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Polar transform network for prostate ultrasound segmentation with uncertainty estimation

Medical Image Analysis 2022年第0期78卷 1页

作者： Xu, Xuanang Sanford, Thomas Turkbey, Baris Xu, Sheng Wood, Bradford J. Yan, Pingkun Department of Biomedical Engineering and the Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute TroyNY12180 United States Department of Urology The State University of New York Upstate Medical University SyracuseNY13210 United States Molecular Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20892 United States Center for Interventional Oncology Radiology & Imaging Sciences at National Institutes of Health BethesdaMD20892 United States

Automatic and accurate prostate ultrasound segmentation is a long-standing and challenging problem due to the severe noise and ambiguous/missing prostate boundaries. In this work, we propose a novel polar transform network (PTN) to handle this problem from a fundamentally new perspective, where the prostate is represented and segmented in the polar coordinate space rather than the original image grid space. This new representation gives a prostate volume, especially the most challenging apex and base sub-areas, much denser samples than the background and thus facilitate the learning of discriminative features for accurate prostate segmentation. Moreover, in the polar representation, the prostate surface can be efficiently parameterized using a 2D surface radius map with respect to a centroid coordinate, which allows the proposed PTN to obtain superior accuracy compared with its counterparts using convolutional neural networks while having significantly fewer (18%∼41%) trainable parameters. We also equip our PTN with a novel strategy of centroid perturbed test-time augmentation (CPTTA), which is designed to further improve the segmentation accuracy and quantitatively assess the model uncertainty at the same time. The uncertainty estimation function provides valuable feedback to clinicians when manual modifications or approvals are required for the segmentation, substantially improving the clinical significance of our work. We conduct a three-fold cross validation on a clinical dataset consisting of 315 transrectal ultrasound (TRUS) images to comprehensively evaluate the performance of the proposed method. The experimental results show that our proposed PTN with CPTTA outperforms the state-of-the-art methods with statistical significance on most of the metrics while exhibiting a much smaller model size. Source code of the proposed PTN is released at https://***/DIAL-RPI/PTN. © 2022 Elsevier B.V.

关键词： Image segmentation

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Flagellum Pumping Efficiency in Shear-Thinning Viscoelastic Fluids

arXiv

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arXiv 2023年

作者： Barrett, Aaron Fogelson, Aaron L. Gregory Forest, M. Gruninger, Cole Lim, Sookkyung Griffith, Boyce E. Department of Mathematics University of Utah Salt Lake CityUT United States Departments of Mathematics and Biomedical Engineering University of Utah Salt Lake CityUT United States Department of Mathematics University of North Carolina Chapel HillNC United States Department of Applied Physical Sciences University of North Carolina Chapel HillNC United States Department of Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Department of Mathematical Sciences University of Cincinnati CincinnatiOH United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

Microorganism motility often takes place within complex, viscoelastic fluid environments, e.g., sperm in cervicovaginal mucus and bacteria in biofilms. In such complex fluids, strains and stresses generated by the microorganism are stored and relax across a spectrum of length and time scales and the complex fluid can be driven out of its linear response regime. Phenomena not possible in viscous media thereby arise from feedback between the swimmer and the complex fluid, making swimming efficiency co-dependent on the propulsion mechanism and fluid properties. Here we parameterize a flagellar motor and filament properties together with elastic relaxation and nonlinear shear-thinning properties of the fluid in a computational immersed boundary model. We then explore swimming efficiency, defined as a particular flow rate divided by the torque required to spin the motor, over this parameter space. Our findings indicate that motor efficiency (measured by the volumetric flow rate) can be boosted or degraded by relatively moderate or strong shear-thinning of the viscoelastic environment. Copyright © 2023, The Authors. All rights reserved.

关键词： Shear thinning

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Vascular tissue engineering from human adipose tissue: fundamental phenotype of its resident microvascular endothelial cells and stromal/stem cells

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Biomaterials and Biosystems 2022年 6卷 100049页

作者： Antonyshyn, Jeremy A. McFadden, Meghan J. Gramolini, Anthony O. Hofer, Stefan O.P. Santerre, J. Paul Institute of Biomedical Engineering University of Toronto Toronto Canada Translational Biology and Engineering Program Ted Rogers Centre for Heart Research Toronto Canada Department of Physiology University of Toronto Toronto Canada Division of Plastic Reconstructive and Aesthetic Surgery University of Toronto Toronto Canada Departments of Surgery and Surgical Oncology University Health Network Toronto Canada Faculty of Dentistry University of Toronto Toronto Canada

Adipose tissue is an abundant, accessible, and uniquely dispensable source of cells for vascular tissue engineering. Despite its intrinsic endothelial cells, considerable effort is directed at deriving endothelium from its resident stem and progenitor cells. Here, we investigate the composition of human adipose tissue and characterize the phenotypes of its constituent cells in order to help ascertain their potential utility for vascular tissue engineering. Unsupervised clustering based on cell-surface protein signatures failed to detect CD45^–CD31^–VEGFR2⁺ endothelial progenitor cells within adipose tissue, but supported further investigation of its resident CD45^–CD31⁺ microvascular endothelial cells (HAMVECs) and CD45^–CD31^– stromal/stem cells (ASCs). The endothelial differentiation of ASCs altered their proteome, but it remained distinct from that of primary endothelial cell controls – as well as HAMVECs – regardless of their arterial-venous specification or macrovascular-microvascular origin. Rather, ASCs retained a proteome indicative of a perivascular phenotype, which was supported by their ability to facilitate the capillary morphogenesis of HAMVECs. This study supports the use of HAMVECs for the generation of endothelium. It suggests that the utility of ASCs for vascular tissue engineering lies in their capacity to remodel the extracellular matrix and to function as mural cells. © 2022 The Authors

关键词： Adipose tissue Adipose tissue-derived stromal/stem cell Endothelial cell Endothelial progenitor cell Proteomics Vascular tissue engineering

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Numerical study of cavitating flow in orifices and its effect on spray characteristics

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Journal of Hydrodynamics 2018年第5期30卷 908-919页

作者： Morteza Ghorbani Mechatronics Engineering Program Faculty of Engineering and Natural Science Sabanci University Department of Biomedical Engineering and Health Systems KTH Royal Institute of Technology

The bubbly flow regime inside orifices has significant effects on several applications, and studying its trend along an orifice could be helpful in identifying the flow mechanism in various situations. The flow regime inside an orifice depends on the situation which has been specified for the orifice. Orifice geometry has a considerable effect on bubbly flow in injectors. Meanwhile, spray characteristics are influenced by the fuel flow inside an orifice, which has strong effects on the mixture of fuel-air. In this study, spray characteristics are studied for different values of the orifice angle. The cavitation phenomenon which occurs inside an orifice varies in intensity and patterns at different angles of the orifice and consequently has diverse effects on spray characteristics. The governing equations are solved by the SIMPLE algorithm. The spray flow is modeled by the discrete droplet method（DDM）, the droplet breakup is modeled by the WAVE model, and the primary breakup is modeled by the DIESEL BREAK UP model. In order to generate cavitation phenomenon inside orifices and investigate its effect on spray characteristics, the angle of orifice with respect to the injector body is varied and the problem is studied for different angles of orifice.

关键词： Cavitation iinjector angle microchannel spray

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Elbow angle estimation for medical rehabilitation device based on EMG sensor with ARIMAX method

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AIP Conference Proceedings 2022年第1期2663卷

作者： Amelia Lita I. Made Mas Dwiyana Prasetya Wibawa Alinda Anggraini Akif Rahmatillah Riries Rulaningtyas Alfian Pramudita Putra Khusnul Ain 1Biomedical Engineering Study Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya 60115 Indonesia

In the development of medical rehabilitation tools, muscle signals or electromyographic (EMG) are often used as feedback from the body in order to facilitate normal movement patterns. Through this signal, the force, torque, and angle can be estimated to produce the desired movement in the robot to assist patients in rehabilitation therapy. There had been various research done on estimating the extremities' joint angle, including the system identification method with Auto-Regressive Integrated Moving Average with Exogenous Input (ARIMAX) model structure. This research aims to model biceps brachii's EMG signal and the elbow joint angle using the ARIMAX model structure. In modeling, the order of the model was selected using the methods of minimizing the AIC (Akaike Information Criteria) and RMSE (Root Mean Square Error) values. The reported results showed the comparison of the outcome and model orders from three data sets with a frequency sampling of 47.6690 Hz, l66.3248 Hz, and 935.6743 Hz, respectively. The frequency sampling of l66.3248 Hz results showed the best accuracy performance of the ARIMAX model structure. The model order which is selected based on the minimization of the RMSE value obtained the best estimate, while the order models were selected based on the minimization of the AIC value showed a more consistent performance on the data estimation and validation.

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Serum proteomic approach to identifying differentially expressed proteins in effusive feline infectious peritonitis

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Scientific Reports 2025年第1期15卷 1-12页

作者： Moyadee, Wassamon Roytrakul, Sittiruk Jaresitthikunchai, Janthima Phaonakrop, Narumon Choowongkomon, Kiattawee Ploypetch, Sekkarin Tansakul, Natthasit Rattanasrisomporn, Amonpun Rattanasrisomporn, Jatuporn Graduate Program in Animal Health and Biomedical Sciences Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand Department of Companion Animal Clinical Sciences Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency Pathum Thani Thailand Department of Biochemistry Faculty of Science Kasetsart University Bangkok Thailand Department of Clinical Sciences and Public Health Faculty of Veterinary Science Mahidol University Nakhon Pathom Thailand Department of Pharmacology Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand Interdisciplinary of Genetic Engineering and Bioinformatics Graduate School Kasetsart University Bangkok Thailand

Feline infectious peritonitis (FIP) is a lethal, viral-induced immune-mediated disease that remains a challenge for diagnosis and treatment in cats. Proteomic profiling, which analyzes the protein content of biological samples, offers the potential to identify novel biomarkers that could improve the diagnosis and management of FIP. This study aims to assess the serum proteome and identify proteins that differentiate healthy cats from cats diagnosed with effusive FIP using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). A total of 30 cats diagnosed with effusive FIP and 27 clinically normal cats were enrolled. Twenty-three proteins were significantly (p < 0.01, ≥ fivefold change in abundance) differentially expressed between cats with effusive FIP and controls. Among these, the P2X purinoceptor, DNA topoisomerase, Notch receptor 2, and cadherin-17 were identified as key proteins of interest in cats with effusive FIP. Our findings suggest that these differentially expressed proteins could serve as potential diagnostic biomarkers and therapeutic targets for FIP. However, further studies are needed to validate these findings and explore their potential applications. © The Author(s) 2025.

关键词： Biomarkers Cats Coronavirus Feline infectious peritonitis Proteomics Serum

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Product design of memory-boosting jelly drink for young adult

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AIP Conference Proceedings 2022年第1期2537卷

作者： Misri Gozan Brigitta Angelina Cindyara Nayanda Nur Annisa Ruth Silva Amanat Taqwa Woro Bismo 1Bioprocess Engineering Program Department of Chemical Engineering Faculty of Engineering Universitas Indonesia Kampus UI Depok West Java 16424 Indonesia 2Research Center for Biomedical Engineering Faculty of Engineering Universitas Indonesia Kampus UI Depok West Java 16424 Indonesia

Memory loss can occur in an older adult or even a younger age person. From our preliminary survey with 85 respondents, 91% of respondents ever experienced memory loss symptoms, and 63% have ever consumed memory-boosting products. This study examines a product development of a jelly drink for memory boosting, especially for youth and young adults using Brahmi (Bacopa monnieri), one of the herbal plants that can increase cell neurogenesis in the hippocampus. Initially, the needs of the respondents were classified, benchmarked with available similar products, and then transformed into specifications. The concept generation and selection were carried to fulfill the specification, including regulatory requirements. Three concepts were market-tested in jelly drink, milkshake, and syrup, where 53% prefer jelly drink. The final; formulation ingredients include Bacopa monnieri, Honey, Blueberry extract, Sugar, Agar, Jelly, Water, and Sodium benzoate.

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Techno-Economic evaluation of oil palm empty fruit bunch-based encapsulated lignin production process

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AIP Conference Proceedings 2022年第1期2537卷

作者： Muhammad Yusuf Arya Ramadhan Sarah Salsabila Muhammad Arif Darmawan Misri Gozan 1Bioprocess Engineering Program Department of Chemical Engineering Faculty of Engineering Universitas Indonesia Kampus UI Depok West Java 16424 Indonesia 2Research Center for Biomedical Engineering Faculty of Engineering Universitas Indonesia Kampus UI Depok West Java 16424 Indonesia

Oil Palm Empty Fruit Bunch (EFB) is the main solid waste from the palm oil processing industry. One of the main constituent polymers of Oil Palm EFB is lignin. Currently, lignin is used as wood adhesives. The antioxidant activity of lignin has received much attention recently because of the structure of the polyphenols possessed by lignin. Although previous studies have shown that lignin has antioxidant activity, lignin is easily oxidized while in storage. Therefore, we need materials to maintain lignin stability. This research analyzes the investment feasibility of a lignin production plant encapsulated from oil palm empty fruit bunches (EFB) as raw material. The factory will be built in the Kertajaya area, Banten, Indonesia, with a project life span of 15 years and is targeted to meet a 1% market share. This study compared four pretreatment processes: alkaline with NaOH, acid-alkaline, steam explosion, and alkaline with NH4OH. The production process simulation uses the SuperPro Designer v9.5 to obtain mass, energy, and economic parameter data. Simulations show the production of encapsulated lignin with the alkaline pretreatment using the NaOH method as the best alternative with the profitability parameters in the form of NPV, IRR, and PBP, of USD 6,078,000; 35.23 % and 3.19 years, respectively, at the product selling price of USD 40/kg.

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Alleviatory effect of isoquercetin on benign prostatic hyperplasia via IGF-1/PI3K/Akt/mTOR pathway

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Food Science and Human Wellness 2024年第3期13卷 1698-1710页

作者： Young-Jin Choi Meiqi Fan Nishala Erandi Wedamulla Yujiao Tang Eun-Kyung Kim Department of Food Science and Nutrition Dong-A UniversityBusan 49315Republic of Korea Center for Silver-targeted Biomaterials Brain Busan 21 Plus programDong-A UniversityBusan 49315Republic of Korea Department of Health Sciences the Graduate School of Dong-A UniversityBusan 49315Republic of Korea Division of Food Bioscience College of Biomedical and Health SciencesKonkuk UniversityChungju 27478Republic of Korea Department of Export Agriculture Faculty of Animal Science and Export AgricultureUva Wellassa UniversityBadulla 90000Sri Lanka School of Bio-Science and Food Engineering Changchun University of Science and TechnologyChangchun 130600China Nutritional Education Major Graduate School of EducationDong-A UniversityBusan 49315Republic of Korea Nutrinomics Lab.Co. Ltd.Busan 49315Republic of Korea

We evaluated the effect of isoquercetin(quercetin-O-3-glucoside-quercetin,IQ)as a functional component of Abeliophyllum disistichum Nakai ethanol extract(ADLE)on prostate cell proliferation and apoptosis and its effects on the IGF-1/PI3K/Akt/mTOR pathway in benign prostatic hyperplasia(BPH).Metabolites in ADLE were analyzed using UHPLC-qTOF-MS and *** was orally administered(1 or 10 mg/kg)to a testosterone propionate-induced BPH rat model,and its effects on the prostate weight were *** effect of IQ on androgen receptor(AR)signaling was analyzed in LNCaP *** IGF-1 and IQ affect the IGF-1/PI3K/Akt/mTOR pathway in BPH-1 cells was also *** metabolites in ADLE were identified and quantified,which confirmed that ADLE contained abundant IQ(20.88 mg/g).IQ significantly reduced the prostate size in a concentration-dependent manner in a BPH rat model,and significantly decreased the expression of AR signaling factors in the rat prostate tissue and LNCaP cells in a concentration-dependent *** also inhibited the PI3K/AKT/mTOR pathway activated by IGF-1 treatment in BPH-1 *** BPH-1 cells,IQ led to G0/G1 arrest and suppressed the expression of proliferation factors while inducing ***,IQ shows potential for use as a pharmaceutical and nutraceutical for BPH.

关键词： Isoquercetin Benign prostatic hyperplasia Androgen receptor signaling PI3K/Akt/mtor pathway

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Protective effects of naringin on fipronil-induced cardiovascular and renal dysfunctions in rats

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Clinical Traditional Medicine and Pharmacology 2024年第3期5卷 13-21页

作者： Temitayo Olabisi Ajibade Esther Oluwaseyi Oliyide Oluwaseun Olanrewaju Esan Moses Olusola Adetona Omolola Victoria Awoyomi Taiwo Olaide Oyagbemi Adewumi Victoria Adeogun Ademola Adetokunbo Oyagbemi Temidayo Olutayo Omobowale Kehinde Olugboyega Soetan Sanah Malomile Nkadimeng Lyndy Joy McGaw Prudence Ngalula Kayoka-Kabongo Momoh Audu Yakubu Evaristus Nwulia Oluwafemi Omoniyi Oguntibeju Department of Veterinary Physiology and Biochemistry Faculty of Veterinary MedicineUniversity of IbadanIbadanOyo State 200001Nigeria Department of Veterinary Medicine Faculty of Veterinary MedicineUniversity of Ibadan IbadanOyo State 200001Nigeria Department of Anatomy Faculty of Basic Medical SciencesCollege of MedicineUniversity of IbadanIbadanOyo State 200001Nigeria Federal College of Animal Health and Production Technology Moor PlantationIbadanOyo State 200001Nigeria Department of Life and Consumer Sciences Collage of Agriculture and Environmental SciencesUniversity of South Africa Florida CampusUniversity of South AfricaUnisa 0003South Africa Department of Paraclinical Science Faculty of Veterinary ScienceUniversity of PretoriaOnderstepoort01100028South Africa Department of Environmental&Interdisciplinary Sciences College of ScienceEngineering&TechnologyCOPHSTexas Southern UniversityHoustonTX 77587USA Howard University College of MedicineDepartment of Psychiatry and Behavioral SciencesHoward University Hospital2041 Georgia AvenueWashingtonDC 20060USA Department of Biomedical Sciences Faculty of Health and Wellness SciencesCape Peninsula University of TechnologyBellvill 7535South Africa

Background:Naringin as a bioflavanone glycoside is abundant in citrus fruits,which since ancient times have been utilized as natural herbal treatments in traditional *** has potent antioxidant effect that may mitigate oxidative stress mediated cardiovascular and renal dysfunctions in mammalian ***:To explore probable modulatory actions of naringin on fipronil-induced cardio-renal ***:Twenty-four Wistar rats weighing 140±3.0 g were divided into four groups including normal control(saline),10 mg/kg Fipronil(FIP),FIP+100 mg/kg naringin,and 100 mg/kg *** of naringin and fipronil was by oral gavage for 28 consecutive ***,blood pressure monitoring,biochemical assays,histology,and immunohistochemical evaluations were ***:Naringin significantly(P<0.001)lessened blood pressure parameters,oxidative stress markers but significantly(P<0.001)heightened the systemic ***,naringin prevented fipronil-induced histopathological lesions such as congestion and cellular infiltration in cardiac and renal ***,naringin attenuated the immunohistochemical expression of troponin 1 and matrix metalloperoxidase-2 in cardiac tissues,but heightened angiotensin converting enzyme 2 expression in contrast to that of fipronil ***:The observation in this study shows potent attenuation of fipronil-induced toxicity by naringin,through inhibiting processes related to oxidation and inflammation.

关键词： Biomarkers of cardiorenal dysfunction Fipronil toxicity Naringin Immunohistochemistry

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