BuildMapper: A Fully Learnable Framework for Vectorized Building Contour Extraction

Deep learning based methods have significantly boosted the study of automatic building extraction from remote sensing images. However, delineating vectorized and regular building contours like a human does remains very challenging, due to the difficulty of the methodology, the diversity of building structures, and the imperfect imaging conditions. In this paper, we propose the first end-to-end learnable building contour extraction framework, named BuildMapper, which can directly and efficiently delineate building polygons just as a human does. BuildMapper consists of two main components: 1) a contour initialization module that generates initial building contours; and 2) a contour evolution module that performs both contour vertex deformation and reduction, which removes the need for complex empirical post-processing used in existing methods. In both components, we provide new ideas, including a learnable contour initialization method to replace the empirical methods, dynamic predicted and ground truth vertex pairing for the static vertex correspondence problem, and a lightweight encoder for vertex information extraction and aggregation, which benefit a general contour-based method; and a well-designed vertex classification head for building corner vertices detection, which casts light on direct structured building contour extraction. We also built a suitable large-scale building dataset, the WHU-Mix (vector) building dataset, to benefit the study of contour-based building extraction methods. The extensive experiments conducted on the WHU-Mix (vector) dataset, the WHU dataset, and the CrowdAI dataset verified that BuildMapper can achieve a state-of-the-art performance, with a higher mask average precision (AP) and boundary AP than both segmentation-based and contour-based methods

Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish

The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.</p

DVIS: Decoupled Video Instance Segmentation Framework

Video instance segmentation (VIS) is a critical task with diverse applications, including autonomous driving and video editing. Existing methods often underperform on complex and long videos in real world, primarily due to two factors. Firstly, offline methods are limited by the tightly-coupled modeling paradigm, which treats all frames equally and disregards the interdependencies between adjacent frames. Consequently, this leads to the introduction of excessive noise during long-term temporal alignment. Secondly, online methods suffer from inadequate utilization of temporal information. To tackle these challenges, we propose a decoupling strategy for VIS by dividing it into three independent sub-tasks: segmentation, tracking, and refinement. The efficacy of the decoupling strategy relies on two crucial elements: 1) attaining precise long-term alignment outcomes via frame-by-frame association during tracking, and 2) the effective utilization of temporal information predicated on the aforementioned accurate alignment outcomes during refinement. We introduce a novel referring tracker and temporal refiner to construct the \textbf{D}ecoupled \textbf{VIS} framework (\textbf{DVIS}). DVIS achieves new SOTA performance in both VIS and VPS, surpassing the current SOTA methods by 7.3 AP and 9.6 VPQ on the OVIS and VIPSeg datasets, which are the most challenging and realistic benchmarks. Moreover, thanks to the decoupling strategy, the referring tracker and temporal refiner are super light-weight (only 1.69\% of the segmenter FLOPs), allowing for efficient training and inference on a single GPU with 11G memory. The code is available at \href{https://github.com/zhang-tao-whu/DVIS}{https://github.com/zhang-tao-whu/DVIS}

Chapter 10: Mining Genome-Wide Genetic Markers

Genome-wide association study (GWAS) aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1) An introduction to the background of GWAS. (2) The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3) The limitations of current approaches and future directions

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data

Antenna-Coupled Vacuum Channel Nano-Diode with High Quantum Efficiency

Vacuum channel diodes have the potential to serve as a platform for converting free-space electromagnetic radiation into electronic signals within ultrafast timescales. However, the conversion efficiency is typically very low because conventional vacuum channel diode structures suffer from high surface barriers, especially when using lower energy photon excitation (near-infrared photons or lower). Here, we report on an optical antenna-coupled vacuum channel nano-diode, which demonstartes a greatly improved quantum efficiency up to 4% at 800 nm excitation; an efficiency several orders of magnitude higher than any previously reported value. The nano diodes are formed at the cleaved edge of a metal-insulator-semiconductor (MIS) structure, where a gold thin film with nanohole array serves as both the metal electrode and light-harvesting antenna. At the nanoholes-insulator interface, the tunneling barrier is greatly reduced due to the Coulombic repulsion induced high local electron density, such that the resonant plasmon- induced hot electron population can readily inject into the vacuum channel. The presented vertical tertiary MIS junction enables a new class of high-efficiency, polarization-specific and wavelength- sensitive optical modulated photodetector that has the potential for developing a new generation of opto-electronic systems

Chiral Surface Plasmon Polaritons on Metallic Nanowires

Chiral surface plasmon polaritons (SPPs) can be generated by linearly polarized light incident at the end of a nanowire, exciting a coherent superposition of three specific nanowire waveguide modes. Images of chiral SPPs on individual nanowires obtained from quantum dot fluorescence excited by the SPP evanescent field reveal the chirality predicted in our theoretical model. The handedness and spatial extent of the helical periods of the chiral SPPs depend on the input polarization angle and nanowire diameter as well as the dielectric environment. Chirality is preserved in the free-space output wave, making a metallic nanowire a broad bandwidth subwavelength source of circular polarized photons.Comment: 4 figure

An inventory of invasive alien species in China

Invasive alien species (IAS) are a major global challenge requiring urgent action, and the Strategic Plan for Biodiversity (2011–2020) of the Convention on Biological Diversity (CBD) includes a target on the issue. Meeting the target requires an understanding of invasion patterns. However, national or regional analyses of invasions are limited to developed countries. We identified 488 IAS in China’s terrestrial habitats, inland waters and marine ecosystems based on available literature and field work, including 171 animals, 265 plants, 26 fungi, 3 protists, 11 procaryots, and 12 viruses. Terrestrial plants account for 51.6% of the total number of IAS, and terrestrial invertebrates (104 species) for 21.3%. Of the total numbers, 67.9% of plant IAS and 34.8% of animal IAS were introduced intentionally. All other taxa were introduced unintentionally despite very few animal and plant species that invaded naturally. In terms of habitats, 64.3% of IAS occur on farmlands, 13.9% in forests, 8.4% in marine ecosystems, 7.3% in inland waters, and 6.1% in residential areas. Half of all IAS (51.1%) originate from North and South America, 18.3% from Europe, 17.3% from Asia not including China, 7.2% from Africa, 1.8% from Oceania, and the origin of the remaining 4.3% IAS is unknown. The distribution of IAS can be divided into three zones. Most IAS are distributed in coastal provinces and the Yunnan province; provinces in Middle China have fewer IAS, and most provinces in West China have the least number of IAS. Sites where IAS were first detected are mainly distributed in the coastal region, the Yunnan Province and the Xinjiang Uyghur Autonomous Region. The number of newly emerged IAS has been increasing since 1850. The cumulative number of firstly detected IAS grew exponentially

Relationship between Length and Surface-Enhanced Raman Spectroscopy Signal Strength in Metal Nanoparticle Chains: Ideal Models versus Nanofabrication

We have employed capillary force deposition on ion beam patterned substrates to fabricate chains of 60 nm gold nanospheres ranging in length from 1 to 9 nanoparticles. Measurements of the surface-averaged SERS enhancement factor strength for these chains were then compared to the numerical predictions. The SERS enhancement conformed to theoretical predictions in the case of only a few chains, with the vast majority of chains tested not matching such behavior. Although all of the nanoparticle chains appear identical under electron microscope observation, the extreme sensitivity of the SERS enhancement to nanoscale morphology renders current nanofabrication methods insufficient for consistent production of coupled nanoparticle chains. Notwithstanding this fact, the aggregate data also confirmed that nanoparticle dimers offer a large improvement over the monomer enhancement while conclusively showing that, within the limitations imposed by current state-of-the-art nanofabrication techniques, chains comprising more than two nanoparticles provide only a marginal signal boost over the already considerable dimer enhancement