Article
Multidisciplinary Sciences
Mihkel Pajusalu, Iaroslav Iakubivskyi, Gabriel Jorg Schwarzkopf, Olli Knuuttila, Timo Vaisanen, Maximilian Buhrer, Mario F. Palos, Hans Teras, Guillaume Le Bonhomme, Jaan Praks, Andris Slavinskis
Summary: This paper introduces a newly developed physically-based imaging simulator called SISPO, which is designed for simulating small solar system body fly-by and terrestrial planet surface missions. The simulator utilizes the Blender 3D visualization system and its Cycles rendering engine, supporting physically based rendering and texture generation. It focuses on realistic surface rendering and also includes tools for simulating common image aberrations. Its primary objective is to support small-body space mission design and computer-vision algorithm development.
Article
Computer Science, Interdisciplinary Applications
Abbass Ballit, Mathieu Hivert, Chrystele Rubod, Tien-Tuan Dao
Summary: High-quality gynecologist and midwife training is essential for reducing medical complications and improving maternal and fetal outcomes. While physical and virtual training simulators have been developed, they have limitations in providing a realistic childbirth experience and interactive system. The present study developed a virtual childbirth simulator using Mixed-Reality technology and HyperMSM formulation, which allows for intuitive user interaction and quantitative assessment to enhance trainee's gestures.
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2023)
Article
Immunology
Pengfei Li, Zhifang Hao, Jingyu Wu, Chen Ma, Yintai Xu, Jun Li, Rongxia Lan, Bojing Zhu, Pengyu Ren, Daidi Fan, Shisheng Sun
Summary: This study systematically investigated the protein expression profiles of M1 and M2 phenotypes in human THP-1 and mouse RAW264.7 macrophages, revealing significant divergences between the two cell lines while also identifying some common up-regulated proteins in M1 macrophages. These data serve as important resources for further studies of macrophage-associated diseases in experimental pathology using human and mouse cell line models.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Environmental Studies
Nathan H. Schumaker, Sydney M. Watkins, Julie A. Heinrichs
Summary: As fire frequency and severity increase worldwide, scientists need to incorporate wildfire models into their research, but existing simulators are complex and difficult to use. Therefore, we introduce a user-friendly wildfire simulator, HexFire, designed for non-specialist investigators, and provide a detailed description of its design and mechanisms.
Article
Computer Science, Theory & Methods
Bo Cui, Yun Hu
Summary: This paper proposes a Blockchain Simulator based on Event-Layered Architecture (BSELA), which improves the efficiency and accuracy of blockchain simulation through the event-driven scheduling mechanism and the time advancement mechanism. The experimental results show that our simulator outperforms existing blockchain simulators in terms of efficiency and accuracy, and the tuning mechanism of the object model improves the node-trust network construction and enhances data transfer efficiency and security.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2024)
Article
Environmental Sciences
V. G. Jadhao, Ashish Pandey, S. K. Mishra
Summary: The characterization of a rainfall simulator provides a great opportunity to study soil erosivity without waiting for natural rain. However, precise instrumentation is rarely available to estimate the parameters. Therefore, empirical and conceptual relationships obtained through physically-based modeling can help correlate rain parameters contributing to soil erosion.
ENVIRONMENTAL RESEARCH
(2023)
Article
Chemistry, Analytical
Guelis Montenegro, Roberto Chacon, Ernesto Fabregas, Gonzalo Garcia, Karla Schroder, Alberto Marroquin, Sebastian Dormido-Canto, Gonzalo Farias
Summary: This article presents the development of a model of a spherical robot that uses different control strategies, with the performance of the model analyzed through testing and comparison in a simulator.
Article
Chemistry, Analytical
Riccardo Marini, Konstantin Mikhaylov, Gianni Pasolini, Chiara Buratti
Summary: LoRaWAN is considered a promising low power wide area network communication protocol in large scale Internet of Things due to its flexibility and energy-saving capabilities. Precise network simulators, such as LoRaWANSim developed in MATLAB, are essential for assessing and understanding the trade-offs between parameters and performance of LoRaWAN communication in different application scenarios.
Article
Genetics & Heredity
Manuel Kosters, Johannes Leufken, Sebastian A. Leidel
Summary: SMITER is a Python-based command-line tool designed for simulating LC-MS/MS runs. It features a modular design for easy implementation of noise and fragmentation models, with default support for peptide fragmentation and various other models. SMITER enables the easy, fast, and efficient generation of defined LC-MS/MS datasets for diverse experimental purposes.
Article
Physics, Multidisciplinary
Trinh Dinh Toan, Soi Hoi Lam, Yiik Diew Wong, Meng Meng
Summary: This paper presents the development and validation of a driving simulator for ramp traffic control on expressways using a traffic simulator and control system. The simulator includes a car-following model and a traffic controller, which are harmonized and integrated in a close-loop control manner. The validation results show that the simulated speed is similar to the actual speed, and the aggregated flow rate discrepancies are within a small range, indicating the reliability of the model for traffic simulation and control applications.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Article
Biotechnology & Applied Microbiology
Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrcela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
Summary: CAMPAREE, a simulator developed in Python, provides flexibility for users by separating input sample modeling from library preparation/sequencing, allowing for incorporation of new biological findings and developments in sequencing technologies. By simulating at the level of individual molecules, CAMPAREE has the potential to model a heterogeneous population of transcripts from the same genes with different states of degradation and processing.
Article
Computer Science, Information Systems
Murad M. Shoman, Hocine Imine
Summary: This paper presents the new features implemented on the bicycle simulator developed by PICS-L at Gustave Eiffel University, focusing on studying road-bicycle interactions. The study validated the simulator and developed mathematical model through an experiment involving 36 participants, and will be further utilized for exploring bicycle dynamics, cyclist behavior, and interactions with infrastructure and other road users.
Article
Engineering, Industrial
Loic Desgeorges, Pierre-Yves Piriou, Thibault Lemattre, Hassane Chraibi
Summary: This article lays the mathematical foundations of the PyCATSHOO framework and introduces formal definitions of the structure and operational semantics of its models. These definitions clarify the semantics of PyCATSHOO models and provide a foundation for model checking.
RELIABILITY ENGINEERING & SYSTEM SAFETY
(2021)
Article
Oncology
Fangrong Zhang, Yingchao Wang, Geng Chen, Zhenli Li, Xiaohua Xing, Csilla Putz-Bankuti, Rudolf E. Stauber, Xiaolong Liu, Tobias Madl
Summary: Metabolic reprogramming is a common characteristic of malignancy, including hepatocellular carcinoma (HCC). The study reveals that HCC undergoes global metabolic reprogramming during tumor growth, with metabolic alterations associated with advanced disease stages and poor clinical outcomes. Targeting cancer metabolism can potentially provide effective therapies for HCC while also offering diagnostic and prognostic metabolic biomarkers.
Article
Biochemical Research Methods
Rob Smith, Ryan M. Taylor, John T. Prince
BMC BIOINFORMATICS
(2015)
Article
Biochemical Research Methods
Rob Smith, John T. Prince, Dan Ventura
BMC BIOINFORMATICS
(2015)
Article
Multidisciplinary Sciences
Rebecca L. Plimpton, Jorge Cuellar, Chun Wan J. Lai, Takuma Aoba, Aman Makaju, Sarah Franklin, Andrew D. Mathis, John T. Prince, Jose L. Carrascosa, Jose M. Valpuesta, Barry M. Willardson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biochemical Research Methods
John T. Prince, Rob Smith
JOURNAL OF PROTEOME RESEARCH
(2017)
Article
Biochemical Research Methods
Rob Smith, John T. Prince
Article
Biochemical Research Methods
Ryan Taylor, Ryan H. Miller, Ryan D. Miller, Michael Porter, James Dalgleish, John T. Prince
Review
Biochemical Research Methods
Rob Smith, Dan Ventura, John T. Prince
BRIEFINGS IN BIOINFORMATICS
(2015)
Article
Immunology
Jeffrey K. Schachterle, Ryan M. Stewart, M. Brett Schachterle, Joshua T. Calder, Huan Kang, John T. Prince, David L. Erickson
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2018)
Article
Multidisciplinary Sciences
Shiyang Ma, James Dalgleish, Justin Lee, Chen Wang, Linxi Liu, Richard Gill, Joseph D. Buxbaum, Wendy K. Chung, Hugues Aschard, Edwin K. Silverman, Michael H. Cho, Zihuai He, Iuliana Ionita-Laza
Summary: The study proposes a gene-based testing framework that enhances gene discovery by incorporating long-range chromatin interaction data and leveraging the knockoff framework. Through simulations and applications to multiple diseases and traits, the test shows improved power over other gene-based tests and provides a more focused approach to identifying possible causal genes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Shashi Shrivastav, Hewang Lee, Koji H. Okamoto, Huiyan Lu, Teruhiko D. Yoshida, Khun Zaw Latt, Hidefumi Wakashin, James L. T. J. Dalgleish, Erik H. A. Koritzinsky, Peng A. Xu, Laureano D. Z. Asico, Joon-Yong A. Chung, Stephen Hewitt, John J. B. Gildea, Robin A. Felder, Pedro A. Jose, Avi Z. Rosenberg, Mark A. Knepper, Tomoshige Kino, Jeffrey B. Kopp
Summary: HIV-associated nephropathy (HIVAN) impairs both glomerular and tubular functions. This study found that viral protein R (Vpr) plays an important role in urinary sodium wasting by inhibiting the expression of Na+-Cl- cotransporter (NCC) and reducing the transcriptional activity of mineralocorticoid receptor (MR) in the distal convoluted tubule.
Article
Biotechnology & Applied Microbiology
Shiyang Ma, Chen Wang, Atlas Khan, Linxi Liu, James Dalgleish, Krzysztof Kiryluk, Zihuai He, Iuliana Ionita-Laza
Summary: We propose BIGKnock, a computationally efficient gene-based testing approach that leverages long-range chromatin interaction data and performs conditional genome-wide testing via knockoffs. Applying BIGKnock to the UK Biobank data, we show that it produces smaller sets of significant genes that are likely to contain the causal gene(s), compared to conventional gene-based tests. We also demonstrate its ability to pinpoint potential causal genes at more than 80% of the associated loci.
Review
Oncology
James L. T. Dalgleish, Yonghong Wang, Jack Zhu, Paul S. Meltzer
CANCER INFORMATICS
(2019)
Article
Biochemical Research Methods
Adam C. Swensen, Jordan G. Finnell, Catalina Matias, Andrew J. Gross, John T. Prince, Richard K. Watt, John C. Price
ANALYTICAL BIOCHEMISTRY
(2017)