Phagocytosis is the process by which myeloid phagocytes bind to and internalize potentially dangerous microorganisms1. During phagocytosis, innate immune receptors and associated signalling proteins are localized to the maturing phagosome compartment, forming an immune information processing hub brimming with microorganism-sensing features2-8. Here we developed proximity labelling of phagosomal contents (PhagoPL) to identify proteins localizing to phagosomes containing model yeast and bacteria. By comparing the protein composition of phagosomes containing evolutionarily and biochemically distinct microorganisms, we unexpectedly identified programmed death-ligand 1 (PD-L1) as a protein that specifically enriches in phagosomes containing yeast. We found that PD-L1 directly binds to yeast upon processing in phagosomes. By surface display library screening, we identified the ribosomal protein Rpl20b as a fungal protein ligand for PD-L1. Using an auxin-inducible depletion system, we found that detection of Rpl20b by macrophages cross-regulates production of distinct cytokines including interleukin-10 (IL-10) induced by the activation of other innate immune receptors. Thus, this study establishes PhagoPL as a useful approach to quantifying the collection of proteins enriched in phagosomes during host-microorganism interactions, exemplified by identifying PD-L1 as a receptor that binds to fungi.
The cycling performance of zinc-ion batteries is greatly affected by dendrite formation and side reactions on zinc anode, particularly in scenarios involving high depth of discharge (DOD) and low negative/positive capacity (N/P) ratios in full cells. Herein, drawing upon principles of host-guest interaction chemistry, we investigate the impact of molecular structure of electrolyte additives, specifically the -COOH and -OH groups, on the zinc negative electrode through molecular design. Our findings reveal that molecules containing these groups exhibit strong adsorption onto zinc anode surfaces and chelate with Zn2+, forming a H2O-poor inner Helmholtz plane. This effectively suppresses side reactions and promotes dendrite-free zinc deposition of exposed (002) facets, enhancing stability and reversibility of an average coulombic efficiency of 99.89% with the introduction of Lactobionic acid (LA) additive. Under harsh conditions of 92% DOD, Zn//Zn cells exhibit stable cycling at challenging current densities of 15 mA·cm-2. Even at a low N/P ratio of 1.3, Zn//NH4V4O10 full cells with LA electrolyte exhibit high-capacity retention of 73% after 300 cycles, significantly surpassing that of the blank electrolyte. Moreover, in a conversion type Zn//Br static battery with a high areal capacity (~ 5 mAh·cm-2), LA electrolyte sustains an improved cycling stability of 700 cycles.
Muscle aging contributed to morbidity and mortality in the elderly adults by leading to severe outcomes such as frailty, falls and fractures. Post-transcriptional regulation especially competing endogenous RNA (ceRNA) mechanism may modulate the process of skeletal muscle aging. RNA-seq was performed in quadriceps of 6-month-old (adult) and 22-month-old (aged) male mice to identify differentially expressed ncRNAs and mRNAs and further construct ceRNA networks. Decreased quadriceps-body weight ratio and muscle fiber cross-sectional area as well as histological characteristics of aging were observed in the aged mice. Besides, there were higher expressions of atrogin-1 and MuRF-1 and lower expression of Myog, Myf4 and Myod1 in the quadriceps of aged mice relative to that of adult mice. The expression of 85 lncRNAs, 52 circRNAs, 10 miRNAs and 277 mRNAs were significantly dysregulated in quadriceps between the two groups, among which two ceRNA networks lncRNA 2700081O15Rik/circRNA_0000820-miR-673-3p-Tmem120b were constructed. Level of triglycerides and expression of PPARγ, C/EBPα, FASN and leptin were elevated and the expression of adiponectin was reduced in quadriceps of aged mice compared with that of adult mice. LncRNA 2700081O15Rik/circRNA_0000820-miR-673-3p-Tmem120b were possibly associated with the adipogenesis and fat accumulation in skeletal muscle of age male mice.
Odontogenic infections can spread to the respiratory tract. Despite the known role of Tannerella forsythia as the primary pathogen in periodontitis, the association between T. forsythia infection and risk of pneumonia or lung abscess remains unknown. In this report, we present a case of lung abscess caused by T. forsythia infection. The pathogen was detected by metagenomic next-generation sequencing (mNGS) in the bronchoalveolar lavage fluid of the patient. The clinical characteristics and possible mechanisms of the infection are discussed. T. forsythia is a conditional pathogen that can cause lung abscess in the presence of helper bacteria and reduced host immune status. The course of treatment should be personalized and might be longer than 3 months.
Purpose: This study aims to explore the value of clinical features, CT imaging signs, and radiomics features in differentiating between adults and children with Mycoplasma pneumonia and seeking quantitative radiomic representations of CT imaging signs. Materials and methods: In a retrospective analysis of 981 cases of mycoplasmal pneumonia patients from November 2021 to December 2023, 590 internal data (adults:450, children: 140) randomly divided into a training set and a validation set with an 8:2 ratio and 391 external test data (adults:121; children:270) were included. Using univariate analysis, CT imaging signs and clinical features with significant differences (p < 0.05) were selected. After segmenting the lesion area on the CT image as the region of interest, 1,904 radiomic features were extracted. Then, Pearson correlation analysis (PCC) and the least absolute shrinkage and selection operator (LASSO) were used to select the radiomic features. Based on the selected features, multivariable logistic regression analysis was used to establish the clinical model, CT image model, radiomic model, and combined model. The predictive performance of each model was evaluated using ROC curves, AUC, sensitivity, specificity, accuracy, and precision. The AUC between each model was compared using the Delong test. Importantly, the radiomics features and quantitative and qualitative CT image features were analyzed using Pearson correlation analysis and analysis of variance, respectively. Results: For the individual model, the radiomics model, which was built using 45 selected features, achieved the highest AUCs in the training set, validation set, and external test set, which were 0.995 (0.992, 0.998), 0.952 (0.921, 0.978), and 0.969 (0.953, 0.982), respectively. In all models, the combined model achieved the highest AUCs, which were 0.996 (0.993, 0.998), 0.972 (0.942, 0.995), and 0.986 (0.976, 0.993) in the training set, validation set, and test set, respectively. In addition, we selected 11 radiomics features and CT image features with a correlation coefficient r greater than 0.35. Conclusion: The combined model has good diagnostic performance for differentiating between adults and children with mycoplasmal pneumonia, and different CT imaging signs are quantitatively represented by radiomics.
Backgroud: Acute myocardial infarction (AMI) has a high morbidity rate, high mortality rate, high readmission rate, high health care costs, and a high symptomatic, psychological, and economic burden on patients. Patients with AMI usually present with multiple symptoms simultaneously, which are manifested as symptom clusters. Symptom clusters have a profound impact on the quality of survival and clinical outcomes of AMI patients. Objective: The purpose of this study was to analyze unplanned hospital readmissions among cluster groups within a 1-year follow-up period, as well as to identify clusters of acute symptoms and the characteristics associated with them that appeared in patients with AMI. Methods: Between October 2021 and October 2022, 261 AMI patients in China were individually questioned for symptoms using a structured questionnaire. Mplus 8.3 software was used to conduct latent class analysis in order to find symptom clusters. Univariate analysis is used to examine characteristics associated with each cluster, and multinomial logistic regression is used to analyze a cluster membership as an independent predictor of hospital readmission after 1-year. Results: Three unique clusters were found among the 11 acute symptoms: the typical chest symptom cluster (64.4%), the multiple symptom cluster (29.5%), and the atypical symptom cluster (6.1%). The cluster of atypical symptoms was more likely to have anemia and the worse values of Killip class compared with other clusters. The results of multiple logistic regression indicated that, in comparison to the typical chest cluster, the atypical symptom cluster substantially predicted a greater probability of 1-year hospital readmission (odd ratio 8.303, 95% confidence interval 2.550-27.031, P < 0.001). Conclusion: Out of the 11 acute symptoms, we have found three clusters: the typical chest symptom, multiple symptom, and atypical symptom clusters. Compared to patients in the other two clusters, those in the atypical symptom cluster-which included anemia and a large percentage of Killip class patients-had worse clinical indicators at hospital readmission during the duration of the 1-year follow-up. Both anemia and high Killip classification suggest that the patient's clinical presentation is poor and therefore the prognosis is worse. Intensive treatment should be considered for anemia and high level of Killip class patients with atypical presentation. Clinicians should focus on patients with atypical symptom clusters, enhance early recognition of symptoms, and develop targeted symptom management strategies to alleviate their discomfort in order to improve symptomatic outcomes.
The presence of butylparaben (BP), a prevalent pharmaceutical and personal care product, in surface waters has raised concerns regarding its impact on aquatic ecosystems. Despite its frequent detection, the toxicity of BP to the cyanobacterium Microcystis aeruginosa remains poorly understood. This study investigates the influence of BP on the growth and physiological responses of M. aeruginosa. Results indicate that low concentrations of BP (below 2.5 mg/L) have negligible effects on M. aeruginosa growth, whereas higher concentrations (5 mg/L and 10 mg/L) lead to significant growth inhibition. This inhibition is attributed to the severe disruption of photosynthesis, evidenced by decreased Fv/Fm values and chlorophyll a content. BP exposure also triggers the production of reactive oxygen species (ROS), resulting in elevated activity of antioxidant enzymes. Excessive ROS generation stimulates the production of microcystin-LR (MC-LR). Furthermore, lipid peroxidation and cell membrane damage indicate that high BP concentrations cause cell membrane rupture, facilitating the release of MC-LR into the environment. Transcriptome analysis reveals that BP disrupts energy metabolic processes, particularly affecting genes associated with photosynthesis, carbon fixation, electron transport, glycolysis, and the tricarboxylic acid cycle. These findings underscore the profound physiological impact of BP on M. aeruginosa and highlight its role in stimulating the production and release of MC-LR, thereby amplifying environmental risks in aquatic systems.
The presence of Total Polar Materials (TPM) in edible oils is a crucial indicator for assessing oil quality. It is of paramount importance to develop a rapid and dependable technique for monitoring polarity in frying oil. Sensitive polarity responsive fluorescence carbon dots (F-CDs) were synthesized by using p-phenylenediamine as precursors and 2-formylphenylboronic acid pinacol ester (2-FAPE) as a post-modifier. The construction of the fluorescent probe F-CDs involved a strong intramolecular charge-transfer (ICT) mechanism, with 2-FAPE serving as the electron-withdrawing fluorophore and the π-conjugated structure acting as a potent electron-donating group. A strong linear relationship was observed between the emission wavelength and the TPM value of frying oil within a range of 11% to 30%. Notably, the fluorescence color of the probe transitioned from blue to yellow under UV light at 365 nm as the TMP value increased. This study expands the range of sensing applications for CDs in food safety.
Biotransformation of ursane-type triterpenoid ilexgenin A by endophytic fungi Lasiodiplodia sp. MQD-4 and Pestalotiopsis sp. ZZ-1, isolated from Ilex pubescences and Callicarpa kwangtungensis respectively, was investigated for the first time. Six previously undescribed metabolites (1-6) with 23-norursane triterpenoids skeleton were isolated and their structures were unambiguously established by the analysis of spectroscopic data and single-crystal X-ray crystallographic experiments. Decarboxylation, oxidation, and hydroxylation reactions were observed on the triterpenoid skeleton. Especially, the decarboxylation of C-23 provided definite evidence to understand the biogenetic process of 23-norursane triterpenoids. Moreover, the qualitative analysis of the extract of I. pubescences showed metabolites 1, 3, 4, and 6 could be detected in the originated plant, indicating biotransformation by endophytic fungi is a practical strategy for the isolation of novel natural products. Finally, all isolates were evaluated for the protective activities against H2O2-induced HUVECs dysfunction in vitro. Compound 5 could improve the viability of endothelial cells and decrease the level of intracellular ROS.
Objective: To evaluate the long-term gastrointestinal (GI) symptoms and sleep quality sequelae in adolescents with COVID-19. Methods: Between June and July 2023, an online survey was done in Xiaoshan District, Hangzhou City, Zhejiang Province, China, using the GI Symptom Rating Scale (GSRS) and the Pittsburgh Sleep Quality Inventory (PSQI). Results: GI symptoms in COVID-19 patients increased by 11.86% compared to before infection, while sleep quality decreased by 10.9%. Over time, there was a significant increase in the cumulative incidence rate of GI symptoms and sleep disorders (p < 0.001). Follow-up of COVID-19 positive patients within 6 months of infection showed that GI symptoms and sleep quality began to ease starting from the first month after infection. Further analysis indicated a significant linear relationship between the severity of GI symptoms and sleep quality (R > 0.5, p < 0.001). Moreover, females, older age, and higher education were identified as risk factors influencing the long-term effects of COVID-19. Conclusion: SARS-CoV-2 affects GI symptoms and sleep quality in adolescents during both the acute phase and post-infection periods. Over time, these symptoms gradually alleviate. A significant correlation exists between GI symptoms and sleep quality.
COVID-19 , Gastrointestinal Diseases , Sleep Quality , Sleep Wake Disorders , Humans , COVID-19/epidemiology , COVID-19/complications , Adolescent , Female , Male , Gastrointestinal Diseases/epidemiology , Gastrointestinal Diseases/etiology , China/epidemiology , Retrospective Studies , Sleep Wake Disorders/epidemiology , SARS-CoV-2 , Surveys and Questionnaires , Risk Factors
Reaction of a P/N/S hybrid ligand dpppyatc (N,N-bis((diphenylphosphaneyl)methyl)-N-(pyridin-2-yl)-amino-thiocarbamide) with Au(tht)Cl (tht = tetrahydrothiophene) and [Cu(MeCN)4]BF4 afforded cluster complex [Au2Cu(dpppyatc)2](BF4)2Cl (1). Upon excitation at 480 nm, 1 emitted orange phosphorescence at 646 nm, which was red-shifted to ~698 nm selectively in the presence of ammonia or amine vapor. This chromic photoluminescent response toward ammonia was sensitive and reversible. Complex1 could detect ammonia in aqueous solution down to concentrations of 2 ppm (w/w).
Burns are a global public health problem, which brings great challenges to public health and the economy. Severe burns often lead to systemic infection, shock, multiple organ failure, and even death. With the increasing demand for the therapeutic effect of burn wounds, traditional dressings have been unable to meet people's needs due to their single function and many side effects. In this context, electrospinning shows a great prospect on the way to open up advanced wound dressings that promote wound repairing and prevent infection. With its large specific surface area, high porosity, and similar to natural extracellular matrix (ECM), electrospun nanofibers can load drugs and accelerate wound healing. It provides a promising solution for the treatment and management of burn wounds. This review article introduces the concept of burn and the types of electrospun nanofibers, then summarizes the polymers used in electrospun nanofiber dressings. Finally, the drugs (plant extracts, small molecule drugs and nanoparticles) loaded with electrospun burn dressings are summarized. Some promising aspects for developing commercial electrospun burn dressings are proposed.
Existing RNA in situ imaging strategies mostly utilize parallel repetitive nucleic acid self-assembly to achieve multiple analysis, with limitations of complicated systems and cumbersome steps. Here, a Cas9 code key system with key probe (KP) encoder and CRISPR/Cas9 signal exporter is developed. This system triggers T-protospacer adjacent motif (T-PAM structural transitions of multiple KP encoders to form coding products with uniform single-guide RNA (sgRNA) target sequences as tandem nodes. Only single sgRNA/Cas9 complex is required to cleave multiple coding products, enabling efficient "many-to-one" tandem signaling, and non-collateral cleavage activity-dependent automatic signaling output through active introduction of mismatched bases. Compared with conventional parallel multiple signaling analysis model, the proposed system greatly simplifies reaction process and enhances detection efficiency. Further, a rapid multiple RNA in situ imaging system is developed by combining the Cas9 code key system with a T-strand displacement amplification (T-SDA) signal amplifier. The constructed system is applied to tumor cells and clinicopathology slices, generating clear multi-mRNA imaging profiles in less than an hour with just one step. Therefore, this work provides reliable technical support for clinical tumor typing and molecular mechanism investigation.
BACKGROUND: Sarcopenia is characterized by loss of skeletal muscle mass and function, and is a major risk factor for disability and independence in the elderly. Effective medication is not available. Dietary restriction (DR) has been found to attenuate aging and aging-related diseases, including sarcopenia, but the mechanism of both DR and sarcopenia are incompletely understood. METHODS: In this study, mice body weight, fore and all limb grip strength, and motor learning and coordination performance were first analysed to evaluate the DR effects on muscle functioning. Liquid chromatography-mass spectrometry (LC-MS) was utilized for the metabolomics study of the DR effects on sarcopenia in progeroid DNA repair-deficient Ercc1∆/- and Xpg-/- mice, to identify potential biomarkers for attenuation of sarcopenia. RESULTS: Muscle mass was significantly (P < 0.05) decreased (13-20%) by DR; however, the muscle quality was improved with retained fore limbs and all limbs grip strength in Ercc1∆/- and Xpg-/- mice. The LC-MS results revealed that metabolites and pathways related to oxidative-stress, that is, GSSG/GSH (P < 0.01); inflammation, that is, 9-HODE, 11-HETE (P < 0.05), PGE2, PGD2, and TXB2 (P < 0.01); and muscle growth (PGF2α) (P < 0.01) and regeneration stimulation (PGE2) (P < 0.05) are significantly downregulated by DR. On the other hand, anti-inflammatory indicator and several related metabolites, that is, ß-hydroxybutyrate (P < 0.01), 14,15-DiHETE (P < 0.0001), 8,9-EET, 12,13-DiHODE, and PGF1 (P < 0.05); consumption of sources of energy (i.e., muscle and liver glycogen); and energy production pathways, that is, glycolysis (glucose, glucose-6-P, fructose-6-P) (P < 0.01), tricarboxylic acid cycle (succinyl-CoA, malate) (P < 0.001), and gluconeogenesis-related metabolite, alanine (P < 0.01), are significantly upregulated by DR. The notably (P < 0.01) down-modulated muscle growth (PGF2α) and regeneration (PGE2) stimulation metabolite and the increased consumption of glycogen in muscle and liver may be related to the significantly (P < 0.01) lower body weight and muscle mass by DR. The downregulated oxidative stress, pro-inflammatory mediators, and upregulated anti-inflammatory metabolites resulted in a lower energy expenditure, which contributed to enhanced muscle quality together with upregulated energy production pathways by DR. The improved muscle quality may explain why grip strength is maintained and motor coordination and learning performance are improved by DR in Ercc1∆/- and Xpg-/- mice. CONCLUSIONS: This study provides fundamental supporting information on biomarkers and pathways related to the attenuation of sarcopenia, which might facilitate its diagnosis, prevention, and clinical therapy.
Metabolomics , Sarcopenia , Animals , Mice , Sarcopenia/metabolism , Metabolomics/methods , Aging, Premature/metabolism , Metabolome , Mice, Knockout , Disease Models, Animal , DNA Repair , Male , Caloric Restriction/methods , Muscle, Skeletal/metabolism , DNA-Binding Proteins , Endonucleases
Double-layer quantum systems are promising platforms for realizing novel quantum phases. Here, we report a study of quantum oscillations (QOs) in a weakly coupled double-layer system composed of a large-angle twisted-double-bilayer graphene (TDBG). We quantify the interlayer coupling strength by measuring the interlayer capacitance from the QOs pattern at low temperatures, revealing electron-hole asymmetry. At high temperatures when SdHOs are thermally smeared, we observe resistance peaks when Landau levels (LLs) from two moiré minivalleys are aligned, regardless of carrier density; eventually, it results in a 2-fold increase of oscillating frequency in D, serving as compelling evidence of the magneto-intersub-band oscillations (MISOs) in double-layer systems. The temperature dependence of MISOs suggests that electron-electron interactions play a crucial role and the scattering times obtained from MISO thermal damping are correlated with the interlayer coupling strength. Our study reveals intriguing interplays among Landau quantization, moiré band structure, and scatterings.
Elastic stability is the basis for understanding structural responses to external stimuli in crystalline solids, including melting, incipient plasticity and fracture. In this work, elastic stability is investigated in a series of high-entropy alloys (HEAs) using in situ mechanical tests and atomic-resolution characterization in transmission electron microscopy. Under tensile loading, the HEA lattices are observed to undergo a sudden loss of ordering as the elastic strain reached â½ 10%. Such elastic strain-induced amorphization stands in intrinsic contrast to previously reported dislocation-mediated elastic instability and defect accumulation-mediated amorphization, introducing a form of elastic instability. Together with the first principle calculations and atomic-resolution chemical mapping, we identify that the elastic strain-induced amorphization is closely related to the depressed dislocation nucleation due to the local atomic environment inhomogeneity of HEAs. Our findings provide insights for the understanding of the fundamental nature of physical mechanical phenomena like elastic instability and incipient plasticity.
Paeoniflorin (PF), which is the main component of the Paeonia lactiflora Pall extract, is one of the traditional Chinese medicines. The pharmacological effects associated with PF include antioxidant, immunomodulatory, anti-inflammatory, anticancer, antidepressant-like and neuroprotective effects. Our previous studies had revealed that PF protected melanocytes and inhibited photodamage through the suppression of oxidative stress (OS). As OS plays a vital role in the progression of a variety of diseases, the capacity for PF to suppress OS may exert important effects upon them. However, no review exists on these antioxidant effects of PF as related to various diseases. Therefore, in this review we summarized studies involved with examining the antioxidant effects and molecular mechanisms of PF. Through its capacity to inhibit OS, PF has been shown to exert beneficial effects upon several systems including nervous, cardiac/vascular, digestive, and respiratory as well as specific diseases such as diabetes, autoimmune, pregnancy related, ocular, kidney, dermatology, along with suppression of distal flap necrosis, postoperative adhesions, and hearing loss. Such findings provide new insights and directions for future research directed at the development of PF as a natural antioxidant for the treatment of clinical diseases.
With the increasing trend of global aging, sarcopenia has become a significant public health issue. Goji berry, also known as "Gou qi zi" in China, is a traditional Chinese herb that can enhance the structure and function of muscles and bones. Otherwise, previous excellent publications illustrated that plant-derived exosome-like nanoparticles can exert good bioactive functions in different aging or disease models. Thus, we issued the hypothesis that Gouqi-derived nanovesicles (GqDNVs) may also have the ability to improve skeletal muscle health, though the effect and its mechanism need to be explored. Hence, we have extracted GqDNVs from fresh berries of Lycium barbarum L. (goji) and found that the contents of GqDNVs are rich in saccharides and lipids. Based on the pathway annotations and predictions in non-targeted metabolome analysis, GqDNVs are tightly associated with the pathways in metabolism. In muscle atrophy model mice, intramuscular injection of GqDNVs improves the cross-sectional area of the quadriceps muscle, grip strength and the AMPK/SIRT1/PGC1α pathway expression. After separately inhibiting AMPK or PGC1α in C2C12 cells with dexamethasone administration, we have found that the activated AMPK plays the chief role in improving cell proliferation induced by GqDNVs. Furthermore, the energy-targeted metabolome analysis in the quadriceps muscle demonstrates that the GqDNVs up-regulate the metabolism of amino sugar and nucleotide sugar, autophagy and oxidative phosphorylation process, which indicates the activation of muscle regeneration. Besides, the Spearman rank analysis shows close associations between the quality and function of skeletal muscle, metabolites and expression levels of AMPK and SIRT1. In this study, we provide a new founding that GqDNVs can improve the quality and function of skeletal muscle accompanying the activated AMPK/SIRT1/PGC1α signaling pathway. Therefore, GqDNVs have the effect of anti-aging skeletal muscle as a potential adjuvant or complementary method or idea in future therapy and research.
AMP-Activated Protein Kinases , Dexamethasone , Muscular Atrophy , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha , Signal Transduction , Sirtuin 1 , Animals , Sirtuin 1/metabolism , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Mice , Signal Transduction/drug effects , Dexamethasone/pharmacology , AMP-Activated Protein Kinases/metabolism , Muscular Atrophy/metabolism , Muscular Atrophy/drug therapy , Muscular Atrophy/chemically induced , Cell Line , Drugs, Chinese Herbal/pharmacology , Drugs, Chinese Herbal/chemistry , Male , Muscle, Skeletal/drug effects , Muscle, Skeletal/metabolism , Mice, Inbred C57BL , Nanoparticles/chemistry , Exosomes/metabolism , Exosomes/drug effects
A wealth of experimental evidence has suggested that open chromatin regions (OCRs) are involved in many critical biological activities, such as DNA replication, enhancer activity, and gene transcription. Accurately identifying OCRs in livestock species can provide critical insights into the distribution and characteristics of OCRs for disease treatment in livestock, thereby improving animal welfare. However, most current machine-learning methods for OCR prediction were originally designed for a limited number of model organisms, such as humans and some model organisms, and thus their performance on non-model organisms, specifically livestock, is often unsatisfactory. To bridge this gap, we propose DeepOCR, a lightweight depth-separable residual network model for predicting OCRs in livestock, including chicken, cattle, and sheep. DeepOCR integrates a single convolution layer and two improved residue structure blocks to extract and learn important features from the input DNA sequences. A fully connected layer was also employed to further process the extracted features and improve the robustness of the entire network. Our benchmarking experiments demonstrated superior prediction performance of DeepOCR compared to state-of-the-art approaches on testing datasets of the three species. The source code of DeepOCR is freely available for academic purposes at https://github.com/jasonzhao371/DeepOCR/. We anticipate DeepOCR servers as a practical and reliable computational tool for OCR-related studies in livestock species.
Chromatin , Deep Learning , Livestock , Animals , Livestock/genetics , Chromatin/genetics , Chromatin/chemistry , Chromatin/metabolism , Cattle , Sheep , Chickens
