Efficient COI barcoding using high throughput single-end 400 bp sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Efficient \u3ci\u3eCOI\u3c/i\u3e Barcoding Using High Throughput Single-End 400 bp Sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly, and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Dense RGB-D SLAM with Multiple Cameras

A multi-camera dense RGB-D SLAM (simultaneous localization and mapping) system has the potential both to speed up scene reconstruction and to improve localization accuracy, thanks to multiple mounted sensors and an enlarged effective field of view. To effectively tap the potential of the system, two issues must be understood: first, how to calibrate the system where sensors usually shares small or no common field of view to maximally increase the effective field of view; second, how to fuse the location information from different sensors. In this work, a three-Kinect system is reported. For system calibration, two kinds of calibration methods are proposed, one is suitable for system with inertial measurement unit (IMU) using an improved hand–eye calibration method, the other for pure visual SLAM without any other auxiliary sensors. In the RGB-D SLAM stage, we extend and improve a state-of-art single RGB-D SLAM method to multi-camera system. We track the multiple cameras’ poses independently and select the one with the pose minimal-error as the reference pose at each moment to correct other cameras’ poses. To optimize the initial estimated pose, we improve the deformation graph by adding an attribute of device number to distinguish surfels built by different cameras and do deformations according to the device number. We verify the accuracy of our extrinsic calibration methods in the experiment section and show the satisfactory reconstructed models by our multi-camera dense RGB-D SLAM. The RMSE (root-mean-square error) of the lengths measured in our reconstructed mode is 1.55 cm (similar to the state-of-art single camera RGB-D SLAM systems)

Evaluation and associated factors of public health emergency management among medical college students in a city in Southwest China: a cross-sectional study

Abstract Background Colleges and universities face an increased risk of public health emergencies. Among them, medical colleges and universities deserve more attention as they serve as the play a fundamental role in providing public health emergency services and in cultivating medical professionals. Effectively managing infectious disease prevention and control, as well as responding to public health emergencies in medical colleges and universities, is of great importance for enhancing the capacity of social emergency governance and improving the completeness of the public health system. This study aims to understand the management of public health emergencies in medical colleges in a city in southwest China, explore the factors associated with medical college students’ evaluations, and provide recommendations for emergency management mechanisms in colleges and universities. Methods In total, 781 medical college students were selected through stratified random sampling and surveyed using a questionnaire. The main factors affecting students’ evaluation of emergency management were analyzed using multiple linear regression and structural equation modeling. Results The overall emergency management situation in medical colleges was relatively complete, with satisfactory results. Medical college students’ satisfaction with the timeliness of prevention measures was the highest, while the publicity and education were the lowest. Multiple linear regression analysis showed that grades, emergency education, -simulation training, -information reporting, and dynamic adjustment measures were associated with the evaluation of emergency management by medical students. Conclusions Although the evaluation of emergency management in medical colleges was generally positive, certain limitations still existed. To improve the development of the public health system, colleges and universities should constantly reform and innovate emergency management mechanisms according to the important links in the prevention and control processes

A Color Image Encryption Algorithm Based on Hash Table, Hilbert Curve and Hyper-Chaotic Synchronization

Chaotic systems, especially hyper-chaotic systems are suitable for digital image encryption because of their complex properties such as pseudo randomness and extreme sensitivity. This paper proposes a new color image encryption algorithm based on a hyper-chaotic system constructed by a tri-valued memristor. The encryption process is based on the structure of permutation-diffusion, and the transmission of key information is realized through hyper-chaotic synchronization technology. In this design, the hash value of the plaintext image is used to generate the initial key the permutation sequence with the Hash table structure based on the hyper-chaotic sequence is used to implement pixel-level and bit-level permutation operations. Hilbert curves combining with the ciphertext feedback mechanism are applied to complete the diffusion operation. A series of experimental analyses have been applied to measure the novel algorithm, and the results show that the scheme has excellent encryption performance and can resist a variety of attacks. This method can be applied in secure image communication fields