Seeing Beyond the Brain: Conditional Diffusion Model with Sparse Masked Modeling for Vision Decoding

Decoding visual stimuli from brain recordings aims to deepen our understanding of the human visual system and build a solid foundation for bridging human and computer vision through the Brain-Computer Interface. However, reconstructing high-quality images with correct semantics from brain recordings is a challenging problem due to the complex underlying representations of brain signals and the scarcity of data annotations. In this work, we present MinD-Vis: Sparse Masked Brain Modeling with Double-Conditioned Latent Diffusion Model for Human Vision Decoding. Firstly, we learn an effective self-supervised representation of fMRI data using mask modeling in a large latent space inspired by the sparse coding of information in the primary visual cortex. Then by augmenting a latent diffusion model with double-conditioning, we show that MinD-Vis can reconstruct highly plausible images with semantically matching details from brain recordings using very few paired annotations. We benchmarked our model qualitatively and quantitatively; the experimental results indicate that our method outperformed state-of-the-art in both semantic mapping (100-way semantic classification) and generation quality (FID) by 66% and 41% respectively. An exhaustive ablation study was also conducted to analyze our framework.Comment: 8 pages, 9 figures, 2 tables, accepted by CVPR2023, see https://mind-vis.github.io/ for more informatio

Regional homogeneity alterations of resting-state functional magnetic resonance imaging of chronic rhinosinusitis with olfactory dysfunction

ObjectivesThe aim of this study was to assess the brain functional changes of patients with chronic rhinosinusitis with olfactory dysfunction (CRSwOD) using regional homogeneity (ReHo) of resting-state functional magnetic resonance imaging (MRI) scans, and to better explain the occurrence and development of olfactory decline in patients with chronic sinusitis provides a new idea for the study of more advanced olfactory therapy modalities.MethodsA total of 28 CRSwOD patients, 24 patients with CRS without olfactory dysfunction (CRSsOD), and 25 healthy controls (HCs) were recruited. All subjects underwent olfactory testing, clinical and brief psychological assessments, and MRI scans. A two-sided two-sample t test with AlphaSim correction (voxel-p < 0.001, cluster size >54 voxels) was used to detect differences between CRSwOD, CRSsOD, and HC groups.ResultsCompared with HCs, the ReHo values in traditional olfactory regions (e.g., parahippocampal gyrus (PHG), hippocampal, olfactory cortex) were increased, and ReHo values in the frontal gyrus, middle temporal gyrus, precuneus, and posterior cingulate gyrus were decreased in CRSwOD patients. The ReHo values in the precuneus and posterior cingulate gyrus of CRSwOD patients were negatively correlated with Questionnaire of Olfactory Disorders-Negative Statements (QOD-NS) scores. Compared with CRSsOD patients, the ReHo values in cerebellar regions were increased and those in the inferior temporal gyrus, precuneus, postcentral, and paracentral gyrus were decreased in CRSwOD patients. The receiver operating characteristic (ROC) curve showed that the mean ReHo values significantly differed between the CRSwOD and CRSsOD groups.ConclusionSynchronization of regional brain activity in the regions of the secondary olfactory cortex orbitofrontal cortex (OFC), temporal gyrus, precuneus, and cerebellum may be closely related to the development of olfactory dysfunction. Precuneus and posterior cingulate gyrus may be critical brain areas of action for emotional dysfunction in CRSwOD patients

Identification of ZNF26 as a Prognostic Biomarker in Colorectal Cancer by an Integrated Bioinformatic Analysis

The dysregulation of transcriptional factors (TFs) leads to malignant growth and the development of colorectal cancer (CRC). Herein, we sought to identify the transcription factors relevant to the prognosis of colorectal cancer patients. We found 526 differentially expressed TFs using the TCGA database of colorectal cancer patients (n = 544) for the differential analysis of TFs (n = 1,665) with 210 upregulated genes as well as 316 downregulated genes. Subsequently, GO analysis and KEGG pathway analysis were performed for these differential genes for investigating their pathways and function. At the same time, we established a genetic risk scoring model for predicting the overall survival (OS) by using the mRNA expression levels of these differentially regulated TFs, and defined the CRC into low and high-risk categories which showed significant survival differences. The genetic risk scoring model included four high-risk genes (HSF4, HEYL, SIX2, and ZNF26) and two low-risk genes (ETS2 and SALL1), and validated the OS in two GEO databases (p = 0.0023 for the GSE17536, p = 0.0193 for the GSE29623). To analyze the genetic and epigenetic changes of these six risk-related TFs, a unified bioinformatics analysis was conducted. Among them, ZNF26 is progressive in CRC and its high expression is linked with a poor diagnosis as well. Knockdown of ZNF26 inhibits the proliferative capacity of CRC cells. Moreover, the positive association between ZNF26 and cyclins (CDK2, CCNE2, CDK6, CHEK1) was also identified. Therefore, as a novel biomarker, ZNF26 may be a promising candidate in the diagnosis and prognostic evaluation of colorectal cancer

Growth of PdCoO2 films with controlled termination by molecular-beam epitaxy and determination of their electronic structure by angle-resolved photoemission spectroscopy

Utilizing the powerful combination of molecular-beam epitaxy (MBE) and angle-resolved photoemission spectroscopy (ARPES), we produce and study the effect of different terminating layers on the electronic structure of the metallic delafossite PdCoO2. Attempts to introduce unpaired electrons and synthesize new antiferromagnetic metals akin to the isostructural compound PdCrO2 have been made by replacing cobalt with iron in PdCoO2 films grown by MBE. Using ARPES, we observe similar bulk bands in these PdCoO2 films with Pd-, CoO2-, and FeO2-termination. Nevertheless, Pd- and CoO2-terminated films show a reduced intensity of surface states. Additionally, we are able to epitaxially stabilize PdFexCo1-xO2 films that show an anomaly in the derivative of the electrical resistance with respect to temperature at 20 K, but do not display pronounced magnetic order

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees

Data accessibility statement: Full census data are available upon reasonable request from the ForestGEO data portal, http://ctfs.si.edu/datarequest/ We thank Margie Mayfield, three anonymous reviewers and Jacob Weiner for constructive comments on the manuscript. This study was financially supported by the National Key R&D Program of China (2017YFC0506100), the National Natural Science Foundation of China (31622014 and 31570426), and the Fundamental Research Funds for the Central Universities (17lgzd24) to CC. XW was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB3103). DS was supported by the Czech Science Foundation (grant no. 16-26369S). Yves Rosseel provided us valuable suggestions on using the lavaan package conducting SEM analyses. Funding and citation information for each forest plot is available in the Supplementary Information Text 1.Peer reviewedPostprin

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A Nonlinear Convex Decreasing Weights Golden Eagle Optimizer Technique Based on a Global Optimization Strategy

A novel approach called the nonlinear convex decreasing weights golden eagle optimization technique based on a global optimization strategy is proposed to overcome the limitations of the original golden eagle algorithm, which include slow convergence and low search accuracy. To enhance the diversity of the golden eagle, the algorithm is initialized with the Arnold chaotic map. Furthermore, nonlinear convex weight reduction is incorporated into the position update formula of the golden eagle, improving the algorithm’s ability to perform both local and global searches. Additionally, a final global optimization strategy is introduced, allowing the golden eagle to position itself in the best possible location. The effectiveness of the enhanced algorithm is evaluated through simulations using 12 benchmark test functions, demonstrating improved optimization performance. The algorithm is also tested using the CEC2021 test set to assess its performance against other algorithms. Several statistical tests are conducted to compare the efficacy of each method, with the enhanced algorithm consistently outperforming the others. To further validate the algorithm, it is applied to the cognitive radio spectrum allocation problem after discretization, and the results are compared to those obtained using traditional methods. The results indicate the successful operation of the updated algorithm. The effectiveness of the algorithm is further evaluated through five engineering design tasks, which provide additional evidence of its efficacy