Infertility is a global issue, with approximately 50% of cases attributed to defective spermatogenesis. For studies into spermatogenesis and spermatogenic dysfunction, evaluating the seminiferous tubule stage is essential. However, the current method of evaluation involves labor-intensive and time-consuming manual tasks such as staining, observation, and image analysis. Lack of reproducibility is also a problem owing to the subjective nature of visual evaluation by experts. In this study, we propose a deep learning–based method for automatically and objectively evaluating the seminiferous tubule stage. Our approach automatically predicts which of 12 seminiferous tubule stages is represented in bright-field microscopic images of mouse seminiferous tubules stained by hematoxylin-PAS. For training and validation of our model, we created a dataset of 1229 tissue images, each labeled with one of 12 distinct seminiferous tubule stages. The maximum prediction accuracy was 79.58% which rose to 98.33% with allowance for a prediction error of ±1 stage. Remarkably, although the model was not explicitly trained on the patterns of transition between stages, it inferred characteristic structural patterns involved in the process of spermatogenesis. This method not only advances our understanding of spermatogenesis but also holds promise for improving the automated diagnosis of infertility.
{"title":"Deep learning–based automated prediction of mouse seminiferous tubule stage by using bright-field microscopy","authors":"Y. Tokuoka, Tsutomu Endo, Takashi Morikura, Yuki Hiradate, Masahito Ikawa, Akira Funahashi","doi":"10.1101/2024.08.07.606973","DOIUrl":"https://doi.org/10.1101/2024.08.07.606973","url":null,"abstract":"Infertility is a global issue, with approximately 50% of cases attributed to defective spermatogenesis. For studies into spermatogenesis and spermatogenic dysfunction, evaluating the seminiferous tubule stage is essential. However, the current method of evaluation involves labor-intensive and time-consuming manual tasks such as staining, observation, and image analysis. Lack of reproducibility is also a problem owing to the subjective nature of visual evaluation by experts. In this study, we propose a deep learning–based method for automatically and objectively evaluating the seminiferous tubule stage. Our approach automatically predicts which of 12 seminiferous tubule stages is represented in bright-field microscopic images of mouse seminiferous tubules stained by hematoxylin-PAS. For training and validation of our model, we created a dataset of 1229 tissue images, each labeled with one of 12 distinct seminiferous tubule stages. The maximum prediction accuracy was 79.58% which rose to 98.33% with allowance for a prediction error of ±1 stage. Remarkably, although the model was not explicitly trained on the patterns of transition between stages, it inferred characteristic structural patterns involved in the process of spermatogenesis. This method not only advances our understanding of spermatogenesis but also holds promise for improving the automated diagnosis of infertility.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"50 31","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.09.607305
Jonathan R. Gadsby, P. S. Ioannou, Richard Butler, Julia Mason, Alison Smith, U. Dobramysl, Stacey Chin, Claire L. Dobson, J. Gallop
Filopodia, microspikes and cytonemes are implicated in sensing the environment and in dissemination of morphogens, organelles and pathogens across tissues. Their major structural component is parallel bundles of actin filaments that assemble from the cell membrane. Whilst the length of filopodia is central to their function, it is not known how their lengths are determined by actin bundle dynamics. Here, we identified a set of monoclonal antibodies that lengthen filopodia-like structures formed in a cell-free reconstitution system, and used them to uncover a key molecular switch governing length regulation. Using immunolabelling, enzyme-linked immunosorbent assays, immunoprecipitation and immunoblock experiments, we identified four antibodies that lengthen actin bundles by selectively binding the open DNase 1-binding loop (D-loop) of actin filaments. The antibodies inhibit actin disassembly and their effects can be alleviated by providing additional actin or cofilin. This work indicates that maintaining an open state of the actin filament D-loop is a mechanism of generating the long projections of filopodia-like actin bundles.
丝状体、微钉和细胞核与感知环境以及形态发生器、细胞器和病原体在组织间的传播有关。它们的主要结构成分是由细胞膜组装而成的平行肌动蛋白丝束。虽然丝状体的长度是其功能的核心，但其长度如何由肌动蛋白束动力学决定尚不清楚。在这里，我们发现了一组能延长无细胞重组系统中形成的丝状结构的单克隆抗体，并利用它们发现了调节长度的关键分子开关。通过免疫标记、酶联免疫吸附测定、免疫沉淀和免疫阻断实验，我们确定了四种抗体，它们通过选择性结合肌动蛋白丝的开放 DNase 1 结合环（D-环）来延长肌动蛋白束。这些抗体可抑制肌动蛋白的解体，通过提供额外的肌动蛋白或辅纤蛋白可减轻其影响。这项工作表明，维持肌动蛋白丝 D 环的开放状态是产生丝状肌动蛋白束长突起的一种机制。
{"title":"The open to closed D-loop conformational switch determines length in filopodia-like actin bundles","authors":"Jonathan R. Gadsby, P. S. Ioannou, Richard Butler, Julia Mason, Alison Smith, U. Dobramysl, Stacey Chin, Claire L. Dobson, J. Gallop","doi":"10.1101/2024.08.09.607305","DOIUrl":"https://doi.org/10.1101/2024.08.09.607305","url":null,"abstract":"Filopodia, microspikes and cytonemes are implicated in sensing the environment and in dissemination of morphogens, organelles and pathogens across tissues. Their major structural component is parallel bundles of actin filaments that assemble from the cell membrane. Whilst the length of filopodia is central to their function, it is not known how their lengths are determined by actin bundle dynamics. Here, we identified a set of monoclonal antibodies that lengthen filopodia-like structures formed in a cell-free reconstitution system, and used them to uncover a key molecular switch governing length regulation. Using immunolabelling, enzyme-linked immunosorbent assays, immunoprecipitation and immunoblock experiments, we identified four antibodies that lengthen actin bundles by selectively binding the open DNase 1-binding loop (D-loop) of actin filaments. The antibodies inhibit actin disassembly and their effects can be alleviated by providing additional actin or cofilin. This work indicates that maintaining an open state of the actin filament D-loop is a mechanism of generating the long projections of filopodia-like actin bundles.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"32 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141924500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607036
Haley Q. Marcarian, Anutr Sivakoses, Anika M. Arias, Olivia C. Ihedioha, Benjamin R. Lee, Maria C. Bishop, Alfred L.M. Bothwell
Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers. SIGNIFICANCE STATEMENT We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.
逆行细胞吞噬是一种未得到充分重视的现象，它塑造了许多类型实体瘤周围的免疫微环境。膜结合蛋白从供体免疫细胞通过逆行吞噬作用沉积到受体癌细胞的后果尚不清楚。在此，我们报告了人类透明细胞肾癌肿瘤稳定表达淋巴标记物 CD45、CD56、CD14 和 CD16 的情况。对新鲜肾脏肿瘤进行的流式细胞术显示，肿瘤细胞上的 CD45 表达一致，前面提到的其他标记物也有不同程度的表达。这些结果与我们的免疫荧光分析结果一致，免疫荧光分析还发现淋巴标记物与标准肾肿瘤标记物碳酸酐酶 9（CAIX）共聚焦。RNA 分析表明，在逆行细胞增殖后，肿瘤细胞中与免疫细胞相关的基因明显上调。最后，我们展示了染色体 DNA 在逆行吞噬过程中从免疫细胞转移到肿瘤细胞的证据。这种水平基因转移对受体肿瘤细胞的转录产生了影响，从而形成了同时表达免疫和癌症特异性蛋白的融合表型。这项工作展示了一种新的机制，即通过从浸润淋巴细胞获取表面膜片段和基因组 DNA 来改变肿瘤细胞的蛋白质表达。这些结果改变了我们对肿瘤-免疫细胞相互作用的理解方式，并可能揭示肿瘤发生机制的新见解。此外，对逆行细胞增多症的进一步研究将有助于推动下一代免疫疗法和生物标记物领域的发展，以治疗肾细胞癌和其他类型的癌症。意义声明 我们已经发现，逆行细胞吞噬是人类透明细胞肾癌肿瘤从肿瘤浸润免疫细胞获得淋巴细胞表面蛋白表达的一种机制。除了膜碎片的转移外，我们还提供证据表明，在逆行细胞吞噬过程中，基因组 DNA 会从正常免疫细胞转移到肿瘤细胞。这一过程改变了癌细胞的转录组，使其表达的免疫蛋白（如淋巴细胞标记物 CD45）的 mRNA 明显多于未发生逆行吞噬的肿瘤细胞。这项研究深入分析了癌细胞与肿瘤浸润淋巴细胞之间的相互作用，以及这些相互作用如何改变人类肿瘤的发展。
{"title":"Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer","authors":"Haley Q. Marcarian, Anutr Sivakoses, Anika M. Arias, Olivia C. Ihedioha, Benjamin R. Lee, Maria C. Bishop, Alfred L.M. Bothwell","doi":"10.1101/2024.08.07.607036","DOIUrl":"https://doi.org/10.1101/2024.08.07.607036","url":null,"abstract":"Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers. SIGNIFICANCE STATEMENT We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"58 29","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.08.607200
John B. Linehan, Alexandra Zampetaki, Michael E. Werner, Bryan W. Heck, Paul S. Maddox, Sebastian Fürthauer, A. S. Maddox
The non-muscle actomyosin cytoskeleton generates contractile force through the dynamic rearrangement of its constituent parts. Actomyosin rings are a specialization of the non-muscle actomyosin cytoskeleton that are associated with a number of cell biological processes. To explore how contractile forces are generated by actomyosin rings, we studied three instances of ring closure within the common cytoplasm of the C. elegans oogenic germline: when germline stem cells (GSCs) divide mitotically, when meiotic compartments undergo apoptosis, and when nascent oocytes cellularize. We found that each of these rings closed with unique kinetics, protein density and abundance dynamics. These measurements suggested that the mechanism of contractile force generation varied across the subcellular contexts. Next, we formulated a physical model that related the forces generated by filament-filament interactions to the material properties of these rings that dictate the kinetics of their closure. Using this framework, we related the density of conserved cytoskeletal proteins anillin and myosin to the kinematics of ring closure. We found that actomyosin ring closure results from the asymmetric distribution of protein along the length of F-actin, which occurs naturally due to differences in crosslinker and NMMII bundle size. Our work predicts that the role of myosin varies across these ring types, due in part to its distribution along F-actin and motoring.
{"title":"Cellular context specific tuning of actomyosin ring contractility within a common cytoplasm","authors":"John B. Linehan, Alexandra Zampetaki, Michael E. Werner, Bryan W. Heck, Paul S. Maddox, Sebastian Fürthauer, A. S. Maddox","doi":"10.1101/2024.08.08.607200","DOIUrl":"https://doi.org/10.1101/2024.08.08.607200","url":null,"abstract":"The non-muscle actomyosin cytoskeleton generates contractile force through the dynamic rearrangement of its constituent parts. Actomyosin rings are a specialization of the non-muscle actomyosin cytoskeleton that are associated with a number of cell biological processes. To explore how contractile forces are generated by actomyosin rings, we studied three instances of ring closure within the common cytoplasm of the C. elegans oogenic germline: when germline stem cells (GSCs) divide mitotically, when meiotic compartments undergo apoptosis, and when nascent oocytes cellularize. We found that each of these rings closed with unique kinetics, protein density and abundance dynamics. These measurements suggested that the mechanism of contractile force generation varied across the subcellular contexts. Next, we formulated a physical model that related the forces generated by filament-filament interactions to the material properties of these rings that dictate the kinetics of their closure. Using this framework, we related the density of conserved cytoskeletal proteins anillin and myosin to the kinematics of ring closure. We found that actomyosin ring closure results from the asymmetric distribution of protein along the length of F-actin, which occurs naturally due to differences in crosslinker and NMMII bundle size. Our work predicts that the role of myosin varies across these ring types, due in part to its distribution along F-actin and motoring.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"59 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.606919
Bhavna Gupta, Brandon Kepros, Jann B. Landgraf, Michael F. Becker, Wen Li, Erin K. Purcell, James R. Siegenthaler
Neurochemical sensing with implantable devices has gained remarkable attention over the last few decades. A promising area of this research is the progress of novel electrodes as electrochemical tools for neurotransmitter detection in the brain. The boron-doped diamond (BDD) electrode is one such candidate that previously has been reported for its excellent electrochemical properties, including a wide working potential, superior chemical inertness and mechanical stability, good biocompatibility and resistance to fouling. Meanwhile, limited research has been conducted on the BDD as a microelectrode for neurochemical detection. Our team has developed a freestanding, all diamond microelectrode consisting of a boron-doped polycrystalline diamond core, encapsulated in an insulating polycrystalline diamond shell, with a cleaved planar tip for electrochemical sensing. This all-diamond electrode is advantageous due to its – (1) batch fabrication using wafer technology that eliminates traditional hand fabrication errors and inconsistencies, (2) absence of metal-based wires, or foundations, to improve biocompatibility and flexibility, and (3) sp3 carbon surface with resistance to biofouling, i.e. adsorption of proteins or unwanted molecules at the electrode surface in a biological environment that impedes overall electrode performance. Here, we provide findings on further in vitro testing and development of the freestanding boron-doped diamond microelectrode (BDDME) for neurotransmitter detection using fast scan cyclic voltammetry (FSCV). In this report, we elaborate on – 1) an updated fabrication scheme and work flow to generate all diamond BDDMEs, 2) slow scan cyclic voltammetry measurements of reference and target analytes to understand basic electrochemical behavior of the electrode, and 3) FSCV characterization of common neurotransmitters, and overall favorability of serotonin (5-HT) detection. The BDDME showed a 2-fold increased FSCV response for 5-HT in comparison to dopamine (DA), with a limit of detection of 0.16 µM for 5-HT and 0.26 µM for DA. These results are intended to expand on the development of the next generation BDDME and guide future in vivo experiments, adding to the growing body of literature on implantable devices for neurochemical sensing.
{"title":"All-Diamond Boron-Doped Microelectrodes for Neurochemical Sensing with Fast-Scan Cyclic Voltammetry","authors":"Bhavna Gupta, Brandon Kepros, Jann B. Landgraf, Michael F. Becker, Wen Li, Erin K. Purcell, James R. Siegenthaler","doi":"10.1101/2024.08.07.606919","DOIUrl":"https://doi.org/10.1101/2024.08.07.606919","url":null,"abstract":"Neurochemical sensing with implantable devices has gained remarkable attention over the last few decades. A promising area of this research is the progress of novel electrodes as electrochemical tools for neurotransmitter detection in the brain. The boron-doped diamond (BDD) electrode is one such candidate that previously has been reported for its excellent electrochemical properties, including a wide working potential, superior chemical inertness and mechanical stability, good biocompatibility and resistance to fouling. Meanwhile, limited research has been conducted on the BDD as a microelectrode for neurochemical detection. Our team has developed a freestanding, all diamond microelectrode consisting of a boron-doped polycrystalline diamond core, encapsulated in an insulating polycrystalline diamond shell, with a cleaved planar tip for electrochemical sensing. This all-diamond electrode is advantageous due to its – (1) batch fabrication using wafer technology that eliminates traditional hand fabrication errors and inconsistencies, (2) absence of metal-based wires, or foundations, to improve biocompatibility and flexibility, and (3) sp3 carbon surface with resistance to biofouling, i.e. adsorption of proteins or unwanted molecules at the electrode surface in a biological environment that impedes overall electrode performance. Here, we provide findings on further in vitro testing and development of the freestanding boron-doped diamond microelectrode (BDDME) for neurotransmitter detection using fast scan cyclic voltammetry (FSCV). In this report, we elaborate on – 1) an updated fabrication scheme and work flow to generate all diamond BDDMEs, 2) slow scan cyclic voltammetry measurements of reference and target analytes to understand basic electrochemical behavior of the electrode, and 3) FSCV characterization of common neurotransmitters, and overall favorability of serotonin (5-HT) detection. The BDDME showed a 2-fold increased FSCV response for 5-HT in comparison to dopamine (DA), with a limit of detection of 0.16 µM for 5-HT and 0.26 µM for DA. These results are intended to expand on the development of the next generation BDDME and guide future in vivo experiments, adding to the growing body of literature on implantable devices for neurochemical sensing.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"38 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141924187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607018
Nathalie Liegel, Daniel Schneider, Edmund Wascher, Laura-Isabelle Klatt, Stefan Arnau
In some situations, e.g., when we expect to gain a reward in case of good performance, goal-driven top-down attention is particularly strong. Little is known about the task specificity of such increases of top-down attention due to environmental factors. To understand to what extent performance-contingent reward prospects can result in specific and unspecific changes in cognitive processing, we here investigate reward effects under different levels of task specification. Thirty-two participants performed a visual or an auditory discrimination task cued by two consecutive visual stimuli: First, a reward cue indicated if good performance was rewarded. Second, a task cue announced either which of the two tasks would follow (precise cue) or that both tasks would follow equally likely (imprecise cue). Reward and task cue preciseness both significantly improved performance. Moreover, the response time difference between precisely and imprecisely cued trials was significantly stronger in rewarded than in unrewarded trials. These effects were reflected in ERP slow wave amplitudes: Reward and preciseness both significantly enhanced the contingent negative variation (CNV) prior to the task stimulus. In an early CNV time interval, both factors also showed an interaction. A negative slow wave prior to the task cue was also significantly enhanced for rewarded trials. This effect correlated with the reward difference in response times. These results indicate that reward prospects trigger task-specific changes in preparatory top-down attention which can flexibly adapt over time and across different task requirements. This highlights that a reward-induced increase of cognitive control can occur on different specificity levels.
{"title":"The effect of performance contingent reward prospects flexibly adapts to more versus less specific task goals","authors":"Nathalie Liegel, Daniel Schneider, Edmund Wascher, Laura-Isabelle Klatt, Stefan Arnau","doi":"10.1101/2024.08.07.607018","DOIUrl":"https://doi.org/10.1101/2024.08.07.607018","url":null,"abstract":"In some situations, e.g., when we expect to gain a reward in case of good performance, goal-driven top-down attention is particularly strong. Little is known about the task specificity of such increases of top-down attention due to environmental factors. To understand to what extent performance-contingent reward prospects can result in specific and unspecific changes in cognitive processing, we here investigate reward effects under different levels of task specification. Thirty-two participants performed a visual or an auditory discrimination task cued by two consecutive visual stimuli: First, a reward cue indicated if good performance was rewarded. Second, a task cue announced either which of the two tasks would follow (precise cue) or that both tasks would follow equally likely (imprecise cue). Reward and task cue preciseness both significantly improved performance. Moreover, the response time difference between precisely and imprecisely cued trials was significantly stronger in rewarded than in unrewarded trials. These effects were reflected in ERP slow wave amplitudes: Reward and preciseness both significantly enhanced the contingent negative variation (CNV) prior to the task stimulus. In an early CNV time interval, both factors also showed an interaction. A negative slow wave prior to the task cue was also significantly enhanced for rewarded trials. This effect correlated with the reward difference in response times. These results indicate that reward prospects trigger task-specific changes in preparatory top-down attention which can flexibly adapt over time and across different task requirements. This highlights that a reward-induced increase of cognitive control can occur on different specificity levels.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"32 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141924505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607044
J.M. Trinidad-Barnech, J.R. José Sotelo-Silveira, D. Fernandez Do Porto, P. Smircich
Kinetoplastids belong to the supergroup Discobids, an early divergent eukaryotic clade. Although the amount of genomic information on these parasites has grown substantially, assigning gene functions through traditional sequence-based homology methods remains challenging. Recently, significant advancements have been made in in silico protein structure prediction and algorithms for rapid and precise large-scale protein structure comparisons. In this work, we developed a protein structure-based homology search pipeline (ASC, Annotation by Structural Comparisons) and applied it to annotate all kinetoplastid proteins available in TriTrypDB. Our pipeline assigned functional annotation to 23,000 hypothetical proteins across all 35 kinetoplastid species in the database. Among these, we identified ubiquitous eukaryotic proteins that had not been previously detected in kinetoplastid genomes. The resulting annotations (KASC, Kinetoplastid Annotation by Structural Comparison) are openly available to the community (kasc.fcien.edu.uy). Author Summary Kinetoplastids are a group of parasites that cause severe diseases in the poorest regions of the world. Despite the increasing amount of genomic information available on these parasites, predicting the function of many of their genes using traditional methods has been difficult. Recently, there have been significant advancements in predicting protein structures and comparing them on a large scale. In this study, we created a new method called ASC (Annotation by Structural Comparisons) to find functions for all the kinetoplastid genes listed in the TriTrypDB database. Our strategy successfully assigned functions to 23,000 proteins in kinetoplastids. Among these, we discovered important proteins found in all eukaryotes that had not been previously identified in kinetoplastids. This information (KASC, Kinetoplastid Annotation by Structural Comparison) is freely available at kasc.fcien.edu.uy.
Kinetoplastids 属于 Discobids 超群，是一个早期分化的真核生物支系。尽管有关这些寄生虫的基因组信息量已大幅增加，但通过传统的基于序列的同源性方法来确定基因功能仍然具有挑战性。最近，硅学蛋白质结构预测和快速精确的大规模蛋白质结构比较算法取得了重大进展。在这项工作中，我们开发了基于蛋白质结构的同源性搜索管道（ASC，Annotation by Structural Comparisons），并将其应用于注释 TriTrypDB 中的所有动植体蛋白质。我们的管道为数据库中所有 35 个核原生动物物种的 23,000 个假定蛋白质分配了功能注释。在这些蛋白质中，我们发现了以前未在核原生质体基因组中检测到的普遍存在的真核蛋白质。由此产生的注释（KASC，Kinetoplastid Annotation by Structural Comparison）可向社区公开（kasc.fcien.edu.uy）。作者简介 Kinetoplastids 是一类寄生虫，在世界上最贫穷的地区引起严重的疾病。尽管有关这些寄生虫的基因组信息越来越多，但用传统方法预测其许多基因的功能一直很困难。最近，在预测蛋白质结构并对其进行大规模比较方面取得了重大进展。在这项研究中，我们创建了一种名为 ASC（通过结构比较进行注释）的新方法，为 TriTrypDB 数据库中列出的所有动植体基因寻找功能。我们的策略成功地为 23,000 个核原生动物蛋白质分配了功能。在这些蛋白质中，我们发现了所有真核生物中都有的重要蛋白质，而这些蛋白质以前从未在核原生质中发现过。这些信息（KASC，Kinetoplastid Annotation by Structural Comparison）可在 kasc.fcien.edu.uy 免费获取。
{"title":"Expanding kinetoplastid genome annotation through protein structure comparison","authors":"J.M. Trinidad-Barnech, J.R. José Sotelo-Silveira, D. Fernandez Do Porto, P. Smircich","doi":"10.1101/2024.08.07.607044","DOIUrl":"https://doi.org/10.1101/2024.08.07.607044","url":null,"abstract":"Kinetoplastids belong to the supergroup Discobids, an early divergent eukaryotic clade. Although the amount of genomic information on these parasites has grown substantially, assigning gene functions through traditional sequence-based homology methods remains challenging. Recently, significant advancements have been made in in silico protein structure prediction and algorithms for rapid and precise large-scale protein structure comparisons. In this work, we developed a protein structure-based homology search pipeline (ASC, Annotation by Structural Comparisons) and applied it to annotate all kinetoplastid proteins available in TriTrypDB. Our pipeline assigned functional annotation to 23,000 hypothetical proteins across all 35 kinetoplastid species in the database. Among these, we identified ubiquitous eukaryotic proteins that had not been previously detected in kinetoplastid genomes. The resulting annotations (KASC, Kinetoplastid Annotation by Structural Comparison) are openly available to the community (kasc.fcien.edu.uy). Author Summary Kinetoplastids are a group of parasites that cause severe diseases in the poorest regions of the world. Despite the increasing amount of genomic information available on these parasites, predicting the function of many of their genes using traditional methods has been difficult. Recently, there have been significant advancements in predicting protein structures and comparing them on a large scale. In this study, we created a new method called ASC (Annotation by Structural Comparisons) to find functions for all the kinetoplastid genes listed in the TriTrypDB database. Our strategy successfully assigned functions to 23,000 proteins in kinetoplastids. Among these, we discovered important proteins found in all eukaryotes that had not been previously identified in kinetoplastids. This information (KASC, Kinetoplastid Annotation by Structural Comparison) is freely available at kasc.fcien.edu.uy.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"18 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.08.606705
Jeanne Hsieh, Megan A. L. Hall, Mohammad Shameem, Patrick J. Ernst, Forum Kamdar, Bhairab N. Singh, Robert L. Meisel, Brenda M. Ogle
Hypertrophic cardiomyopathy (HCM) is characterized by myocyte hypertrophy, sarcomere disarray, and myocardial fibrosis, leading to significant morbidity and mortality. As the most common inherited cardiomyopathy, HCM largely results from mutations in sarcomeric protein genes. Current treatments for HCM primarily focus on alleviating late-stage symptoms, with a critical gap in the detailed understanding of early-stage deficiencies that drive disease progression. We recently showed, in monolayers of cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) with MYH7 R723C and MYH6 R725C mutations, altered expression of several extracellular matrix (ECM)-related genes with associated defects in cardiomyocyte-ECM adhesion. To better evaluate the cardiomyocyte-ECM interface and pathological ECM dynamics in early-stage HCM, here we adopted a 3D engineered heart tissue (EHT) model containing both cardiomyocytes and fibroblasts, the primary contributor to ECM remodeling. Mutant EHTs showed aberrant cardiomyocyte distribution, augmented calcium handling, and force generation compared to controls. Altered proteoglycan deposition and increased phosphorylated focal adhesion kinase (pFAK) further indicated changes in ECM composition and connectivity. Elevated transforming growth factor beta-1 (TGF-β1) secretion and a higher proportion of activated fibroblasts were identified in mutant EHTs, along with sustained TGF-β1 transcription specifically in mutant cardiomyocytes. Remarkably, blocking TGF-β1 receptor signaling reduced fibroblast activation and contraction force to control levels. This study underscores the early interplay of mutant hiPSC-CMs with fibroblasts, wherein mutant cardiomyocytes initiate fibroblast activation via TGF-β1 overexpression, independent of the immune system. These findings provide a promising foundation for developing and implementing novel strategies to treat HCM well before the manifestation of clinically detectable fibrosis and cardiac dysfunction.
{"title":"HCM-associated mutations in MYH6/7 drive pathologic expression of TGF-β1 in cardiomyocytes within weeks of developmental specification","authors":"Jeanne Hsieh, Megan A. L. Hall, Mohammad Shameem, Patrick J. Ernst, Forum Kamdar, Bhairab N. Singh, Robert L. Meisel, Brenda M. Ogle","doi":"10.1101/2024.08.08.606705","DOIUrl":"https://doi.org/10.1101/2024.08.08.606705","url":null,"abstract":"Hypertrophic cardiomyopathy (HCM) is characterized by myocyte hypertrophy, sarcomere disarray, and myocardial fibrosis, leading to significant morbidity and mortality. As the most common inherited cardiomyopathy, HCM largely results from mutations in sarcomeric protein genes. Current treatments for HCM primarily focus on alleviating late-stage symptoms, with a critical gap in the detailed understanding of early-stage deficiencies that drive disease progression. We recently showed, in monolayers of cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) with MYH7 R723C and MYH6 R725C mutations, altered expression of several extracellular matrix (ECM)-related genes with associated defects in cardiomyocyte-ECM adhesion. To better evaluate the cardiomyocyte-ECM interface and pathological ECM dynamics in early-stage HCM, here we adopted a 3D engineered heart tissue (EHT) model containing both cardiomyocytes and fibroblasts, the primary contributor to ECM remodeling. Mutant EHTs showed aberrant cardiomyocyte distribution, augmented calcium handling, and force generation compared to controls. Altered proteoglycan deposition and increased phosphorylated focal adhesion kinase (pFAK) further indicated changes in ECM composition and connectivity. Elevated transforming growth factor beta-1 (TGF-β1) secretion and a higher proportion of activated fibroblasts were identified in mutant EHTs, along with sustained TGF-β1 transcription specifically in mutant cardiomyocytes. Remarkably, blocking TGF-β1 receptor signaling reduced fibroblast activation and contraction force to control levels. This study underscores the early interplay of mutant hiPSC-CMs with fibroblasts, wherein mutant cardiomyocytes initiate fibroblast activation via TGF-β1 overexpression, independent of the immune system. These findings provide a promising foundation for developing and implementing novel strategies to treat HCM well before the manifestation of clinically detectable fibrosis and cardiac dysfunction.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"53 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.08.607243
Katherine M. Casazza, Gregory M. Williams, Lauren Johengen, Gavin Twoey, J. Surtees
Mismatch repair (MMR) is a highly conserved DNA repair pathway that recognizes mispairs that occur spontaneously during DNA replication and coordinates their repair. In Saccharomyces cerevisiae, Msh2-Msh3 and Msh2-Msh6 initiate MMR by recognizing and binding insertion deletion loops (in/dels) up to ∼ 17 nucleotides (nt.) and base-base mispairs, respectively; the two complexes have overlapping specificity for small (1-2 nt.) in/dels. The DNA-binding specificity for the two complexes resides in their respective mispair binding domains (MBDs) and have distinct DNA-binding modes. Msh2-Msh3 also plays a role in promoting CAG/CTG trinucleotide repeat (TNR) expansions, which underlie many neurodegenerative diseases such as Huntington’s Disease and Myotonic Dystrophy Type 1. Models for Msh2-Msh3’s role in promoting TNR tracts expansion have invoked its specific DNA-binding activity and predict that the TNR structure alters its DNA binding and downstream activities to block repair. Using a chimeric Msh complex that replaces the MBD of Msh6 with the Msh3 MBD, we demonstrate that Msh2-Msh3 DNA-binding activity is not sufficient to promote TNR expansions. We propose a model for Msh2-Msh3-mediated TNR expansions that requires a fully functional Msh2-Msh3 including DNA binding, coordinated ATP binding and hydrolysis activities and interactions with Mlh complexes that are analogous to those required for MMR. Article Summary The mismatch repair (MMR) protein complex Msh2-Msh3 promotes trinucleotide repeat (TNR) expansions that can lead to neurodegenerative diseases, while the Msh2-Msh6 complex does not. We tested the hypothesis that Msh2-Msh3’s specific DNA binding activity is sufficient to promote TNR expansions, using a chimeric MSH complex in vivo and in vitro. We found that the Msh2-Msh3-like DNA-binding was not sufficient to promote TNR expansions. Our findings indicate that Msh2-Msh3 plays an active, pathogenic role in promoting TNR expansions beyond simply binding to TNR structures.
错配修复（MMR）是一种高度保守的 DNA 修复途径，它能识别 DNA 复制过程中自发发生的错配并协调其修复。在酿酒酵母（Saccharomyces cerevisiae）中，Msh2-Msh3 和 Msh2-Msh6 分别通过识别和结合插入缺失环（in/dels）（最大可达 17 个核苷酸（nt.））和碱基碱基误码配对来启动 MMR；这两个复合体对小的（1-2 nt.）in/dels 具有重叠的特异性。这两种复合物的 DNA 结合特异性存在于各自的错配结合域（MBD）中，并具有不同的 DNA 结合模式。Msh2-Msh3 还在促进 CAG/CTG 三核苷酸重复（TNR）扩增方面发挥作用，而这种扩增是亨廷顿氏病和 1 型肌营养不良症等多种神经退行性疾病的基础。Msh2-Msh3在促进TNR片段扩增中的作用模型援引了其特定的DNA结合活性，并预测TNR结构会改变其DNA结合和下游活动，从而阻碍修复。利用用 Msh3 MBD 取代 Msh6 MBD 的嵌合 Msh 复合物，我们证明 Msh2-Msh3 的 DNA 结合活性不足以促进 TNR 扩增。我们提出了一个Msh2-Msh3介导的TNR扩展模型，该模型需要一个全功能的Msh2-Msh3，包括DNA结合、协调的ATP结合和水解活性以及与Mlh复合物的相互作用，这些与MMR所需的类似。文章摘要 错配修复（MMR）蛋白复合物 Msh2-Msh3 可促进三核苷酸重复（TNR）扩增，从而导致神经退行性疾病，而 Msh2-Msh6 复合物则不会。我们利用体内和体外的嵌合 MSH 复合物，检验了 Msh2-Msh3 的特异性 DNA 结合活性是否足以促进 TNR 扩增的假设。我们发现，类似 Msh2-Msh3 的 DNA 结合不足以促进 TNR 扩增。我们的研究结果表明，Msh2-Msh3 在促进 TNR 扩增方面发挥着积极的致病作用，而不仅仅是与 TNR 结构结合。
{"title":"Msh2-Msh3 DNA-binding is not sufficient to promote trinucleotide repeat expansions in Saccharomyces cerevisiae","authors":"Katherine M. Casazza, Gregory M. Williams, Lauren Johengen, Gavin Twoey, J. Surtees","doi":"10.1101/2024.08.08.607243","DOIUrl":"https://doi.org/10.1101/2024.08.08.607243","url":null,"abstract":"Mismatch repair (MMR) is a highly conserved DNA repair pathway that recognizes mispairs that occur spontaneously during DNA replication and coordinates their repair. In Saccharomyces cerevisiae, Msh2-Msh3 and Msh2-Msh6 initiate MMR by recognizing and binding insertion deletion loops (in/dels) up to ∼ 17 nucleotides (nt.) and base-base mispairs, respectively; the two complexes have overlapping specificity for small (1-2 nt.) in/dels. The DNA-binding specificity for the two complexes resides in their respective mispair binding domains (MBDs) and have distinct DNA-binding modes. Msh2-Msh3 also plays a role in promoting CAG/CTG trinucleotide repeat (TNR) expansions, which underlie many neurodegenerative diseases such as Huntington’s Disease and Myotonic Dystrophy Type 1. Models for Msh2-Msh3’s role in promoting TNR tracts expansion have invoked its specific DNA-binding activity and predict that the TNR structure alters its DNA binding and downstream activities to block repair. Using a chimeric Msh complex that replaces the MBD of Msh6 with the Msh3 MBD, we demonstrate that Msh2-Msh3 DNA-binding activity is not sufficient to promote TNR expansions. We propose a model for Msh2-Msh3-mediated TNR expansions that requires a fully functional Msh2-Msh3 including DNA binding, coordinated ATP binding and hydrolysis activities and interactions with Mlh complexes that are analogous to those required for MMR. Article Summary The mismatch repair (MMR) protein complex Msh2-Msh3 promotes trinucleotide repeat (TNR) expansions that can lead to neurodegenerative diseases, while the Msh2-Msh6 complex does not. We tested the hypothesis that Msh2-Msh3’s specific DNA binding activity is sufficient to promote TNR expansions, using a chimeric MSH complex in vivo and in vitro. We found that the Msh2-Msh3-like DNA-binding was not sufficient to promote TNR expansions. Our findings indicate that Msh2-Msh3 plays an active, pathogenic role in promoting TNR expansions beyond simply binding to TNR structures.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"69 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607010
Tim J. van der Zee, Paolo Tecchio, Daniel Hahn, B. Raiteri
Background Brightness-mode (B-mode) ultrasound is a valuable tool to non-invasively image skeletal muscle architectural changes during movement, but automatically estimating architectural features such as fascicle length remains a major challenge. Existing fascicle tracking algorithms either require time-consuming drift corrections or yield noisy estimates that require post-processing. We therefore aimed to develop an algorithm that tracks fascicles without drift and noise across a range of experimental conditions and image acquisition settings. Methods We applied a Kalman filter to combine fascicle length and fascicle angle estimates from existing and openly available UltraTrack and TimTrack algorithms into a hybrid algorithm called UltraTimTrack. We applied the hybrid algorithm to ultrasound image sequences collected from the human medial gastrocnemius of healthy individuals (N=8, 4 women), who performed cyclical submaximal plantar flexion contractions or remained at rest during passive ankle joint rotations at given frequencies and amplitudes whilst seated in a dynamometer chair. We quantified the algorithm’s tracking accuracy, noise, and drift as the respective mean, cycle-to-cycle, and accumulated between-contraction variability in fascicle length and fascicle angle. We expected UltraTimTrack’s estimates to be less noisy and to drift less across experimental conditions and image acquisition settings, compared with estimates from its parent algorithms. Results The proposed algorithm had low-noise estimates like UltraTrack and was drift-free like TimTrack across the broad range of conditions we tested. Estimated fascicle length and fascicle angle deviations accumulated to 2.1 ± 1.3 mm (mean ± s.d.) and 0.8 ± 0.7 deg, respectively, over 120 cyclical contractions. Average cycle-to-cycle variability was 1.4 ± 0.4 mm and 0.6 ± 0.3 deg, respectively. In comparison, UltraTrack had similar cycle-to-cycle variability (1.1 ± 0.3 mm, 0.5 ± 0.1 deg) but greater cumulative deviation (67.0 ± 59.3 mm, 9.3 ± 8.6 deg), whereas TimTrack had similar cumulative deviation (1.9 ± 2.2 mm, 0.9 ± 1.0 deg) but greater variability (3.5 ± 1.0 mm, 1.4 ± 0.5 deg). UltraTimTrack was significantly less affected by experimental conditions and image acquisition settings than its parent algorithms. It also performed well on a previously published image sequence from the human tibialis anterior, yielding a smaller root-mean-square deviation from manual tracking (fascicle length: 2.7 mm, fascicle angle: 0.7 deg) than a recently proposed hybrid algorithm (fascicle length: 4.5 mm, fascicle angle: 0.8 deg) and a machine-learning (DL_Track) algorithm (fascicle length: 8.2 mm, fascicle angle: 4.8 deg). Conclusion We developed a Kalman-filter-based method to improve fascicle tracking from B-mode ultrasound image sequences. The proposed algorithm provides low-noise, drift-free estimates of muscle architectural changes that may better inform muscle function interpretations.
{"title":"UltraTimTrack: a Kalman-filter-based algorithm to track muscle fascicles in ultrasound image sequences","authors":"Tim J. van der Zee, Paolo Tecchio, Daniel Hahn, B. Raiteri","doi":"10.1101/2024.08.07.607010","DOIUrl":"https://doi.org/10.1101/2024.08.07.607010","url":null,"abstract":"Background Brightness-mode (B-mode) ultrasound is a valuable tool to non-invasively image skeletal muscle architectural changes during movement, but automatically estimating architectural features such as fascicle length remains a major challenge. Existing fascicle tracking algorithms either require time-consuming drift corrections or yield noisy estimates that require post-processing. We therefore aimed to develop an algorithm that tracks fascicles without drift and noise across a range of experimental conditions and image acquisition settings. Methods We applied a Kalman filter to combine fascicle length and fascicle angle estimates from existing and openly available UltraTrack and TimTrack algorithms into a hybrid algorithm called UltraTimTrack. We applied the hybrid algorithm to ultrasound image sequences collected from the human medial gastrocnemius of healthy individuals (N=8, 4 women), who performed cyclical submaximal plantar flexion contractions or remained at rest during passive ankle joint rotations at given frequencies and amplitudes whilst seated in a dynamometer chair. We quantified the algorithm’s tracking accuracy, noise, and drift as the respective mean, cycle-to-cycle, and accumulated between-contraction variability in fascicle length and fascicle angle. We expected UltraTimTrack’s estimates to be less noisy and to drift less across experimental conditions and image acquisition settings, compared with estimates from its parent algorithms. Results The proposed algorithm had low-noise estimates like UltraTrack and was drift-free like TimTrack across the broad range of conditions we tested. Estimated fascicle length and fascicle angle deviations accumulated to 2.1 ± 1.3 mm (mean ± s.d.) and 0.8 ± 0.7 deg, respectively, over 120 cyclical contractions. Average cycle-to-cycle variability was 1.4 ± 0.4 mm and 0.6 ± 0.3 deg, respectively. In comparison, UltraTrack had similar cycle-to-cycle variability (1.1 ± 0.3 mm, 0.5 ± 0.1 deg) but greater cumulative deviation (67.0 ± 59.3 mm, 9.3 ± 8.6 deg), whereas TimTrack had similar cumulative deviation (1.9 ± 2.2 mm, 0.9 ± 1.0 deg) but greater variability (3.5 ± 1.0 mm, 1.4 ± 0.5 deg). UltraTimTrack was significantly less affected by experimental conditions and image acquisition settings than its parent algorithms. It also performed well on a previously published image sequence from the human tibialis anterior, yielding a smaller root-mean-square deviation from manual tracking (fascicle length: 2.7 mm, fascicle angle: 0.7 deg) than a recently proposed hybrid algorithm (fascicle length: 4.5 mm, fascicle angle: 0.8 deg) and a machine-learning (DL_Track) algorithm (fascicle length: 8.2 mm, fascicle angle: 4.8 deg). Conclusion We developed a Kalman-filter-based method to improve fascicle tracking from B-mode ultrasound image sequences. The proposed algorithm provides low-noise, drift-free estimates of muscle architectural changes that may better inform muscle function interpretations.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"50 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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