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Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.

BackgroundToxicity on social media, encompassing behaviors such as harassment, bullying, hate speech, and the dissemination of misinformation, has become a pressing social concern in the digital age. Its prevalence intensifies during periods of social crises and unrest, eroding a sense of safety and community. Such toxic environments can adversely impact the mental well-being of those exposed and further deepen societal divisions and polarization. The 2022 mpox outbreak, initially called “monkeypox” but later renamed to reduce stigma and address societal concerns, provides a relevant context for this issue. ObjectiveIn this study, we conducted a comprehensive analysis of the toxic online discourse surrounding the 2022 mpox outbreak. We aimed to dissect its origins, characterize its nature and content, trace its dissemination patterns, and assess its broader societal implications, with the goal of providing insights that can inform strategies to mitigate such toxicity in future crises. MethodsWe collected >1.6 million unique tweets and analyzed them with 5 dimensions: context, extent, content, speaker, and intent. Using topic modeling based on bidirectional encoder representations from transformers and social network community clustering, we delineated the toxic dynamics on Twitter. ResultsBy categorizing topics, we identified 5 high-level categories in the toxic online discourse on Twitter, including disease (20,281/43,521, 46.6%), health policy and health care (8400/43,521, 19.3%), homophobia (10,402/43,521, 23.9%), politics (2611/43,521, 6%), and racism (1784/43,521, 4.1%). Across these categories, users displayed negativity or controversial views on the mpox outbreak, highlighting the escalating political tensions and the weaponization of stigma during this infodemic. Through the toxicity diffusion networks of mentions (17,437 vertices with 3628 clusters), retweets (59,749 vertices with 3015 clusters), and the top users with the highest in-degree centrality, we found that retweets of toxic content were widespread, while influential users rarely engaged with or countered this toxicity through retweets. ConclusionsOur study introduces a comprehensive workflow that combines topical and network analyses to decode emerging social issues during crises. By tracking topical dynamics, we can track the changing popularity of toxic content on the internet, providing a better understanding of societal challenges. Network dynamics highlight key social media influencers and their intentions, suggesting that engaging with these central figures in toxic discourse can improve crisis communication and guide policy making.

Effects of graded dietary iron (Fe) levels on coho salmon Oncorhynchus kisutch (Walbaum, 1792) post-smolts were assessed by determining the growth performance, Fe deposited in tissue, liver and serum antioxidant and immunity responses. Six experimental diets containing graded Fe (FeSO4·7 H2O as a Fe source) levels of 23.70, 42.40, 63.80, 89.30, 102.70 and 125.70 mg/kg were made and fed to three replicate groups of fish. A total 180 coho salmon post-smolts (188.28 ± 0.40 g) were randomly distributed to 18 floating cages (water volume 1000-L) with a flow-through system for 10 weeks, and fed three times daily until satiation. The results showed that the final body weight (FBW) and specific growth rate (SGR) were increased (p < 0.05) with increasing Fe content (from 23.70 to 89.30 mg/kg) in the diet, and significantly decreased (p < 0.05) in these traits were recorded when dietary Fe supplementation was further increased (from 89.30 to 125.70 mg/kg). However, feed conversion ratio (FCR) showed the opposite trend. Survival rate, morphological indices, and body proximate compositions did not differ significantly among the groups (p > 0.05). Nevertheless, the Fe contents in the whole body and muscle exhibited a steady rise (linear, p < 0.05), meanwhile, the liver Fe content significantly increased with increasing dietary Fe levels (linear and quadratic, p < 0.05). Increasing dietary Fe levels increased (p < 0.05) the hemoglobin (Hb), erythrocyte counts and hematocrit. In serum, lysozyme activity was significantly increased in 89.30 mg/kg diets ( p < 0.05). There was a significant increase in liver and serum superoxide dismutase (SOD) and catalase activities in response to the Fe levels in the diet, whereas a significant quadratic decrease in malondialdehyde levels (p < 0.05). Quadratic regression analysis of SGR and FCR against dietary Fe levels indicated that the optimal dietary Fe requirements were estimated to be 100.00 mg/kg and 104.17 mg/kg. Broken-line model analyses of the hepatic Fe content and SOD activity, the Hb content in the blood, and serum SOD activity against dietary Fe levels indicated that the optimal dietary Fe levels are 85.01, 87.53, 87.04, 91.23 mg/kg in Oncorhynchus kisutch post-smolts, respectively.

To evaluate the impact of nutritional tea polyphenols (TPs) on body composition, growth, biochemical markers, antioxidant capacity, and hemato-immunological levels, a ten-week feeding experiment was carried out on coho salmon (Oncorhynchus kisutch, 180.51 ± 0.15 g). The control group was fed a basal diet; the T1, T2, T3, and T4 groups were fed 0.005%, 0.01%, 0.02%, and 0.04% TPs, respectively. These results demonstrate that adding TPs significantly (p < 0.05) increased the coho salmon fish’s weight gain (WG), relative growth rate (RGR), condition factor (CF), feed efficacy (FE), daily growth rate (DGR), and specific growth rate (SGR). There was no discernible difference in the body compositions of the treated TPs and the control group (p > 0.05). In addition, the T3 group showed a significant (p < 0.05) decrease in GPT, LDL, HDL, TC, and CAT. Fish given a 0.02% diet containing TPs had significantly lower levels of malondialdehyde (MDA) in their liver; yet, the TP-treated groups had higher levels of SOD and CAT than the control (p < 0.05). The data analysis shows a significant rise in lysozyme, respiratory burst activity, bactericidal activity, and blood hematological parameters in the 0.01–0.04% TP groups. According to these findings, TPs could be a useful dietary supplement for raising the antioxidant status, growth parameters, haemato-immunological response, and whole-body composition of coho salmon fish.

A 10-week growth trial was carried out to study the impact of dietary manganese (Mn) level on growth, tissue Mn content and anti-oxidative capacity of coho salmon (Oncorhynchus kisutch) post-smolts (186.51 ± 1.43 g). Six iso-nitrogenous (42.40% Protein) and iso-lipidic (10.27% Lipid) purified diets based on casein-gelatin were formulated to contain varied graded (MnSO4·H2O as a Mn source) levels of 0.40, 9.50, 16.80, 25.80, 33.40 and 41.20 Mn mg/kg. Fish were reared in a freshwater flow-through rearing system and fed to apparent satiation 3 times daily. No significant effects were found on the survival rate, morphological indices, whole-body proximate composition (p > .05) among the groups. However, higher dietary Mn supplementation level than 25.80 mg/kg improved the growth performance, increased the deposition of Mn in whole-body and vertebral, improved hepatic digestive enzyme activity, enhanced anti-oxidative enzyme activities, and decreased the malondialdehyde content in liver and serum (p

A 10-week feeding trial was conducted to investigate the dietary pyridoxine requirements of coho salmon (Oncorhynchus kisutch) post-smolts with an initial mean body weight of 180.22 ± 0.41 g. Seven diets were prepared with gradient pyridoxine levels of 0.32, 1.25, 2.56, 4.08, 8.24, 16.02, and 32.32 mg/kg, respectively, and each diet was assigned to three replication groups of 10 fish. The results revealed that coho salmon fed the diet with pyridoxine supplementation gained more final body weight (FBW), specific growth rate (SGR), and better feed conversion ratio (FCR). FBW and SGR of the fish fed the diet with 8.24 mg/kg pyridoxine were significantly higher than those of the other groups (P0.05) significant impact on the whole-body composition including moisture, ash, crude lipid, and crude protein. The hepatic pyridoxine concentration, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) activities increased significantly with dietary pyridoxine levels increasing from 0.32 to 4.08 mg/kg (P0.05). The coho salmon fed the diet with 8.24 mg/kg pyridoxine achieved the maximum superoxide dismutase and catalase, as well as the minimum total cholesterol, triglyceride, and malondialdehyde. Broken line analysis of SGR, FCR, AST, and ALT activities reflected the optimal dietary pyridoxine requirements for coho salmon post-smolts from 3.92 to 7.08 mg/kg diet.

Here, the authors characterize the gut microbiome fermentation properties and therapeutic potential of chemically diverse synthetic glycans (SGs), showing they promote specific shifts in taxonomic and metabolite profiles, and exhibit therapeutic benefits in mouse models of colonic inflammation, together implying SGs as a potential avenue to treat disease by modulating the composition and metabolites produced by the gut microbiome.

The suitable dietary L-lysine concentration for coho salmon (Oncorhynchus kisutch) alevins was assessed by a dose response feeding trial. Six experimental diets were made with graded L-lysine concentrations of 2.29%, 2.81%, 3.32%, 3.80%, 4.27%, and 4.78% of the dry matter, respectively, each of which was fed to triplicate groups of 100 alevins (initial body weight: 0.30 ± 0.01 g) in 18 plastic baskets (water volume 240 L). The alevins were cultured in a flowing freshwater system and fed manually to apparent satiation four times a day for 12 weeks. The survival rate of alevins did not differ significantly among the dietary groups. The specific growth rate (SGR), protein efficiency ratio (PER), and body protein deposition (BPD) increased significantly (p < 0.05) with the increase in dietary lysine concentration up to 3.80% and then reduced as lysine level further increased. The feed conversion ratio (FCR) had an inverse trend to SGR. The whole-body crude protein content of the alevins increased significantly with increasing dietary lysine level, while crude lipid content showed the opposite trend. In comparison, the contents of morphological indices, whole-body moisture, and ash were not affected significantly (p > 0.05) by the different dietary lysine concentrations. The highest contents of lysine, arginine, and total essential amino acids (EAAs) were observed in the group with 4.27% dietary lysine concentration, which did not differ significantly from those in the 3.32%, 3.80%, and 4.78% groups but was significantly higher than those in the 2.29% and 2.81% groups. Similarly, valine had the highest content in the group with 4.78%. The variations in dietary lysine had no significant impacts on other EAA and non-EAA contents except glycine, which increased with increasing dietary lysine level. Second-order polynomial model analyses based on SGR, PER, BPD, and FCR evaluated the optimum L-lysine requirements of coho salmon alevins as 3.74%, 3.73%, 3.91%, and 3.77% of the diet or 6.80%, 6.78%, 7.11%, and 6.85% of dietary proteins, respectively.

We investigated effect of dietary iron (Fe) on the lipid deposition, nutritional element, and muscle quality in coho salmon. Four level Fe diets at 23.7, 46.4, 77.3, and 127.7 mg/kg were fed to the post-larval coho salmon for 12 weeks. Our results showed that dietary Fe decreased the content of triglyceride and the activity of fatty acid synthetase, ATP-citrate lyase, and acetyl-CoA carboxylase. The content of Fe in muscle was increased with increasing dietary Fe levels, and dietary Fe affected the content of nutritional elements. In addition, dietary Fe levels affected the composition of fatty acids and the content of free amino acids, and increased muscle fiber size. The lower dietary Fe levels also affected the hardness, chewiness, resilience, springiness, cohesiveness, and gumminess of salmon muscle. In all, dietary Fe inhibited the lipid deposition and affected the content of nutritional element and muscle quality in coho salmon.

The present study evaluated the effects of partially substituting fish meal (FM) with poultry by-product meal (PBPM) on the growth, muscle composition, and tissue biochemical parameters of coho salmon (Oncorhynchus kisutch) post-smolts. Five isonitrogenous (7.45% nitrogen) and isoenergetic (18.61 MJ/kg gross energy) experimental diets were made by substituting 0%, 10%, 20%, 40%, and 60% FM protein with PBPM protein, which were designated accordingly as PBPM0 (the control), PBPM10, PBPM20, PBPM40, and PBPM60, respectively. Each diet was fed to triplicates of ten post-smolts (initial individual body weight, 180.13 ± 1.32 g) in three floating cages three times daily (6:50, 11:50, and 16:50) to apparent satiation for 84 days. Both specific growth rate (SGR) and protein efficiency ratio did not differ significantly (p > 0.05) among the control, PBPM10, and PBPM20 groups, which were remarkably (p < 0.05) higher than those of the PBPM40 and PBPM60 groups. Feed conversion ratio varied inversely with SGR. The PBPM replacement had no remarkable effects on the morphological indices and proximal muscle components. The control and PBPM10 groups led to significantly higher muscle contents of leucine, lysine, and methionine than groups of higher PBPM inclusion. The groups of PBPM40 and PBPM60 obtained significantly (p < 0.05) higher serum alanine aminotransferase and aspartate aminotransferase activities than the control and low PBPM inclusion groups. The control group had significantly higher albumin and total cholesterol contents than the groups with PBPM inclusion. The control group had significantly higher triglycerides content than the PBPM60 group. The PBPM60 group had significantly lower contents of high-density lipoprotein, low-density lipoprotein, and total protein than the control and PBPM10 groups. The high PBPM replacement level up to 40% and 60% had adverse effects on hepatic malondialdehyde levels. The catalase and superoxide dismutase activities were not affected by low PBPM inclusion, but significantly decreased in high-PBPM-inclusion groups. Based on broken-line regression analysis of SGR and PER, the optimum dietary PBPM replacing level was evaluated to be 16.63–17.50% of FM protein for coho salmon post-smolts.

In the present study, we evaluated the effects of dietary lipid levels on the anti-oxidant responses, initial immunity, and mTOR signaling in the liver of coho salmon Oncorhynchus kisutch. The post-larval coho salmon were fed four isonitrogenous experimental diets with crude lipid levels of 6.6%, 10.56%, 18.91%, and 26.91% for 12 weeks, respectively. Compared to the control group (6.6% dietary lipid level), the activities of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), peroxidase (POD), glutathione peroxidase (GSH-PX), and total antioxidant capacity (TAC) were enhanced by 10.56% and 18.91% dietary lipid levels in the liver of coho salmon. However, no significant difference was observed on these anti-oxidant enzyme activities when the fish were fed 26.91% lipid level diet. Compared to the control group (6.6% dietary lipid level), the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) as well as the generation of hydroxy radical (·OH) and superoxide anion (O2·-) were decreased by 10.56% and 18.91% dietary lipid levels. In addition, the gene and protein expression level of PI3K, Akt, and mTOR was induced by 10.56%, 18.91%, and 26.91% dietary lipid levels. The gene expression level of IL-1β, IL-6, and TNFα was also increased with the increase of dietary lipid levels. The result of hepatic tissue sections showed that the cellular morphology of liver was affected by the higher dietary lipid levels. In conclusion, the dietary lipid levels affected the anti-oxidant responses, initial immunity, and mTOR signaling in the liver of post-larval coho salmon.

In this study, post-larval coho salmon Oncorhynchus kisutch (initial weight 0.37 ± 0.03 g) were fed with 6 experimental diets with increasing manganese (Mn) content (2.4, 8.5, 14.8, 19.8, 24.6, and 33.7 mg kg−1) for 12 weeks. Our results indicated that the feed conversion rate (FCR), specific growth rate (SGR), condition factor (CF), crude protein, moisture, crude lipid, ash, whole-body Mn, and vertebral Mn were affected by the elevation of Mn content in the diet. The activities of hepatic GSH-PX, Mn-SOD, and CAT were enhanced with increasing Mn content in the diet and reached the highest value at 19.8 mg kg−1 Mn. However, the level of hydrogen peroxide (H2O2), superoxide anion (O2·−), and malondialdehyde (MDA) was reduced with increasing Mn content in the diet. In addition, the activity of hepatic lipase (HL) and lipoprotein lipase (LPL) was increased with the elevation of dietary Mn content and reached a peak value at 14.8 mg kg−1 Mn. The activity of fatty acid synthetase (FAS) and the content of nonesterified fatty acid (NEFA) were increased following the elevation of Mn content from 2.4 to 19.8 mg kg−1 in the diet. The results indicated that the appropriate dietary Mn supplementation improved the feeding efficiency, lipid metabolism, and antioxidant capacity of coho salmon. The dietary Mn requirement for post-larval coho salmon was 17.35 mg kg−1 and 19.75 mg kg−1 based on the SGR and FCR, respectively. An optimal dietary level of Mn enhances hepatic lipid metabolism, and the signaling pathway of PI3K/AKT/mTOR may be involved in regulating the activity of enzymes related to lipid metabolism.

A 12-week feeding trial aimed to evaluate the effects of dietary linoleic acid (LA, 18:2n-6) on the growth performance, fatty acid profile, and lipid metabolism enzyme activities of coho salmon (Oncorhynchus kisutch) alevins. Six experimental diets (47% crude protein and 15% crude lipid) were formulated to contain graded LA levels of 0.11%, 0.74%, 1.37%, 2.00%, 2.63%, and 3.26%. Each diet was fed to triplicate groups of 50 alevins with an initial body weight of 0.364 ± 0.002 g, which were randomly assigned to 18 white plastic tanks (0.8 × 0.6 × 0.6 m, 240 L/tank). Fish were reared in a freshwater flow-through rearing system and fed to apparent satiation four times daily. The survival rate was not significantly different among the treatments (p > 0.05). However, the 1.37% LA group significantly improved the final body weight and specific growth rate (SGR) (p < 0.05) of alevins. The feed conversion ratio (FCR) in the 1.37% LA group was significantly lower than those in other groups (p < 0.05). The whole-body lipid content significantly decreased (p < 0.05) with dietary LA levels increasing from 0.74% to 2.00%. The fatty acid composition of the total lipid in muscle was closely correlated with those in the diets. The dietary LA level of 1.37% led to significantly higher activities of liver lipoprotein lipase (LPL) and hepatic lipase (HL) than those of other groups (p < 0.05). Hepatic malate dehydrogenase (MDH) and fatty acid synthase (FAS) decreased with the increase in the dietary LA levels from 0.11% to 1.37%. The lowest MDH and FAS activities were obtained in the 1.37% LA group (p < 0.05). This study indicated that an appropriate amount of dietary LA was beneficial for the growth and lipid metabolism of coho salmon alevins, and the results of the quadratic regression analysis of the SGR and FCR indicated that the optimal dietary LA requirements were 1.25% and 1.23% for coho salmon alevins, respectively.

Reopening amid the COVID-19 pandemic has triggered a battle on social media. The supporters perceived that the lockdown policy could damage the economy and exacerbate social inequality. By contrast, the opponents believed it was necessary to contain the spread and ensure a safe environment for recovery. Anatomy into the battle is of importance to address public concerns, beliefs, and values, thereby enabling policymakers to determine the appropriate solutions to implement reopening policy. To this end, we investigated over 1.5 million related Twitter postings from April 17 to May 30, 2020. With the aid of natural language processing (NLP) techniques and machine learning classifiers, we classified each tweet into either a "supporting" or "opposing" class and then investigated the public perception from temporal and spatial perspectives. From the temporal dimension, we found that both political and scientific news that were extensively discussed on Twitter led to the perception of opposing reopening. Further, being the first mover with full reopen adversely affected the public reaction to reopening policy, while being the follower or late mover resulted in positive responses. From the spatial dimension, the correlation and regression analyses suggest that the state-level perception was very likely to be associated with political affiliation and health value.

The rapid advancements in generative AI models present new opportunities in the education sector. However, it is imperative to acknowledge and address the potential risks and concerns that may arise with their use. We analyzed Twitter data to identify critical concerns related to the use of ChatGPT in education. We employed BERT-based topic modeling to conduct a discourse analysis and social network analysis to identify influential users in the conversation. While Twitter users generally expressed a positive attitude toward using ChatGPT, their concerns converged into five categories: academic integrity, impact on learning outcomes and skill development, limitation of capabilities, policy and social concerns, and workforce challenges. We also found that users from the tech, education, and media fields were often implicated in the conversation, while education and tech individual users led the discussion of concerns. Based on these findings, the study provides several implications for policymakers, tech companies and individuals, educators, and media agencies. In summary, our study underscores the importance of responsible and ethical use of AI in education and highlights the need for collaboration among stakeholders to regulate AI policy.

In order to enhance the efficiency of offshore companies, a multi-objective scheduling system based on hybrid non-dominated sorting genetic algorithm was proposed. An optimized model for multi-objective and multi-execution mode was constructed under the condition of taking time, cost, and resource into account, and then the mathematical model for the same was established. Moreover, the key techniques of the proposed system were elaborated, and the flowchart was designed. Aiming at the weaknesses of non-dominated sorting genetic algorithm which is short for non-dominated sorting genetic algorithm-II in the facet of local search and computational efficiency, Pareto-dominated simulated annealing algorithm was applied in search global solution. Finally, by simulation examples and industrial application, the robustness and outperformance of the improved algorithm were verified.

Aimed at enhancing the effectiveness and efficiency for offshore platform project scheduling, a multiagent collaborative scheduling model based on the analysis of distributed offshore platform project scheduling was proposed. The functional definitions and internal structure of agents in the proposed system were analyzed. Moreover, in order to explore the cooperative way of agents, communication mechanism was presented and a negotiation model was elaborated. Then, system architecture and hardware architecture were constructed to lay a foundation to develop the collaborative scheduling system. Finally, an intelligent algorithm based on Bayesian method was designed to verify the negotiation model and a prototype system was developed to test the feasibility and rationality.