ARTICLE | doi:10.20944/preprints201808.0112.v2
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: remote sensing; image classification; fully connected conditional random fields (FC-CRF); convolutional neural networks (CNN)
Online: 28 November 2018 (07:11:42 CET)
The interpretation of land use and land cover (LULC) is an important issue in the fields of high-resolution remote sensing (RS) image processing and land resource management. Fully training a new or existing convolutional neural network (CNN) architecture for LULC classification requires a large amount of remote sensing images. Thus, fine-tuning a pre-trained CNN for LULC detection is required. To improve the classification accuracy for high resolution remote sensing images, it is necessary to use another feature descriptor and to adopt a classifier for post-processing. A fully connected conditional random fields (FC-CRF), to use the fine-tuned CNN layers, spectral features, and fully connected pairwise potentials, is proposed for image classification of high-resolution remote sensing images. First, an existing CNN model is adopted, and the parameters of CNN are fine-tuned by training datasets. Then, the probabilities of image pixels belong to each class type are calculated. Second, we consider the spectral features and digital surface model (DSM) and combined with a support vector machine (SVM) classifier, the probabilities belong to each LULC class type are determined. Combined with the probabilities achieved by the fine-tuned CNN, new feature descriptors are built. Finally, FC-CRF are introduced to produce the classification results, whereas the unary potentials are achieved by the new feature descriptors and SVM classifier, and the pairwise potentials are achieved by the three-band RS imagery and DSM. Experimental results show that the proposed classification scheme achieves good performance when the total accuracy is about 85%.
ARTICLE | doi:10.20944/preprints202104.0180.v1
Subject: Physical Sciences, Optics And Photonics Keywords: MEMS Mirror Arrays; Laser beam; Fraunhofer Diffraction; Optical Intensity
Online: 6 April 2021 (13:47:01 CEST)
Compared with liquid crystal clad waveguide, MEMS mirror has some merits, such as high-er-transmissivity, lager-angle of scanning, faster scanning speed and so on. Furthermore, MEMS mirror arrays perform more superior than MEMS mirror when they steer laser beam, which make MEMS arrays much more suitable to be used in devising compact Lidar. Before assembling a Lidar with MEMS arrays, the optical intensity and distributions of the laser diffracted by MEMS arrays should be analyzed, but few published papers about this issue are available so far, this paper will focus on this issue about MEMS arrays. Firstly, the complex amplitudes of laser which is diffracted by 1-D and 2-D arrays are presented, respectively. Then the optical intensity and distributions on the observation plane are presented. Finally, the simulation diagrams of these distributions are shown, and the correctness of the results is indirectly verified by Young’s dou-ble-slit experiment. The results gotten in this letter are essential to design a compacted Lidar based on MEMS arrays.
ARTICLE | doi:10.20944/preprints202304.0445.v1
Subject: Engineering, Marine Engineering Keywords: underwater wireless optical communication; LED; blue-green light communication
Online: 17 April 2023 (10:31:41 CEST)
Underwater wireless optical communication (UWOC) is acknowledged as a useful way to transmit data in ocean for short distance application. Carrying UWOC device on mobile platform is quite practical in ocean engineering, which is helpful to exploit its advantages. In application, such platform needs camera to observe surroundings and guide its action. Since the majority of ocean is always dark, active illumination is necessary to imaging. Once UWOC worked in such environment, its performance is affected by the illumination light noise. In this paper, we study the influence of underwater LED illumination on bidirectional UWOC with Monte Carlo method. We simulate forward noise from the LED illumination to the opposite receiver in the cooperative terminal, and the backscattering noise on the adjacent receiver in the same terminal. The results show that the forward noise is reduced with the increase of absorption coefficient, scattering coefficient, transmitting distance, and separated distance between receiver and the optical axis of LED. But it becomes greater with FOV of receiver. The backscattering noise is reduced with the increase of absorption coefficient and separated distance between receiver and LED. But it becomes greater with FOV and scattering coefficient, while it has little relation with transmitting distance. In order to reduce such two kind noises, besides inserting optical filter in the receivers and narrow their field, the optical axis of LED light should keep away from the receivers. The results in this paper is helpful for UWOC application.
ARTICLE | doi:10.20944/preprints202309.0998.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: burned areas; restoration; two-way indicator species analysis (TWINSPAN); detrended correspondence analysis (DCA); detrended canonical correspondence analysis (DCCA)
Online: 15 September 2023 (03:58:41 CEST)
Fire is a common natural disturbance in forest ecosystems and plays an important role in subsequent vegetation patterns. Based on the spatial sequence method instead of the time successional sequence method, this study selected burned areas in different locations in the Anning River Basin, which contains typical dry valleys. Quadrat surveys and quantitative classification were used to identify the vegetation classification, distribution pattern, and environmental interpretation during the natural restoration process after forest fire. The results showed that: (1) the vegetation community in the early stage of natural recovery after forest fire disturbance could be divided into seven community types, and Quercus guyavaefolia H. Leveille (Qg) was the dominant species in the community; (2) vegetation samples could be divided into five ecological types, and the classification and distribution pattern of community types in this region changed most obviously with altitude; and (3) detrended correspondence analysis could clearly classify vegetation community types, and detrended canonical correspondence analysis could well reveal the relationships between species and environmental factors. This study provides a scientific basis guiding the restoration of ecosystem structural stability and biodiversity in burned areas.
ARTICLE | doi:10.20944/preprints202308.1667.v1
Subject: Biology And Life Sciences, Toxicology Keywords: Inosine 5’-monophosphate (IMP); AMPK; Acetyl-CoA; ACC; Lipohyperplasia
Online: 24 August 2023 (04:12:23 CEST)
Inosine 5'-monophoaphate (IMP) allows animals to sense umami. Intake of IMP in C57/KsJ-db/db (db/db) mice induced lipohyperplasia causing the liver cirrhosis, however, how to that of in normal mammals injure health is still unclear. Thus, we had investigated that intake of IMP in C57BL/6J mice effected its metabolic functions. We found that intake of 255 M/d IMP in C57BL/6J mice for 4 months induced hyperlipidemia and body fat rate raised. In mechanism, the expressions of ACC1 and phosphorylated ACC2 in hepatocytes were increased though IMP promoting phosphorylation of AMPK. The increased ACC1 promoted the conversion of acetyl-CoA into TG. These TG were transported out of hepatocytes to avoid NAFLD, causing a deficiency of acetyl-CoA in liver, and then the increased phosphorylated ACC2 promoted cytoplasm fatty acids into mitochondria to convert into acetyl-CoA though the fatty acids β-oxidation pathway, causing a deficiency of fatty acids. Therefore, liver enhanced the absorption of exogenous fatty acids, which were converted into TG caused lipohyperplasia. Moreover, intake of IMP in normal mice induced complement system weaken in liver causing mild inflammation. Our data not only alerted that humans avoid excessive intake of IMP, but also provided novel insights into the adipose of metabolic dysfunctions.
ARTICLE | doi:10.20944/preprints202310.0518.v1
Subject: Physical Sciences, Radiation And Radiography Keywords: Compton camera; wide-energy range; Monte Carlo simulation; scintillation detector; image reconstruction
Online: 9 October 2023 (11:08:24 CEST)
(1) Background: The imaging energy range of a typical Compton camera is limited due to the fact that scattered gamma photons are seldom fully absorbed when the incident energies are above 3 MeV. Further improving the upper energy limit of gamma-ray imaging has important application significance in active interrogation of special nuclear materials and chemical warfare agents, as well as range verification of proton therapy; (2) Methods: To realize gamma-ray imag-ing in a wide energy range of 0.3~7 MeV, a principle prototype, named a portable three-layer Compton camera, was developed using the scintillation detector that consist of an silicon photo-multiplier array coupled with a Gd3Al2Ga3O12:Ce pixelated scintillator array. Implemented in a list-mode maximum likelihood expectation maximization algorithm, a far-field energy-domain imaging method based on two-interaction and three-interaction events was applied to estimate the initial energy and spatial distribution of gamma-ray sources. The simulation model of detec-tors was established based on Monte Carlo simulation toolkit Geant4. The reconstructed images of a 133Ba, a 137Cs and a 60Co point-like sources were successfully obtained with our prototype in laboratory tests and compared with simulation studies; (3) Results: The proportion of effective imaging events accounted for about 2%, which made our prototype realize reconstructing the distribution of a 0.05 μSv/h 137Cs source in 10 seconds. The angular resolution for resolving two 137Cs point-like sources was 15°. Additional simulated imaging of the 6.13 MeV gamma-rays from 14.1 MeV neutron scattering with water preliminarily demonstrated the imaging capability for high incident energy; (4) Conclusions: We concluded that the prototype had good imaging per-formance in a wide energy range (0.3~7 MeV), which showed potential in several MeV gam-ma-ray imaging applications.
ARTICLE | doi:10.20944/preprints201910.0146.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: NGS data analysis; bioinformatics pipelines; NGS pipelines
Online: 8 April 2020 (06:21:10 CEST)
Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in fastq format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal
ARTICLE | doi:10.20944/preprints202006.0089.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Wuhua yellow chicken; whole genome resequencing; heritable variation; selection signal
Online: 7 June 2020 (14:42:23 CEST)
Chickens have extensive phenotypic variation. The Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken in China, characterized by white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of traits associated with WHYC is still poorly understood. In this study, whole genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 SNPs and 1,069,574 InDels were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. A comparative genomic analysis of WHYC and other yellow-feathered chicken showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interaction. Several genes associated with disease resistance were identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, PMEL and TYRP1 may contribute to the coloring of white feathers in WHYC. These findings improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: patient; COVID-19; asymptomatic contact
Online: 9 March 2020 (10:34:58 CET)
An outbreak caused by coronavirus disease 2019 (COVID-19) occurred in Wuhan City, Hubei Province, China, in December 2019. Up to March 2, 2020, at least 80180 cases have been reported. Most of the patients had a history of visiting Hubei Province or contacting with people who had ever stayed in or passed by Hubei Province, or exposed to symptoms. Some patients got infected only from asymptomatic contacts. This study aimed to report the epidemic features and lab identification of a patient confirmed with COVID-19 infection only from asymptomatic contact.