ARTICLE | doi:10.20944/preprints201807.0487.v1
Subject: Materials Science, General Materials Science Keywords: diffraction contrast tomography; Al-La dendrite; lamellar eutectic; lifted multicut
Online: 25 July 2018 (13:31:53 CEST)
It is important for researchers in material domain to reconstruct and visualize the microstructure of alloy, which helps discover morphologies and properties that can only be found in three dimensional and microscopic space. However, because of the limitation of state-of-the-art sensors, the internal microstructure of the material is not easy to obtain. In this paper, a novel automatic 3D reconstruction method is proposed using diffraction contrast tomography technology to capture the 3D microstructure of Al-La alloy. The pipeline of the proposed method starts from the imaging of Al-La alloy with the LabDCT technique from Carl Zeiss AG, which produces a sequence of 2D microstructure sections. Then, a segmentation algorithm based on superpixel and lifted multicut is proposed to extract the 2D microstructure in an image section. Finally, 2D segmentations are joined together to reconstruct and visulize the 3D microstructure. As a result, a novel morphology of Al-La alloy is recovered with both dendrite and lamellar morphologies. The proposed method has the advantage of the ability to losslessly recover the internal microstructure.
ARTICLE | doi:10.20944/preprints202010.0444.v1
Subject: Engineering, Automotive Engineering Keywords: staggered SAR; low oversampling; compressed sensing (CS); NUFFT
Online: 21 October 2020 (16:41:58 CEST)
This paper focuses on processing low oversampling echo data of staggered synthetic aperture radar (SAR). In staggered mode, the non-uniformly sampling and irregular loss of echo data cause azimuth ambiguity which severely degrades the imaging quality. To solve this problem, we propose a compressed sensing (CS) method in which the non-uniform fast Fourier transform (NUFFT) technique is adopted to obtain uniform azimuth spectrum, and the fast iterative shrinkage thresholding algorithm (FISTA) is utilized to efficiently reconstruct the ambiguity-free image from in-complete echo data. Simulation results demonstrate the proposed method can effectively suppress the azimuth ambiguity in the vicinity of targets.
REVIEW | doi:10.20944/preprints202003.0271.v2
Subject: Medicine & Pharmacology, Ophthalmology Keywords: Coronavirus; 2019-nCOV; SARS-CoV-2; transmission; infection; conjunctiva; eye
Online: 24 March 2020 (06:42:35 CET)
The outbreak of recently identified 2019 novel coronavirus (2019-nCOV) infection has become a world-wide health threat. Currently, more information is needed for further understanding the transmission, clinical characteristics, and infection control procedures of 2019-nCOV. Recently, the role of the eye in transmitting 2019-nCOV has been intensively discussed. Previous investigations about other high infectious human COVs, that is, severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV), may provide helpful information. In this review, we describe the genomics and morphology of human CoVs, the epidemiology, systemic and ophthalmic manifestations, mechanisms of human CoVs infection, and infection control procedures. The role of the eye in the transmission of SARS-CoV and 2019-nCOV is discussed. Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of ocular surface and upper respiratory tract is connected by nasolacrimal duct and share same entry receptors for some respiratory viruses. The eye is rarely involved in human CoVs infection, conjunctivitis is quite rare in patients with SARS-CoV and 2019-nCoV infection, and COV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with SARS-CoV and 2019-nCoV infection is also very low, which imply that the eye is neither a preferred organ of human COVs infection, nor is a preferred gateway of entry for human COVs to infect respiratory tract. However, pathogens exposed to the ocular surface might be transported to nasal and nasopharyngeal mucosa by constant tear rinsing through lacrimal duct, and then cause respiratory tract infection. Considering close doctor-patient contact is quite common in ophthalmic practice which are apt to transmit human COVs by droplets and fomites, hand hygiene and personal protection are still highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice.
ARTICLE | doi:10.20944/preprints202208.0341.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: Schizophrenia; cell types proportions; differential expression genes; functional pathways; CIBERSORTx
Online: 18 August 2022 (10:54:05 CEST)
Schizophrenia (SCZ) is a severe mental disorder that may result in hallucinations, delusions, and extremely disordered thinking. How each cell type in the brain contributes to SCZ occurrence is still unclear. Here, we leveraged the human dorsolateral prefrontal cortex bulk RNA-seq data, then used the RNA-seq deconvolution algorithm CIBERSORTx to generate SCZ brain single-cell RNA-seq data for a comprehensive analysis to understand SCZ-associated brain cell types and gene expression changes. Firstly, we observed that the proportions of brain cell types in SCZ differed from normal samples. Among these cell types, astrocyte, pericyte, and PAX6 cells were found to have a higher proportion in SCZ patients (astrocyte: SCZ = 0.163, Control = 0.145, P.adj = 4.9×10-4; pericyte: SCZ = 0.057, Control = 0.066, P.adj = 1.1×10-4; PAX6 : SCZ = 0.014, Control = 0.011, P.adj = 0.014), while the L5/6_IT_CAR3 cells and LAMP5 cells are the exact opposite (L5/6_IT_Car3 : SCZ = 0.102, Control = 0.108, P.adj = 0.016; LAMP5 : SCZ = 0.057, Control = 0.066, P.adj = 2.2×10-6). Next, we investigated gene expression in cell types and functional pathways in SCZ. We observed chemical synaptic transmission dysregulation in two types of GABAergic neurons (PVALB and LAMP5), and immune reaction involvement in GABAergic neurons (SST) and non-neuronal cell types (endothelial and oligodendrocyte). Furthermore, we observed that some differential expression genes from bulk RNA-seq displayed cell-type-specific abnormal in the expression of molecules in SCZ. Finally, the cell types with the SCZ-related transcriptomic changes could be considered to belong to the same module since we observed two major similar coordinated transcriptomic changes across these cell types. Together, our results offer novel insights into cellular heterogeneity and the molecular mechanisms underlying SCZ.
ARTICLE | doi:10.20944/preprints202208.0355.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: developmental delay; de novo mutation; protein-protein interaction; PPI interface; protein in-teractome; PsymuKB
Online: 19 August 2022 (04:50:42 CEST)
Mutations, especially those at the protein-protein interaction (PPI) interface, have been associated with various diseases. Meanwhile, though de novo mutations (DNMs) have been proven important in neuropsychiatric disorders, such as developmental delay (DD), the relationship between PPI interface DMNs and DD has not been well studied. Here we curated developmental delay DNM datasets from the PsyMuKB database and showed that DD patients showed a higher rate and deleteriousness in DNM missense on the PPI interface than sibling control. Next, we identified 302 DD-related PsychiPPIs, defined as PPI harboring a statistically significant number of DNM missenses at their interface, and 42 DD candidate genes from PsychiPPI. We then observed that PsychiPPIs preferentially affected hub proteins in the human protein interactome network. When analyzing DD candidate genes using gene ontology and gene spatio-expression, we found that PsychiPPI genes carrying PPI interface mutations, such as FGFR3 and ALOX5, were enriched in development-related pathways and the development of the neocortex, and cerebellar cortex, suggesting their potential involvement in the etiology of DD. Our results demonstrated that DD patients carried an excess burden of PPI-truncating DNM, which could be used to efficiently search for disease-related genes and mutations in large-scale sequencing studies. In conclusion, our comprehensive study indicated the significant role of PPI interface DNMs in developmental delay pathogenicity.