Automated segmentation and recognition of C. elegans whole-body cells.

MOTIVATION: Motivation: Accurate segmentation and recognition of Caenorhabditis elegans cells are critical for various biological studies, including gene expression, cell lineages and cell fates analysis at single-cell level. However, the highly dense distribution, similar shapes, and inhomogeneous intensity profiles of whole-body cells in 3D fluorescence microscopy images make automatic cell segmentation and recognition a challenging task. Existing methods either rely on additional fiducial markers or only handle a subset of cells. Given the difficulty or expense associated with generating fiducial features in many experimental settings, a marker-free approach capable of reliably segmenting and recognizing C. elegans whole-body cells is highly desirable. RESULTS: We report a new pipeline, called Automated Segmentation and Recognition (ASR) of cells, and applied it to 3D fluorescent microscopy images of L1-stage C. elegans with 558 whole-body cells. A novel displacement vector field based deep learning model is proposed to address the problem of reliable segmentation of highly crowded cells with blurred boundary. We then realize the cell recognition by encoding and exploiting statistical priors on cell positions and structural similarities of neighboring cells. To the best of our knowledge, this is the first method successfully applied to the segmentation and recognition of C. elegans whole-body cells. The ASR segmentation module achieves an F1-score of 0.8956 on a dataset of 116 C. elegans image stacks with 64728 cells (Accuracy 0.9880, AJI 0.7813). Based on the segmentation results, the ASR recognition module achieved an average accuracy of 0.8879. We also show ASR's applicability to other cell types, e.g. platynereis and rat kidney cells. AVAILABILITY: The code is available at https://github.com/reaneyli/ASR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluating serum CXCL12, sCD22, Lp-PLA2 levels and ratios as biomarkers for diagnosis of Alzheimer's disease.

BACKGROUND: Grasping the underlying mechanisms of Alzheimer's disease (AD) is still a work in progress, and existing diagnostic techniques encounter various obstacles. Therefore, the discovery of dependable biomarkers is essential for early detection, tracking the disease's advancement, and steering treatment strategies. AIM: To explore the diagnostic potential of serum CXCL12, sCD22, Lp-PLA2, and their ratios in AD, aiming to enhance early detection and inform targeted treatment strategies. METHODS: The study was conducted in Dongying people's Hospital from January 2021 to December 2022. Participants included 60 AD patients (AD group) and 60 healthy people (control group). Using a prospective case-control design, the levels of CXCL12, sCD22 and Lp-PLA2 and their ratios were detected by enzyme-linked immunosorbent assay kit in the diagnosis of AD. The differences between the two groups were analyzed by statistical methods, and the corresponding ratio was constructed to improve the specificity and sensitivity of diagnosis. RESULTS: Serum CXCL12 levels were higher in the AD group (47.2 ± 8.5 ng/mL) than the control group (32.8 ± 5.7 ng/mL, P < 0.001), while sCD22 levels were lower (14.3 ± 2.1 ng/mL vs 18.9 ± 3.4 ng/mL, P < 0.01). Lp-PLA2 levels were also higher in the AD group (112.5 ± 20.6 ng/mL vs 89.7 ± 15.2 ng/mL, P < 0.05). Significant differences were noted in CXCL12/sCD22 (3.3 vs 1.7, P < 0.001) and Lp-PLA2/sCD22 ratios (8.0 vs 5.2, P < 0.05) between the groups. Receiver operating characteristic analysis confirmed high sensitivity and specificity of these markers and their ratios in distinguishing AD, with area under the curves ranging from 0.568 to 0.787. CONCLUSION: Serum CXCL12 and Lp-PLA2 levels were significantly increased, while sCD22 were significantly decreased, as well as increases in the ratios of CXCL12/sCD22 and Lp-PLA2/sCD22, are closely related to the onset of AD. These biomarkers and their ratios can be used as potential diagnostic indicators for AD, providing an important clinical reference for early intervention and treatment.

The golden key to open mystery boxes of SMARCA4-deficient undifferentiated thoracic tumor: focusing immunotherapy, tumor microenvironment and epigenetic regulation.

SMARCA4-deficient undifferentiated thoracic tumor is extremely invasive. This tumor with poor prognosis is easily confused with SMARCA4-deficent non-small cell lung cancer or sarcoma. Standard and efficient treatment has not been established. In this review, we summarized the etiology, pathogenesis and diagnosis, reviewed current and proposed innovative strategies for treatment and improving prognosis. Immunotherapy, targeting tumor microenvironment and epigenetic regulator have improved the prognosis of cancer patients. We summarized clinicopathological features and immunotherapy strategies and analyzed the progression-free survival (PFS) and overall survival (OS) of patients with SMARCA4-UT who received immune checkpoint inhibitors (ICIs). In addition, we proposed the feasibility of epigenetic regulation in the treatment of SMARCA4-UT. To our knowledge, this is the first review that aims to explore innovative strategies for targeting tumor microenvironment and epigenetic regulation and identify potential benefit population for immunotherapy to improve the prognosis.

Maternal exposure to particulate matter from duck houses restricts fetal growth due to inflammatory damage and oxidative stress.

The composition of particulate matter (PM) in poultry farms differs significantly from that of atmospheric PM as there is a higher concentration of microbes on farms. To assess the health effects of PM from poultry farms on pregnant animals, we collected PM from duck houses using a particulate sampler, processed it via centrifugation and vacuum concentration, and subsequently exposed the mice to airborne PM at 0.48 mg/m3 (i.e., low concentration group) and 1.92 mg/m3 (i.e., high concentration group) on the fifth day of pregnancy. After exposure until the twentieth day of pregnancy or spontaneous delivery, mice were euthanized for sampling. The effects of PM from duck houses on the pregnancy toxicity of mice were analyzed using histopathological analysis, enzyme-linked immunosorbent assay, and quantitative real-time polymerase chain reaction (qPCR). The results showed that exposure to PM had adverse effects on pregnant mice that reduced their feed intake in both groups. Microscopic lesions were observed in the lungs and placentas of pregnant mice, and the lesions worsened with increased PM concentrations, as shown by alveolar wall thickening, the infiltration of inflammatory cells in pulmonary interstitium, congestion, edema, and cellular degeneration of placenta. In pregnant mice in the high concentration group, exposure to PM significantly increased the expression of inflammatory cytokines in the lungs and placentas, caused oxidative stress, and decreased estrogen level in the blood. Exposure to PM also resulted in the reduced litter sizes of pregnant mice and shorter body and tail lengths in the fetuses delivered. Beyond that, exposure to PM significantly downregulated the levels of antioxidant factor superoxide dismutase and neurotrophic factor Ngf in the brains of fetuses. Collectively, exposure to a high concentration of PM by inhalation among pregnant mice caused significant pregnancy toxicity that led to abnormal fetal development due to inflammatory damage and oxidative stress. These findings established a foundation for future studies on the underlying mechanisms of pregnancy toxicity induced by exposure to PM.

A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans.

Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool) to automate cell identity assignment in three-dimensional image stacks of L1 larvae and profile reporter expression of 620 transcription factors in every cell. Transcription factor profile-based clustering analysis defines 80 cell types distinct from conventional phenotypic cell types and identifies three general phenotypic modalities related to these classifications. First, transcription factors are broadly downregulated in quiescent stage Hermaphrodite Specific Neurons, suggesting stage- and cell type-specific variation in transcriptome size. Second, transcription factor expression is more closely associated with morphology than other phenotypic modalities in different pre- and post-differentiation developmental stages. Finally, embryonic cell lineages can be associated with specific transcription factor expression patterns and functions that persist throughout postembryonic life. This study presents a comprehensive transcription factor atlas for investigation of intra-cell type heterogeneity.

Enriched switching in a donor-acceptor Stenhouse adduct via reversible covalent bonding.

We have utilized reversible covalent bonding to expand the accessible states of a molecular switch. Introducing a hydroxyl group onto the donor moiety of a donor-acceptor Stenhouse adduct (DASA) imparts an acidity response by forming an oxazolidine ring through intramolecular nucleophilic addition. Furthermore, we observed distinct color changes under cryogenic conditions, extending the thermal responsiveness beyond the cyclization equilibrium observed at elevated temperatures. These unique responses present promising prospects for diverse applications compared to traditional photoinduced binary isomerization.

Cross-linked poly(ester urethane)/starch composite films with high starch content as sustainable food-packaging materials: Influence of cross-link density.

This study focused on the development of cross-linked poly(ester urethane)/starch (PEUST) composites containing 50 wt% starch content for food-packaging materials. The NCO-terminated poly(caprolactone-urethane) prepolymer (PCUP) was first synthesized through bulk condensation. Then, low-moisture starch (0.21 wt%) and PCUP-based PEUST films were fabricated through an intensive extrusion process, followed by thermo-compression molding. The chemical structure of PCUP and PEUST was confirmed using Fourier transform infrared spectroscopy. Moreover, a comprehensive evaluation was conducted to assess the influence of cross-link density on the physicochemical properties of the composite films. The results showed that an increase in the cross-link density within the composites improved component compatibility and tensile strength but reduced crystallinity, water sensitivity, hydrolytic degradability, and water vapor permeability (WVP) of the films. In addition, the cytotoxicity tests were conducted to evaluate the safety of the composite films, and the high cell viability demonstrated non-toxicity for food application. The PEUST-II films with moderate cross-link density exhibited a suitable degradation rate (27.7 % weight loss at degradation for 140 d), optimal tensile properties (tensile strength at break: 12.4 MPa; elongation at break: 352 %), and low WVP (68.4 g/(m2⋅24h) at 30 % relative humidity). These characteristics make them highly promising as fresh-keeping food packaging.

PLZF protein forms a complex with protein TET1 to target TCF7L2 in undifferentiated spermatogonia.

The transcription factor promyelocytic leukemia zinc finger (PLZF, also known as ZBTB16) is critical for the self-renewal of spermatogonial stem cells (SSCs). However, the function of PLZF in SSCs is not clear. Here, we found that PLZF acted as an epigenetic regulator of stem cell maintenance and self-renewal of germ cells. The PLZF protein interacts with the ten-eleven translocation 1 (TET1) protein and subsequently acts as a modulator to regulate the expression of self-renewal-related genes. Furthermore, Transcription Factor 7-like 2 (TCF7L2) is promoted by the coordination of PLZF and Tri-methylation of lysine 4 on histone H3 (H3K4me3). In addition, testicular single-cell sequencing indicated that TCF7L2 is commonly expressed in the PLZF cluster. We demonstrated that PLZF directly targets TCF7L2 and alters the landscape of histone methylation in the SSCs nucleus. Meanwhile, the RD domain and Zn finger domain of PLZF synergize with H3K4me3 and directly upregulate TCF7L2 expression at the transcriptional level. Additionally, we identified a new association between PLZF and the histone methyltransferase EZH2 at the genomic level. Our study identified a new association between PLZF and H3K4me3, established the novel PLZF&TET1-H3K4me3-TCF7L2 axis at the genomic level which regulates undifferentiated spermatogonia, and provided a platform for studying germ cell development in male domestic animals.

Studies on the airborne bacterial communities and antimicrobial resistance genes in duck houses based on metagenome and PCR analysis.

The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods. The results showed that the bacterial communities in the air of duck houses were mainly Actinobacteria, Firmicutes, Proteobactria, Chlamydia, and Bcateroidetes at the phylum level. At the genus level, the air was dominated by Corynebacterium, Jeotgalicoccus, Staphylococcus, Brevibacterium, and Megacoccus, and contained some pathogenic bacteria such as Staphylococcus aureus, Corynebacterium diphtheriae, Klebsiella oxytoca, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were also potential hosts for ARGs. The airborne ARGs were mainly macrolides (10.97%), penicillins (10.73%), cephalosporins (8.91%), streptozotocin (8.91%), and aminoglycosides (8.02%). PCR detected 27 ARGs in airborne culturable microorganisms, and comparative analysis between PCR and the metagenomic data revealed that a total of 9 ARGs were found to the same, including macrolides ErmA, ErmF, tetracyclines tetG, tetX, methicarbamazepines dfrA12, dfrA15, aminoglycosides APH3-VI, ANT2-Ⅰ, and sulfonamides sul2. Moreover, inhalation exposure modeling showed that the workers in duck houses inhaled higher concentrations of ARB, human pathogenic bacteria (HPB) and human pathogenic antibiotic-resistant bacteria (HPARB) than hospital workers. These results provide new insights into airborne microorganisms and ARGs in animal farms and lay the foundation for further study.

LncRNA LINK-A Remodels Tissue Inflammatory Microenvironments to Promote Obesity.

High-fat diet (HFD)-induced obesity is a crucial risk factor for metabolic syndrome, mainly due to adipose tissue dysfunctions associated with it. However, the underlying mechanism remains unclear. This study has used genetic screening to identify an obesity-associated human lncRNA LINK-A as a critical molecule bridging the metabolic microenvironment and energy expenditure in vivo by establishing the HFD-induced obesity knock-in (KI) mouse model. Mechanistically, HFD LINK-A KI mice induce the infiltration of inflammatory factors, including IL-1ß and CXCL16, through the LINK-A/HB-EGF/HIF1α feedback loop axis in a self-amplified manner, thereby promoting the adipose tissue microenvironment remodeling and adaptive thermogenesis disorder, ultimately leading to obesity and insulin resistance. Notably, LINK-A expression is positively correlated with inflammatory factor expression in individuals who are overweight. Of note, targeting LINK-A via nucleic acid drug antisense oligonucleotides (ASO) attenuate HFD-induced obesity and metabolic syndrome, pointing out LINK-A as a valuable and effective therapeutic target for treating HFD-induced obesity. Briefly, the results reveale the roles of lncRNAs (such as LINK-A) in remodeling tissue inflammatory microenvironments to promote HFD-induced obesity.

Nephropathy Is Aggravated by Fatty Acids in Diabetic Kidney Disease through Tubular Epithelial Cell Necroptosis and Is Alleviated by an RIPK-1 Inhibitor.

Introduction: Diabetic kidney disease (DKD), one of the leading causes of end-stage renal disease, has complex pathogenic mechanisms and few effective clinical therapies. DKD progression is accompanied by the loss of renal resident cells, followed by chronic inflammation and extracellular matrix deposition. Necroptosis is a newly discovered form of regulated cell death and is a major form of intrinsic cell loss in certain diabetic complications such as cardiomyopathy, intestinal disease, and retinal neuropathy; however, its significance in DKD is largely unknown. Methods: In this study, the expression of necroptosis marker phosphorylated MLKL (p-MLKL) in renal biopsy tissues of patients with DKD was detected using immunofluorescence and semiquantified using immunohistochemistry. The effects of different disease-causing factors on necroptosis activation in human HK-2 cells were evaluated using immunofluorescence and Western blotting. db/db diabetic mice were fed a high-fat diet to establish an animal model of DKD with significant renal tubule damage. Mice were treated with the RIPK1 inhibitor RIPA-56 to evaluate its renal protective effects. mRNA transcriptome sequencing was used to explore the changes in signaling pathways after RIPA-56 treatment. Oil red O staining and electron macroscopy were used to observe lipid droplet accumulation in renal biopsy tissues and mouse kidney tissues. Results: Immunostaining of phosphorylated RIPK1/RIPK3/MLKL verified the occurrence of necroptosis in renal tubular epithelial cells of patients with DKD. The level of the necroptosis marker p-MLKL correlated positively with the severity of renal functional, pathological damages, and lipid droplet accumulation in patients with DKD. High glucose and fatty acids were the main factors causing necroptosis in human renal tubular HK-2 cells. Renal function deterioration and renal pathological injury were accelerated, and the necroptosis pathway was activated in db/db mice fed a high-fat diet. Application of RIPA-56 effectively reduced the degree of renal injury, inhibited the necroptosis pathway activation, and reduced necroinflammation and lipid droplet accumulation in the renal tissues of db/db mice fed a high-fat diet. Conclusion: The present study revealed the role of necroptosis in the progression of DKD and might provide a new therapeutic target for the treatment of DKD.

InDel and CNV within the AKAP13 Gene Revealing Strong Associations with Growth Traits in Goat.

A-kinase-anchoring protein 13 (AKAP13) is a member of the AKAP protein family that has been found to be associated with bone formation. Thus, we investigated the AKAP13 gene as a potential candidate gene for molecular-marker-assisted selection (MAS) in breeding. Our aim was to explore genetic variations (InDel and CNV) within the AKAP13 gene of Shaanbei white cashmere (SBWC) goats and analyze their relationship with growth traits. Ultimately, we identified three InDel loci (16-bp deletion, 15-bp insertion, and 25-bp deletion) and three CNVs, and the 16-bp and 15-bp loci were significantly associated with goat body length (p < 0.05). Both the 16-bp deletion variant and the 15-bp insertion variant facilitated an increase in body length in goats. In addition to this, there was a certain superposition effect between 16-bp and 15-bp loci, although there was no linkage. Additionally, the CNV1 locus was significantly correlated with body height and body length of goats (p < 0.05), and CNV2 was significantly correlated with chest depth, chest circumference, and cannon circumference of goats (p < 0.05). Individuals with gain type showed excellent growth performance. In conclusion, the InDel and CNV loci that we have identified could possibly serve as effective molecular markers in goat breeding, which is very essential for improving efficiency and success of breeding. Moreover, our findings provide a new avenue for further research into the function of the AKAP13 gene.

The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats.

Selenium (Se) is an important microelement for animal health. However, the knowledge about the effects of Se supplementation on rumen eukaryotic community remains less explored. In this study, the ruminal eukaryotic diversity in three months old Shaanbei white cashmere wether goats, with body weight (26.18 ± 2.71) kg, fed a basal diet [0.016 mg/kg Se dry matter (DM), control group (CG)] were compared to those animals given basal diet supplemented with different levels of organic Se in the form of Selenohomolanthionine (SeHLan), namely low Se group (LSE, 0.3 mg/kg DM), medium Se group (MSE, 0.6 mg/kg Se DM) and high Se group (HSE, 1.2 mg/kg DM) using 18S rRNA amplicon sequencing. Illumina sequencing generated 2,623,541 reads corresponding to 3123 operational taxonomic units (OTUs). Taxonomic analysis revealed that Eukaryota (77.95%) and Fungi (14.10%) were the dominant eukaryotic kingdom in all samples. The predominant rumen eukaryotic phylum was found to be Ciliophora (92.14%), while fungal phyla were dominated by Ascomycota (40.77%), Basidiomycota (23.77%), Mucoromycota (18.32%) and unidentified_Fungi (13.89%). The dominant eukaryotic genera were found to be Entodinium (55.44%), Ophryoscolex (10.51%) and Polyplastron (10.19%), while the fungal genera were dominanted by Mucor (15.39%), Pichia (9.88%), Aspergillu (8.24%), Malassezia (7.73%) and unidentified_Neocallimastigaceae (7.72%). The relative abundance of eukaryotic genera Ophryoscolex, Enoploplastron and fungal genus Mucor were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Spearman correlation analysis revealed that the ciliate protozoa and fungi were negatively correlated with each other. The results of this study provided newer information about the effects of Se on rumen eukaryotic diversity patterns using 18s rRNA high-throughput sequencing technology.

M1 polarization of chicken macrophage HD11 can be activated by duck Tembusu virus via MyD88-NF-κB-mediated signaling pathway.

Duck Tembusu virus (DTMUV) has caused significant economic losses to the global duck industry since its outbreak in 2010. The macrophages act as the key immune cell, and its polarization in different functional states is very important for host's immune responses and microbial infections. Avian macrophages are the main target cells of DTMUV, its polarization induced by DTMUV and the underlying mechanisms were explored in this study. Through quantitative real-time PCR, nitrite assay, and flow cytometry analysis, we found that DTMUV caused severe inflammatory responses in chicken macrophage line HD11 by reprogramming the expression of M1- and M2-associated genes, leading to the polarization of HD11 macrophage to M1-type. In term of mechanism, transcriptomics was performed to analyze the M1-type polarization triggered by DTMUV, it was found that most differential genes were implicated in biological processes, and DTMUV infection significantly activated innate immune signaling pathways, including cytokine-cytokine receptor interaction, MAPK signaling pathway. Moreover, transcription factors NF-κB and AP1 also be activated after viral infection. However, further validation analysis by inhibitors and siRNAs of NF-κB and AP1 showed that NF-κB molecule was essential for DTMUV-induced M1 polarization in HD11 cell, but not AP1. Additionally, the inhibiting assays targeting MyD88 and TRIF molecules were conducted to determine their effect on NF-κB and M1-associated genes upregulated by DTMUV. The results showed that although the inhibition of both MyD88 and TRIF significantly downregulated the mRNA level of NF-κB, but the expression of M1-associated genes such as CD86 was lower in MyD88 inhibition group than in the other group, indicating that the role of MyD88 in mediating M1 polarization induced by DTMUV was more important. Overall, these results demonstrated that DTMUV infection induces M1-type polarization in chicken macrophage HD11 through MyD88-NF-κB signaling pathways. This finding will lay the foundation for further study the pathogenesis of DTMUV, and provide new insights into the prevention and control of this disease.

New insight into copy number variations of goat SMAD2 gene and their associations with litter size and semen quality.

Copy number variations (CNV) contribute significantly to genetic variations. Numerous studies have shown that CNV affects phenotypic traits in livestock. The SMAD family member 2 (SMAD2) is a leading candidate gene in reproduction and has a crucial effect on litter size. Additionally, SMAD2 is also required for male reproduction and influences male germ cell development. However, there are no reports on investigating the effect of CNVs in the SMAD2 gene on reproductive traits in goat. Therefore, the goal of this study was to explore associations between CNV of the SMAD2 gene and litter size and semen quality in Shaanbei white cashmere (SBWC) goats. In this study, two CNVs within the SMAD2 were identified in 352 SBWC goats (50 males and 302 females). The association analysis revealed that only CNV2 was significantly associated with female goat first-born litter size (P = 3.59 × 10-4), male semen concentration (P < 0.01), ejaculation volume, live sperm count, and sperm deformity rate (P < 0.05). In terms of phenotypic performance, the individuals with loss genotypes outperformed those with other genotypes. CNV1 and CNV2 genotype combinations containing their dominant genotypes were also associated with goat litter size (P = 1.7 × 10-5), but no differences in semen quality were found. In summary, CNV2 of the SMAD2 gene is useful for molecular marker-assisted selection breeding, as it is associated with essential goat reproductive traits.

Vegetarians have an indirect positive effect on sleep quality through depression condition.

This study aimed to assess the association between a vegetarian diet and sleep quality among Chinese healthy adults and explore potential contributing factors. A cross-sectional study was conducted with 280 vegetarians and 280 age- and sex-matched omnivores from Shanghai, China. The Pittsburgh Sleep Quality Index (PSQI) and the Central Depression Scale (CES-D) were used to assess sleep and depression condition, respectively. A validated semi-quantitative food frequency questionnaires (SQFFQ) was employed to assess dietary intakes, and body composition was measured with InBody720. Multi-linear regression and logistic regression analysis were performed for the data analysis. The sleep quality was significantly better in the vegetarians than in the omnivores (PSQI score: 2.80 ± 2.02 vs. 3.27 ± 1.90, p = 0.005). The proportion of vegetarians who reported self-satisfied sleep was also higher than that of the omnivores (84.6% vs. 76.1%, p = 0.011). However, after adjusted for the depression condition (CES-D scores), the difference in sleep quality between vegetarians and omnivores became insignificant (p = 0.053). Compared to omnivores, vegetarians had lower depression scores (CES-D: 9.37 ± 6.24 vs. 10.94 ± 7.00, p = 0.006). After controlling for confounding factors, there was positive association between depression condition and sleep quality (ß = 0.106, 95%CI: 0.083 to 0.129, p < 0.001). Similarly, participants with better CES-D score had a lower risk of sleep disorders after controlling for the same confounding factors (OR = 1.109, 95%CI: 1.072 to 1.147, p < 0.001). Different contributing factors were reported in the vegetarian group and omnivore group. In conclusion, a vegetarian diet might improve sleep quality by moderating mental health, particularly depression condition.

Gut Microbiota Taxon-Dependent Transformation of Microglial M1/M2 Phenotypes Underlying Mechanisms of Spatial Learning and Memory Impairment after Chronic Methamphetamine Exposure.

Methamphetamine (METH) exposure may lead to cognitive impairment. Currently, evidence suggests that METH exposure alters the configuration of the gut microbiota. However, the role and mechanism of the gut microbiota in cognitive impairment after METH exposure are still largely unknown. Here, we investigated the impact of the gut microbiota on the phenotype status of microglia (microglial phenotypes M1 and microglial M2) and their secreting factors, the subsequent hippocampal neural processes, and the resulting influence on spatial learning and memory of chronically METH-exposed mice. We determined that gut microbiota perturbation triggered the transformation of microglial M2 to M1 and a subsequent change of pro-brain-derived neurotrophic factor (proBDNF)-p75NTR-mature BDNF (mBDNF)-TrkB signaling, which caused reduction of hippocampal neurogenesis and synaptic plasticity-related proteins (SYN, PSD95, and MAP2) and, consequently, deteriorated spatial learning and memory. More specifically, we found that Clostridia, Bacteroides, Lactobacillus, and Muribaculaceae might dramatically affect the homeostasis of microglial M1/M2 phenotypes and eventually contribute to spatial learning and memory decline after chronic METH exposure. Finally, we found that fecal microbial transplantation could protect against spatial learning and memory decline by restoring the microglial M1/M2 phenotype status and the subsequent proBDNF-p75NTR/mBDNF-TrkB signaling in the hippocampi of chronically METH-exposed mice. IMPORTANCE Our study indicated that the gut microbiota contributes to spatial learning and memory dysfunction after chronic METH exposure, in which microglial phenotype status plays an intermediary role. The elucidated "specific microbiota taxa-microglial M1/M2 phenotypes-spatial learning and memory impairment" pathway would provide a novel mechanism and elucidate potential gut microbiota taxon targets for the no-drug treatment of cognitive deterioration after chronic METH exposure.

Intramolecular charge transfer enables highly-efficient X-ray luminescence in cluster scintillators.

Luminescence clusters composed of organic ligands and metals have gained significant interests as scintillators owing to their great potential in high X-ray absorption, customizable radioluminescence, and solution processability at low temperatures. However, X-ray luminescence efficiency in clusters is primarily governed by the competition between radiative states from organic ligands and nonradiative cluster-centered charge transfer. Here we report that a class of Cu4I4 cubes exhibit highly emissive radioluminescence in response to X-ray irradiation through functionalizing biphosphine ligands with acridine. Mechanistic studies show that these clusters can efficiently absorb radiation ionization to generate electron-hole pairs and transfer them to ligands during thermalization for efficient radioluminescence through precise control over intramolecular charge transfer. Our experimental results indicate that copper/iodine-to-ligand and intraligand charge transfer states are predominant in radiative processes. We demonstrate that photoluminescence and electroluminescence quantum efficiencies of the clusters reach 95% and 25.6%, with the assistance of external triplet-to-singlet conversion by a thermally activated delayed fluorescence matrix. We further show the utility of the Cu4I4 scintillators in achieving a lowest X-ray detection limit of 77 nGy s-1 and a high X-ray imaging resolution of 12 line pairs per millimeter. Our study offers insights into universal luminescent mechanism and ligand engineering of cluster scintillators.

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.