Akhila Krishna, Ravi Kant Gupta, Pranav Jeevan, Amit Sethi
{"title":"Advancing Gene Selection in Oncology: A Fusion of Deep Learning and Sparsity for Precision Gene Selection","authors":"Akhila Krishna, Ravi Kant Gupta, Pranav Jeevan, Amit Sethi","doi":"arxiv-2403.01927","DOIUrl":"https://doi.org/arxiv-2403.01927","url":null,"abstract":"Gene selection plays a pivotal role in oncology research for improving\u0000outcome prediction accuracy and facilitating cost-effective genomic profiling\u0000for cancer patients. This paper introduces two gene selection strategies for\u0000deep learning-based survival prediction models. The first strategy uses a\u0000sparsity-inducing method while the second one uses importance based gene\u0000selection for identifying relevant genes. Our overall approach leverages the\u0000power of deep learning to model complex biological data structures, while\u0000sparsity-inducing methods ensure the selection process focuses on the most\u0000informative genes, minimizing noise and redundancy. Through comprehensive\u0000experimentation on diverse genomic and survival datasets, we demonstrate that\u0000our strategy not only identifies gene signatures with high predictive power for\u0000survival outcomes but can also streamlines the process for low-cost genomic\u0000profiling. The implications of this research are profound as it offers a\u0000scalable and effective tool for advancing personalized medicine and targeted\u0000cancer therapies. By pushing the boundaries of gene selection methodologies,\u0000our work contributes significantly to the ongoing efforts in cancer genomics,\u0000promising improved diagnostic and prognostic capabilities in clinical settings.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140035448","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}
Roman Cherniha, Joanna Stachowska-Pietka, Jacek Waniewski
{"title":"A Mathematical Model for Two Solutes Transport in a Poroelastic Material and Its Applications","authors":"Roman Cherniha, Joanna Stachowska-Pietka, Jacek Waniewski","doi":"arxiv-2403.00216","DOIUrl":"https://doi.org/arxiv-2403.00216","url":null,"abstract":"Using well-known mathematical foundations of the elasticity theory, a\u0000mathematical model for two solutes transport in a poroelastic material (soft\u0000tissue is a typical example) is suggested. It is assumed that molecules of\u0000essentially different sizes dissolved in fluid and are transported through\u0000pores of different sizes. The stress tensor, the main force leading to the\u0000material deformation, is taken not only in the standard linear form but also\u0000with an additional nonlinear part. The model is constructed in 1D space and\u0000consists of six nonlinear equations. It is shown that the governing equations\u0000are integrable in stationary case, therefore all steady-state solutions are\u0000constructed. The obtained solutions are used in an example for healthy and\u0000tumour tissue, in particular, tissue displacements are calculated and compared\u0000for parameters taken from experimental data in cases of the linear and\u0000nonlinear stress tensors. Since the governing equations are non-integrable in\u0000non-stationary case, the Lie symmetry analysis is used in order to construct\u0000time-dependent exact solutions. Depending on parameters arising in the\u0000governing equations, several special cases with non-trivial Lie symmetries are\u0000identified. As a result, multi-parameter families of exact solutions are\u0000constructed including those in terms of special functions(hypergeometric and\u0000Bessel functions). A possible application of the solutions obtained is\u0000demonstrated.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140035445","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}
Takumi Ogawa, Shuji Koyama, Toshihiro Omori, Kenji Kikuchi, Helene de Maleprade, Raymond E. Goldstein, Takuji Ishikawa
{"title":"The Architecture of Sponge Choanocyte Chambers Maximizes Mechanical Pumping Efficiency","authors":"Takumi Ogawa, Shuji Koyama, Toshihiro Omori, Kenji Kikuchi, Helene de Maleprade, Raymond E. Goldstein, Takuji Ishikawa","doi":"arxiv-2402.14364","DOIUrl":"https://doi.org/arxiv-2402.14364","url":null,"abstract":"Sponges, the basalmost members of the animal kingdom, exhibit a range of\u0000complex architectures in which microfluidic channels connect multitudes of\u0000spherical chambers lined with choanocytes, flagellated filter-feeding cells.\u0000Choanocyte chambers can possess scores or even hundreds of such cells, which\u0000drive complex flows entering through porous walls and exiting into the sponge\u0000channels. One of the mysteries of the choanocyte chamber is its spherical\u0000shape, as it seems inappropriate for inducing directional transport since many\u0000choanocyte flagella beat in opposition to such a flow. Here we combine direct\u0000imaging of choanocyte chambers in living sponges with computational studies of\u0000many-flagella models to understand the connection between chamber architecture\u0000and directional flow. We find that those flagella that beat against the flow\u0000play a key role in raising the pressure inside the choanocyte chamber, with the\u0000result that the mechanical pumping efficiency, calculated from the pressure\u0000rise and flow rate, reaches a maximum at a small outlet opening angle.\u0000Comparison between experimental observations and the results of numerical\u0000simulations reveal that the chamber diameter, flagellar wave number and the\u0000outlet opening angle of the freshwater sponge $E. muelleri$, as well as several\u0000other species, are related in a manner that maximizes the mechanical pumping\u0000efficiency. These results indicate the subtle balances at play during\u0000morphogenesis of choanocyte chambers, and give insights into the physiology and\u0000body design of sponges.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139951246","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}
Morteza Rasouligandomani, Alex del Arco, Francis Kiptengwer Chemorion, Marc-Antonio Bisotti, Fabio Galbusera, Jerome Noailly, Miguel Angel Gonzalez Ballester
{"title":"Data Repository of Finite Element Models of Normal and Deformed Thoracolumbar Spine","authors":"Morteza Rasouligandomani, Alex del Arco, Francis Kiptengwer Chemorion, Marc-Antonio Bisotti, Fabio Galbusera, Jerome Noailly, Miguel Angel Gonzalez Ballester","doi":"arxiv-2402.13041","DOIUrl":"https://doi.org/arxiv-2402.13041","url":null,"abstract":"Adult spine deformity (ASD) is prevalent and leads to a sagittal misalignment\u0000in the vertebral column. Computational methods, including Finite Element (FE)\u0000Models, have emerged as valuable tools for investigating the causes and\u0000treatment of ASD through biomechanical simulations. However, the process of\u0000generating personalized FE models is often complex and time-consuming. To\u0000address this challenge, we present a repository of FE models with diverse spine\u0000morphologies that statistically represent real geometries from a cohort of\u0000patients. These models are generated using EOS images, which are utilized to\u0000reconstruct 3D surface spine models. Subsequently, a Statistical Shape Model\u0000(SSM) is constructed, enabling the adaptation of a FE hexahedral mesh template\u0000for both the bone and soft tissues of the spine through mesh morphing. The SSM\u0000deformation fields facilitate the personalization of the mean hexahedral FE\u0000model based on sagittal balance measurements. Ultimately, this new hexahedral\u0000SSM tool offers a means to generate a virtual cohort of 16807 thoracolumbar FE\u0000spine models, which are openly shared in a public repository.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139921102","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}
Timothy J Tyree, Patrick Murphy, Wouter-Jan Rappel
{"title":"Annihilation dynamics during spiral defect chaos revealed by particle models","authors":"Timothy J Tyree, Patrick Murphy, Wouter-Jan Rappel","doi":"arxiv-2402.10308","DOIUrl":"https://doi.org/arxiv-2402.10308","url":null,"abstract":"Pair-annihilation events are ubiquitous in a variety of spatially extended\u0000systems and are often studied using computationally expensive simulations. Here\u0000we develop an approach in which we simulate the pair-annihilation of spiral\u0000wave tips in cardiac models using a computationally efficient particle model.\u0000Spiral wave tips are represented as particles with dynamics governed by\u0000diffusive behavior and short-ranged attraction. The parameters for diffusion\u0000and attraction are obtained by comparing particle motion to the trajectories of\u0000spiral wave tips in cardiac models during spiral defect chaos. The particle\u0000model reproduces the annihilation rates of the cardiac models and can determine\u0000the statistics of spiral wave dynamics, including its mean termination time. We\u0000show that increasing the attraction coefficient sharply decreases the mean\u0000termination time, making it a possible target for pharmaceutical intervention","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139902790","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}
Sarah Zaidan, Syamsudin Abdillah, Nur Arfian, Wawaimuli Arozal
{"title":"Hypolipidemic effect of brown seaweed (Sargassum crassifolium) extract in vivo (Study of histopathology, mRNA expression, and immunohistochemistry (IHC) with VCAM-1, ICAM-1, and MCP-1 parameters)","authors":"Sarah Zaidan, Syamsudin Abdillah, Nur Arfian, Wawaimuli Arozal","doi":"arxiv-2402.07497","DOIUrl":"https://doi.org/arxiv-2402.07497","url":null,"abstract":"The purpose of this study was to obtain natural drugs from brown seaweed\u0000(Sargassum crassifolium) as antiatherosclerosis candidates through the study of\u0000hypolipidemic mechanisms of action. Modeling of dyslipidemia rats was carried\u0000out by feeding high-fat (HFF) and doses of crude fucoidan 100. 200. 400mg /\u0000KgBB. in both treatments measured blood lipid profile levels taken from the\u0000orbital sinuses. HE's histopathology. mRNA expression. immunohistochemistry\u0000(IHC) with parameters VCAM-1. ICAM-1. and MCP-1 were performed on adipose\u0000tissue. as well as liver. Total cholesterol values 51.07-225.2. triglycerides\u000030.43-115.73. HDL 13.1-24.86 mg/dl and LDL 20.22-189.68 mg/dl. In the treatment\u0000of crude fucoidan obtained the result of p value < {alpha} (0.05.\u0000Histopathological features of adipose tissue after administration of HFF for 60\u0000days resulted in an increase in adipose cell size. and the liver experienced\u0000structural damage and inflammation. but after 21 days of treatment the\u0000morphological picture of adipose tissue was similar to normal morphology and\u0000the liver also decreased in severity and inflammation. The results of\u0000histochemical staining after treatment showed a positive staining part on\u0000MCP-1. The result of p value < {alpha} (0.05) of mRNA expression for\u0000administration of 3 treatment doses. A dyslipidemic mouse model with HFF\u0000administration for 60 days succeeded in becoming a dyslipidemic rat. and crude\u0000fucoidan had hypolipidemic activity. Doses of 100. 200. and 400 mg/KgBB crude\u0000fucoidan showed improvement in adipose and liver morphological features of\u0000severity and inflammation of dyslipidemic rats and decreased mRNA expression.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139773560","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}
Mariia Soloviova, Juan Carlos Beltran Vargas, Luis Fernandez de Castro, Juan Belmonte-Beitia, Víctor M. Pérez-García, Magdalena Caballero
{"title":"A mathematical model for fibrous dysplasia: The role of the flow of mutant cells","authors":"Mariia Soloviova, Juan Carlos Beltran Vargas, Luis Fernandez de Castro, Juan Belmonte-Beitia, Víctor M. Pérez-García, Magdalena Caballero","doi":"arxiv-2402.07724","DOIUrl":"https://doi.org/arxiv-2402.07724","url":null,"abstract":"Fibrous dysplasia (FD) is a mosaic non-inheritable genetic disorder of the\u0000skeleton in which normal bone is replaced by structurally unsound fibro-osseous\u0000tissue. There is no curative treatment for FD, partly because its\u0000pathophysiology is not yet fully known. We present a simple mathematical model\u0000of the disease incorporating its basic known biology, to gain insight on the\u0000dynamics of the involved bone-cell populations, and shed light on its\u0000pathophysiology. Our mathematical models account for the dynamic evolution over\u0000time of several interacting populations of bone cells averaged over a volume of\u0000bone of sufficient size in order to obtain consistent results. We develop an\u0000analytical study of the model and study its basic properties. The existence and\u0000stability of steady states are studied, an analysis of sensitivity on the model\u0000parameters is done, and different numerical simulations provide findings in\u0000agreement with the analytical results. We discuss the model dynamics match with\u0000known facts on the disease, and how some open questions could be addressed\u0000using the model.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139772442","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}
{"title":"Single-channel and multi-channel electrospinning for the fabrication of PLA/PCL tissue engineering scaffolds: comparative study of the materials physicochemical and biological properties","authors":"Semen Goreninskii, Ulyana Chernova, Elisaveta Prosetskaya, Alina Laushkina, Alexander Mishanin, Alexey Golovkin, Evgeny Bolbasov","doi":"arxiv-2403.00767","DOIUrl":"https://doi.org/arxiv-2403.00767","url":null,"abstract":"Fabrication of tissue engineering scaffolds with tailored physicochemical and\u0000biological characteristics is a relevant task in biomedical engineering. The\u0000present work was focused at the evaluation of the effect of fabrication\u0000approach (single-channel or multi-channel electrospinning) on the properties of\u0000the fabricated poly(lactic acid)(PLA)/poly(epsilon-caprolactone)(PCL) scaffolds\u0000with various polymer mass ratios (1/0, 2/1, 1/1, 1/2, and 0/1). The scaffolds\u0000with same morphology (regardless of electrospinning variant) were fabricated\u0000and characterized using SEM, water contact angle measurement, FTIR, XRD,\u0000tensile testing and in vitro experiment with multipotent mesenchymal stem\u0000cells. It was demonstrated, that multi-channel electrospinning prevents\u0000intermolecular interactions between the polymer components of the scaffold,\u0000preserving their crystal structure, what affects the mechanical characteristics\u0000of the scaffold (particularly, leads to 2-fold difference in elongation).\u0000Better adhesion of multipotent mesenchymal stem cells on the surface of the\u0000scaffolds fabricated using multichannel electrospinning was demonstrated.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140035712","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}
{"title":"A model for membrane degradation using a gelatin invadopodia assay","authors":"Giorgia Ciavolella, Nathalie Ferrand, Michèle Sabbah, Benoît Perthame, Roberto Natalini","doi":"arxiv-2404.05730","DOIUrl":"https://doi.org/arxiv-2404.05730","url":null,"abstract":"One of the most crucial and lethal characteristics of solid tumors is\u0000represented by the increased ability of cancer cells to migrate and invade\u0000other organs during the so-called metastatic spread. This is allowed thanks to\u0000the production of matrix metalloproteinases (MMPs), enzymes capable of\u0000degrading a type of collagen abundant in the basal membrane separating the\u0000epithelial tissue from the connective one. In this work, we employ a\u0000synergistic experimental and mathematical modelling approach to explore the\u0000invasion process of tumor cells. A athematical model composed of\u0000reaction-diffusion equations describing the evolution of the tumor cells\u0000density on a gelatin substrate, MMPs enzymes concentration and the degradation\u0000of the gelatin is proposed. This is completed with a calibration strategy. We\u0000perform a sensitivity analysis and explore a parameter estimation technique\u0000both on synthetic and experimental data in order to find the optimal parameters\u0000that describe the in vitro experiments. A comparison between numerical and\u0000experimental solutions ends the work.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584832","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}
Jixin Hou, Xianyan Chen, Taotao Wu, Ellen Kuhl, Xianqiao Wang
{"title":"Automated Data-Driven Discovery of Material Models Based on Symbolic Regression: A Case Study on Human Brain Cortex","authors":"Jixin Hou, Xianyan Chen, Taotao Wu, Ellen Kuhl, Xianqiao Wang","doi":"arxiv-2402.05238","DOIUrl":"https://doi.org/arxiv-2402.05238","url":null,"abstract":"We introduce a data-driven framework to automatically identify interpretable\u0000and physically meaningful hyperelastic constitutive models from sparse data.\u0000Leveraging symbolic regression, an algorithm based on genetic programming, our\u0000approach generates elegant hyperelastic models that achieve accurate data\u0000fitting through parsimonious mathematic formulae, while strictly adhering to\u0000hyperelasticity constraints such as polyconvexity. Our investigation spans\u0000three distinct hyperelastic models -- invariant-based, principal stretch-based,\u0000and normal strain-based -- and highlights the versatility of symbolic\u0000regression. We validate our new approach using synthetic data from five classic\u0000hyperelastic models and experimental data from the human brain to demonstrate\u0000algorithmic efficacy. Our results suggest that our symbolic regression robustly\u0000discovers accurate models with succinct mathematic expressions in\u0000invariant-based, stretch-based, and strain-based scenarios. Strikingly, the\u0000strain-based model exhibits superior accuracy, while both stretch- and\u0000strain-based models effectively capture the nonlinearity and\u0000tension-compression asymmetry inherent to human brain tissue. Polyconvexity\u0000examinations affirm the rigor of convexity within the training regime and\u0000demonstrate excellent extrapolation capabilities beyond this regime for all\u0000three models. However, the stretch-based models raise concerns regarding\u0000potential convexity loss under large deformations. Finally, robustness tests on\u0000noise-embedded data underscore the reliability of our symbolic regression\u0000algorithms. Our study confirms the applicability and accuracy of symbolic\u0000regression in the automated discovery of hyperelastic models for the human\u0000brain and gives rise to a wide variety of applications in other soft matter\u0000systems.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139772437","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}