WPU-Net: Boundary Learning by Using Weighted Propagation in Convolution Network

Deep learning has driven a great progress in natural and biological image processing. However, in material science and engineering, there are often some flaws and indistinctions in material microscopic images induced from complex sample preparation, even due to the material itself, hindering the detection of target objects. In this work, we propose WPU-net that redesigns the architecture and weighted loss of U-Net, which forces the network to integrate information from adjacent slices and pays more attention to the topology in boundary detection task. Then, the WPU-net is applied into a typical material example, i.e., the grain boundary detection of polycrystalline material. Experiments demonstrate that the proposed method achieves promising performance and outperforms state-of-the-art methods. Besides, we propose a new method for object tracking between adjacent slices, which can effectively reconstruct 3D structure of the whole material. Finally, we present a material microscopic image dataset with the goal of advancing the state-of-the-art in image processing for material science.Comment: technical repor

Direction-oriented Multi-objective Learning: Simple and Provable Stochastic Algorithms

Multi-objective optimization (MOO) has become an influential framework in many machine learning problems with multiple objectives such as learning with multiple criteria and multi-task learning (MTL). In this paper, we propose a new direction-oriented multi-objective problem by regularizing the common descent direction within a neighborhood of a direction that optimizes a linear combination of objectives such as the average loss in MTL. This formulation includes GD and MGDA as special cases, enjoys the direction-oriented benefit as in CAGrad, and facilitates the design of stochastic algorithms. To solve this problem, we propose Stochastic Direction-oriented Multi-objective Gradient descent (SDMGrad) with simple SGD type of updates, and its variant SDMGrad-OS with an efficient objective sampling in the setting where the number of objectives is large. For a constant-level regularization parameter $\lambda$, we show that SDMGrad and SDMGrad-OS provably converge to a Pareto stationary point with improved complexities and milder assumptions. For an increasing $\lambda$, this convergent point reduces to a stationary point of the linear combination of objectives. We demonstrate the superior performance of the proposed methods in a series of tasks on multi-task supervised learning and reinforcement learning. Code is provided at https://github.com/ml-opt-lab/sdmgrad

Stress Evolution in Nanocrystalline Diamond Films Produced by Chemical Vapor Deposition

Nanocrystalline diamond films were grown on silicon substrates by microwave plasma enhanced chemical vapor deposition with 1% methane, 2%–10% hydrogen, and argon. High resolution transmission electron microscope images and selected area electron diffraction patterns confirm that the films consist of 10–20 nm sized diamond grains. The residual and intrinsic stresses were investigated using wafer curvature. Intrinsic stresses were always tensile, with higher H2 concentrations generally leading to higher stresses. Annealing the films in a hydrogen plasma significantly increased these stresses. These hydrogen induced changes also appear to alter stress levels and stress gradients during the growth process itself. Raman spectra revealed subtle changes in the chemical bonding that were correlated with some of the stress variations. These results suggest that grain boundary bonding and hydrogen induced reactions at the grain boundaries can influence the intrinsic stresses in nanocrystalline diamond films

Monitoring thermal pollution in rivers downstream of dams with Landsat ETM+ thermal infrared images

Dams play a significant role in altering the spatial pattern of temperature in rivers and contribute to thermal pollution, which greatly affects the river aquatic ecosystems. Understanding the temporal and spatial variation of thermal pollution caused by dams is important to prevent or mitigate its harmful effect. Assessments based on in-situ measurements are often limited in practice because of the inaccessibility of water temperature records and the scarcity of gauges along rivers. By contrast, thermal infrared remote sensing provides an alternative approach to monitor thermal pollution downstream of dams in large rivers, because it can cover a large area and observe the same zone repeatedly. In this study, Landsat Enhanced Thematic Mapper Plus (ETM+) thermal infrared imagery were applied to assess the thermal pollution caused by two dams, the Geheyan Dam and the Gaobazhou Dam, located on the Qingjiang River, a tributary of the Yangtze River downstream of the Three Gorges Reservoir in Central China. The spatial and temporal characteristics of thermal pollution were analyzed with water temperatures estimated from 54 cloud-free Landsat ETM+ scenes acquired in the period from 2000 to 2014. The results show that water temperatures downstream of both dams are much cooler than those upstream of both dams in summer, and the water temperature remains stable along the river in winter, showing evident characteristic of the thermal pollution caused by dams. The area affected by the Geheyan Dam reaches beyond 20 km along the downstream river, and that affected by the Gaobazhou Dam extends beyond the point where the Qingjiang River enters the Yangtze River. Considering the long time series and global coverage of Landsat ETM+ imagery, the proposed technique in the current study provides a promising method for globally monitoring the thermal pollution caused by dams in large rivers

Controls on anomalously high porosity/permeability of Middle Jurassic deeply buried tight sandstones in the Taibei Sag, Turpan-Hami Basin, northwestern China: Implications for reservoir quality prediction

The lower member of the Middle Jurassic Xishanyao Formation (J2x1+2) sandstones are significant exploratory targets for hydrocarbon resources in the Taibei Sag of the Turpan-Hami Basin, northwestern China. Formation of anomalously high porosity/permeability in deeply buried J2x1+2 sandstones and reservoir quality prediction were investigated using a variety of petrographic analyses. These results show that the J2x1+2 sandstones are mostly feldspathic litharenites and litharenites, which are characterized by moderate-to good sorting, silty to medium granularity, and point- to long grain contacts. The J2x1+2 sandstone has low porosity (avg 6.0%) and permeability (avg 1.12 mD), but shows anomalously high porosity/permeability at depth interval of 3850–4050 m. There is a noticeable variation in pore types and sizes from intergranular-intragranular dissolution pores with a size mode of 2.0 μm in anomalously high porosity (AHP) sandstones, to major intragranular dissolution pores with a size mode of 0.5 μm in normally high porosity (NHP) sandstones, to most micropores with a size mode of 0.25 μm occurred in the normally low porosity (NLP) sandstones. The compaction is the main cause of porosity destruction, resulting in an average porosity loss of 89.6%. However, the authigenic minerals have relatively little influence on reservoir quality. The combination of nappe tectonics and well-sorted particles alleviated the compaction and thus preserved more intergranular pores in the AHP sandstones. Dissolution further increases the porosity and eventually forms the AHP sandstones. The strong carbonate-cemented facies (SCC), tightly compacted facies (TC), moderately compacted with moderate dissolution facies (MCMD), and weakly compacted with strong dissolution facies (WCSD) are determined in the J2x1+2 sandstones. The sandstones with SCC and TC are recognized as the NLP reservoirs. The MCMD and WCSD correspond to the NHP and AHP reservoirs, respectively. The reservoir quality predicted using the constructed diagenetic facies charts is in good agreement with the photomicrograph observations and physical property tests. Additionally, the AHP reservoirs are still developed in the deeply buried sandstones with depths larger than 4000 m

Characterization of the RNA-binding properties of the triple-gene-block protein 2 of Bamboo mosaic virus

The triple-gene-block protein 2 (TGBp2) of Bamboo mosaic virus (BaMV) is a transmembrane protein which was proposed to be involved in viral RNA binding during virus transport. Here, we report on the RNA-binding properties of TGBp2. Using tyrosine fluorescence spectroscopy and UV-crosslinking assays, the TGBp2 solubilized with Triton X-100 was found to interact with viral RNA in a non-specific manner. These results raise the possibility that TGBp2 facilitates intracellular delivery of viral RNA through non-specific protein-RNA interaction

MicroRNA gga-miR-200a-3p modulates immune response via MAPK signaling pathway in chicken afflicted with necrotic enteritis

International audienceAbstractMicroRNAs (miRNAs) are small non-coding RNAs that contribute to host immune response as post-transcriptional regulation. The current study investigated the biological role of the chicken (Gallus gallus) microRNA-200a-3p (gga-miR-200a-3p), using 2 necrotic enteritis (NE) afflicted genetically disparate chicken lines, 6.3 and 7.2, as well as the mechanisms underlying the fundamental signaling pathways in chicken. The expression of gga-miR-200a-3p in the intestinal mucosal layer of NE-induced chickens, was found to be upregulated during NE infection in the disease-susceptible chicken line 7.2. To validate the target genes, we performed an overexpression analysis of gga-miR-200a-3p using chemically synthesized oligonucleotides identical to gga-miR-200a-3p, reporter gene analysis including luciferase reporter assay, and a dual fluorescence reporter assay in cultured HD11 chicken macrophage cell lines. Gga-miR-200a-3p was observed to be a direct transcriptional repressor of ZAK, MAP2K4, and TGFβ2 that are involved in mitogen-activated protein kinase (MAPK) pathway by targeting the 3′-UTR of their transcripts. Besides, gga-miR-200a-3p may indirectly affect the expression of protein kinases including p38 and ERK1/2 at both transcriptional and translational levels, suggesting that this miRNA may function as an important regulator of the MAPK signaling pathway. Proinflammatory cytokines consisting of IL-1β, IFN-γ, IL-12p40, IL-17A, and LITAF belonging to Th1 and Th17-type cytokines, were upregulated upon gga-miR-200a-3p overexpression. These findings have enhanced our knowledge of the immune function of gga-miR-200a-3p mediating the chicken immune response via regulation of the MAPK signaling pathway and indicate that this miRNA may serve as an important biomarker of diseases in domestic animals

Causal networks of phytoplankton diversity and biomass are modulated by environmental context

Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmental factors is challenging due to their complex and context-dependent interactions (e.g., a nutrient-dependent relationship between diversity and biomass). Consequently, studies that only consider separable, unidirectional effects can produce divergent conclusions and equivocal ecological implications. To address this complexity, we use empirical dynamic modeling to assemble causal networks for 19 natural aquatic ecosystems (N24◦~N58◦) and quantified strengths of feedbacks among phytoplankton diversity, phytoplankton biomass, and environmental factors. Through a cross-system comparison, we identify macroecological patterns; in more diverse, oligotrophic ecosystems, biodiversity effects are more important than environmental effects (nutrients and temperature) as drivers of biomass. Furthermore, feedback strengths vary with productivity. In warm, productive systems, strong nitrate-mediated feedbacks usually prevail, whereas there are strong, phosphate-mediated feedbacks in cold, less productive systems. Our findings, based on recovered feedbacks, highlight the importance of a network view in future ecosystem management

The Stable Association of Virion with the Triple-geneblockProtein 3-based Complex of Bamboo mosaic virus

The triple-gene-block protein 3 (TGBp3) of Bamboo mosaic virus (BaMV) is an integral endoplasmic reticulum (ER) membraneprotein which is assumed to form a membrane complex to deliver the virus intracellularly. However, the virus entity that isdelivered to plasmodesmata (PD) and its association with TGBp3-based complexes are not known. Results from chemicalextraction and partial proteolysis of TGBp3 in membrane vesicles revealed that TGBp3 has a right-side-out membranetopology; i.e., TGBp3 has its C-terminal tail exposed to the outer surface of ER. Analyses of the TGBp3-specificimmunoprecipitate of Sarkosyl-extracted TGBp3-based complex revealed that TGBp1, TGBp2, TGBp3, capsid protein (CP),replicase and viral RNA are potential constituents of virus movement complex. Substantial co-fractionation of TGBp2, TGBp3and CP, but not TGBp1, in the early eluted gel filtration fractions in which virions were detected after TGBp3-specificimmunoprecipitation suggested that the TGBp2- and TGBp3-based complex is able to stably associate with the virion. Thisnotion was confirmed by immunogold-labeling transmission electron microscopy (TEM) of the purified virions. In addition,mutational and confocal microscopy analyses revealed that TGBp3 plays a key role in virus cell-to-cell movement byenhancing the TGBp2- and TGBp3-dependent PD localization of TGBp1. Taken together, our results suggested that the cellto-cell movement of potexvirus requires stable association of the virion cargo with the TGBp2- and TGBp3-based membranecomplex and recruitment of TGBp1 to the PD by this complex