Positioning of nuclei generated from arrangements of actin filaments.

a, Results of the identification and matching of real and generated nuclei by an automatic counting of the whole generated dataset and by manual counting of a subset of images. Stained nuclei refer to those recorded directly using fluorescent microscopy. Generated nuclei are those produced by the neural network using actin filament arrangements. Matched nuclei are those generated at less than 4 μm of its real counterpart. b, Manual (left) and automatic (right) processing of the same image. In manual processing the profile of the nuclei is drawn to calculate the centroid and the nuclei matched by comparison with the real counterpart. On the other hand, the automatic processing automatically identified the nuclei and generated their bounding boxes, matching generated and real nuclei based on the maximization of the overlapping areas of the bounding boxes. c, Several examples of generated nuclei (red) and their corresponding real nuclei (blue). The first three images (green frame) correspond to nuclei generated within the average nuclear radius (4 μm) from their real position. The last image (red frame) corresponds to a mismatch, where the generated nucleus is too far from its real position (See S2 Fig in S1 File for full images; Bars are 20 μm). d, Example of a cell and the relative distance of 4 μm within the cytoplasm. The probability of randomly positioning the nucleus within the cytoplasm can be identified as the ratio of possible matched positions for the centroid (green area) with respect to all possible positions (orange area). Those possible positions of the centroid located at less than the nuclear radius from the edges of the cell (red area) are discarded under the premise that the nucleus cannot be positioned partially outside the cell (See S3 Fig in S1 File for further analysis of probabilities; Bar is 20 μm). e, Distribution of the distances of the generated nuclei respect their real position. 71% of the nuclei are situated at less than 4 μm of their real position. f, Distribution of distances of the generated nuclei considered matched (<4 μm). 40% of the matched nuclei are located at less than 1μm from their real position.</p

Demonstration of a correlation between arrangements of actin filaments and nuclear position.

Actin filaments and nuclei information was isolated using non-overlapping fluorophores (Alexa Fluor 488 and SyTOX Deep Red). Then, 80% of the dataset of filaments was used as input to train a transformer-based network using the corresponding paired nuclei to evaluate the proximity to the real solution. The process iteration resulted in a fully trained network that was then used to generate the nuclei of the remaining 20% filament images of the dataset. The generated nuclei and their real counterparts were identified, and the coordinates of their centroids were determined to evaluate the network’s ability to predict the nuclear position using only actin filament arrangements.</p

Assessing the performance of TFill network and comparison with state-of-the-art generative models.

a, Encoder and Decoder layers comprise of a traditional convolutional neural network (CNN)-based ResNet block. b, The detailed architecture of the transformer encoder with self-attention mechanism. c, Reconstruction loss convergence as a function of iterations. d, Visual comparison of TFill generated nuclei images with trending image translation models. e, Quantitative comparison of TFill generated images with other image translation models using various metrics from computer vision (↓ Lower is better; ↑ Higher is better).</p

This contains three additional figures on the performance of the generative network, the generation of nuclei, and the statistical analysis.

The cell image database used in this research is available in the supplementary file “NIH3T3_ImageDataset-20220519T022044Z-001.zip”. The network source code can be found at: https://github.com/JGFermart/NuclearPrediction. (PDF)</p

Table_1_Metagenomic insights into the modulatory effects of kelp powder (Thallus laminariae)-Treated dairy milk on growth performances and physiological lipometabolic processes of kunming mice.XLSX

Kelp powder, supplemented with a dairy cow diet, effectively improved the milk polyunsaturated fatty acids (PUFAs) content. However, little information exists on the downstream effects of the kelp-treated milk on body health, gut microbiota, and nutrient metabolism. For this purpose, 48 3-week old Kunming (KM) male mice with an average body weight of 16.1 g ± 0.2 g were randomly divided into the control treatment (CON, fed with standard chow), the common milk supplement treatment (Milk), and the kelp powder-treated milk supplement treatment (KPM). The experiment lasted for 35 days, with a 7-day long adaptive period and a 28-day long main trial. Phenotypic parameters including growth performances and serum lipids-related parameters were first measured, and results indicated that Milk and KPM supplement significantly promoted the total body weight gain (P < 0.05), while significantly decreasing the feed conversion ratio compared with CON (P < 0.05). No significant differences were observed in the blood lipids content among all three treatments, however, the triglyceride content showed a decreasing trend after KPM supplement treatment. Further, activities of liver lipometabolic-related enzymes were investigated to determine the underlying factors that impacted physiological lipid metabolism. KPM treatment showed a significant reductive effect on the activity of lipogenesis-related enzymes, such as FAS and ACC, while a significant stimulative effect on the activity of lipolysis-related enzymes included the ATGL and CPT1 compared with CON (P < 0.05). Finally, gastrointestinal tract development and cecal microbiota community that correlated with body lipid degradation and absorption were measured to determine the underlying mechanism of KPM supplementation on physiological lipid metabolism. Results indicated that supplementation with KPM significantly enhanced cecal bacteria diversity which was reflected in the significant increase of Chao1 and ACE indexes. Besides, starch-degraded bacteria such as Faecalibacterium, Ruminococcaceae, and Streptococcus are significant decreased (P < 0.05), while cellulose-degraded bacteria including Parabacteroides, Prevotella, Lactobacillus, Clostridium, and Bifidobacterium are significantly increased (P < 0.05) after KPM supplement, which may further restrict the energy generation and therefore reduce the lipid deposition. In summary, kelp supplement helped increase the milk PUFAs content, enhance the bacterial diversity and relative abundances of probiotics, which finally modulated physiological lipid metabolism, and promote growth performances.</p

Table_2_Rumen Microbial Metabolic Responses of Dairy Cows to the Honeycomb Flavonoids Supplement Under Heat-Stress Conditions.XLSX

Flavonoids played critical roles in stabilizing microbial homoeostasis when animals suffered exoteric stresses. However, whether flavonoids attenuated heat stress of dairy cows is still not clear. Therefore, in the present article, flavonoids extracted from honeycomb were supplemented to investigate the production, digestibility, and rumen microbial metabolism responses of cows under heat stress conditions. A total of 600 multiparous dairy herds were randomly allotted into the control treatment (CON), the heat stress (HS) treatment, and the honeycomb flavonoids supplement under heat stress conditions (HF) treatment for a 30-day-long trial. Each treatment contains 4 replicates, with 50 cows in each replicate. Production performances including dry matter intake (DMI), milk production, and milk quality were measured on the basis of replicate. Furthermore, two cows of each replicate were selected for the measurement of the nutrient digestibility, the ruminal fermentable parameters including ruminal pH, volatile fatty acids, and ammonia-N, and the rumen microbial communities and metabolism. Results showed that HF effectively increased DMI, milk yield, milk fat, and ruminal acetate content (p < 0.05) compared with HS. Likewise, digestibility of NDF was promoted after HF supplement compared with HS. Furthermore, relative abundances of rumen microbial diversities especially Succiniclasticum, Pseudobutyrivibrio, Acetitomaculum, Streptococcus, and Succinivibrio, which mainly participated in energy metabolism, significantly improved after HF supplement. Metabolomic investigation showed that HF supplement significantly upregulated relative content of lipometabolic-related metabolites such as phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, and phosphatidylethanolamine, while it downregulated biogenic amines. In summary, HF supplement helps proliferate microbial abundances, which further promoted fiber digestibility and energy provision, and ultimately enhances the production performances of dairy cows under heat stress conditions.</p

Table_1_Rumen Microbial Metabolic Responses of Dairy Cows to the Honeycomb Flavonoids Supplement Under Heat-Stress Conditions.XLSX

Flavonoids played critical roles in stabilizing microbial homoeostasis when animals suffered exoteric stresses. However, whether flavonoids attenuated heat stress of dairy cows is still not clear. Therefore, in the present article, flavonoids extracted from honeycomb were supplemented to investigate the production, digestibility, and rumen microbial metabolism responses of cows under heat stress conditions. A total of 600 multiparous dairy herds were randomly allotted into the control treatment (CON), the heat stress (HS) treatment, and the honeycomb flavonoids supplement under heat stress conditions (HF) treatment for a 30-day-long trial. Each treatment contains 4 replicates, with 50 cows in each replicate. Production performances including dry matter intake (DMI), milk production, and milk quality were measured on the basis of replicate. Furthermore, two cows of each replicate were selected for the measurement of the nutrient digestibility, the ruminal fermentable parameters including ruminal pH, volatile fatty acids, and ammonia-N, and the rumen microbial communities and metabolism. Results showed that HF effectively increased DMI, milk yield, milk fat, and ruminal acetate content (p < 0.05) compared with HS. Likewise, digestibility of NDF was promoted after HF supplement compared with HS. Furthermore, relative abundances of rumen microbial diversities especially Succiniclasticum, Pseudobutyrivibrio, Acetitomaculum, Streptococcus, and Succinivibrio, which mainly participated in energy metabolism, significantly improved after HF supplement. Metabolomic investigation showed that HF supplement significantly upregulated relative content of lipometabolic-related metabolites such as phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, and phosphatidylethanolamine, while it downregulated biogenic amines. In summary, HF supplement helps proliferate microbial abundances, which further promoted fiber digestibility and energy provision, and ultimately enhances the production performances of dairy cows under heat stress conditions.</p