-
Materials Today. Bio Jun 2024This study introduces a novel mechanobiology assay, named "i-Rheo-optical assay", that integrates rheology with optical microscopy for analysing the viscoelastic...
This study introduces a novel mechanobiology assay, named "i-Rheo-optical assay", that integrates rheology with optical microscopy for analysing the viscoelastic properties of multicellular spheroids. These spheroids serve as three-dimensional models resembling tissue structures. The innovative technique enables real-time observation and quantification of morphological responses to applied stress using a cost-effective microscope coverslip for constant compression force application. By bridging a knowledge gap in biophysical research, which has predominantly focused on the elastic properties while only minimally exploring the viscoelastic nature in multicellular systems, the i-Rheo-optical assay emerges as an effective tool. It facilitates the measurement of broadband viscoelastic compressional moduli in spheroids, here derived from cancer (PANC-1) and non-tumoral (NIH/3T3) cell lines during compression tests. This approach plays a crucial role in elucidating the mechanical properties of spheroids and holds potential for identifying biomarkers to discriminate between healthy tissues and their pathological counterparts. Offering comprehensive insights into the biomechanical behaviour of biological systems, i-Rheo-optical assay marks a significant advancement in tissue engineering, cancer research, and therapeutic development.
PubMed: 38693994
DOI: 10.1016/j.mtbio.2024.101066 -
Science Advances May 2024Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity,... (Review)
Review
Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity, reproducibility, and generalizability. These failures can hinder scientific progress, lead to false consensus around invalid claims, and undermine the credibility of ML-based science. ML methods are often applied and fail in similar ways across disciplines. Motivated by this observation, our goal is to provide clear recommendations for conducting and reporting ML-based science. Drawing from an extensive review of past literature, we present the REFORMS checklist (recommendations for machine-learning-based science). It consists of 32 questions and a paired set of guidelines. REFORMS was developed on the basis of a consensus of 19 researchers across computer science, data science, mathematics, social sciences, and biomedical sciences. REFORMS can serve as a resource for researchers when designing and implementing a study, for referees when reviewing papers, and for journals when enforcing standards for transparency and reproducibility.
Topics: Machine Learning; Consensus; Humans; Reproducibility of Results; Science
PubMed: 38691601
DOI: 10.1126/sciadv.adk3452 -
PNAS Nexus Apr 2024Optical fibers aim to image in vivo biological processes. In this context, high spatial resolution and stability to fiber movements are key to enable decision-making...
Optical fibers aim to image in vivo biological processes. In this context, high spatial resolution and stability to fiber movements are key to enable decision-making processes (e.g. for microendoscopy). Recently, a single-pixel imaging technique based on a multicore fiber photonic lantern has been designed, named computational optical imaging using a lantern (COIL). A proximal algorithm based on a sparsity prior, dubbed SARA-COIL, has been further proposed to solve the associated inverse problem, to enable image reconstructions for high resolution COIL microendoscopy. In this work, we develop a data-driven approach for COIL. We replace the sparsity prior in the proximal algorithm by a learned denoiser, leading to a plug-and-play (PnP) algorithm. The resulting PnP method, based on a proximal primal-dual algorithm, enables to solve the Morozov formulation of the inverse problem. We use recent results in learning theory to train a network with desirable Lipschitz properties, and we show that the resulting primal-dual PnP algorithm converges to a solution to a monotone inclusion problem. Our simulations highlight that the proposed data-driven approach improves the reconstruction quality over variational SARA-COIL method on both simulated and real data.
PubMed: 38689704
DOI: 10.1093/pnasnexus/pgae164 -
PloS One 2024Bovine tuberculosis is usually diagnosed using tuberculin skin tests or at post-mortem. Recently, we have developed a serological test for bovine tuberculosis in cattle...
Bovine tuberculosis is usually diagnosed using tuberculin skin tests or at post-mortem. Recently, we have developed a serological test for bovine tuberculosis in cattle which shows a high degree of accuracy using serum samples. Here, we have assessed the performance of the test using individual bovine milk samples. The diagnostic specificity estimate using the high sensitivity setting of the test was 99.7% (95% CI: 99.2-99.9). This estimate was not altered significantly by tuberculin boosting. The relative sensitivity estimates of the test using the high sensitivity setting in milk samples from comparative skin test positive animals was 90.8% (95% CI: 87.1-93.6) with boosting. In animals with lesions, the relative sensitivity was 96.0% (95% CI: 89.6-98.7). Analysis of paired serum and milk samples from skin test positive animals showed correlation coefficients ranging from 0.756-0.955 for individual antigens used in the test. Kappa analysis indicated almost perfect agreement between serum and milk results, while McNemar marginal homogeneity analysis showed no statistically significant differences between the two media. The positive and negative likelihood ratio were 347.8 (95% CI: 112.3-1077.5) and 0.092 (95% CI: 0.07-0.13) respectively for boosted samples from skin test positive animals. The results show that the test has high sensitivity and specificity in individual milk samples and thus milk samples could be used for the diagnosis of bovine tuberculosis.
Topics: Animals; Cattle; Milk; Tuberculosis, Bovine; Sensitivity and Specificity; Antibodies, Bacterial; Tuberculin Test; Mycobacterium bovis; Female; Antigens, Bacterial
PubMed: 38687765
DOI: 10.1371/journal.pone.0301609 -
Particle and Fibre Toxicology Apr 2024Plastic accumulation in the environment is rapidly increasing, and nanoplastics (NP), byproducts of environmental weathering of bulk plastic waste, pose a significant...
Plastic accumulation in the environment is rapidly increasing, and nanoplastics (NP), byproducts of environmental weathering of bulk plastic waste, pose a significant public health risk. Particles may enter the human body through many possible routes such as ingestion, inhalation, and skin absorption. However, studies on NP penetration and accumulation in human skin are limited. Loss or reduction of the keratinized skin barrier may enhance the skin penetration of NPs. The present study investigated the entry of NPs into a human skin system modeling skin with compromised barrier functions and cellular responses to the intracellular accumulations of NPs. Two in vitro models were employed to simulate human skin lacking keratinized barriers. The first model was an ex vivo human skin culture with the keratinized dermal layer (stratum corneum) removed. The second model was a 3D keratinocyte/dermal fibroblast cell co-culture model with stratified keratinocytes on the top and a monolayer of skin fibroblast cells co-cultured at the bottom. The penetration and accumulation of the NPs in different cell types were observed using fluorescent microscopy, confocal microscopy, and cryogenic electron microscopy (cryo-EM). The cellular responses of keratinocytes and dermal fibroblast cells to stress induced by NPs stress were measured. The genetic regulatory pathway of keratinocytes to the intracellular NPs was identified using transcript analyses and KEGG pathway analysis. The cellular uptake of NPs by skin cells was confirmed by imaging analyses. Transepidermal transport and penetration of NPs through the skin epidermis were observed. According to the gene expression and pathway analyses, an IL-17 signaling pathway was identified as the trigger for cellular responses to internal NP accumulation in the keratinocytes. The transepidermal NPs were also found in co-cultured dermal fibroblast cells and resulted in a large-scale transition from fibroblast cells to myofibroblast cells with enhanced production of α-smooth muscle actin and pro-Collagen Ia. The upregulation of inflammatory factors and cell activation may result in skin inflammation and ultimately trigger immune responses.
Topics: Keratinocytes; Humans; Coculture Techniques; Fibroblasts; Nanoparticles; Skin Absorption; Skin; Microplastics; Cells, Cultured; Particle Size
PubMed: 38685063
DOI: 10.1186/s12989-024-00583-9 -
EMBO Reports May 2024The article processing charges associated with open-access publishing are unaffordable for some scientists. One solution is to break the APC down into its component... (Review)
Review
The article processing charges associated with open-access publishing are unaffordable for some scientists. One solution is to break the APC down into its component parts, enabling scientists to spread the costs over multiple providers and several years. [Image: see text]
Topics: Humans; Animals
PubMed: 38684908
DOI: 10.1038/s44319-024-00138-1 -
Gastroenterology Report 2024Visceral fat represents a metabolically active entity linked to adverse metabolic sequelae of obesity. We aimed to determine if celiac artery mesenteric fat thickness...
BACKGROUND
Visceral fat represents a metabolically active entity linked to adverse metabolic sequelae of obesity. We aimed to determine if celiac artery mesenteric fat thickness can be reliably measured during endoscopic ultrasound (EUS), and if these measurements correlate with metabolic disease burden.
METHODS
This was a retrospective analysis of patients who underwent celiac artery mesenteric fat measurement with endosonography (CAMEUS) measurement at a tertiary referral center, and a validation prospective trial of patients with obesity and nonalcoholic steatohepatitis who received paired EUS exams with CAMEUS measurement before and after six months of treatment with an intragastric balloon.
RESULTS
CAMEUS was measured in 154 patients [56.5% females, mean age 56.5 ± 18.0 years, body mass index (BMI) 29.8 ± 8.0 kg/m] and was estimated at 14.7 ± 6.5 mm. CAMEUS better correlated with the presence of non-alcoholic fatty liver disease (NAFLD) ( = 0.248, <0.001) than BMI ( = 0.153, <0.001), and significantly correlated with metabolic parameters and diseases. After six months of intragastric balloon placement, the prospective cohort experienced 11.7% total body weight loss, 1.3 points improvement in hemoglobin A1c (=0.001), and a 29.4% average decrease in CAMEUS (-6.4±5.2 mm, <0.001). CAMEUS correlated with improvements in weight ( = 0.368), aspartate aminotransferase to platelet ratio index ( = 0.138), and NAFLD activity score ( = 0.156) (all <0.05).
CONCLUSIONS
CAMEUS is a novel measure that is significantly correlated with critical metabolic indices and can be easily captured during routine EUS to risk-stratify susceptible patients. This station could allow for EUS access to sampling and therapeutics of this metabolic region.
PubMed: 38681751
DOI: 10.1093/gastro/goae039 -
Frontiers in Neuroinformatics 2024simulations are a powerful tool in modern neuroscience for enhancing our understanding of complex brain systems at various physiological levels. To model biologically...
INTRODUCTION
simulations are a powerful tool in modern neuroscience for enhancing our understanding of complex brain systems at various physiological levels. To model biologically realistic and detailed systems, an ideal simulation platform must possess: (1) high performance and performance scalability, (2) flexibility, and (3) ease of use for non-technical users. However, most existing platforms and libraries do not meet all three criteria, particularly for complex models such as the Hodgkin-Huxley (HH) model or for complex neuron-connectivity modeling such as gap junctions.
METHODS
This work introduces , an exascale-ready, flexible library for simulating HH models on multi-FPGA platforms. Utilizing FPGA-based Data-Flow Engines (DFEs) and the dataflow programming paradigm, ExaFlexHH addresses all three requirements. The library is also parameterizable and compliant with NeuroML, a prominent brain-description language in computational neuroscience. We demonstrate the performance scalability of the platform by implementing a highly demanding extended-Hodgkin-Huxley (eHH) model of the Inferior Olive using ExaFlexHH.
RESULTS
Model simulation results show linear scalability for unconnected networks and near-linear scalability for networks with complex synaptic plasticity, with a 1.99 × performance increase using two FPGAs compared to a single FPGA simulation, and 7.96 × when using eight FPGAs in a scalable ring topology. Notably, our results also reveal consistent performance efficiency in GFLOPS per watt, further facilitating exascale-ready computing speeds and pushing the boundaries of future brain-simulation platforms.
DISCUSSION
The ExaFlexHH library shows superior resource efficiency, quantified in FLOPS per hardware resources, benchmarked against other competitive FPGA-based brain simulation implementations.
PubMed: 38680548
DOI: 10.3389/fninf.2024.1330875 -
Cognition Jul 2024Voices are fundamentally social stimuli, and their importance to the self may be underpinned by how far they can be used to express the self and achieve communicative...
Voices are fundamentally social stimuli, and their importance to the self may be underpinned by how far they can be used to express the self and achieve communicative goals. This paper examines how self-bias and agency over a synthesised voice is altered when that voice is used to represent the self in social interaction. To enable participants to use a new voice, a novel two-player game was created, in which participants communicated online using a text-to-speech (TTS) synthesised voice. We then measured self-bias and sense of agency attributed to this synthesised voice, comparing participants who had used their new voice to interact with another person (n = 44) to a control group of participants (n = 44) who had been only briefly exposed to the voices. We predicted that the new, synthesised self-voice would be more perceptually prioritised after it had been self-produced. Further, that participants' sense of agency over the voice would be increased, if they had experienced self-producing the voice, relative to those who only owned it. Contrary to the hypothesis, the results indicated that both experimental participants and control participants similarly prioritised the new synthesised voice and experienced a similar degree of agency over it, relative to voices owned by others. Critically then, being able to produce the new voice in a social interaction did not modulate bias towards it nor participant's sense of agency over it. These results suggest that merely having ownership over a new voice may be sufficient to generate a perceptual bias and a sense of agency over it.
Topics: Humans; Female; Male; Adult; Young Adult; Voice; Self Concept; Social Interaction; Ownership; Adolescent
PubMed: 38678806
DOI: 10.1016/j.cognition.2024.105804 -
Sensors (Basel, Switzerland) Apr 2024Electric-field energy harvesters (EFEHs) have emerged as a promising technology for harnessing the electric field surrounding energized environments. Current research...
Electric-field energy harvesters (EFEHs) have emerged as a promising technology for harnessing the electric field surrounding energized environments. Current research indicates that EFEHs are closely associated with Tribo-Electric Nano-Generators (TENGs). However, the performance of TENGs in energized environments remains unclear. This work aims to evaluate the performance of TENGs in electric-field energy harvesting applications. For this purpose, TENGs of different sizes, operating in single-electrode mode were conceptualized, assembled, and experimentally tested. Each TENG was mounted on a 1.5 HP single-phase induction motor, operating at nominal parameters of 8 A, 230 V, and 50 Hz. In addition, the contact layer was mounted on a linear motor to control kinematic stimuli. The TENGs successfully induced electric fields and provided satisfactory performance to collect electrostatic charges in fairly variable electric fields. Experimental findings disclosed an approximate increase in energy collection ranging from 1.51% to 10.49% when utilizing TENGs compared to simple EFEHs. The observed correlation between power density and electric field highlights TENGs as a more efficient energy source in electrified environments compared to EFEHs, thereby contributing to the ongoing research objectives of the authors.
PubMed: 38676124
DOI: 10.3390/s24082507