Using Unreliable Pseudo-Labels for Label-Efficient Semantic Segmentation

The crux of label-efficient semantic segmentation is to produce high-quality pseudo-labels to leverage a large amount of unlabeled or weakly labeled data. A common practice is to select the highly confident predictions as the pseudo-ground-truths for each pixel, but it leads to a problem that most pixels may be left unused due to their unreliability. However, we argue that every pixel matters to the model training, even those unreliable and ambiguous pixels. Intuitively, an unreliable prediction may get confused among the top classes, however, it should be confident about the pixel not belonging to the remaining classes. Hence, such a pixel can be convincingly treated as a negative key to those most unlikely categories. Therefore, we develop an effective pipeline to make sufficient use of unlabeled data. Concretely, we separate reliable and unreliable pixels via the entropy of predictions, push each unreliable pixel to a category-wise queue that consists of negative keys, and manage to train the model with all candidate pixels. Considering the training evolution, we adaptively adjust the threshold for the reliable-unreliable partition. Experimental results on various benchmarks and training settings demonstrate the superiority of our approach over the state-of-the-art alternatives

Atomistically-informed continuum modeling and isogeometric analysis of 2D materials over holey substrates

This work develops, discretizes, and validates a continuum model of a molybdenum disulfide (MoS$_2$) monolayer interacting with a periodic holey silicon nitride substrate via van der Waals (vdW) forces. The MoS$_2$ layer is modeled as a geometrically nonlinear Kirchhoff-Love shell, and vdW forces are modeled by a Lennard-Jones potential, simplified using approximations for a smooth substrate topography. The material parameters of the shell model are calibrated by comparing small-strain tensile and bending tests with atomistic simulations. This model is efficiently discretized using isogeometric analysis (IGA) for the shell structure and a pseudo-time continuation method for energy minimization. The IGA shell model is validated against fully-atomistic calculations for several benchmark problems with different substrate geometries. The continuum simulations reproduce deflections, strains and curvatures predicted by atomistic simulations, which are known to strongly affect the electronic properties of MoS$_2$, with deviations well below the modeling errors suggested by differences between the widely-used reactive empirical bond order and Stillinger-Weber interatomic potentials. Agreement with atomistic results depends on geometric nonlinearity in some cases, but a simple isotropic St. Venant-Kirchhoff model is found to be sufficient to represent material behavior. We find that the IGA discretization of the continuum model has a much lower computational cost than atomistic simulations, and expect that it will enable efficient design space exploration in strain engineering applications. This is demonstrated by studying the dependence of strain and curvature in MoS$_2$ over a holey substrate as a function of the hole spacing on scales inaccessible to atomistic calculations. The results show an unexpected qualitative change in the deformation pattern below a critical hole separation

Quantum-informed simulations for mechanics of materials: DFTB+MBD framework

peer reviewedThe macroscopic behaviors of materials are determined by interactions that occur at multiple lengths and time scales. Depending on the application, describing, predicting, and understanding these behaviors may require models that rely on insights from atomic and electronic scales. In such cases, classical simplified approximations at those scales are insufficient, and quantum-based modeling is required. In this paper, we study how quantum effects can modify the mechanical properties of systems relevant to materials engineering. We base our study on a high-fidelity modeling framework that combines two computationally efficient models rooted in quantum first principles: Density Functional Tight Binding (DFTB) and many-body dispersion (MBD). The MBD model is applied to accurately describe non-covalent van der Waals interactions. Through various benchmark applications, we demonstrate the capabilities of this framework and the limitations of simplified modeling. We provide an open-source repository containing all codes, datasets, and examples presented in this work. This repository serves as a practical toolkit that we hope will support the development of future research in effective large-scale and multiscale modeling with quantum-mechanical fidelity

The History and Prediction of Prebiotics and Postbiotics: A Patent Analysis

Prebiotics and postbiotics have gained attention as functional food additives due to their substantial influence on the gut microbiome and potential implications for human health on a broader scale. In addition, the number of patents for these additives has also increased, yet their functional classification has been problematic. In this study, we classified 2215 patents granted from 2001 to 2020 by functionality to enable predictions of future development directions. These patents encompassed subjects as diverse as feed supplementation, regulation of intestinal homeostasis, prevention of gastrointestinal ailments, targeted drug administration and augmentation of drug potency. The progression of patents issued during this time frame could be divided into three phases: occasional accounts prior to 2001, a period from 2001 to 2013 during which an average of 42 patents were issued annually, followed by a surge exceeding 140 patents annually after 2013. The latter increase has indicated that pre- and post-biotics have been recognized as biologically relevant. Patent mining therefore can enable forecasts of the future trajectory of these biologics and provide insights to evaluate their advancement. Moreover, this research is the first attempt to generalize and predict the directions of prebiotics and postbiotics using patent information and offers a comprehensive perspective for the potential utilization of prebiotics and postbiotics across a wide variety of fields.<br/

Atomistically-informed continuum modeling and isogeometric analysis of 2D materials over holey substrates

This work develops, discretizes, and validates a continuum model of a molybdenum disulfide (MoS2) monolayer interacting with a periodic holey silicon nitride (Si3N4) substrate via van der Waals (vdW) forces. The MoS2 layer is modeled as a geometrically nonlinear Kirchhoff–Love shell, and vdW forces are modeled by a Lennard-Jones (LJ) potential, simplified using approximations for a smooth substrate topography. Both the shell model and LJ interactions include novel extensions informed by close comparison with fully-atomistic calculations. The material parameters of the shell model are calibrated by comparing small-strain tensile and bending tests with atomistic simulations. This model is efficiently discretized using isogeometric analysis (IGA) for the shell structure and a pseudo-time continuation method for energy minimization. The IGA shell model is validated against fully-atomistic calculations for several benchmark problems with different substrate geometries. Agreement with atomistic results depends on geometric nonlinearity in some cases, but a simple isotropic St.Venant–Kirchhoff model is found to be sufficient to represent material behavior. We find that the IGA discretization of the continuum model has a much lower computational cost than atomistic simulations, and expect that it will enable efficient design space exploration in strain engineering applications. This is demonstrated by studying the dependence of strain and curvature in MoS2 over a holey substrate as a function of the hole spacing on scales inaccessible to atomistic calculations. The results show an unexpected qualitative change in the deformation pattern below a critical hole separation

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Cinnamomum camphora ('Gantong 1')

Cinnamomum camphora is one of the most commonly used tree species in landscaping. Improving its ornamental traits, particularly bark and leaf colors, is one of the key breeding goals. The basic helix-loop-helix (bHLH) transcription factors (TFs) are crucial in controlling anthocyanin biosynthesis in many plants. However, their role in C. camphora remains largely unknown. In this study, we identified 150 bHLH TFs (CcbHLHs) using natural mutant C. camphora 'Gantong 1', which has unusual bark and leaf colors. Phylogenetic analysis revealed that 150 CcbHLHs were divided into 26 subfamilies which shared similar gene structures and conserved motifs. According to the protein homology analysis, we identified four candidate CcbHLHs that were highly conserved compared to the TT8 protein in A. thaliana. These TFs are potentially involved in anthocyanin biosynthesis in C. camphora. RNA-seq analysis revealed specific expression patterns of CcbHLHs in different tissue types. Furthermore, we verified expression patterns of seven CcbHLHs (CcbHLH001, CcbHLH015, CcbHLH017, CcbHLH022, CcbHLH101, CcbHLH118, and CcbHLH134) in various tissue types at different growth stages using qRT-PCR. This study opens a new avenue for subsequent research on anthocyanin biosynthesis regulated by CcbHLH TFs in C. camphora

Self-assembly of H2S-responsive nanoprodrugs based on natural rhein and geraniol for targeted therapy against <i>Salmonella Typhimurium</i>

Salmonellosis is a globally extensive food-borne disease, which threatens public health and results in huge economic losses in the world annually. The rising prevalence of antibiotic resistance in Salmonella poses a significant global concern, emphasizing an imperative to identify novel therapeutic agents or methodologies to effectively combat this predicament. In this study, self-assembly hydrogen sulfide (H2S)-responsive nanoprodrugs were fabricated with poly(α-lipoic acid)-polyethylene glycol grafted rhein and geraniol (PPRG), self-assembled into core–shell nanoparticles via electrostatic, hydrophilic and hydrophobic interactions, with hydrophilic exterior and hydrophobic interior. The rhein and geraniol are released from self-assembly nanoprodrugs PPRG in response to Salmonella infection, which is known to produce hydrogen sulfide (H2S). PPRG demonstrated stronger antibacterial activity against Salmonella compared with rhein or geraniol alone in vitro and in vivo. Additionally, PPRG was also able to suppress the inflammation and modulate gut microbiota homeostasis. In conclusion, the as-prepared self-assembly nanoprodrug sheds new light on the design of natural product active ingredients and provides new ideas for exploring targeted therapies for specific Enteropathogens

Clinical evidence of acupuncture and moxibustion for irritable bowel syndrome: A systematic review and meta-analysis of randomized controlled trials

BackgroundAcupuncture and moxibustion have been widely used in the treatment of Irritable Bowel Syndrome (IBS). But the evidence that acupuncture and moxibustion for IBS reduction of symptom severity and abdominal pain, and improvement of quality of life is scarce.MethodsPubMed, Embase, Cochrane Library, Web of Science, Chinese National Knowledge Infrastructure (CNKI), Chinese Scientific Journals Database (VIP), Wanfang Database, China Biomedical Literature Service System (SinoMed), and unpublished sources were searched from inception until June 30, 2022. The quality of RCTs was assessed with the Cochrane Collaboration risk of bias tool. The strength of the evidence was evaluated with the Grading of Recommendations Assessment, Development and Evaluation system (GRADE). Trial sequential analysis (TSA) was conducted to determine whether the participants in the included trials had reached optimal information size and whether the cumulative data was adequately powered to evaluate outcomes.ResultsA total of 31 RCTs were included. Acupuncture helped reduce the severity of symptoms more than pharmaceutical drugs (MD, −35.45; 95% CI, −48.21 to −22.68; I2 = 71%). TSA showed the cumulative Z score crossed O'Brien-Fleming alpha-spending significance boundaries. Acupuncture wasn't associated with symptom severity reduction (SMD, 0.03, 95% CI, −0.25 to 0.31, I2 = 46%), but exhibited therapeutic benefits on abdominal pain (SMD, −0.24; 95% CI, −0.48 to −0.01; I2 = 8%) compared to sham acupuncture. Moxibustion show therapeutic benefits compared to sham moxibustion on symptom severity (SMD, −3.46, 95% CI, −5.66 to −1.27, I2 = 95%) and abdominal pain (SMD, −2.74, 95% CI, −4.81 to −0.67, I2 = 96%). Acupuncture (SMD, −0.46; 95% CI, −0.68 to −0.24; I2 = 47%) and the combination of acupuncture and moxibustion (SMD, −2.00; 95% CI, −3.04 to −0.96; I2 = 90%) showed more benefit for abdominal pain compared to pharmacological medications as well as shams. Acupuncture (MD, 4.56; 95% CI, 1.46–7.67; I2 = 79%) and moxibustion (MD, 6.97; 95% CI, 5.78–8.16; I2 = 21%) were more likely to improve quality of life than pharmaceutical drugs.ConclusionAcupuncture and/or moxibustion are beneficial for symptom severity, abdominal pain and quality of life in IBS. However, in sham control trials, acupuncture hasn't exhibited robust and stable evidence, and moxibustion's results show great heterogeneity. Hence, more rigorous sham control trials of acupuncture or moxibustion are necessary.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=262118, identifier CRD42021262118

Numerical Methods for Continuum Mechanics with Nonlocal Interactions: Weak Form Peridynamics and Nanoscale Strain Engineering

Nonlocal interactions raise numerical challenges such as high computational cost and geometric complexity. In the context of continuum mechanics, this thesis studies numerical methods for two nonlocal problems: weak form peridynamics and nanoscale strain engineering.Unlike the classical local theory, the weak formulation of peridynamics involves a double integral and the additional integral operator needs an efficient quadrature rule. For this reason, the thesis investigates convergence behaviours of a promising quadrature rule based on Generalized Moving Least Squares (GMLS) when applied to the double integral. For uniform discretizations, second-order convergence is observed with a mesh extension for global symmetrical inner quadrature. For non-uniform discretizations, a proposed strategy for symmetrically placing inner quadrature points shows decaying second-order convergence, while increasing the number of outer quadrature points leads to a more persistent convergence behaviour. Numerical tests in 1D demonstrate the above properties and 2D tests show consistent behaviours.Nanoscale strain engineering aims at tuning the electronic properties of a semiconductor by modulating its nanoscale stain field, and the nonlocal interaction through Van der Waals forces is a possible mechanism for the modulation. To better understand the interaction process, based on the Lennard-Jones (LJ) model, the thesis builds a continuum model to simulate nonlocal interactions between a monolayer MoS2 and a multihole Si3N4 substrate. A low-dimensional model is first built as a proof of concept before considering the real problem. The monolayer MoS2 is then modeled by a Kirchhoff–Love shell while the integration of LJ potential over the substrate is approximated by a Riemann sum in a finite range and optimized using octrees. An alternative approach based on a semi-infinite integral is proposed for the integration over curved substrates, as a preliminary study for future work