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PloS One 2024This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital...
This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital management of cultural heritage. By introducing an improved Genetic Algorithm (GA), digital management and access efficiency are enhanced, to bring substantial optimization and innovation to the digital management of cultural heritage. Based on the collection of art museums, this study first integrates the collection's images, texts, and metadata with multi-source intelligent information to achieve a more accurate and comprehensive description of digital content. Second, a GA is introduced, and a GA 2 Convolutional Neural Network (GA2CNN) optimization model combining domain knowledge is proposed. Moreover, the convergence speed of traditional GA is improved to adapt to the characteristics of cultural heritage data. Lastly, the Convolutional Neural Network (CNN), GA, and GA2CNN are compared to verify the proposed system's superiority. The results show that in all models, the sample output results' actual value is 2.62, which represents the real data observation results. For sample number 5, compared with the actual value of 2.62, the predicted values of the GA2CNN and GA models are 2.6177 and 2.6313, and their errors are 0.0023 and 0.0113. The CNN model's predicted value is 2.6237, with an error of 0.0037. It can be found that the network fitting accuracy after optimization of the GA2CNN model is high, and the predicted value is very close to the actual value. The digital retrieval system integrated with the GA2CNN model has a good performance in enhancing retrieval efficiency and accuracy. This study provides technical support for the digital organization and display of cultural heritage and offers valuable references for innovative exploration of museum information management in the digital era.
Topics: Museums; Algorithms; Neural Networks, Computer; Information Storage and Retrieval; Art; Humans
PubMed: 38917118
DOI: 10.1371/journal.pone.0305690 -
BioRxiv : the Preprint Server For... Jun 2024Methodological advances in neuroscience have enabled the collection of massive datasets which demand innovative approaches for scientific communication. Existing...
Methodological advances in neuroscience have enabled the collection of massive datasets which demand innovative approaches for scientific communication. Existing platforms for data storage lack intuitive tools for data exploration, limiting our ability to interact effectively with these brain-wide datasets. We introduce two public websites: Data and Atlas developed for the International Brain Laboratory which provide access to millions of behavioral trials and hundreds of thousands of individual neurons. These interfaces allow users to discover both the raw and processed brain-wide data released by the IBL at the scale of the whole brain, individual sessions, trials, and neurons. By hosting these data interfaces as websites they are available cross-platform with no installation. By releasing each site's code as a modular open-source framework, other researchers can easily develop their own web interfaces and explore their own data. As neuroscience datasets continue to expand, customizable web interfaces offer a glimpse into a future of streamlined data exploration and act as blueprints for future tools.
PubMed: 38915704
DOI: 10.1101/2024.06.07.597950 -
BioRxiv : the Preprint Server For... Jun 2024Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of the...
BACKGROUND
Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of the VCF data model (either as text or packed binary) emphasises efficient retrieval of all data for a given variant, but accessing data on a field or sample basis is inefficient. Biobank scale datasets currently available consist of hundreds of thousands of whole genomes and hundreds of terabytes of compressed VCF. Row-wise data storage is fundamentally unsuitable and a more scalable approach is needed.
RESULTS
We present the VCF Zarr specification, an encoding of the VCF data model using Zarr which makes retrieving subsets of the data much more efficient. Zarr is a cloud-native format for storing multi-dimensional data, widely used in scientific computing. We show how this format is far more efficient than standard VCF based approaches, and competitive with specialised methods for storing genotype data in terms of compression ratios and calculation performance. We demonstrate the VCF Zarr format (and the vcf2zarr conversion utility) on a subset of the Genomics England aggV2 dataset comprising 78,195 samples and 59,880,903 variants, with a 5X reduction in storage and greater than 300X reduction in CPU usage in some representative benchmarks.
CONCLUSIONS
Large row-encoded VCF files are a major bottleneck for current research, and storing and processing these files incurs a substantial cost. The VCF Zarr specification, building on widely-used, open-source technologies has the potential to greatly reduce these costs, and may enable a diverse ecosystem of next-generation tools for analysing genetic variation data directly from cloud-based object stores.
PubMed: 38915693
DOI: 10.1101/2024.06.11.598241 -
BioRxiv : the Preprint Server For... Jun 2024Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT's DNA synthesis...
Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT's DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants in high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell History Recording by Ordered Insertion (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested , revealing concordance between each variant's bias and the bias determined from the multiplexed high throughput assay. Overall, our work, and the multiplex assay it features, should support the continued development of TdT-based DNA recorders, applications of TdT, and further study of the biology of TdT.
PubMed: 38915690
DOI: 10.1101/2024.06.11.598561 -
BioRxiv : the Preprint Server For... Jun 2024Entomopathogenic nematodes (EPNs) exhibit a bending-elastic instability, or kink, before becoming airborne, a feature hypothesized but not proven to enhance jumping...
Entomopathogenic nematodes (EPNs) exhibit a bending-elastic instability, or kink, before becoming airborne, a feature hypothesized but not proven to enhance jumping performance. Here, we provide the evidence that this kink is crucial for improving launch performance. We demonstrate that EPNs actively modulate their aspect ratio, forming a liquid-latched closed loop over a slow timescale (1 s), then rapidly open it (10 µs), achieving heights of 20 body lengths (BL) and generating ∼ 10 W/Kg of power. Using jumping nematodes, a bio-inspired Soft Jumping Model (SoftJM), and computational simulations, we explore the mechanisms and implications of this kink. EPNs control their takeoff direction by adjusting their head position and center of mass, a mechanism verified through phase maps of jump directions in simulations and SoftJM experiments. Our findings reveal that the reversible kink instability at the point of highest curvature on the ventral side enhances energy storage using the nematode's limited muscular force. We investigated the impact of aspect ratio on kink instability and jumping performance using SoftJM, and quantified EPN cuticle stiffness with AFM, comparing it with . This led to a stiffness-modified SoftJM design with a carbon fiber backbone, achieving jumps of ∼25 BL. Our study reveals how harnessing kink instabilities, a typical failure mode, enables bidirectional jumps in soft robots on complex substrates like sand, offering a novel approach for designing limbless robots for controlled jumping, locomotion, and even planetary exploration.
PubMed: 38915562
DOI: 10.1101/2024.06.07.598012 -
BioRxiv : the Preprint Server For... Jun 2024We implemented a multimodal set of functional imaging techniques optimized for deep-tissue imaging to investigate how cancer cells invade surrounding tissues and how...
We implemented a multimodal set of functional imaging techniques optimized for deep-tissue imaging to investigate how cancer cells invade surrounding tissues and how their physiological properties change in the process. As a model for cancer invasion of the extracellular matrix, we created 3D spheroids from triple-negative breast cancer cells (MDA-MB-231) and non-tumorigenic breast epithelial cells (MCF-10A). We analyzed multiple hallmarks of cancer within the same spheroid by combining a number of imaging techniques, such as metabolic imaging of NADH by Fluorescence Lifetime Imaging Microscopy (NADH-FLIM), hyperspectral imaging of a solvatochromic lipophilic dye (Nile Red) and extracellular matrix imaging by Second Harmonic Generation (SHG). We included phasor-based bioimage analysis of spheroids at three different time points, tracking both morphological and biological properties, including cellular metabolism, fatty acids storage, and collagen organization. Employing this multimodal deep-imaging framework, we observed and quantified cancer cell plasticity in response to changes in the environment composition.
PubMed: 38915530
DOI: 10.1101/2024.06.10.598307 -
BioRxiv : the Preprint Server For... Jun 2024Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. Here, we leveraged a diversity outbred mouse population to map the...
UNLABELLED
Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. Here, we leveraged a diversity outbred mouse population to map the genetic drivers of fresh/stored RBC metabolism and extravascular hemolysis upon storage and transfusion in 350 mice. We identify the ferrireductase Steap3 as a critical regulator of a ferroptosis-like process of lipid peroxidation. Steap3 polymorphisms were associated with RBC iron content, in vitro hemolysis, and in vivo extravascular hemolysis both in mice and 13,091 blood donors from the Recipient Epidemiology and Donor evaluation Study. Using metabolite Quantitative Trait Loci analyses, we identified a network of gene products (FADS1/2, EPHX2 and LPCAT3) - enriched in donors of African descent - associated with oxylipin metabolism in stored human RBCs and related to Steap3 or its transcriptional regulator, the tumor protein TP53. Genetic variants were associated with lower in vivo hemolysis in thousands of single-unit transfusion recipients.
HIGHLIGHTS
Steap3 regulates lipid peroxidation and extravascular hemolysis in 350 diversity outbred miceSteap3 SNPs are linked to RBC iron, hemolysis, vesiculation in 13,091 blood donorsmQTL analyses of oxylipins identified ferroptosis-related gene products FADS1/2, EPHX2, LPCAT3Ferroptosis markers are linked to hemoglobin increments in transfusion recipients.
PubMed: 38915523
DOI: 10.1101/2024.06.11.598512 -
BioRxiv : the Preprint Server For... Jun 2024facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD...
facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations. The key ingredient of the generalized Rouse model is the Zimm matrix that we compute from equilibrium MMC simulations. We compute two flavors of Zimm matrices, one referred to as the single-chain model that accounts only for intra-chain contacts, and the other referred to as a collective model, that accounts for inter-chain interactions. The single-chain model systematically overestimates the storage and loss moduli, whereas the collective model reproduces the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two models proves to be most accurate. In line with the theory of Rouse, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic versus dominantly viscous behaviors is influenced by the totality of the relaxation modes. Hence, our analysis suggests that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain distributions of relaxation times that underlie the dynamics within condensates.
PubMed: 38915484
DOI: 10.1101/2024.06.11.598543 -
Communications Biology Jun 2024Red blood cell (RBC) transfusions facilitate many life-saving acute and chronic interventions. Transfusions are enabled through the gold-standard hypothermic storage of...
Red blood cell (RBC) transfusions facilitate many life-saving acute and chronic interventions. Transfusions are enabled through the gold-standard hypothermic storage of RBCs. Today, the demand for RBC units is unfulfilled, partially due to the limited storage time, 6 weeks, in hypothermic storage. This time limit stems from high metabolism-driven storage lesions at +1-6 °C. A recent and promising alternative to hypothermic storage is the supercooled storage of RBCs at subzero temperatures, pioneered by our group. Here, we report on long-term supercooled storage of human RBCs at physiological hematocrit levels for up to 23 weeks. Specifically, we assess hypothermic RBC additive solutions for their ability to sustain supercooled storage. We find that a commercially formulated next-generation solution (Erythro-Sol 5) enables the best storage performance and can form the basis for further improvements to supercooled storage. Our analyses indicate that oxidative stress is a prominent time- and temperature-dependent injury during supercooled storage. Thus, we report on improved supercooled storage of RBCs at -5 °C by supplementing Erythro-Sol 5 with the exogenous antioxidants, resveratrol, serotonin, melatonin, and Trolox. Overall, this study shows the long-term preservation potential of supercooled storage of RBCs and establishes a foundation for further improvement toward clinical translation.
Topics: Erythrocytes; Humans; Blood Preservation; Cold Temperature; Antioxidants; Oxidative Stress; Cryopreservation; Time Factors
PubMed: 38914723
DOI: 10.1038/s42003-024-06463-4 -
Scientific Reports Jun 2024We explore light storage in antirelaxation-coated and buffer-gas-filled alkali vapor cells, employing electromagnetically induced transparency (EIT) in warm rubidium...
We explore light storage in antirelaxation-coated and buffer-gas-filled alkali vapor cells, employing electromagnetically induced transparency (EIT) in warm rubidium vapor. We conduct a comparative study of light storage performance under identical experimental conditions for these two cell types. Using a buffer-gas-filled cell resulted in approximately a tenfold improvement in memory efficiency and storage time compared to antirelaxation-coated cells. Moreover, we demonstrate that memory efficiency can be further enhanced by choosing a near-resonant EIT -scheme over a resonant one. Our findings provide valuable insights for optimizing light storage, thereby contributing to the development of field-deployable quantum memories.
PubMed: 38914638
DOI: 10.1038/s41598-024-63489-8