The central dogma of gene expression considers RNA as the carrier of genetic information from DNA to protein. However, it has become more and more clear that RNA plays more important roles than ...simply being the information carrier. Recently, whole genome transcriptomic analyses have identified large numbers of dynamically expressed long noncoding RNAs (lncRNAs), many of which are involved in a variety of biological functions. Even so, the functions and molecular mechanisms of most lncRNAs still remain elusive. Therefore, it is necessary to develop computational methods to predict the function of lncRNAs in order to accelerate the study of lncRNAs. Here, we review the recent progress in the identification of lncRNAs, the molecular functions and mechanisms of lncRNAs, and the computational methods for predicting the function of lncRNAs.
•GoFDR predicts GO functions using sequence alignment prepared from PSI-BLAST.•GoFDR identifies the Functional Discriminating Residues for each target GO.•GoFDR applies score-probability table to ...convert raw scores to probabilities.•GoFDR ranked one of the best methods in CAFA2 experiment.
In this study, we developed a method named GoFDR for predicting Gene Ontology (GO)-based protein functions. The input for GoFDR is simply a query sequence-based multiple sequence alignment (MSA) produced by PSI-BLAST. For each GO term annotated to the sequences in the MSA, GoFDR identifies a number of functionally discriminating residues (FDRs) specific to the GO term, and scores the query sequence using a position specific scoring matrix (PSSM) constructed for the FDRs. The raw score is then converted into a probability score according to a score-to-probability table prepared from training sequences. GoFDR outperformed three sequence-based methods for predicting GO functions in a benchmark of 18,520 sequences. In addition, GoFDR was ranked one of the top methods according to the preliminary evaluation report released by the 2nd Critical Assessment of Function Annotation (CAFA2) project. Finally, we applied GoFDR to the complete human proteome sequences, and showed that the predictions made by GoFDR with high confidence significantly expanded current annotations of human proteome. As such, GoFDR is of great value not only for annotating protein functions in newly sequenced genomes, but also for characterizing the function of proteins of interest.
Regional Style and Color Transfer Ding, Zhicheng; Li, Panfeng; Yang, Qikai ...
arXiv (Cornell University),
06/2024
Paper, Journal Article
Odprti dostop
This paper presents a novel contribution to the field of regional style transfer. Existing methods often suffer from the drawback of applying style homogeneously across the entire image, leading to ...stylistic inconsistencies or foreground object twisted when applied to image with foreground elements such as person figures. To address this limitation, we propose a new approach that leverages a segmentation network to precisely isolate foreground objects within the input image. Subsequently, style transfer is applied exclusively to the background region. The isolated foreground objects are then carefully reintegrated into the style-transferred background. To enhance the visual coherence between foreground and background, a color transfer step is employed on the foreground elements prior to their rein-corporation. Finally, we utilize feathering techniques to achieve a seamless amalgamation of foreground and background, resulting in a visually unified and aesthetically pleasing final composition. Extensive evaluations demonstrate that our proposed approach yields significantly more natural stylistic transformations compared to conventional methods.
Regional Style and Color Transfer Ding, Zhicheng; Li, Panfeng; Yang, Qikai ...
2024 5th International Conference on Computer Vision, Image and Deep Learning (CVIDL),
2024-April-19
Conference Proceeding
Odprti dostop
This paper presents a novel contribution to the field of regional style transfer. Existing methods often suffer from the drawback of applying style homogeneously across the entire image, leading to ...stylistic inconsistencies or foreground object twisted when applied to images with foreground elements such as person figures. To address this limitation, we propose a new approach that leverages a segmentation network to precisely isolate foreground objects within the input image. Subsequently, style transfer is applied exclusively to the background region. The isolated foreground objects are then carefully reintegrated into the style-transferred background. To enhance the visual coherence between foreground and background, a color transfer step is employed on the foreground elements prior to their reincorporation. Finally, we utilize feathering techniques to achieve a seamless amalgamation of foreground and background, resulting in a visually unified and aesthetically pleasing final composition. Extensive evaluations demonstrate that our proposed approach yields significantly more natural stylistic transformations compared to conventional methods.
The change of macrofaunal bioturbation potential (BP) under environmental stress has application value in ecological restoration and ecological models. Single and combined toxic effects of metals ...cadmium and copper on the BP of polychaete Perinereis aibuhitensis were studied. The distribution of tracer sand showed a negative correlation between the transportation capacity of P. aibuhitensis and the Cd concentration; Cu stress indicated a stronger ability of promoting downward transportation, and the linear relationship with concentration was not so obvious as Cd. The toxicity stress of Cd and Cu also showed a significant effect on the oxidation-reduction potential (ORP) in the sediment matrix. There was a certain synergistic effect between cadmium and copper, and toxicity effects were associated with metal concentration and stress duration. In the later stage of the combined experiment, P. aibuhitensis avoided living in depth near the bottom, especially when the concentrations of Cd and Cu were high. For the bioturbation model, it was suggested that the two parameters of mobility and reworking would be reduced by half or one category scale depending on the cadmium and copper concentration and stress duration. The results can be used for ecological restoration prediction and ecological risk assessment; it is necessary to carry out more studies with a variety of environmental factors and indicators, since a variety of coexisted pollutants would show complex influence on the BP of macrobenthos.
•Cd and Cu stress can change the bioturbation potential of Perinereis aibuhitensis.•BP of P. aibuhitensis depends on both Cd–Cu pollution degree and stress duration.•Combined stress reduced the ability transporting downward by limiting living depth.
The Cathaysia Block is located in South China, along the western margin of the Pacific plate, and well known for its widespread granitoids and rich poly-metallic mineralization. Despite the numerous ...studies conducted in this region, some key questions are still in debate, which revolve around the detailed crustal architecture, the boundary between the western and eastern part of Cathaysia Block, and the geodynamic evolution and metallogenic settings in the Cathaysia Block. In this study, we have conducted a dense broad-band seismic observation in the Cathaysia Block, and obtained the fine crustal structure of it by using P-wave receiver functions and analyzing other geophysical and geological studies comprehensively. Our study has following findings: (1) the crust of the Cathaysia Block is ~31.5 km thick, thinner than that of the global continent, and is interpreted to have been thinned since the Late Mesozoic; (2) the Vp/Vs ratio of the Cathaysia Block is lower than that of the global continent, which implies there is no extensive underplating beneath the Cathaysia Block, or that the magma may be confined at bottom of the crust and formed a velocity gradient belt around Moho; (3) Zhenghe-Dapu fault is marked as the structural boundary between the western and eastern Cathaysia Block; (4) the western and eastern Cathaysia Block have different intra-crustal structures, petrochronology features and mineralization settings; (5) the subduction of the paleo-Pacific plate and the following roll-back could be responsible for the geodynamic evolution of the crustal deformation, as well as the widespread magmatism and mineralization.
•Fine crustal structure of Cathaysia is obtained by new seismic survey.•Zhenghe-Dapu fault is the boundary between the east and west Cathaysia.•No extensive magmatic underplating beneath the Cathaysia Block.•Two-stage paleo-Pacific subduction led to the crustal structure of Cathaysia.
Geophysical methods identify lithospheric structures and potential fluid conduits. Tectonicblock boundaries acted as fluid conduits for ore development. The Late Mesozoic Fe–Cu (Au) mineral system of ...LYMB was formed by multi-level sources, processes, and conduits communicating each other within an exceptional lithospheric architecture.
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•An extensive ore system occurred in the Lower Yangtze Metallogenic Belt.•Geophysical methods identify lithospheric structures and potential fluid conduits.•Tectonic block boundaries acted as fluid conduits for ore development.
Diverse seismic (active and passive) and magnetotelluric (MT) surveys have been conducted in the past decade over the Lower Yangtze Metallogenic Belt (LYMB) and adjacent areas, in eastern China. We present an integrated interpretation of these data describing the lithospheric architecture of an extensive Fe–Cu system in the LYMB. A combination of anomalous geophysical features has been observed in the sub-continental lithospheric mantle (SCLM) and asthenospheric mantle, which include: anomalously thin lithosphere (thickness ~70 km), low S- and P-wave seismic velocity in the upper mantle (70–150 km), and a dipping high-conductivity body extending from the lower crust to the asthenosphere (~150 km). We interpret these features to be the result of lithospheric delamination and asthenospheric upwelling during Late Mesozoic orogenesis. Melts and metal-rich (e.g., Cu, and Au) fluids produced by the asthenosphere would have metasomatized the lithospheric conduits (faults) and the lower part of the SCLM. Therefore, we suggest that these areas acted as the primary source regions for the Fe–Cu (Au) mineral system in the LYMB. Seismic reflection profiles across different parts of the LYMB reveal various large-scale structures, including crustal wedges, Moho stacks, mega-thrusts, and even lower crust underthrusting at block boundaries; these features are consistent with collisional orogeny. The spatial coincidence of major block boundaries with the distribution of deposits is evidence that deep-penetrating boundary faults acted as conduits for migrating magmas/fluids from lower crust to the upper crust. Conductive zones in the crust beneath the LYMB are interpreted as the result of alteration by fluids within the conduits. We conclude that the Late Mesozoic Fe–Cu (Au) mineral system of LYMB was formed by during an intra-continental orogeny with multi-level sources, processes, and conduits communicating each other within an exceptional lithospheric architecture.
Background and Purpose
Pyroptosis is a lytic form of pro‐inflammatory cell death characterised as caspase 1 dependent with canonical NLRP3 inflammasome‐induced gasdermin D (GSDMD) activation. We ...aimed to investigate the role of acinar pyroptotic cell death in pancreatic injury and systemic inflammation in AP.
Experimental Approach
Pancreatic acinar pyroptotic cell death pathway activation upon pancreatic toxin stimulation in vitro and in vivo was investigated. Effects of pharmacological (NLRP3 and caspase‐1 inhibitors), constitutive (Nlrp3−/−, Casp1−/− and Gsdmd−/−) and acinar cell conditional (Pdx1CreNlrp3Δ/Δ and Pdx1CreGsdmdΔ/Δ) genetic inhibition on pyroptotic acinar cell death, pancreatic necrosis and systemic inflammation were assessed using mouse AP models (caerulein, sodium taurocholate and l‐arginine). Effects of Pdx1CreGsdmdΔ/Δ versus myeloid conditional knockout (Lyz2CreGsdmdΔ/Δ) and Gsdmd−/− versus receptor‐interacting protein 3 (RIP3) inhibitor were compared in CER‐AP.
Key Results
There was consistent pyroptotic acinar cell death upon pancreatic toxin stimulation both in vitro and in vivo, which was significantly reduced by pharmacological or genetic pyroptosis inhibition. Pdx1CreGsdmdΔ/Δ but not Lyz2CreGsdmdΔ/Δ mice showed significantly reduced pyroptotic acinar cell death, pancreatic necrosis and systemic inflammation in caerulein‐AP. Co‐application of RIP3 inhibitor on Gsdmd−/− mice further increased protection on caerulein‐AP.
Conclusion and Implications
This work demonstrates a critical role for NLRP3 inflammasome and GSDMD activation‐mediated pyroptosis in acinar cells, linking pancreatic necrosis and systemic inflammation in AP. Targeting pyroptosis signalling pathways holds promise for specific AP therapy.
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•Mesozoic Mo-associated granitoids on the Jiaodong Peninsula occurred at ca.160 Ma and 117 Ma.•North China Block lower crust served as source for the Mo-associated ...granitoids.•Different magma sources controlled by crustal architectures led to Mo endowment diversity along the Dabie-Sulu Orogen.
Recent studies have demonstrated a linkage between the crustal architecture and the location of magmatic–hydrothermal Cu deposits in collisional orogens. However, if and how the crustal architecture controls the distribution of magmatic–hydrothermal Mo deposits in collisional orogens is unclear. Here, we present zircon U–Pb dating, geochemical and Sr–Nd–Hf–O isotopic data for granitoids associated with Mesozoic Mo mineralization on the Jiaodong Peninsula which exhibits substantial endowment differences to the Dabie Orogen. Geochronology data show that the Mo-associated granitoids occurred at ca. 160 Ma and 117 Ma. The Jurassic Mo-associated monzogranite was derived from melting of the thickened North China Block lower crust in a subduction-related setting. The Early Cretaceous Mo-associated granodiorite and granite were originated from a modified North China Block thorough crust–mantle interactions, induced by rollback of the Paleo-Pacific Plate. Our results complemented by published data indicate a crustal architecture characterized by South China Block gneisses overlying North China Block lower crust in the Sulu Orogen and wedging into the North China Block in the Jiaobei Terrane. By comparing the Mo–associated granitoids in Dabie Orogen and Jiaodong Peninsula, we conclude that magma source differences controlled by crustal architectures lead to Mo endowment diversities along the Dabie–Sulu Orogen.
The Middle and Lower Reaches of the Yangtze River metallogenic belt (MLYMB) is one of the most important Fe‐Cu polymetallic belts in China. However, the mechanism and deep geodynamical process for ...the formation of this belt are still controversial. Here, we obtain the crustal and the uppermost mantle structures using ambient noise data from a dense seismic profile. A low velocity zone is revealed beneath the Moho of MLYMB, interpreted as the source of the deep mineralization materials. In addition, a low velocity layer (LVL) and a high velocity layer (HVL) are observed in the crust of the southern segment of the profile. The LVL is interpreted as a tectonic detachment layer between the upper and the lower crust, and the HVL is interpreted as the aggregation zone for mineralizing melts or crystallized magma chambers. Based on the observed velocity features, we propose a three‐stage model for the formation of ore deposits in MLYMB. Our model suggests that an upwelling of asthenosphere triggered by the delamination of a previously thickened lithosphere leads to the partial melting of upper mantle rocks, which eventually ponders under the Moho. The magma then infiltrates through the ductile lower crust and reaches a depth of ∼7–13 km, forming a minerals‐enriched magma chamber. Minerals‐rich hot fluids originating from the magma chamber continue to move upward along the pre‐existent faults and the minerals finally precipitate in dense veinlets when reaching shallow depths, forming the ore deposits in and around the MLYMB.
Plain Language Summary
The formation of large‐scale mineral deposits is closely related to the lithosphere structure. The Middle and Lower Reaches of the Yangtze River metallogenic belt (MLYMB) is an ideal place to study the mineral system, as it is one of the most important Fe‐Cu polymetallic metallogenic belts in Eastern China and contains more than 200 ore deposits. Yet the mechanism and deep geodynamical process for the formation of this belt are still controversial. In this study, we construct a high‐resolution seismic model of the crust and the uppermost mantle using ambient noise data from a dense seismic profile. Our result reveals velocity features closely related to the metallogenic process in this region. Based on the observed velocity features, we propose a three‐stage model for the formation of the ore deposits in MLYMB, which is of great importance for the development of “mineral system” approaches to the exploration of minerals worldwide.
Key Points
We obtain a fine Vs structure of the crust and uppermost mantle beneath the MLYMB
We observe velocity features closely related to the metallogenic process of MLYMB
We propose a three‐stage metallogenic process for the origin of the MLYMB
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