Red blood cell flickering activity locally controlled by holographic optical tweezers.

Red blood cells possess a singular mechanobiology, enabling efficient navigation through capillaries smaller than their own size. Their plasma membrane exhibits non-equilibrium shape fluctuation, often reported as enhanced flickering activity. Such active membrane motion is propelled by motor proteins that mediate interactions between the spectrin skeleton and the lipid bilayer. However, modulating the flickering in living red blood cells without permanently altering their mechanical properties represents a significant challenge. In this study, we developed holographic optical tweezers to generate a force field distributed along the equatorial membrane contour of individual red blood cells. In free-standing red blood cells, we observed heterogeneous flickering activity, attributed to localized membrane kickers. By employing holographic optical forces, these active kickers can be selectively halted under minimal invasion. Our findings shed light on the dynamics of membrane flickering and established a manipulation tool that could open new avenues for investigating mechanotransduction processes in living cells.

Excess endocrine growth hormone in acromegaly promotes the aggressiveness and metastasis of triple-negative breast cancer.

Pituitary adenoma-induced excess endocrine growth hormone (GH) secretion can lead to breast cancer development and metastasis. Herein, we used an acromegaly mouse model to investigate the role of excess endocrine GH on triple-negative breast cancer (TNBC) growth and metastasis. Additionally, we aimed to elucidate the molecular mechanism of transcription factor 20 (TCF20)/nuclear factor erythroid 2-related factor 2 (NRF2) signaling-mediated aggressiveness and metastasis of TNBC. Excess endocrine GH induced TCF20 activates the transcription of NRF2 and NRF2-target genes to facilitate TNBC metastasis. Inhibition of GH receptor (GHR) and TCF20 activity using the GHR antagonist or small-interfering RNA-induced gene knockdown resulted in reduced tumor volume and metastasis, suggesting that excess endocrine GH stimulates TCF20/NRF2 pathways in TNBC and promotes metastasis to the lung. GHR inhibitors present an effective therapeutic strategy to prevent TNBC cell growth and metastasis. Our findings revealed functional and mechanistic roles of the GH-TCF20-NRF2 signaling axis in TBNC progression.

Hydrothermal regulation of MnO2 on a wood-based RGO composite for achieving wide voltage windows and high energy density supercapacitors.

The increasing need for improved energy storage devices renders it particularly important that inexpensive electrodes with high capacitance, excellent cycling stability, and environment-friendly characteristics are developed. In this study, a wood-derived carbon@reduced graphene (WRG) conductive precursor with an average conductivity of 15.38 S/m was firstly synthesized. The binder-free WRG-MnO2 electrode was successfully constructed by growing MnO2 onto a WRG under hydrothermal conditions. The asymmetric supercapacitor assembled with the WRG-20MnO2 cathode exhibited excellent electrochemical capacitive behavior with a voltage window of 0-2 V, maximum energy density of 52.3 Wh kg-1, and maximum power density of 1642.7 W kg-1, which is mainly due to the distinctive icicle-shaped structure of the MnO2. Thus, a facile strategy for developing high-performance hierarchical porous carbon electrodes that can be used in supercapacitors was developed herein, which may provide new opportunities to improve the high added value of poplar wood.

Language model and its interpretability in biomedicine: A scoping review.

With advancements in large language models, artificial intelligence (AI) is undergoing a paradigm shift where AI models can be repurposed with minimal effort across various downstream tasks. This provides great promise in learning generally useful representations from biomedical corpora, at scale, which would empower AI solutions in healthcare and biomedical research. Nonetheless, our understanding of how they work, when they fail, and what they are capable of remains underexplored due to their emergent properties. Consequently, there is a need to comprehensively examine the use of language models in biomedicine. This review aims to summarize existing studies of language models in biomedicine and identify topics ripe for future research, along with the technical and analytical challenges w.r.t. interpretability. We expect this review to help researchers and practitioners better understand the landscape of language models in biomedicine and what methods are available to enhance the interpretability of their models.

Analysis and prediction in SCR experiments using GPT-4 with an effective chain-of-thought prompting strategy.

This study explores the use of large language models (LLMs) in interpreting and predicting experimental outcomes based on given experimental variables, leveraging the human-like reasoning and inference capabilities of LLMs, using selective catalytic reduction of NOx with NH3 as a case study. We implement the chain of thought (CoT) concept to formulate logical steps for uncovering connections within the data, introducing an "Ordered-and-Structured" CoT (OSCoT) prompting strategy. We compare the OSCoT strategy with the more conventional "One-Pot" CoT (OPCoT) approach and with human experts. We demonstrate that GPT-4, equipped with this new OSCoT prompting strategy, outperforms the other two settings and accurately predicts experimental outcomes and provides intuitive reasoning for its predictions.

Bioinformatics analysis identifies TGF-ß signaling pathway-associated molecular subtypes and gene signature in diabetic foot.

The role of transforming growth factor ß (TGF-ß) in inflammation and immune response is established, but the mechanism of TGF-ß signaling pathway-related genes (TRGs) in diabetic foot ulcer (DFU) is not fully understood. We aimed to investigate the contribution of TRGs in the identification, molecular categorization, and immune infiltration of DFU through bioinformatics analysis. TGF-ß signaling pathway is activated in DFU. 33 TRGs were upregulated. Regression analysis revealed TGFBR1 and TGFB1 as significant differential expression core genes, validated by quantitative real-time PCR. The diagnostic model with core genes had high clinical validity (AUC = 0.909). Core gene expression was associated with immune cell infiltration. A total of 5672 genes showed differential expression in TGF-related patterns, with differences in biological functions and immune infiltration. TGF-ß signaling pathway may be critical in DFU development.

Canagliflozin combined with aerobic exercise protects against chronic heart failure in rats.

To determine the efficacy and potential protective mechanism of canagliflozin combined with aerobic exercise in treating chronic heart failure (CHF). Isoproterenol was injected into rats to create CHF models. The rats were then subsequently divided into saline, canagliflozin (3 mg/kg/d), aerobic exercise training, and canagliflozin combined with aerobic exercise training. Compared to the CHF group, the canagliflozin combined with the aerobic exercise group had superior ventricular remodeling and cardiac function. In rats treated with canagliflozin combined with aerobic exercise, the expression of cytochrome P450 (CYP) 4A3, CYP4A8, COL1A1, COL3A1, and FN1 was reduced, while the expression of CYP26B1, ALDH1A2, and CYP1A1 increased significantly. Additionally, canagliflozin combined with aerobic exercise decreased the phosphorylation of AKT and ERK1/2. Canagliflozin combined with aerobic exercise has a positive effect on the development of CHF via the regulation of retinol metabolism and the AKT/ERK signaling pathway.

Exploring the relationship among soccer-related knowledge, attitude, practice, and self-health in Chinese campus soccer education.

China has promoted campus soccer for over a decade due to its potential health benefits. The study aimed to explore soccer knowledge (SK), soccer attitude (SA), soccer practice (SP), and health status among Chinese freshmen and sophomore undergraduates who had received campus soccer education. Of the 7419 participants, 1,069 were valid and included in the analysis. Structural equation modeling (SEM) results indicated SK is positively associated with SA (p < 0.001), but negatively with SP (p < 0.01). SA was positively linked to SP (p < 0.001). SK indirectly affected SP through SA (Z = 13.677). Random forest-tree-structured Parzen estimators (RF-TPE) with SHAP indicated SP holds primary importance with a strong negative impact on health. Additionally, differences in rankings for SK, SA, and SP were observed among gender and urban-rural groups. These results reveal current campus soccer education is suboptimal to health promotion.

Structural and vibrational properties of Sb2S3: Practical methodologies for accelerated research and application of this low dimensional material.

Recently, the interest for the family of low dimensional materials has increased significantly due to the anisotropic nature of their fundamental properties. Among them, antimony sulfide (Sb2S3) is considered a suitable material for various solid-state devices. Although the main advantages and physicochemical properties of Sb2S3 are known, some doubtful information remains in literature and methodologies to easily assess its critical properties are missing. In this study, an advanced characterization of several types of Sb2S3 samples, involving the Rietveld refinement of structural properties, and Raman spectroscopy analysis, completed with lattice dynamics investigations reveal important insights into the structural and vibrational characteristics of the material. Based on the gathered data, fast, non-destructive, and non-invasive methodologies for assessment of the crystallographic orientation and point defect concentration of Sb2S3 are proposed. With a high resolution in-sample and in-situ assessment, these methodologies will serve for accelerating the research and application of Sb2S3 in the research field.

Linel2D-Net: A deep learning approach to solving 2D linear elastic boundary value problems on image domains.

Efficient solution of physical boundary value problems (BVPs) remains a challenging task demanded in many applications. Conventional numerical methods require time-consuming domain discretization and solving techniques that have limited throughput capabilities. Here, we present an efficient data-driven DNN approach to non-iterative solving arbitrary 2D linear elastic BVPs. Our results show that a U-Net-based surrogate model trained on a representative set of reference FDM solutions can accurately emulate linear elastic material behavior with manifold applications in deformable modeling and simulation.

Mitochondria-ER contact sites expand during mitosis.

Mitochondria-ER contact sites (MERCS) are involved in energy homeostasis, redox and Ca2+ signaling, and inflammation. MERCS are heavily studied; however, little is known about their regulation during mitosis. Here, we show that MERCS expand during mitosis in three cell types using various approaches, including transmission electron microscopy, serial EM coupled to 3D reconstruction, and a split GFP MERCS marker. We further show enhanced Ca2+ transfer between the ER and mitochondria using either direct Ca2+ measurements or by quantifying the activity of Ca2+-dependent mitochondrial dehydrogenases. Collectively, our results support a lengthening of MERCS in mitosis that is associated with improved Ca2+ coupling between the two organelles. This augmented Ca2+ coupling could be important to support the increased energy needs of the cell during mitosis.

Laser-induced voltage of table salt for deep ultraviolet pulsed laser detection.

To meet the requirements of fast response and simple process of deep ultraviolet (UV) pulsed laser detector, table salt (TS) was used as laser detection material in combination with a variable resistor to achieve single-pulse laser detection. Under the irradiation of a KrF excimer laser, the laser-induced voltage (LIV) of TS was influenced by the dynamic process of laser-induced plasma, and the whole process was well fitted with the sum of the three exponential functions. As the applied bias voltage (Vb) and incident laser energy (Ein) increased, the LIV amplitude (Vp) increased and the response time decreased. When the variable resistor (R) was reduced to 14.7 Ω, the response time of LIV decreased from ∼300 µs to ∼20 ns, which is the same as the duration of laser pulse. This research provided a simple, low-cost, and fast method for the detection of UV single-pulse laser based on the laser-TS interaction.

Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution.

Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.

Extracellular matrix protein composition dynamically changes during murine forelimb development.

The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome was assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system. This resource will guide future research investigating the role of the matrisome during complex tissue development.

Microglia-endothelial cross-talk regulates diabetes-induced retinal vascular dysfunction through remodeling inflammatory microenvironment.

Inflammation-mediated crosstalk between neuroglial cells and endothelial cells (ECs) is a fundamental feature of many vascular diseases. Nevertheless, the landscape of inflammatory processes during diabetes-induced microvascular dysfunction remains elusive. Here, we applied single-cell RNA sequencing to elucidate the transcriptional landscape of diabetic retinopathy (DR). The transcriptome characteristics of microglia and ECs revealed two microglial subpopulations and three EC populations. Exploration of intercellular crosstalk between microglia and ECs showed that diabetes-induced interactions mainly participated in the inflammatory response and vessel development, with colony-stimulating factor 1 (CSF1) and CSF1 receptor (CSF1R) playing important roles in early cell differentiation. Clinically, we found that CSF1/CSF1R crosstalk dysregulation was associated with proliferative DR. Mechanistically, ECs secrete CSF1 and activate CSF1R endocytosis and the CSF1R phosphorylation-mediated MAPK signaling pathway, which elicits the differentiation of microglia and triggers the secretion of inflammatory factors, and subsequently foster angiogenesis by remodeling the inflammatory microenvironment through a positive feedback mechanism.

Spider webs capture environmental DNA from terrestrial vertebrates.

Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.

Computational screening and functional tuning of chemically stable metal organic frameworks for I2/CH3I capture in humid environments.

High chemical stability is of vital significance in rendering metal organic frameworks (MOFs) as promising adsorbents for capturing leaked radioactive nuclides, under real nuclear industrial conditions with high humidity. In this work, grand canonical Monte Carlo (GCMC) and density functional theory (DFT) methods have been employed to systematically evaluate I2/CH3I capture performances of 21 experimentally confirmed chemically stable MOFs in humid environments. Favorable structural factors and the influence of hydrophilicity for iodine capture were unveiled. Subsequently, the top-performing MIL-53-Al with flexible tunability was functionalized with different functional groups to achieve the better adsorption performance. It has been revealed that the adsorption affinity and pore volume were two major factors altered by the functionalization of polar functional groups, which collectively influenced the iodine adsorption properties. In general, this work has screened the chemically stable high-performance MOF iodine adsorbents and provided comprehensive insights into the key factors affecting I2/CH3I uptake and separation in humid environments.

Dual hybrid frameworks combining graph convolutional network with decoding for covering location problem.

The Covering Location Problem (CLP) is widely used for the efficient facility distribution. However, existing algorithms for this problem suffer from long computation times or suboptimal solutions. To address this, we propose two methods based on graph convolutional networks (GCN) to solve two types of covering location problems: the location set covering problem and the maximum covering location problem. The first method, GCN-Greedy, is a supervised algorithm that synergized with the Greedy algorithm as decoder. It designs a specialized loss function to train the model, tailored to the characteristics of the two covering location problems. The second method, reinforcement learning based on GCN with auto-regressive decoder (GCN-AR-RL), represents a reinforcement learning framework that integrates a GCN encoder with an auto-regressive decoder. The experimental results of these models demonstrate the remarkable accuracy and performance advantages. Additionally, we apply these two models to the realistic dataset and achieve good performance.

PERCEPT: Replacing binary p-value thresholding with scaling for more nuanced identification of sample differences.

Key to a biologists' capacity to understand data is the ability to make meaningful conclusions about differences in experimental observations. Typically, data are noisy, and conventional methods rely on replicates to average out noise and enable univariate statistical tests to assign p-values. Yet thresholding p-values to determine significance is controversial and often misleading, especially for omics datasets with few replicates. This study introduces PERCEPT, an alternative that transforms data using an ad-hoc scaling factor derived from p-values. By applying this method, low confidence effects are suppressed compared to high confidence ones, enabling clearer patterns to emerge from noisy datasets. The effectiveness of PERCEPT scaling is demonstrated using simulated datasets and published omics studies. The approach reduces the exclusion of datapoints, enhances accuracy, and enables nuanced interpretation of data. PERCEPT is easy to apply for the non-expert in statistics and provides researchers a straightforward way to improve data-driven analyses.

The first specific probe for pyrrolidine with multifunction by the interaction mechanism of atomic economic reaction.

Pyrrolidine (PyD) has an important impact on the environment and human health. However, there is currently no method for trace detection of PyD. Here, we successfully designed diaminomethylene-4H-pyran (1) as the first specific fluorescent probe for PyD. Only by adding PyD to probe 1, there is blue fluorescence at 455 nm, and the color of the solution changes from colorless to yellow. The detection limit is 1.12 × 10-6 M, and the response time is less than 5 min. Meanwhile, probe 1 can also sense the gaseous PyD and detect PyD in actual water samples. Moreover, due to the low biological toxicity, probe 1 can detect the exogenous PyD in zebrafish. The preliminary mechanism shows that probe 1 and PyD undergo a combination-type chemical reaction to generate a new substance 1-PyD. Therefore, the 100% atom utilization reaction enables probe 1 to exhibit specific adsorption and removal of PyD.