DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock.

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.

[The cup safe-zone and optimum combination of the acetabular and femoral anteversions that fulfills the desired range of motion of the hip].

OBJECTIVE: To investigate safe range of acetabular prosthesis angle and the optimum combination of cup and neck in the range of activities of daily living (ADL). METHODS: A three-dimensional generic parametric and kinematic simulation module of THA was developed. Range of motion (ROM) of flexion > or = 110 degrees, internal-rotation > or = 30 degrees at 90 degrees flexion, extension > or = 30 degrees and external rotation > or = 40 degrees were defined as the normal criteria for desired ROM for activities of daily living (ADL), and ROM of flexion > or = 120 degrees, internal-rotation > or = 45 degrees at 90 degrees flexion, extension > or = 30 degrees and external rotation > or = 40 degrees as the severe criteria. The range of the changes in the general head-neck ratios (GR), the femoral neck anteversion (FA), the operative anteversion (OA) and operative inclination (OI) of the cup component were 2-2.92, 0 degrees-30 degrees, 0 degrees-70 degrees, 10 degrees-60 degrees respectively. For the collodiaphyseal angle (CCD) of 135 degrees, the corresponding OA related to the OI which every 5 degrees was calculated, and described using dots and lines in a coordinate system in which OI of acetabular cup was the horizontal ordinate and OA of acetabular cup was the vertical ordinate. All data was analyzed by SAS 6.12 software. RESULTS: Large GR greatly increased the size of safe range and it was recommended that GR be more than 2.37 when the CCD-angle was 135 degrees as it further increases the size of safezone. The size of cup safety range of the severe criteria was smaller than normal criteria. When the CCD-angle was 135 degrees, the optimum relationship between OA of acetabular and FA of the normal criteria and the severe criteria can be estimated by the formula: Y1=-0.816X1 + 39.76 (R2=0.993), Y2=-0.873X2 + 47.04 (R2=0.999) respectively. CONCLUSION: Large GR greatly increases the size of safe-zone and it is recommended that GR be more than 2.37, so it extends the acceptable range of error that clinicians cannot avoid it completely. The larger range of the hip motion, the smaller size of the cup safe-zone,but can retrieve by increase the GR. The OA is negative with FA.

In vivo anthelmintic activity of five alkaloids from Macleaya microcarpa (Maxim) Fedde against Dactylogyrus intermedius in Carassius auratus.

The present study aims to evaluate the anthelmintic properties of aerial part of Macleaya microcarpa (Maxim) Fedde. Bioassay-guided fractionation and isolation of the compounds with anthelmintic activity were performed on the ethanolic extract of M. microcarpa yielding five bioactive alkaloids namely: sanguinarine, cryptopine, beta-allocryptopine, protopine and 6-methoxyl-dihydro-chelerythrine by comparing spectral data (UV, NMR, and EI-MS) with literature values. According to in vivo anthelmintic assays, they were found to be 100% effective at the concentrations of 0.7, 8.0, 8.0, 16.0 and 7.0 mgl(-1), and the median effective concentration (EC(50)) values for the five compounds were 0.37, 3.31, 4.64, 8.13 and 3.63 mgl(-1), respectively. Additionally, the acute toxicity on goldfish for the five active compounds was also investigated with median lethal concentrations (LC(50)) values of 1.13, 16.12, 15.88, 21.69 and 10.91 mgl(-1), respectively. The resulting therapeutic indices for sanguinarine, cryptopine, beta-allocryptopine, protopine and 6-methoxyl-dihydro-chelerythrine were 3.03, 4.82, 3.40, 2.66 and 2.99 correspondingly. Correlations analysis between the logP and EC(50), LC(50) of the five alkaloids revealed that the activity of the five alkaloids was well correlated with their hydrophobicity and r(2)=0.45 is for anthelmintic activity while r(2)=0.47 is for acute toxicity for goldfish, respectively. These results provided evidence that the studied plant extract, as well as the isolated compounds, especially sanguinarine, might be potential plant-based medicines for the treatment of D. intermedius infection.