Biology subjects

Zheng, Z.

Publications and source records attributed to Zheng, Z..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Immune regulators EDS1 and PAD4 constrain ADR1-dependent disease resistance in rice

Withdrawal StatementThe authors have withdrawn this manuscript owing to finding inconsistencies in genotyping of kitaake rice eds1 pad4 double mutant lines and to establishing that combined loss of EDS1 and PAD4 does not underlie the stunted autoimmune-like phenotype reported in this preprint. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors: Jane Parker, Thomas Kroj and Haitao Cui (co-corresponding)

plant biology↗

bioRxiv2024

CPT1A Mediates Radiation Sensitivity in Colorectal Cancer

The prevalence and mortality rates of colorectal cancer (CRC) are increasing worldwide. Radiation resistance hinders radiotherapy, a standard treatment for advanced CRC, leading to local recurrence and metastasis. Elucidating the molecular mechanisms underlying radioresistance in CRC is critical to enhance therapeutic efficacy and patient outcomes. Bioinformatic analysis and tumour tissue examination were conducted to investigate the CPT1A mRNA and protein levels in CRC and their correlation with radiotherapy efficacy. Furthermore, lentiviral overexpression and CRISPR/Cas9 lentiviral vectors, along with in vitro and in vivo radiation experiments, were used to explore the effect of CPT1A on radiosensitivity. Additionally, transcriptomic sequencing, molecular biology experiments, and bioinformatic analyses were employed to elucidate the molecular mechanisms by which CPT1A regulates radiosensitivity. CPT1A was significantly downregulated in CRC and negatively correlated with responsiveness to neoadjuvant radiotherapy. Functional studies suggested that CPT1A mediates radiosensitivity, influencing reactive oxygen species (ROS) scavenging and DNA damage response. Transcriptomic and molecular analyses highlighted the involvement of the peroxisomal pathway. Mechanistic exploration revealed that CPT1A downregulates the FOXM1-SOD1/SOD2/CAT axis, moderating cellular ROS levels after irradiation and enhancing radiosensitivity. CPT1A downregulation contributes to radioresistance in CRC by augmenting the FOXM1-mediated antioxidant response. Thus, CPT1A is a potential biomarker of radiosensitivity and a novel target for overcoming radioresistance, offering a future direction to enhance CRC radiotherapy.

cancer biology↗

bioRxiv2024

The heritability and structural correlates of brain entropy

Brain entropy (BEN) quantifies the temporal complexity of spontaneous neural activity, which has been increasingly recognized as providing important insights into cognitive functions and psychiatric disorders. However, its heritability and structural underpinnings are not well understood. Here, we utilize sample entropy to calculate BEN in healthy young adults using resting-state fMRI from the Human Connectome Project. We show that BEN is significantly heritable in broad brain regions. Heritability estimates exhibit regional variability, with lower heritability in the limbic and subcortical networks than in other networks. We further relate BEN to structural features including surface area (SA), cortical myelination (CM), cortical thickness (CT), and subcortical volumes (SV). We find that BEN is negatively correlated with SA in most cortical regions, but is positively correlated with CM in the prefrontal cortex, lateral temporal lobe, precuneus, lateral parietal cortex, and cingulate cortex. Only a few cortical regions show significant correlations between BEN and CT. By decomposing correlations into genetic and environmental components, we observe that most of BEN-SA correlations are associated with shared genetic and environmental effects. BEN-CM correlations are mainly attributed to shared environmental effects. BEN-CT correlations are partly related to shared environmental effects. We find no significant associations between BEN and SV. Collectively, our work establishes the genetic basis and structural correlates of resting-state fMRI-based BEN, supporting its potential application as an endophenotype for psychiatric disorders.

neuroscience↗

bioRxiv2024

Limited Cell-Autonomous Anticancer Mechanisms in Long-Lived Bats

Bats are remarkably long-lived for their size with many species living more than 20-40 years, suggesting that they possess efficient anti-aging and anti-cancer defenses. Here we investigated requirements for malignant transformation in primary bat fibroblasts in four bat species - little brown bat (Myotis lucifugus), big brown bat (Eptesicus fuscus), cave nectar bat (Eonycteris spelaea) and Jamaican fruit bat (Artibeus jamaicensis) - spanning the bat evolutionary tree and including the longest-lived genera. We show that bat fibroblasts do not undergo replicative senescence and express active telomerase. Bat cells displayed attenuated stress induced premature senescence with a dampened secretory phenotype. Unexpectedly, we discovered that bat cells could be readily transformed by only two oncogenic perturbations or "hits": inactivation of either p53 or pRb and activation of oncogenic RASV12. This was surprising because other long-lived mammalian species require up to five hits for malignant transformation. Additionally, bat fibroblasts exhibited increased p53 and MDM2 transcript levels, and elevated p53-dependent apoptosis. The little brown bat showed a genomic duplication of the p53 gene. We hypothesize that bats evolved enhanced p53 activity through gene duplications and transcriptional upregulation as an additional anti-cancer strategy, similar to elephants. In summary, active telomerase and the small number of oncogenic hits sufficient to malignantly transform bat cells suggest that in vivo bats rely heavily on non-cell autonomous mechanisms of tumor suppression.

cell biology↗

bioRxiv2024

Disentangling Mnemonic Metacognition from Confidence by Communication between the Precuneus and Hippocampus

Metacognition, the ability to introspectively monitor ones own performance, remains an area with poorly understood neural mechanisms, particularly regarding the intercommunication among various brain regions. Recent studies have identified the precuneus as a key region in mnemonic metacognitive tasks, while the hippocampus is recognized for its role in memory function. This study aimed to investigate the role of the precuneus and hippocampus in mnemonic metacognition by utilizing intracranial electrode recordings from patients with intractable epilepsy to analyze the correlational dynamics between these regions. Our findings revealed that high gamma activity serve as a key feature in both the precuneus and hippocampus for confidence judgment. Based on signal detection theory (SDT), we discovered that high gamma activity in the precuneus is significantly linked to type 2 sensitivity (meta-d), while hippocampal high gamma activity was primarily linked to type 1 sensitivity (d). Additionally, the correlation between high gamma activity in the hippocampus and precuneus was exclusively related to type 2 sensitivity (meta-d). Temporal analysis indicated that the hippocampus is initially engaged for the memory process, followed by its joint engagement together with the precuneus for confidence generation. These findings elucidate the distinct electrophysiological roles of the hippocampus and precuneus in mnemonic metacognition, providing deeper insights into the neural mechanisms underlying this cognitive process.

neuroscience↗

bioRxiv2024

RinRK1 Promotes Accumulation of Nod Factor Receptors in Nanodomain-like structures at the tip of infected root hairs

Legume-rhizobia root-nodule symbioses involve the recognition of rhizobial Nod factor (NF) signals by NF receptors, triggering both nodule organogenesis and rhizobial infection. RinRK1 is induced by NF signaling and is essential for infection thread (IT) formation in Lotus japonicus. However, the precise mechanism underlying this process remains unknown. Here, we show that RinRK1 interacts with the extracellular domains of NF receptors NFR1 and NFR5 to promote their accumulation at root hair tips in response to rhizobia or NFs. Furthermore, Flotillin 1 (Flot1), a nanodomain-organizing protein, associates with the kinase domains of NFR1, NFR5 and RinRK1. RinRK1 promotes the interactions between Flot1 and NFR1 or NFR5 and both RinRK1 and Flot1 are necessary for the accumulation of NFR1 and NFR5 at root hair tips upon NF stimulation. Our study show that RinRK1 and Flot1 play a crucial role in NF receptor complex assembly within localized plasma membrane signaling centers to promote symbiotic infection.

plant biology↗

bioRxiv2024

Marsilea: An intuitive generalized visualization paradigm for complex datasets

Contemporary data visualization is challenged by the growing complexity and size of datasets, often comprising numerous interrelated features. Traditional visualization methods struggle to capture these complex relationships fully or are specialized to a domain requiring familiarity with multiple visualization tools. We introduce a novel and intuitive general visualization paradigm, termed "cross-layout visualization", which integrates multiple plot types in a cross-like structure. This paradigm allows for a central main plot surrounded by secondary plots, each capable of layering additional features for enhanced context and understanding. To operationalize this paradigm, we present "Marsilea", a Python library designed for creating complex visualizations with ease. Marsilea is notable for its modularity, diverse plot types, compatibility with various data formats, and is available in a coding-free web-based interface for users of all experience levels. We showcase its versatility and broad applicability by re-creating existing visualizations and creating novel visualizations that include elements such as heatmaps, sequence motifs, and set intersections that are typically beyond the scope of existing general visualization tools. The cross-layout paradigm, exemplified by Marsilea, offers a flexible, customizable, and intuitive approach to complex data visualization, promising to enhance data analysis across scientific domains.

bioinformatics↗

bioRxiv2024

Scaffold-Lab: Critical Evaluation and Ranking of Protein Backbone Generation Methods in A Unified Framework

De novo protein design has undergone a rapid development in recent years, especially for backbone generation, which stands out as more challenging yet valuable, offering the ability to design novel protein folds with fewer constraints. However, a comprehensive delineation of its potential for practical application in protein engineering remains lacking, as does a standardized evaluation framework to accurately assess the diverse methodologies within this field. Here, we proposed Scaffold-Lab benchmark focusing on evaluating unconditional generation across metrics like designability, novelty, diversity, efficiency and structural properties. We also extrapolated our benchmark to include the motif-scaffolding problem, demonstrating the utility of these conditional generation models. Our findings reveal that FrameFlow and RFdiffusion in unconditional generation along with Rfdiffusion and GPDL in conditional generation showcased the most outstanding performances. Furthermore, we described a systematic study to investigate conditional generation and applied it to the motif-scaffolding task, offering a novel perspective for the analysis and development of conditional protein design methods. All data and scripts will be available at https://github.com/Immortals-33/Scaffold-Lab.

bioinformatics↗

bioRxiv2024

Unfolded Von Willebrand Factor Binds Protein S and Reduces Anticoagulant Activity

Protein S (PS), the critical plasma cofactor for the anticoagulants tissue factor (TF) pathway inhibitor (TFPI) and activated protein C (APC), circulates in two functionally distinct pools: free (anticoagulant) or bound to complement component 4b-binding protein (C4BP) (anti-inflammatory). Acquired free PS deficiency is detected in several viral infections, but its cause is unclear. Here, we identified a shear-dependent interaction between PS and von Willebrand Factor (VWF) by mass spectrometry. Consistently, plasma PS and VWF comigrated in both native and agarose gel electrophoresis. The PS/VWF interaction was blocked by TFPI but not APC, suggesting an interaction with the C-terminal sex hormone binding globulin (SHBG) region of PS. Microfluidic systems, mimicking arterial laminar flow or disrupted turbulent flow, demonstrated that PS stably binds VWF as VWF unfolds under turbulent flow. PS/VWF complexes also localized to platelet thrombi under laminar arterial flow. In thrombin generation-based assays, shearing plasma decreased PS activity, an effect not seen in the absence of VWF. Finally, free PS deficiency in COVID-19 patients, measured using an antibody that binds near the C4BP binding site in SHBG, correlated with changes in VWF, but not C4BP, and with thrombin generation. Our data suggest that PS binds to a shear-exposed site on VWF, thus sequestering free PS and decreasing its anticoagulant activity, which would account for the increased thrombin generation potential. As many viral infections present with free PS deficiency, elevated circulating VWF, and increased vascular shear, we propose that the PS/VWF interaction reported here is a likely contributor to virus-associated thrombotic risk. Key PointsO_LIVon Willebrand Factor (VWF) binds Protein S (PS) in a shear-dependent manner, reducing the free PS pool and its anticoagulant activity. C_LIO_LIThe PS/VWF complex forms under turbulent flow conditions, is stable in whole blood, and localizes to growing platelet thrombi. C_LI

biochemistry↗

bioRxiv2024

Comparative transcriptome analysis provides insights into the resistance regulation mechanism and inhibitory effect of fungicide phenamacril in Fusarium asiaticum

Fusarium asiaticum is a destructive phytopathogenic fungus that causes Fusarium head blight of wheat (FHB), leading to serious yield and economic losses to cereal crops worldwide. Our previous studies indicated that target-site mutations (K216R/E, S217P/L, or E420K/G/D) of Type I myosin FaMyo5 conferred high resistance to phenamacril. Here, we first constructed a sensitive strain H1S and point mutation resistant strains HA, HC and H1R. Then we conducted comparative transcriptome analysis of these strains in F. asiaticum after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment. Results indicated that 2135 genes were differentially expressed (DEGs) among the sensitive and resistant strains. Among them, the DEGs encoding ammonium transporter MEP1/MEP2, nitrate reductase, copper amine oxidase 1, 4-aminobutyrate aminotransferase, amino-acid permease inda1, succinate-semialdehyde dehydrogenase, 2, 3-dihydroxybenzoic acid decarboxylase, etc., were significantly up-regulated in all the phenamacril-resistant strains. Compared to the control group, a total of 1778 and 2097 DEGs were identified in these strains after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment, respectively. These DEGs involved in 4-aminobutyrate aminotransferase, chitin synthase 1, multiprotein-bridging factor 1, transcriptional regulatory protein pro-1, amino-acid permease inda1, ATP-dependent RNA helicase DED, acetyl-coenzyme A synthetase, sarcoplasmic/endoplasmic reticulum calcium ATPase 2, etc., showed significantly down-regulated expression in phenamacril-sensitive strain but not in resistant strains after phenamacril treatment. In addition, cyanide hydratase, mating-type protein MAT-1, putative purine nucleoside permease, plasma membrane protein yro2, etc., showed significantly co-down-regulated expression in all the strains after phenamacril treatment. Taken together, This study provide deep insights into the resistance regulation mechanism and inhibitory effect of fungicide phenamacril and these new annotated proteins or enzymes are worth for the discovery of new fungicide targets. Author summaryFungicide phenamacril resistance occur in F. asiaticum and the resistance regulation mechanis are systematic and complex. Here, we conducted comparative transcriptome analysis of a sensitive strain H1S and point mutation resistant strains HA, HC and H1R in F. asiaticum after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment. Among these annotated proteins or enzymes, amino-acid permease inda1, 1, 4-aminobutyrate aminotransferase, chitin synthase 1, multiprotein-bridging factor 1, ATP-dependent RNA helicase DED, acetyl-coenzyme A synthetase, sarcoplasmic/endoplasmic reticulum calcium ATPase 2, cyanide hydratase, mating-type protein MAT-1, putative purine nucleoside permease, plasma membrane protein yro2, etc., were involved in the resistance regulation mechanism and inhibitory effect of fungicide phenamacril. Our paper provides a reference basis for the study of drug resistance in other microorganisms. In addition, the relevant proteins or enzymes annotated in our study also have reference value for the discovery of new fungicide targets.

pathology↗

bioRxiv2024

Monocyte-derived fibrocytes contribute to nucleus pulposus fibrosis and intervertebral disc degeneration

Fibrotic remodeling of nucleus pulposus (NP) leads to structural and mechanical anomalies of intervertebral discs that prone to degeneration, leading to low back pain incidence and disability. Emergence of fibroblastic cells in disc degeneration has been reported, yet their nature and origin remain elusive. In this study, we performed an integrative analysis of multiple single-cell RNA sequencing datasets to interrogate the cellular heterogeneity and fibroblast-like entities in degenerative human NP specimens. We found that disc degeneration severity is associated with an enrichment of fibrocyte-like phenotype, characterized by CD45 and collagen I dual positivity, and expression of myofibroblast marker -smooth muscle actin. Refined clustering and classification distinguished the fibrocyte-like populations as subtypes in the NP cells - and immunocytes-clusters, expressing disc degeneration markers HTRA1 and ANGPTL4 and genes related to response to TGF-{beta}. In injury-induced mouse disc degeneration model, fibrocyte-like cells were found recruited into the NP undergoing fibrosis and adopted a myofibroblast phenotype. Depleting the fibrocyte-like cells in CD11b-DTR mice in which monocytic lineages were ablated by diphtheria toxin could markedly attenuate fibrous modeling and myofibroblast formation in the NP of the degenerative discs, and prevent disc height loss and histomorphological abnormalities. Marker analysis supports that disc degeneration progression is dependent on a function of CD45+COL1A1+ and SMA+ cells. Our findings reveal that fibrocyte-like cells play a pivotal role in NP fibrosis and may therefore be a target for modifying disc degeneration and promoting its repair.

physiology↗

bioRxiv2024

Identification of a distinct cluster of GDF15high macrophages exhibiting anti-inflammatory activities

Macrophage-mediated inflammatory response may have crucial roles in the pathogenesis of a variety of human diseases. Growth differentiation factor 15 (GDF15) is a cytokine of the transforming growth factor-{beta} superfamily, with potential anti-inflammatory activities. Previous studies observed in human lungs some macrophages which expressed a high level of GDF15. In the present study, we employed multiple techniques, including immunofluorescence, flow cytometry, and single-cell RNA sequencing, in order to further clarify the identity of such GDF15high macrophages. We demonstrated that macrophages derived from human peripheral blood mononuclear cells and rat bone marrow mononuclear cells by in vitro differentiation with granulocyte-macrophage colony stimulating factor contained a minor population ([~]1%) of GDF15high cells. GDF15high macrophages did not exhibit a typical M1 or M2 phenotype, but had a unique molecular signature as revealed by single-cell RNA sequencing. Functionally, GDF15high macrophages were associated with reduced responsiveness to pro-inflammatory activation; furthermore, GDF15high macrophages could inhibit the pro-inflammatory functions of other macrophages via a paracrine mechanism. We further confirmed that GDF15 per se was a key mediator of the anti-inflammatory effects of GDF15high macrophage. Also, we provided direct evidence showing that GDF15high macrophages were also present in other macrophage-residing human tissues in addition to the lungs. Our results suggest that the GDF15high macrophage may represent a distinct cluster of macrophage cells with intrinsic anti-inflammatory functions. The (patho)physiological importance of these cells in vivo warrants further investigation.

immunology↗

bioRxiv2023

Internal Dynamics Interact with Proprioceptive Feedback During Movement Execution in an RNN Model of Motor Cortex

Proprioceptive feedback provides the information about the state of the body, which is critical in motor control. However, the contribution of proprioceptive feedback to motor cortical activity during voluntary movement execution is unclear. Here, we built an recurrent neural network model of motor cortex that receives proprioceptive feedback, and optimized it to control a virtual arm to perform a delayed-reach task. Simulated neural activity is similar to real data, indicating that our model captures the motor cortical dynamics. We further disrupted recurrent connectivity and proprioceptive feedback to dissect their contribution, and found that internal dynamics dominate in neural population activity, while proprioceptive feedback controls movement termination. Moreover, proprioceptive feedback improves the networks robustness against noisy initial conditions. We further investigated the relative importance of the components in proprioceptive feedback and found that the feedback of hand velocity contributes most to the similarity between simulation and real data. Finally, we show that our motor cortex model can be implemented in the sensorimotor system, demonstrating our models biological plausibility. In summary, motor command may arise from the intersection between recurrent dynamics in motor cortex and proprioceptive feedback.

neuroscience↗

bioRxiv2023

Limitation of switching sensory information flow in flexible perceptual decision making

Humans can flexibly change rules to categorize sensory stimuli, but their performance degrades immediately after a task switch. This switch cost is believed to reflect a limitation in cognitive control, although the bottlenecks responsible for this remain controversial. Here, we show that humans exhibit a brief reduction in the efficiency of converting sensory inputs into decision evidence immediately after changing rules in perceptual tasks. Participants performed a flexible face categorization task in which they classified parametrically generated face stimuli based on one of two rules, switching every few trials. Although participants were always informed of a rule switch by a context cue, they showed a specific pattern of increase in reaction times, regardless of the time they were given to prepare for the switch. Psychophysical reverse correlation and computational modeling revealed a reduction in sensory weighting immediately after a rule switch, which recovered within a few hundred milliseconds after stimulus presentation. Furthermore, this cost depends on the sensory features being switched, suggesting a major bottleneck at the stage of adjusting the sensory information flow. We propose that decision-making circuits cannot fully adjust their sensory readout based on an abstract context cue alone, but rather require the presence of an actual stimulus to tune it, leading to a limitation in flexible perceptual decision making.

neuroscience↗

bioRxiv2023

Perception of Motion Salience Shapes the Emergence of Collective Motions

As one of the most common and spectacular manifestations of coordinated behavior, collective motion is the spontaneous emergence of the ordered movement in a system consisting of many self-propelled agents, e.g., flocks of birds, schools of fish, herds of animals, and human crowds. Despite extensive studies on collective motions, a systems-level understanding of different motion patterns of collective behaviors is still lacking. This further hinders the adoption of bio-inspired mechanisms for applications of swarm robotics. Here, by leveraging three large bird-flocking datasets, we systematically investigate the emergence of different patterns of collective motions: mobbing, circling, and transit. We find that flocks with higher maneuverable motions (i.e., mobbing and circling) prefer to evolve a more nested structure of leader-follower (LF) relations and a clear hierarchy to mitigate the damage of individual freedom to group cohesion. In contrast, flocks with smooth motion (i.e., transit) do not display this tactful strategy to organize the group. To explain this empirical finding, we propose a measure based on the perception of motion salience (MS) to quantify the trade-off between individual freedom and group cohesion. Moreover, we perform the correlation analysis between LF and MS, finding that individuals with higher MS tend to lead the group with higher maneuverable motions. Those findings prompt us to develop a swarm model with adaptive MS-based (AMS) interactions and confirm that AMS interactions are responsible for the emergence of nested and hierarchical LF relations in the flocks with highly maneuverable motions. Finally, we implement AMS interactions in swarm robotics that consists of [~]102 miniature mobile robots. The swarm experiments of collective following and collective evacuation demonstrate that AMS interactions not only empower the swarm to promptly respond to the transient perturbation but also strengthen the self-organization of collective motions in terms of temporal cognition.

animal behavior and cognition↗

bioRxiv2023

Well-Paired-Seq2: High-Throughput and High-Sensitivity Strategy for Characterizing Low RNA-Content Cell/Nucleus Transcriptomes

High-throughput single-cell RNA sequencing (scRNA-seq) is recognized as a powerful technology for disentangling the heterogeneity of cellular states. However, the Poisson-dependent cell capture and low sensitivity in scRNA-seq methods pose challenges for throughput and for samples with low RNA-content. Herein, to address these challenges, we developed Well-Paired-Seq2 (WPS2) based on size-exclusion and locally quasi-static hydrodynamic principles to realize high efficiency of cell utilization, single cell/bead pairing, and cell-free RNA removal. WPS2 exploits molecular crowding effect, tailing activity enhancement in reverse transcription, and homogeneous enzymatic reaction in the initial bead-based amplification to achieve 3116 genes and 8447 transcripts. With an average of [~]20,000 reads per cell, WPS2 detected 1420 more genes and 4864 more transcripts than our previous Well-Paired-Seq. Using WPS2, we overcame the Poisson limit for the capture of both cells and beads and accurately characterized transcriptomes of low RNA-content single cells and nuclei with high sensitivity. WPS2 was further applied to comprehensively profile transcriptomes from frozen clinical samples. We found that clear cell renal cell carcinoma (ccRCC) has a complex microenvironment, and that chromophobe renal cell carcinoma (chRCC) exhibits abundant copy number variations (CNVs). In addition, metanephric adenoma (MA) was characterized at single-cell level for the first time and some potentially specific markers were revealed. With the advantages of high sensitivity, high throughput, and high fidelity, we anticipate that WPS2 will be broadly applicable in basic and clinical research.

genetics↗

bioRxiv2023

Investigation of contributions from cortical and subcortical brain structures for speech decoding

Language impairments often arise from severe neurological disorders, prompting the development of neural prosthetics based on electrophysiological signals for the restoration of comprehensible language information. Previous decoding efforts have focused mainly on signals from the cerebral cortex, neglecting the potential contributions of subcortical brain structures to speech decoding in brain-computer interfaces (BCIs). This study aims to explore the role of subcortical structures for speech decoding by utilizing stereotactic electroencephalography (sEEG). Two native Mandarin Chinese speakers, who underwent sEEG implantation for pharmaco-resistant epilepsy, participated in this study. sEEG contacts were primarily located in the superior temporal gyrus, middle temporal gyrus, inferior temporal gyrus, thalamus, hippocampus, insular gyrus, amygdala, and parahippocampal gyrus. The participants were asked to read Chinese text, which included 407 Chinese characters (covering all Chinese syllables), displayed on a screen after receiving prompts. 1-30, 30-70 and 70-150 Hz frequency band powers of sEEG signals were used as key features. A deep learning model based on long short-term memory (LSTM) was developed to evaluate the contribution of different brain structures during encoding of speech. Prediction of speech characteristics of consonants (articulatory place and manner) and tone within single words based on the selected features and electrode contact locations was made. Cortical signals were generally better at articulatory place prediction (86.5% accuracy, chance level = 12.5%), while cortical and subcortical signals predicted articulatory manner at similar level (51.5% vs 51.7% accuracy, respectively, chance level = 14.3%). Subcortical signals generated better prediction for tone (around 58.3% accuracy, chance level = 25%). Superior temporal gyrus remains highly relevant during speech decoding for both consonants and tone. Prediction reached the highest level when cortical and subcortical inputs were combined, especially for tone prediction. Our findings indicate that both cortical and subcortical structures can play crucial roles for speech decoding, each contributing to different aspects of speech.

neuroscience↗

bioRxiv2023

Auxetic patch material exhibits systolic thickening and restores pump function in a finite element model of acute myocardial infarction repair

Passive mechanical reinforcement of the infarcted heart has been shown to counteract infarct expansion and left ventricular (LV) functional degradation. However, traditional patch plasty of the ischemic region also restricts diastolic filling, reducing cardiac output. These negative side-effects can be minimized with strategic modification of the standard patch, suggesting further functional improvements could be possible through a broader exploration of patch materials. This study examines the potential advantages of a patch graft with auxetic properties, having a negative Poissons ratio ({nu} < 0). For preliminary evaluation, an established finite element model of LV biomechanics pre- and post-acute infarction, originally developed for modeling patch plasty with non-auxetic, or meiotic, materials, was modified to simulate epicardial implantation of auxetic patch materials. A homogeneous auxetic patch graft ({nu} = -0.2) exhibited radial thickening during systole, driven by tension on the patch from the neighboring contracting myocardium; but the patch thickness expanded away from the LV cavity and therefore did not improve ventricular mechanics compared to a standard meiotic patch graft ({nu} = 0.4). Alternatively, a heterogeneous auxetic patch design with an outer reinforcement layer caused inwardly-directed systolic thickening that restored the LV pressure-volume relationship toward baseline function, without adversely affecting fiber stress in the border zone or remote myocardium compared to the meiotic patch. This computational modeling study demonstrates the potential to harness auxetic mechanical properties for improving LV pump function in the setting of acute myocardial infarction, motivating further experimental validation of auxetic metamaterial patch devices for surgical repair of injured myocardium.

bioengineering↗