Biology subjects

Wen, Y.

Publications and source records attributed to Wen, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

What genes and regulatory sequences critically differentiate modern humans from apes and archaic humans, which share highly similar genomes but show distinct phenotypes, has puzzled researchers for decades. Previous studies examined species-specific protein-coding genes and related regulatory sequences, revealing that birth, loss, and changes in these genes and sequences can drive speciation and evolution. However, investigations of species-specific lncRNA genes and related regulatory sequences, which regulate substantial genes, remain limited. We identified human-specific (HS) lncRNAs from GENCODE-annotated human lncRNAs, predicted their DNA binding domains (DBDs) and binding sites (DBSs), analyzed DBS sequences in modern humans (CEU, CHB, and YRI), archaic humans (Altai Neanderthals, Denisovans, and Vindija Neanderthals), and chimpanzees, and investigated how HS lncRNAs and their DBSs have influenced gene expression in archaic and modern humans. Our results suggest that these lncRNAs and DBSs have substantially reshaped gene expression. This reshaping has evolved continuously from archaic to modern humans, enabling humans to adapt to new environments and lifestyles, promoting brain evolution, and resulting in cross-population differences. The parallel analysis of gene expression in GTEx tissues by HS TFs and their DBSs indicates that HS lncRNAs have reshaped gene expression in the brain more significantly than HS TFs.

genomics↗

bioRxiv2023

A single-cell atlas of the single versus multiple parous Hu Sheep ovary

In the modern sheep production system, the reproductive performance of ewes determines the economic profitability of farming. The mechanism of difference in litter size is important for the selection and breeding of high-fecundity ewes. Hu sheep is a high-quality sheep breed with high fecundity in China and is ideal for investigating high reproductive traits. In the current study, the sheep with lambing number [≥]3 in three consecutive lambing records were assigned to the HLS group, and lambing number = 1 as the LLS group selected from the same farm with three consecutive lambing. Three randomly picked ewes were slaughtered within 12 h of estrus, and unilateral ovarian tissue was collected and analyzed by single-cell RNA sequencing in each group. A total of five types of somatic cells were identified, and corresponding expression profiles were mapped in the ovaries of the Hu sheep. Additionally, the results of the difference in ovary somatic cell expression profiles between HLS and LLS present that the differences between multiples vs. singleton Hu sheep were mainly clustered in the GCs. In addition, 4 granulosa cell subtypes were identified. GeneSwitches results revealed the opening of JPH1 expression and the closure of LOC101112291, which leads to different evolutionary directions of the granular cells. The expression levels of FTH1 and FTL in GCs of Hu sheep in the HLS group were significantly higher, which inhibited necroptosis and ferroptosis of mural- GCs from decreasing follicular atresia. This study constructed the cellular atlas of the ovary and revealed related biological characteristics at the cellular molecular level. It provides a theoretical basis for the mechanisms underlying the differences in ovulation numbers, which contributes to breeding high-fertility sheep and molecular genetics-based selection.

zoology↗

bioRxiv2023

An ex vivo model of interactions between extracellular vesicles and peripheral mononuclear blood cells in whole blood

Extracellular vesicles (EVs) can be loaded with therapeutic cargo and engineered for retention by specific body sites; therefore, they have great potential for targeted delivery of biomolecules to treat diseases. However, the pharmacokinetics and biodistribution of EVs in large animals remain relatively unknown, especially in primates. We recently reported that when cell culture-derived EVs are administered intravenously to Macaca nemestrina (pig-tailed macaques), they differentially associate with specific subsets of peripheral blood mononuclear cells (PBMCs). More than 60% of CD20+ B cells were observed to associate with EVs for up to 1 hr post-intravenous administration. To investigate these associations further, we developed an ex vivo model of whole blood collected from healthy pig-tailed macaques. Using this ex vivo system, we found that labeled EVs preferentially associate with B cells in whole blood at levels similar to those detected in vivo. This study demonstrates that ex vivo blood can be used to study EV-blood cell interactions.

immunology↗

bioRxiv2023

A Quadrivalent mRNA immunization elicits potent immune responses against vaccinia and monkeypox viral antigens - a step closer to a broad orthopoxvirus vaccine

The global outbreak of the 2022 monkeypox virus infection of human raised the public health concerns of the threat of human-to-human transmission of zoonotic diseases. Given the evidence that other orthopoxviruses including cowpox and camelpox were also reported infectious to human, and that the reemerging risk of smallpox as a bioterrorist or accidental laboratory escape exists, there is an urgent need to develop a poxvirus vaccine with a broad protection of orthopoxviruses to stockpile for future emergency. Extensive studies of vaccinia virus (VACV) suggested that multiple VACV antigens, such as A27, L1, A33 and B5, showed high level similarity in terms of immunogenicity to their respective homologous antigens of other orthopoxviruses. These findings paved the ground for VACV antigens to be used as potential vaccine targets for development of a universal poxvirus vaccine. In this study, we construct a novel poxvirus vaccine candidate, mRNA-ALAB-LNP, encoding four vaccinia viral antigens A27, L1, A33 and B5. Strong anti-L1-specific antibody and moderate anti-A33-, anti-A27- and anti-B5-specific antibody responses were induced in mice after a single immunization. The antibody responses to all four antigens were significantly boosted after the second shot with all IgG titers >5 logs and highest being anti-A33 IgG. The high level of binding antibodies showed potent neutralizing capability against vaccinia virus. Specific IFN-{gamma} responses were detected to all four antigens with the highest cellular response being that induced by the same antigen, A33. When evaluating the cross reactivity, equivalent or better serum IgG responses were seen in responses to corresponding monkeypox antigens A35, M1, A29 and B6, in comparison to vaccinia antigens. Apparently, the mRNA vaccine encoding four vaccinia antigens induced immunity not only to vaccinia virus but also to monkeypox, suggesting that the mRNA-ALAB may be a candidate for potential vaccine development against infection of monkeypox, smallpox and possibly other orthopoxviruses.

immunology↗

bioRxiv2023

Biomaterial based implants caused remote liver fatty deposition through activated blood-derived Kupffer cells

Understanding the foreign-body response (FBR) of biomaterials is a prerequisite for the prediction of its clinical application, and the present assessments mainly rely on in vitro cell culture and in situ histopathology. However, remote organs responses after biomaterials implantation is unclear. Here, by leveraging body-wide-transcriptomics data, we performed in-depth systems analysis of biomaterials - remote organs crosstalk after abdominal implantation of polypropylene and silk fibroin using a rodent model, demonstrating local implantation caused remote organs responses dominated by acute-phase responses, immune system responses and lipid metabolism disorders. Of note, liver function was specially disturbed, defined as hepatic lipid deposition. Combining flow cytometry analyses and liver monocyte recruitment inhibition experiments, we proved that blood derived monocyte-derived Kupffer cells in the liver underlying the mechanism of abnormal lipid deposition induced by local biomaterials implantation. Moreover, from the perspective of temporality, the remote organs responses and liver lipid deposition of silk fibroin group faded away with biomaterial degradation and restored to normal at end, which highlighted its superiority of degradability. These findings were further indirectly evidenced by human blood biochemical examination from 141 clinical cases of hernia repair using silk fibroin mesh and polypropylene mesh. In conclusion, this study provided knowledge of biomaterials-body interactions. It is of great important for future development of biomaterial devices for clinical application. One Sentence SummaryAbdominal local biomaterials implantation induces remote organ fatty deposition through activated blood-derived Kupffer cells.

pharmacology and toxicology↗

bioRxiv2023

Hepatic conversion of acetyl-CoA to acetate plays crucial roles in energy stresses

Accumulating evidences indicate that acetate is increased in energy stresses such as diabetes mellitus and prolonged starvation. However, it is largely unknown how and where acetate is produced and what is its biological significance. We observed overproduction of acetate in an amount comparable to ketone bodies in patients and mice with diabetes or starvation. Mechanistically, ACOT 12&8 are dramatically upregulated in liver to convert FFA-derived acetyl-CoA to acetate and CoA. This conversion not only provides large amount of acetate which fuels brain preferentially rather than muscle, but also recycles CoA which is required for sustained fatty acid oxidation and ketogenesis. Taken together, we suggest that acetate is an emerging novel "ketone body" and may be used as a parameter to evaluate the progression of energy stress in the future.

biochemistry↗

bioRxiv2022

ZBTB20 is Essential for Cochlear Maturation and Hearing in Mice

The mammalian cochlear epithelium undergoes substantial remodeling and maturation before the onset of hearing. However, very little is known about the transcriptional network governing cochlear late-stage maturation and particularly the differentiation of its lateral non-sensory region. Here we establish ZBTB20 as an essential transcription factor required for cochlear terminal differentiation and maturation and hearing. ZBTB20 is abundantly expressed in the developing and mature cochlear non-sensory epithelial cells, with transient expression in immature hair cells and spiral ganglion neurons. Otocyst-specific deletion of Zbtb20 causes profound deafness with reduced endolymph potential in mice. The subtypes of cochlear epithelial cells are normally generated but their postnatal development is arrested in the absence of ZBTB20, as manifested by an immature appearance of the organ of Corti, malformation of tectorial membrane, a flattened spiral prominence, and a lack of identifiable Boettcher cells. Furthermore, these defects are related with a failure in the terminal differentiation of the non-sensory epithelium covering the outer border Claudius cells, outer sulcus root cells and spiral prominence epithelial cells. Transcriptome analysis shows ZBTB20 regulates genes coding for tectorial membrane proteins in the greater epithelial ridge, and those preferentially expressed in root cells and spiral prominence epithelium. Our results point to ZBTB20 as an essential regulator for postnatal cochlear maturation and particularly for the terminal differentiation of cochlear lateral non-sensory domain.

developmental biology↗

bioRxiv2022

Estrogens dynamically regulate neurogenesis in the dentate gyrus of adult female rats

Estrone and estradiol differentially modulate neuroplasticity and cognition, but how they influence maturation pathways of new neurons in the adult hippocampus is not known. The present study assessed the effects of estrone and estradiol on various aspects of neurogenesis in the dentate gyrus (DG) of ovariectomized young adult Sprague-Dawley rats using daily subcutaneous injections of 17{beta}-estradiol or estrone. Rats were injected with a DNA synthesis marker, 5-bromo-2-deoxyuridine (BrdU), and were perfused one, two, or three weeks after BrdU injection and treatment. Immunofluorescent labelling for GFAP/Sox2 was used to examine the density of neural stem/progenitor cells and Ki67 for cell proliferation. Double-immunofluorescent labelling of BrdU with doublecortin (DCX) or NeuN was used to examine the attrition and maturation of adult-born neurons over time. Length of time post ovariectomy was associated with a reduction in neural stem/progenitor cells in the DG. Estrogens had effects on different components of neurogenesis after one week of exposure but not after prolonged treatment. Estradiol enhanced, whereas estrone reduced, cell proliferation after one week but not after longer exposure to hormones. Both estrogens increased the density of BrdU/DCX-ir cells after one week of exposure but showed greater attrition of new neurons between one and two weeks after exposure, suggesting that the effects of estrogens on neurogenesis were not sustained. These results demonstrate that estrogens modulate several aspects of adult hippocampal neurogenesis differently in the short term, but may lose their ability to influence neurogenesis after long-term exposure.

neuroscience↗

bioRxiv2022

Toward a generalizable deep CNN for neural drive estimation across muscles and participants

High-density electromyography (HD-EMG) decomposition algorithms are used to identify individual motor unit spike trains, which collectively constitute the neural code of movements, to predict motor intent. This approach has advanced from offline to online decomposition, from isometric to dynamic contractions, leading to a wide range of neural-machine interface applications. However, current online methods need offline retraining when applied to the same muscle on a different day or to a different person, which limits their applications in a real-time neural-machine interface. We proposed a deep convolutional neural network (CNN) framework for neural drive estimation, which captures general spatiotemporal properties of motor unit action potentials to generalize its application without retraining to HD-EMG data recorded in separate sessions, muscles, and participants. We recorded HD-EMG signals from the vastus medialis and vastus lateralis muscles while participants performed isometric contractions during two sessions separated by approximately 20 months. We identified motor unit spike trains from HD-EMG signals using a blind source separation (BSS) method, and then used the cumulative spike train (CST) of these motor units and the HD-EMG signals to train and validate the deep CNN. On average, the correlation coefficients between CST from BSS and that from deep CNN were 0.977{+/-}0.007 for leave-one-out across-sessions-and-muscles validation and 0.985{+/-}0.005 for leave-one-out across-participants validation. When trained with more than four datasets, the performance of deep CNN saturated at 0.979{+/-}0.001 for cross validations across muscles, sessions, and participants. Therefore, we can conclude that the deep CNN is generalizable across the afore-mentioned conditions without retraining. We could potentially generate a robust deep CNN to estimate neural drive to muscles for neural-machine interfaces.

neuroscience↗

bioRxiv2022

CausalCell: applying causal discovery to single-cell analyses

Correlation between objects does not answer many scientific questions because of the lack of causal but the excess of spurious information and is prone to happen by coincidence. Causal discovery infers causal relationships from data upon conditional independence test between objects without prior assumptions (e.g., variables have linear relationships and data follow the Gaussian distribution). Causal interactions within and between cells provide valuable information for investigating gene regulation, identifying diagnostic and therapeutic targets, and designing experimental and clinical studies. The rapid increase of single-cell data permits inferring causal interactions in many cell types. However, because no algorithms have been designed for handling abundant variables and few algorithms have been evaluated using real data, how to apply causal discovery to single-cell data remains a challenge. We report a pipeline and web server (http://www.gaemons.net/causalcell/causalDiscovery/) for accurately and conveniently performing causal discovery. The pipeline has been developed upon the benchmarking of 18 algorithms and the analyses of multiple datasets. Our applications indicate that only complicated algorithms can generate satisfactorily reliable results. Critical issues are discussed, and tips for best practices are provided.

bioinformatics↗

bioRxiv2022

Analysis of the mechanism of castor tolerance to Cd metal based on proteomics and metabolomics

The pollution of soil with heavy metals is an increasingly serious worldwide problem, and cadmium (Cd) has attracted attention because of its high toxicity to almost all plants. Since castor tolerates the accumulation of heavy metals, it has the potential for heavy metal soil remediation. We studied the mechanism of the tolerance of castor to Cd stress treatments at three doses: 300 mg/L, 700 mg/L, and 1,000 mg/L. Our research provides new ideas for revealing the defense and detoxification mechanisms of Cd-stressed castor. By combining the results of physiology, differential proteomics and comparative metabolomics, we conducted a comprehensive analysis of the networks that regulate the response of castor to Cd stress. The physiological results mainly emphasize the super-sensitive responses of castor plant roots to Cd stress and the effects of Cd stress on plants antioxidant system, ATP synthesis and ion homeostasis. We confirmed these results at the protein and metabolite levels. At the same time, proteomics and metabolomics show that castor plants mainly block the root systems absorption of Cd2+ by enhancing the strength of the cell wall, and inducing programmed cell death in response to the three different doses of Cd stress. In addition, the plasma membrane ATPase encoding gene (RcHA4), which was significantly upregulated in our differential proteomics and RT-qPCR studies, was transgenically overexpressed in wild type Arabidopsis thaliana for functional verification. The results indicated that this gene plays an important role in improving plant Cd tolerance.

molecular biology↗

bioRxiv2022

A point mutation in Chl biosynthesis gene Mg-chelatase I subunit influences on leaf color and metabolism in strawberry

Magnesium chelatase catalysis the insertion of magnesium into protoporphyrin IX is a vital step in chlorophyll biogenesis. It consists of three subunits, CHLI, CHLD and CHLH. The CHLI subunit is an ATPase and hydrolysis ATP in the catalysis. However, its key point on influencing flavonoid biosynthesis and chlorophyll accumulation under different light density was still unknown. In this study, we identified an N-Ethyl-N-nitrosourea (ENU) mutant, p240 from strawberry Fragaria pentaphylla that has yellow-green leaves and lower chlorophyll level. We verified the mutation occurs in the 186th amino acid of CHLI subunit, which is conserved in most photosynthetic organism. Mutants generated from RNAi and CRISPR/Cas9 gene editing confirmed this phenotype. In addition, we found that FpCHLI was localized in chloroplast and its subcellular location have not been changed by mutation. Further study showed that the interaction between FpCHLI and FpCHLD were not affected by mutagenesis. In contrast, all types of mutants showed reduced ATPase and magnesium chelatase activity indicating mutagenesis decreased enzymatic activities. Furthermore, mutagenesis suppressed the biosynthesis of Mg-proto IX. Metabolites analysis of gene knock-out mutant and WT revealed that CHLI may help to keep stabilizing the flavonoid level in leaves. Furthermore, both p240 and chli mutants are light sensitive, which has yellow leaves under high light but pale green leaves under poor light. The photosynthesis ability of mutants was also increased under shade. Moreover, stomatal apertures of mutants were wider than WT. Taken together, these results suggest that CHLI plays an important role in both leaf coloration and metabolism.

plant biology↗

bioRxiv2022

One-Pot Endonucleolytically Exponentiated Rolling Circle Amplification by CRISPR-Cas12a Affords Sensitive, Expedited Isothermal Detection of MicroRNAs

MicroRNAs (miRNAs) are a class of short non-coding RNAs that play essential roles in gene expression regulation. While miRNAs offer a promising source for developing potent cancer biomarkers, the progress towards clinical utilities remains largely limited, due in part to the long-standing challenge in sensitive, specific, and robust detection of miRNAs in human biofluids. Emerging next-generation molecular technologies, such as the CRISPR-based methods, promise to transform nucleic acid testing. The prevailing strategy used in existing CRISPR-based methods is to hyphenate two separate reactions for pre-amplification, e.g., rolling circle amplification (RCA), and amplicon detection by Cas12a/13a trans-cleavage in tandem. Thus, existing CRISPR-based miRNA assays require multiple manual steps and lack the analytical performance of the gold standard, RT-qPCR. Radically deviating from the existing strategies, we developed a one-step, one-pot isothermal miRNA assay termed "Endonucleolytically eXponenTiated Rolling circle Amplification with the dual-functional CRISPR-Cas12a" (EXTRA-CRISPR) to afford RT-PCR-like performance for miRNA detection. We demonstrated the superior analytical performance of our EXTRA-CRISPR assay to detect miRNAs (miR-21, miR-196a, miR-451a, and miR-1246) in plasma extracellular vesicles, which allowed us to define a potent EV miRNA signature for detection of pancreatic cancer. The analytical and diagnostic performance of our one-pot assay were shown to be comparable with that of the commercial RT-qPCR assays, while greatly simplifying and expediting the analysis workflow. Therefore, we envision that our technology provides a promising tool to advance miRNA analysis and clinical marker development for liquid biopsy-based cancer diagnosis and prognosis.

bioengineering↗

bioRxiv2022

Structural insights into the viral proteins binding by TRIM7 reveal a general C-terminal glutamine recognition mechanism

The E3 ligase TRIM7 has emerged as a critical player in viral infection and pathogenesis. A recent study found that TRIM7 inhibits human enteroviruses through ubiquitination and proteasomal degradation of viral 2BC protein by targeting the 2C moiety of 2BC protein. Here, we report the crystal structures of TRIM7 in complex with 2C, where the C-terminal region of 2C is inserted into a positively charged groove of the TRIM7 PRY-SPRY domain. Structure-guided biochemical studies revealed the C-terminus glutamine residue of 2C as the primary determinant for TRIM7 binding. Such a glutamine-end motif binding mechanism can be successfully extended to other substrates of TRIM7. More importantly, leveraged by this finding, we were able to identify norovirus and SARS-CoV-2 proteins, and physiological proteins, as new TRIM7 substrates. We further show that TRIM7 may function as a restriction factor to promote the degradation of the viral proteins of norovirus and SARS-CoV-2, thereby restoring the Type I interferon immune response and inhibiting viral infection. Several crystal structures of TRIM7 in complex with SARS-CoV-2 proteins are also determined, and a conserved C-terminus glutamine-specific interaction is observed. These findings unveil a common recognition mode by TRIM7, providing the foundation for further mechanistic characterization of antiviral and cellular functions of TRIM7.

biochemistry↗

bioRxiv2022

Assessing base-resolution DNA mechanics on the genome scale

Intrinsic DNA properties such as bending play a crucial role in diverse biological systems. A recent advantage in the high-throughput method called loop-seq makes it possible to determine bendability of hundred thousand 50-bp DNA duplexes in one experiment. However, its still infeasible to assess whole sequence bendability in large genomes such as human, which needs thousands of loop-seq experiments. Here we introduce BendNet - a neural network to accurately predict the intrinsic DNA bending at base-resolution by only given DNA sequences. BendNet can increase the resolution of experimental results, and can predict DNA bendability for any new given sequences in high accuracy. We applied BendNet to the human genome and observed high-stiffness regions located at both transcriptional start sites and transcriptional end sites. Such stiffness patterns are different for coding and non-coding genes, which matches distinct nucleosome occupancy patterns. As expected, most transcription factors (TFs) bind in DNA of low bendability. In contrast, we observed an unusually high bendability within binding elements of specific TFs such as EBF1 and regulators of genome folding such as CTCF. These factors either co-bind or compete with nucleosomes to carry out their functions. More interestingly, CTCF binding regions exhibit the highest bendability than other DNA elements, implying their potential role in trapping and holding the CTCF in the exact locations to make sure CTCF as stable anchor in loop extrusion process. Our work provides a tool to assess DNA bendability for large-scale DNA sequences and expands our understanding on DNA mechanics in chromatin regulation and genome folding.

genomics↗

bioRxiv2022

Combating the SARS-CoV-2 Omicron variant with non-Omicron neutralizing antibodies

The highly mutated and transmissible Omicron variant has provoked serious concerns over its decreased sensitivity to the current coronavirus disease 2019 (COVID-19) vaccines and evasion from most anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies (NAbs). In this study, we explored the possibility of combatting the Omicron variant by constructing bispecific antibodies based on non-Omicron NAbs. We engineered ten IgG-like bispecific antibodies with non-Omicron NAbs named GW01, 16L9, 4L12, and REGN10987 by fusing the single-chain variable fragments (scFvs) of two antibodies through a linker and then connecting them to the Fc region of IgG1. Surprisingly, eight out of ten bispecific antibodies showed high binding affinity to the Omicron receptor-binding domain (RBD) and exhibited extreme breadth and potency against pseudotyped SARS-CoV-2 variants of concern (VOCs) including Omicron, as well as authentic Omicron(+R346K) variants. Six bispecific antibodies containing the cross-NAb GW01 neutralized Omicron variant and retained their abilities to neutralize other sarbecoviruses. Bispecific antibodies inhibited Omicron infection by binding to the ACE2 binding site. A cryo-electron microscopy (cryo-EM) structure study of the representative bispecific antibody FD01 in complex with the Omicron spike (S) revealed 5 distinct trimers and one unique bi-trimer conformation. The structure and mapping analyses of 34 Omicron S variant single mutants elucidated that two scFvs of the bispecific antibody synergistically induced the RBD-down conformation into 3-RBD-up conformation, enlarged the interface area, accommodated the S371L mutation, improved the affinity between a single IgG and the Omicron RBD, and hindered ACE2 binding by forming bi-trimer conformation. Our study offers an important foundation for anti-Omicron NAb design. Engineering bispecific antibodies based on non-Omicron NAbs may provide an efficient solution to combat the Omicron variant.

microbiology↗

bioRxiv2022

JWA deficiency accelerates aging through disrupting intestinal epithelial homeostasis via Notch1/PPARγ/Stat5 axis

Aging usually suppresses the renewal and regeneration of intestinal epithelium. The imbalance of intestinal epithelial homeostasis may also be a promoter for aging. JWA responds to oxidative stress and repairs damaged DNA; it participates in multiple cellular processes like cell proliferation and differentiation. Here we identified JWA as a new aging-associated gene, whose deletion-accelerated aging in mice was related to intestinal epithelium atrophy. We further knocked out intestinal epithelial JWA and found it disrupted intestinal epithelial homeostasis, thus promoting aging in mice. Mechanistically, we discovered that JWA deficiency promoted Notch1 ubiquitination degradation via ERK/Fbxw7 cascade and interfered with the PPAR{gamma}/Stat5 signal axis. This reduced the intestinal stem cell function and altered the intestinal epithelial cell lineage distribution, finally suppressing the renewal and regeneration of intestinal epithelium. Our results demonstrated that JWA is a new aging-associated gene essential for the renewal and regeneration of intestinal epithelium. We also provide a new idea that maintaining intestinal epithelial homeostasis may be a potential anti-aging strategy in humans or mammals.

developmental biology↗

bioRxiv2022

A deep CNN framework for neural drive estimation from HD-EMG across contraction intensities and joint angles

ObjectivePrevious studies have demonstrated promising results in estimating the neural drive to muscles, the net output of all motoneurons that innervate the muscle, using high-density electromyography (HD-EMG) for the purpose of interfacing with assistive technologies. Despite the high estimation accuracy, current methods based on neural networks need to be trained with specific motor unit action potential (MUAP) shapes updated for each condition (i.e., varying muscle contraction intensities or joint angles). This preliminary step dramatically limits the potential generalization of these algorithms across tasks. We propose a novel approach to estimate the neural drive using a deep convolutional neural network (CNN), which can identify the cumulative spike train (CST) through general features of MUAPs from a pool of motor units. MethodsWe recorded HD-EMG signals from the gastrocnemius medialis muscle under three isometric contraction scenarios: 1) trapezoidal contraction tasks with different intensities, 2) contraction tasks with a trapezoidal or sinusoidal torque target, and 3) trapezoidal contraction tasks at different ankle angles. We applied a convolutive blind source separation (BSS) method to decompose HD-EMG signals to CST and segmented both signals into windows to train and validate the deep CNN. Then, we optimized the structure of the deep CNN and validated its generalizability across contraction tasks within each scenario. ResultsWith the optimal configuration for the HD-EMG data window (overlap of 20 data points and window length of 40 data points), the deep CNN estimated the CST close to that from BSS, with a correlation coefficient higher than 0.96 and normalized root-mean-square-error lower than 7% with respect to the BSS (golden standard) within each scenario. ConclusionThe proposed deep CNN framework can utilize data from different contraction tasks (e.g., different intensities), learn general features of MUAP variants, and estimate the neural drive for other contraction tasks. SignificanceWith the proposed deep CNN, we could potentially build a neuraldrive-based human-machine interface that is generalizable to different contraction tasks without retraining.

bioengineering↗