The generation and primary migration of hydrocarbons in organic-rich shale leaves void space in organic matter, which is the porosity associated with organic matter commonly observed under scanning ...electron microscope (SEM). In this study, Middle Devonian black shale core samples were collected from three wells penetrating the organic-rich Marcellus Shale and the organic-lean Mahantango Formation in Pennsylvania and West Virginia. Pyrolysis, ion milled SEM and low-pressure nitrogen adsorption analysis were conducted to investigate the organic richness and the properties of the pore system. Vitrinite reflectance (Ro) values in the range of 1.36%–2.89% represent a maturity spectrum covering the wet-gas to post-mature zones. In general, the pore system is composed of organic matter-hosted pores and mineral-hosted pores. However, the dominant pore types and pore sizes vary stratigraphically across lithology and abundance of organic matter. All the organic matter observed in this study shows an amorphous occurrence. Pore space between mineral grains (both silt-size and clay-size) can be filled by organic matter, which contains secondary porosity generated by thermal cracking of kerogen. Mineral-hosted pores are concentrated in organic-lean samples in which secondary organic matter could not fill most of the primary pore space. The destruction of primary mineral-hosted pores and the generation of secondary organic matter-hosted pores were observed. TOC values show positive correlations with the porosity, specific surface area, and the abundance of micropores. Increasing thermal maturity correlates with a significant decrease of pore volume and surface area, primarily through diminishing or vanishing of micropores. The richness and thermal maturity of organic matter in organic-rich Devonian shale can be effective parameters for evaluation of reservoir quality and upscaling the appraisal.
•The pore structure of the Marcellus Shale and Mahantango Formation were characterized.•The evolution of the pore system is driven by compaction, cementation, and organic matter maturation.•A stratigraphic distribution of pore networks is identified and classified into four pore facies.•The mechanism of generation and preservation of organic matter hosted porosity is discussed.•The storage capacity also shows a stratigraphic distribution with respect to the pore system.
Source-Free Domain Adaptation (SFDA) is becoming topical to address the challenge of distribution shift between training and deployment data, while also relaxing the requirement of source data ...availability during target domain adaptation. In this paper, we focus on SFDA for semantic segmentation, in which pseudo labeling based target domain self-training is a common solution. However, pseudo labels generated by the source models are particularly unreliable on the target domain data due to the domain shift issue. Therefore, we propose to use Bayesian Neural Network (BNN) to improve the target self-training by better estimating and exploiting pseudo-label uncertainty. With the uncertainty estimation of BNNs, we introduce two novel self-training based components: Uncertainty-aware Online Teacher-Student Learning (UOTSL) and Uncertainty-aware FeatureMix (UFM). Extensive experiments on two popular benchmarks, GTA5 → Cityscapes and SYNTHIA → Cityscapes, show the superiority of our proposed method with mIoU gains of 3.6% and 5.7% over the state-of-the-art respectively.
Deep Learning for Free-Hand Sketch: A Survey Xu, Peng; Hospedales, Timothy M.; Yin, Qiyue ...
IEEE transactions on pattern analysis and machine intelligence,
2023-Jan.-1, 2023-Jan, 2023-1-1, 20230101, Letnik:
45, Številka:
1
Journal Article
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Free-hand sketches are highly illustrative, and have been widely used by humans to depict objects or stories from ancient times to the present. The recent prevalence of touchscreen devices has made ...sketch creation a much easier task than ever and consequently made sketch-oriented applications increasingly popular. The progress of deep learning has immensely benefited free-hand sketch research and applications. This paper presents a comprehensive survey of the deep learning techniques oriented at free-hand sketch data, and the applications that they enable. The main contents of this survey include: (i) A discussion of the intrinsic traits and unique challenges of free-hand sketch, to highlight the essential differences between sketch data and other data modalities, e.g., natural photos. (ii) A review of the developments of free-hand sketch research in the deep learning era, by surveying existing datasets, research topics, and the state-of-the-art methods through a detailed taxonomy and experimental evaluation. (iii) Promotion of future work via a discussion of bottlenecks, open problems, and potential research directions for the community.
Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent ...homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.
Recent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., ...digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals. However, these studies are relatively limited in the scope of species that have been examined. Here we present a dataset that includes paired wild and captive samples from mammalian taxa across six Orders to investigate generalizable patterns of the effects captivity on mammalian gut bacteria. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the taxa surveyed, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that demonstrated larger shifts in relative abundance between the captive and wild states included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.
Down syndrome (DS), or trisomy 21, is one of the critical risk factors for early-onset Alzheimer's disease (AD), implicating key roles for chromosome 21-encoded genes in the pathogenesis of AD. We ...previously identified a role for the deubiquitinase USP25, encoded on chromosome 21, in regulating microglial homeostasis in the AD brain; however, whether USP25 affects amyloid pathology remains unknown. Here, by crossing 5×FAD AD and Dp16 DS mice, we observed that trisomy 21 exacerbated amyloid pathology in the 5×FAD brain. Moreover, bacterial artificial chromosome (BAC) transgene-mediated USP25 overexpression increased amyloid deposition in the 5×FAD mouse brain, whereas genetic deletion of Usp25 reduced amyloid deposition. Furthermore, our results demonstrate that USP25 promoted β cleavage of APP and Aβ generation by reducing the ubiquitination and lysosomal degradation of both APP and BACE1. Importantly, pharmacological inhibition of USP25 ameliorated amyloid pathology in the 5×FAD mouse brain. In summary, we identified the DS-related gene USP25 as a critical regulator of AD pathology, and our data suggest that USP25 serves as a potential pharmacological target for AD drug development.
Increasing evidence points to inflammation as one of the key players in diabetes-mediating adverse effects to the neuronal and vascular components of the retina. Sustained inflammation induces ...biochemical and molecular changes, ultimately contributing to retinal complications and vision loss in diabetic retinopathy. In this review, we describe changes involving metabolic abnormalities secondary to hyperglycemia, oxidative stress, and activation of transcription factors, together with neuroglial alterations in the diabetic retina. Changes in biochemical pathways and how they promote pathophysiologic developments involving proinflammatory cytokines, chemokines, and adhesion molecules are discussed. Inflammation-mediated leukostasis, retinal ischemia, and neovascularization and their contribution to pathological and clinical stages leading to vision loss in diabetic retinopathy (DR) are highlighted. In addition, potential treatment strategies involving fibrates, connexins, neuroprotectants, photobiomodulation, and anti-inflammatory agents against the development and progression of DR lesions are reviewed. The importance of appropriate animal models for testing novel strategies against DR lesions is discussed; in particular, a novel nonhuman primate model of DR and the suitability of rodent models are weighed. The purpose of this review is to highlight our current understanding of the pathogenesis of DR and to summarize recent advances using novel approaches or targets to investigate and inhibit the retinopathy.
Ferroptosis is a form of regulated cell death that may facilitate the selective elimination of tumor cells. The tumor suppressor p53 (TP53) has been demonstrated to promote ferroptosis via a ...transcription-dependent mechanism. Here, we show that TP53 limits erastin-induced ferroptosis by blocking dipeptidyl-peptidase-4 (DPP4) activity in a transcription-independent manner. Loss of TP53 prevents nuclear accumulation of DPP4 and thus facilitates plasma-membrane-associated DPP4-dependent lipid peroxidation, which finally results in ferroptosis. These findings reveal a direct molecular link between TP53 and DPP4 in the control of lipid metabolism and may provide a precision medicine strategy for the treatment of colorectal cancer by induction of ferroptosis.
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•TP53 inhibits ferroptosis in human colorectal cancer (CRC) cells•TP53 mediates SLC7A11C expression in human CRC cells•DPP4 mediates ferroptosis in TP53-deficient CRC cells•Loss of TP53 enhances the anticancer activity of erastin in vivo
Xie et al. find that TP53 antagonizes ferroptosis in colorectal cancer (CRC) cells by favoring the localization of DPP4 toward a nuclear, enzymatically inactive pool. This pathway is different from the previously identified function of TP53 as a positive regulator of ferroptosis in non-CRC cells.
In the presence of drought and other desiccating stresses, plants synthesize and redistribute the phytohormone abscisic acid (ABA). ABA promotes plant water conservation by acting on specialized ...cells in the leaf epidermis, guard cells, which border and regulate the apertures of stomatal pores through which transpirational water loss occurs. Following ABA exposure, solute uptake into guard cells is rapidly inhibited and solute loss is promoted, resulting in inhibition of stomatal opening and promotion of stomatal closure, with consequent plant water conservation. There is a wealth of information on the guard cell signaling mechanisms underlying these rapid ABA responses. To investigate ABA regulation of gene expression in guard cells in a systematic genome-wide manner, we analyzed data from global transcriptomes of guard cells generated with Affymetrix ATH1 microarrays, and compared these results to ABA regulation of gene expression in leaves and other tissues.
The 1173 ABA-regulated genes of guard cells identified by our study share significant overlap with ABA-regulated genes of other tissues, and are associated with well-defined ABA-related promoter motifs such as ABREs and DREs. However, we also computationally identified a unique cis-acting motif, GTCGG, associated with ABA-induction of gene expression specifically in guard cells. In addition, approximately 300 genes showing ABA-regulation unique to this cell type were newly uncovered by our study. Within the ABA-regulated gene set of guard cells, we found that many of the genes known to encode ion transporters associated with stomatal opening are down-regulated by ABA, providing one mechanism for long-term maintenance of stomatal closure during drought. We also found examples of both negative and positive feedback in the transcriptional regulation by ABA of known ABA-signaling genes, particularly with regard to the PYR/PYL/RCAR class of soluble ABA receptors and their downstream targets, the type 2C protein phosphatases. Our data also provide evidence for cross-talk at the transcriptional level between ABA and another hormonal inhibitor of stomatal opening, methyl jasmonate.
Our results engender new insights into the basic cell biology of guard cells, reveal common and unique elements of ABA-regulation of gene expression in guard cells, and set the stage for targeted biotechnological manipulations to improve plant water use efficiency.
Despite the growth of photoredox methods in academia, application of photoredox at scale in the pharmaceutical and fine chemical industries has been slow. In this report, a photoredox ...trifluoromethylation of a thiophenol was modified from the original literature report, and the mechanism was investigated to define the key scale-up parameters. The mechanistic insight was leveraged in the design and execution of two different reactor designs: an LED-based plug flow photoreactor and a laser-based continuous stirred tank photoreactor. In one of the first examples of commercial-scale photoredox chemistry, the process was scaled to provide over 500 kg of the desired intermediate and amended to fully continuous manufacturing.
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