An efficient ANN SoC for detecting Alzheimer's disease based on recurrent computing.

Alzheimer's Disease (AD) is an irreversible, degenerative condition that, while incurable, can have its progression slowed or impeded. While there are numerous methods utilizing neural networks for AD detection, there is a scarcity of High-performance AD detection chips. Moreover, excessively complex neural networks are not conducive to on-chip implementation and clinical applications. This study addresses the challenges of high misdiagnosis rates and significant hardware costs inherent in traditional AD detection techniques. A novel and efficient AD detection framework based on a recurrent computational strategy is proposed. The framework harnesses an Artificial Neural Network (ANN) embedded within a System on Chip (SoC) to perform sophisticated Electroencephalogram (EEG) analysis. The approach began by employing a reduced IEEE754 single-precision encoding method to hardware-encode the preprocessed EEG data, thereby minimizing the memory storage area. Next, data remapping techniques were utilized to ensure the continuity of the input data read addresses and reduce the memory access pressure during neural network computations. Subsequently, hierarchical and Processing Element (PE) reuse technologies were leveraged to perform the multiply-accumulate operations of the ANN. Finally, a step function was chosen to establish binary classification circuits dedicated to AD detection. Experimental results indicate that the optimized SoC achieves a 70 % reduction in area and a 50 % reduction in power consumption compared to traditional designs. For various neural network models, the detection model proposed in this paper incurs less overhead, with a training speed 3 to 4 times faster than other traditional models, and a high accuracy rate of 98.53 %.

Characterization of circulating tumor cells in patients with metastatic bladder cancer utilizing functionalized microfluidics.

Assessing the molecular profiles of bladder cancer (BC) from patients with locally advanced or metastatic disease provides valuable insights, such as identification of invasive markers, to guide personalized treatment. Currently, most molecular profiling of BC is based on highly invasive biopsy or transurethral tumor resection. Liquid biopsy takes advantage of less-invasive procedures to longitudinally profile disease. Circulating tumor cells (CTCs) isolated from blood are one of the key analytes of liquid biopsy. In this study, we developed a protein and mRNA co-analysis workflow for BC CTCs utilizing the graphene oxide (GO) microfluidic chip. The GO chip was conjugated with antibodies against both EpCAM and EGFR to isolate CTCs from 1 mL of blood drawn from BC patients. Following CTC capture, protein and mRNA were analyzed using immunofluorescent staining and ion-torrent-based whole transcriptome sequencing, respectively. Elevated CTC counts were significantly associated with patient disease status at the time of blood draw. We found a count greater than 2.5 CTCs per mL was associated with shorter overall survival. The invasive markers EGFR, HER2, CD31, and ADAM15 were detected in CTC subpopulations. Whole transcriptome sequencing showed distinct RNA expression profiles from patients with or without tumor burden at the time of blood draw. In patients with advanced metastatic disease, we found significant upregulation of metastasis-related and chemotherapy-resistant genes. This methodology demonstrates the capability of GO chip-based assays to identify tumor-related RNA signatures, highlighting the prognostic potential of CTCs in metastatic BC patients.

BioTrojans: viscoelastic microvalve-based attacks in flow-based microfluidic biochips and their countermeasures.

Flow-based microfluidic biochips (FMBs) are widely used in biomedical research and diagnostics. However, their security against potential material-level cyber-physical attacks remains inadequately explored, posing a significant future challenge. One of the main components, polydimethylsiloxane (PDMS) microvalves, is pivotal to FMBs' functionality. However, their fabrication, which involves thermal curing, makes them susceptible to chemical tampering-induced material degradation attacks. Here, we demonstrate one such material-based attack termed "BioTrojans," which are chemically tampered and optically stealthy microvalves that can be ruptured through low-frequency actuations. To chemically tamper with the microvalves, we altered the associated PDMS curing ratio. Attack demonstrations showed that BioTrojan valves with 30:1 and 50:1 curing ratios ruptured quickly under 2 Hz frequency actuations, while authentic microvalves with a 10:1 ratio remained intact even after being actuated at the same frequency for 2 days (345,600 cycles). Dynamic mechanical analyzer (DMA) results and associated finite element analysis revealed that a BioTrojan valve stores three orders of magnitude more mechanical energy than the authentic one, making it highly susceptible to low-frequency-induced ruptures. To counter BioTrojan attacks, we propose a security-by-design approach using smooth peripheral fillets to reduce stress concentration by over 50% and a spectral authentication method using fluorescent microvalves capable of effectively detecting BioTrojans.

Differential expression of ion channel coding genes in the endometrium of women experiencing recurrent implantation failures.

Our study probed the differences in ion channel gene expression in the endometrium of women with Recurrent Implantation Failure (RIF) compared to fertile women. We analyzed the relative expression of genes coding for T-type Ca2+, ENaC, CFTR, and KCNQ1 channels in endometrial samples from 20 RIF-affected and 10 control women, aged 22-35, via microarray analysis and quantitative real-time PCR. Additionally, we examined DNA methylation in the regulatory region of KCNQ1 using ChIP real-time PCR. The bioinformatics component of our research included Gene Ontology analysis, protein-protein interaction networks, and signaling pathway mapping to identify key biological processes and pathways implicated in RIF. This led to the discovery of significant alterations in the expression of ion channel genes in RIF women's endometrium, most notably an overexpression of CFTR and reduced expression of SCNN1A, SCNN1B, SCNN1G, CACNA1H, and KCNQ1. A higher DNA methylation level of KCNQ1's regulatory region was also observed in RIF patients. Gene-set enrichment analysis highlighted a significant presence of genes involved with ion transport and membrane potential regulation, particularly in sodium and calcium channel complexes, which are vital for cation movement across cell membranes. Genes were also enriched in broader ion channel and transmembrane transporter complexes, underscoring their potential extensive role in cellular ion homeostasis and signaling. These findings suggest a potential involvement of ion channels in the pathology of implantation failure, offering new insights into the mechanisms behind RIF and possible therapeutic targets.

Impedance Characteristics of Microfluidic Channels and Integrated Coplanar Parallel Electrodes as Design Parameters for Whole-Channel Analysis in Organ-on-Chip Micro-Systems.

Microfluidics have revolutionized cell culture by allowing for precise physical and chemical environmental control. Coupled with electrodes, microfluidic cell culture can be activated or have its changes sensed in real-time. We used our previously developed reliable and stable microfluidic device for cell growth and monitoring to design, fabricate, and characterize a whole-channel impedance-based sensor and used it to systematically assess the electrical and electrochemical influences of microfluidic channel boundaries coupled with varying electrode sizes, distances, coatings, and cell coverage. Our investigation includes both theoretical and experimental approaches to investigate how design parameters and insulating boundary conditions change impedance characteristics. We examined the system with various solutions using a frequency range of 0.5 Hz to 1 MHz and a modulation voltage of 50 mV. The results show that impedance is directly proportional to electrode distance and inversely proportional to electrode coating, area, and channel size. We also demonstrate that electrode spacing is a dominant factor contributing to impedance. In the end, we summarize all the relationships found and comment on the appropriateness of using this system to investigate barrier cells in blood vessel models and organ-on-a-chip devices. This fundamental study can help in the careful design of microfluidic culture constructs and models that require channel geometries and impedance-based biosensing.

A Device-on-Chip Solution for Real-Time Diffuse Correlation Spectroscopy Using FPGA.

Diffuse correlation spectroscopy (DCS) is a non-invasive technology for the evaluation of blood perfusion in deep tissue. However, it requires high computational resources for data analysis, which poses challenges in its implementation for real-time applications. To address the unmet need, we developed a novel device-on-chip solution that fully integrates all the necessary computational components needed for DCS. It takes the output of a photon detector and determines the blood flow index (BFI). It is implemented on a field-programmable gate array (FPGA) chip including a multi-tau correlator for the calculation of the temporal light intensity autocorrelation function and a DCS analyzer to perform the curve fitting operation that derives the BFI at a rate of 6000 BFIs/s. The FPGA DCS system was evaluated against a lab-standard DCS system for both phantom and cuff ischemia studies. The results indicate that the autocorrelation of the light correlation and BFI from both the FPGA DCS and the reference DCS matched well. Furthermore, the FPGA DCS system was able to achieve a measurement rate of 50 Hz and resolve pulsatile blood flow. This can significantly lower the cost and footprint of the computational components of DCS and pave the way for portable, real-time DCS systems.

Centrifugal Microfluidic Cell Culture Platform for Physiologically Relevant Virus Infection Studies: A Case Study with HSV-1 Infection of Periodontal Cells.

Static well plates remain the gold standard to study viral infections in vitro, but they cannot accurately mimic dynamic viral infections as they occur in the human body. Therefore, we established a dynamic cell culture platform, based on centrifugal microfluidics, to study viral infections in perfusion. To do so, we used human primary periodontal dental ligament (PDL) cells and herpes simplex virus-1 (HSV-1) as a case study. By microscopy, we confirmed that the PDL cells efficiently attached and grew in the chip. Successful dynamic viral infection of perfused PDL cells was monitored using fluorescent imaging and RT-qPCR-based experiments. Remarkably, viral infection in flow resulted in a gradient of HSV-1-infected cells gradually decreasing from the cell culture chamber entrance towards its end. The perfusion of acyclovir in the chip prevented HSV-1 spreading, demonstrating the usefulness of such a platform for monitoring the effects of antiviral drugs. In addition, the innate antiviral response of PDL cells, measured by interferon gene expression, increased significantly over time in conventional static conditions compared to the perfusion model. These results provide evidence suggesting that dynamic viral infections differ from conventional static infections, which highlights the need for more physiologically relevant in vitro models to study viral infections.

Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons.

Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfiguration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.

Analysis of okadaic acid using electrochemiluminescence imaging on microfluidic biosensing chip.

The sensitivity and specificity of electrochemiluminescence (ECL)-based biosensor directly rely on the property of luminophor, the type of sensing carriers and the effectiveness of signal amplification used in the sensor design, which poses a major challenge to manage these elements simultaneously. In this work, an aggregation-induced electrochemiluminescence (AIECL) microfluidic sensing chip using 4',4″,4‴,4‴'-(ethene-1,1,2,2-tetrayl)tetrabiphenyl-4-carboxylic acid (TPE)-derived hafnium-based metal-organic framework (Hf-MOF) as emitter was developed. An easily overlooked marine pollutant, okadaic acid (OA) with different concentrations ranging from 5.00 ng/mL to 1.50 × 104 ng/mL at the electrode is visualized imaging benefit from high luminescence efficiency of Hf-MOF coupled the rolling circle amplification strategy assisted by trans-cleavage activity of CRISPR/Cas12a. These highlights will solve the long-lasting task in the accurate analysis of small molecule pollutants, which can be able to provide more worthy reference solution about construction of novel ECL luminophor and signal extraction of low-abundance disease-related biomarkers.

Predicting anti-tumor efficacy of multi-functional nanomedicine on decellularized hepatocellular carcinoma-on-a-chip.

Traditional hepatocellular carcinoma-chip models lack the cell structure and microenvironments necessary for high pathophysiological correlation, leading to low accuracy in predicting drug efficacy and high production costs. This study proposed a decellularized hepatocellular carcinoma-on-a-chip model to screen anti-tumor nanomedicine. In this model, human hepatocellular carcinoma (HepG2) and human normal liver cells (L02) were co-cultured on a three-dimensional (3D) decellularized extracellular matrix (dECM) in vitro to mimic the tumor microenvironments of human hepatocellular carcinoma in vivo. Additionally, a smart nanomedicine was developed by encapsulating doxorubicin (DOX) into the ferric oxide (Fe3O4)-incorporated liposome nanovesicle (NLV/Fe+DOX). NLV/Fe+DOX selectively killed 78.59% ± 6.78% of HepG2 cells through targeted delivery and synergistic chemo-chemodynamic-photothermal therapies, while the viability of surrounding L02 cells on the chip model retained high, at over 90.0%. The drug efficacy tested using this unique chip model correlated well with the results of cellular and animal experiments. In summary, our proposed hepatocellular carcinoma-chip model is a low-cost yet accurate drug-testing platform with significant potential for drug screening.

Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag.

An understanding of the mechanisms and logic by which transcription factors coordinate gene regulation requires delineation of their genomic interactions at a genome-wide scale. Chromatin immunoprecipitation-sequencing (ChIP-seq) and more recent techniques, including CUT&Tag, typically reveal thousands of genomic interactions by transcription factors, but without insight into their functional roles. Due to cost and time considerations, optimization of ChIP experimental conditions is typically carried out only with representative interaction sites rather than through genome-wide analyses. Here, we describe insights gained from the titration of two chemical crosslinking reagents in genome-wide ChIP-seq experiments examining two members of the NF-κB family of transcription factors: RelA and c-Rel. We also describe a comparison of ChIP-seq and CUT&Tag. Our results highlight the large impact of ChIP-seq experimental conditions on the number of interactions detected, on the enrichment of consensus and non-consensus DNA motifs for the factor, and on the frequency with which the genomic interactions detected are located near potential target genes. We also found considerable consistency between ChIP-seq and CUT&Tag results, but with a substantial fraction of genomic interactions detected with only one of the two techniques. Together, the results demonstrate the dramatic impact of experimental conditions on the results obtained in a genome-wide analysis of transcription factor binding, highlighting the need for further scrutiny of the functional significance of these condition-dependent differences.

Studies of the interaction of graphene oxide (GO) with endothelial cells under static and flow conditions.

Graphene oxide, due to its unique properties, has several potential applications in biomedicine, especially as a drug carrier. Despite emerging studies on its cytotoxicity and uptake into cells, there are still gaps in knowledge on this area. When analyzing the internalization of nanomaterials, many different factors must be considered, including particle size, surface modifications, and interactions with biological fluids that can change their properties. In the present study, we evaluated the effects of graphene oxide fractions in different sizes and samples incubated in human serum on endothelial cells (HUVECs). In addition, the study was conducted in both macroscale and microscale using Cell-on-a-Chip technology to better replicate in vivo conditions. Our findings indicate that samples incubated with serum reduce the efficiency of fraction uptake into cells. It was also observed that the uptake efficiency of graphene oxide (GO) fractions is higher in the microscale (in more real to in vivo environment) compared to the macroscale. Our research has shown that in order to determine the correct interaction of new materials into mammalian cells, it is necessary to take into account many different biochemical and physical factors.

Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells.

Transcription factor (TF) gene knockout or knockdown experiments provide comprehensive downstream effects on gene regulation. However, distinguishing primary direct effects from secondary effects remains challenging. To assess the direct effect of TF binding events, we present a protocol for establishing a doxycycline (Dox)-inducible CRISPRd system in human pluripotent stem cells (hPSCs). We describe the steps for establishing CRISPRd host hPSCs, designing and preparing single-guide RNA (sgRNA) expression lentivirus vectors, generating CRISPRd hPSCs transduced with sgRNAs, and analyzing CRISPRd TF-block effects by chromatin immunoprecipitation (ChIP)-qPCR. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.

Design and implementation of a lab-on-a-chip for assisted reproductive technologies.

Introduction: The microfluidic device is highly optimized to remove oocytes from the cumulus-corona cell mass surrounding them. Additionally, it effectively captures and immobilizes the oocytes, aiding in assessing their quality and facilitating the injection of sperm into the oocyte. In this study, a novel microfluidic chip was designed and manufactured using conventional soft lithography methods. Methods: This research proposes the utilization of a microfluidic chip as a substitute for the conventional manual procedures involved in oocyte denudation, trapping, and immobilization. The microfluidic chip was modeled and simulated using COMSOL Multiphysics® 5.2 software to optimize and enhance its design and performance. The microfluidic chip was fabricated using conventional injection molding techniques on a polydimethylsiloxane substrate by employing soft lithography methods. Results: A hydrostatic force was applied to guide the oocyte through predetermined pathways to eliminate the cumulus cells surrounding the oocyte. The oocyte was subsequently confined within the designated trap region by utilizing hydraulic resistance along the paths and immobilized by applying vacuum force. Conclusion: The application of this chip necessitates a lower level of operator expertise compared to enzymatic and mechanical techniques. Moreover, it is feasible to continuously monitor the oocyte's state throughout the procedure. There is a reduced need for cultural media compared to more standard approaches.

Potential value of animal microphysiological systems.

Microphysiological systems (MPS) are designed to recapitulate aspects of tissue/organ physiology in vivo, thereby providing potential value in safety and efficacy assessments of FDA-regulated products and regulatory decision-making. While there have been significant advances in the development, use, and proposals of qualification criteria for human organ MPS, there remains a gap in the development using animal tissues. Animal MPS may be of value in many areas including the study of zoonotic diseases, assessment of the safety and efficacy of animal therapeutics, and possibly reduction of the use of animals in regulatory submissions for animal therapeutics. In addition, the development of MPS from various animal species enables comparison to animal in vivo data. This comparison, while not always critical for all contexts of use, could help gain confidence in the use and application of human MPS data for regulatory decision-making and for the potential identification of species-specific effects. The use of animal MPS is consistent with the replacement, reduction, and refinement (3Rs) principles of animal use by identifying toxic compounds before conducting in vivo studies and identifying the appropriate species for testing.

Microphysiological systems (MPS) mimic aspects of organs in humans or animals. These systems may provide information useful for FDA-regulated products. While there have been significant advances in the development of MPS made from human cells, there remains a gap in the development of MPS using animal cells. FDA believes animal MPS may be of value in many areas including the study of diseases transmitted from animals to humans, assessment of the safety and efficacy of animal drugs, and reduction of the use of animals in regulatory submissions. The development of animal MPS enables comparison to data from studies conducted in animals. This comparison provides confidence in the use of human MPS data for regulatory decision-making. The use of animal MPS is consistent with the 3Rs principles of animal use by allowing identification of toxic compounds before conducting animal studies and by helping select the appropriate species for further testing.

Forming Single-Cell-Derived Colon Cancer Organoid Arrays on a Microfluidic Chip for High Throughput Tumor Heterogeneity Analysis.

Single-cell-derived tumor organoids (STOs) possess a distinct genetic background, making them valuable tools for demonstrating tumor heterogeneity. In order to fulfill the high throughput demands of STO assays, we have developed a microfluidic chip containing 30 000 microwells, which is dedicated to a single cell culture approach for selective expansion and differential induction of cancer stem cells. The microwells are coated with a hydrophilic copolymer to eliminate cell adhesion, and the cell culture is supported by poly(ethylene glycol) (PEG) to establish a nonadhesive culture environment. By utilizing an input cell density of 7 × 103·mL-1, it is possible to construct a 4000 single cell culture system through stochastic cell occupation. We demonstrate that the addition of 15% PEG10000 in the cell culture medium effectively prevents cell loss while facilitating tumor stem cell expansion. As were demonstrated by HCT116, HT29, and SW480 colon cancer cells, the microfluidic approach achieved a STO formation rate of ∼20%, resulting in over 800 STOs generated from a single culture. Comprehensive analysis through histomorphology, immunohistochemistry, drug response evaluation, assessment of cell invasion, and biomarker detection reveals the heterogeneity among individual STOs. Specifically, the smaller STOs exhibited higher invasion and drug resistance capabilities compared with the larger ones. The developed microfluidic approach effectively facilitates STO formation and offers promising prospects for investigating tumor heterogeneity, as well as conducting personalized therapy-focused drug screening.

Decoding Clonal Hematopoiesis: Emerging Themes and Novel Mechanistic Insights.

Clonal hematopoiesis (CH), the relative expansion of mutant clones, is derived from hematopoietic stem cells (HSCs) with acquired somatic or cytogenetic alterations that improve cellular fitness. Individuals with CH have a higher risk for hematological and non-hematological diseases, such as cardiovascular disease, and have an overall higher mortality rate. Originally thought to be restricted to a small fraction of elderly people, recent advances in single-cell sequencing and bioinformatics have revealed that CH with multiple expanded mutant clones is universal in the elderly population. Just a few years ago, phylogenetic reconstruction across the human lifespan and novel sensitive sequencing techniques showed that CH can start earlier in life, decades before it was thought possible. These studies also suggest that environmental factors acting through aberrant inflammation might be a common theme promoting clonal expansion and disease progression. However, numerous aspects of this phenomenon remain to be elucidated and the precise mechanisms, context-specific drivers, and pathways of clonal expansion remain to be established. Here, we review our current understanding of the cellular mechanisms driving CH and specifically focus on how pro-inflammatory factors affect normal and mutant HSC fates to promote clonal selection.

Development of a Bladder Cancer-on-a-Chip Model to Assess Bladder Cancer Cell Invasiveness.

We have developed a bladder cancer-on-a-chip model which supports the 3D growth of cells and can be used to assess and quantify bladder cancer cell invasiveness in a physiologically appropriate environment. Three bladder cancer cell lines (T24, J82, and RT4) were resuspended in 50% Matrigel® and grown within a multi-channel organ-on-a-chip system. The ability of live cells to invade across into an adjacent 50% Matrigel®-only channel was assessed over a 2-day period. Cell lines isolated from patients with high-grade bladder cancer (T24 and J82) invaded across into the Matrigel®-only channel at a much higher frequency compared to cells isolated from a patient with low-grade cancer (RT4) (p < 0.001). The T24 and J82 cells also invaded further distances into the Matrigel®-only channel compared to the RT4 cells (p < 0.001). The cell phenotype within the model was maintained as assessed by cell morphology and immunohistochemical analysis of E-cadherin. Treatment with ATN-161, an α5ß1 integrin inhibitor and well-known migrastatic drug, caused a dose-dependent decrease in the invasiveness of the J82 cells (p < 0.01). The combined data demonstrate that our bladder cancer-on-a-chip model supports the retention of the bladder cancer cell phenotype and can be used to reproducibly assess and quantify the invasiveness of live bladder cancer cells.

A Hybrid Metadetector for Measuring Bell States of Optical Angular Momentum Entanglement.

High-dimensional entanglement of optical angular momentum has shown its enormous potential for increasing robustness and data capacity in quantum communication and information multiplexing, thus offering promising perspectives for quantum information science. To make better use of optical angular momentum entangled states, it is necessary to develop a reliable platform for measuring and analyzing them. Here, we propose a hybrid metadetector of monolayer transition metal dichalcogenide (TMD) integrated with spin Hall nanoantenna arrays for identifying Bell states of optical angular momentum. The corresponding states are converted into path-entangled states of propagative polaritonic modes for detection. Several Bell states in different forms are shown to be identified effectively. TMDs have emerged as an attractive platform for the next generation of on-chip optoelectronic devices. Our work may open up a new horizon for devising integrated quantum circuits based on these two-dimensional van der Waals materials.

GNSS Receiver Fingerprinting Based on Time Skew of Embedded CSAC Clock.

GNSS spoofing has become a significant security vulnerability threatening remote sensing systems. Hardware fingerprint-based GNSS receiver identification is one of the solutions to address this security issue. However, existing research has not provided a solution for distinguishing GNSS receivers of the same specification. This paper first theoretically proves that the CSACs (Chip-Scale Atomic Clocks) used in GNSS receivers have unique hardware noise and then proposes a fingerprinting scheme based on this hardware noise. Experiments based on the neural network method demonstrate that this fingerprint achieved an identification accuracy of 94.60% for commercial GNSS receivers of the same specification and performed excellently in anomaly detection, confirming the robustness of the fingerprinting method. This method shows a new real-time GNSS security monitoring method based on CSACs and can be easily used with any commercial GNSS receivers.