first negative biopsy and from 36 control patients with no PCa found in repeated biopsy for at least 3 years after the first biopsy. We evaluated P. acnes-positive gland frequency and P. acnes-positive macrophage number using enzyme-immunohistochemistry with a P. acnes-specific monoclonal antibody (PAL antibody).The frequency of P. acnes-positive glands was higher in PCa samples than in control samples in both first biopsy samples and in combined first and last biopsy samples (P < 0.001). A frequency greater than the threshold (18.5 and 17.7, respectively) obtained by each receiver operating characteristic curve was an independent risk factor for PCa (P = 0.003 and 0.001, respectively) with odds ratios (14.8 and 13.9, respectively) higher than those of serum PSA titers of patients just before each biopsy (4.6 and 2.3, respectively). The number of P. acnes-positive macrophages did not differ significantly between PCa and control samples.These results suggested that the frequency of P. acnes-positive glands in the first negative prostate biopsy performed due to increased PSA titers can be supportive information for urologists in planning repeated biopsy or follow-up strategies.

BACKGROUND:Sarcoidosis is caused by Th1-type immune responses to unknown agents, and is linked to the infectious agent Propionibacterium acnes. Many strains of P. acnes isolated from sarcoid lesions cause intracellular infection and autophagy may contribute to the pathogenesis of sarcoidosis. We examined whether P. acnes induces autophagy. METHODS:Three cell lines from macrophages (Raw264.7), mesenchymal cells (MEF), and epithelial cells (HeLa) were infected by viable or heat-killed P. acnes (clinical isolate from sarcoid lymph node) at a multiplicity of infection (MOI) of 100 or 1000 for 1 h. Extracellular bacteria were killed by washing and culturing infected cells with antibiotics. Samples were examined by colony assay, electron-microscopy, and fluorescence-microscopy with anti-LC3 and anti-LAMP1 antibodies. Autophagy-deficient (Atg5-/-) MEF cells were also used. RESULTS:Small and large (≥5 μm in diameter) LC3-positive vacuoles containing few or many P. acnes cells (LC3-positive P. acnes) were frequently found in the three cell lines when infected by viable P. acnes at MOI 1000. LC3-positive large vacuoles were mostly LAMP1-positive. A few small LC3-positive/LAMP1-negative vacuoles were consistently observed in some infected cells for 24 h postinfection. The number of LC3-positive P. acnes was decreased at MOI 100 and completely abolished when heat-killed P. acnes was used. LC3-positive P. acnes was not found in autophagy-deficient Atg5-/- cells where the rate of infection was 25.3 and 17.6 times greater than that in wild-type Atg5+/+ cells at 48 h postinfection at MOI 100 and 1000, respectively. Electron-microscopic examination revealed bacterial cells surrounded mostly by a single-membrane including the large vacuoles and sometimes a double or multi-layered membrane, with occasional undigested bacterial cells in ruptured late endosomes or in the cytoplasm. CONCLUSION:Autophagy was induced by intracellular P. acnes infection and contributed to intracellular bacterial killing as an additional host defense mechanism to endocytosis or phagocytosis.