Article
Multidisciplinary Sciences
Ruoqing Xu, Fei Dai, Honggang Wu, Renjie Jiao, Feng He, Jun Ma
Summary: In this study, we investigate the formation of patterns in the embryo of Drosophila along the anterior-posterior axis. By analyzing the dynamic movements of gap gene expression boundaries in relation to embryo length and the Bicoid gradient, we observe the emergence of a global scaling landscape and convergence of pattern scaling characteristics. We demonstrate the contributions of Bicoid input and regulatory dynamics in shaping the embryonic pattern's scaling characteristics.
Article
Computer Science, Artificial Intelligence
Bin Gu, Chenkang Zhang, Zhouyuan Huo, Heng Huang
Summary: This paper proposes a new doubly stochastic optimization algorithm (DSGAM) for solving generalized additive models (GAM). The algorithm can scale up additive models in both sample size and dimensionality, and has been proven to have a fast convergence rate. Experimental results on large-scale benchmark datasets demonstrate the fast convergence and significant reduction in computational time compared with existing algorithms, while maintaining similar generalization performance.
Article
Biology
Yonghyun Song, Changbong Hyeon
Summary: Spatial boundaries in animal development are formed by prepatterning of tissues by signaling molecules called morphogens. The accuracy of boundary location is limited by fluctuations in morphogen concentration, which control the expression level of target genes. Producing more morphogen molecules to reduce fluctuations can lead to more precise target boundaries, but also incurs higher thermodynamic cost. In order to achieve a precise morphogen profile with minimal cost, the characteristic length of the concentration profile should be roughly half the distance to the target boundary position from the source.
Article
Biotechnology & Applied Microbiology
Nuria Blanco-Cabra, Maria Jose Lopez-Martinez, Betsy Veronica Arevalo-Jaimes, Maria Teresa Martin-Gomez, Josep Samitier, Eduard Torrents
Summary: The management of bacterial infections is currently threatened by increasing antimicrobial resistance, chronic biofilm-associated infections, and lack of appropriate treatment approaches. This study introduces a microfluidic platform called BiofilmChip, which provides a straightforward tool for antimicrobial biofilm susceptibility testing, suitable for use in routine clinical laboratories.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Thermodynamics
Kazem Mehrabanian, Ali Abbas Nejad
Summary: Proper estimation of the heat source is crucial for destroying cancerous cells through hyperthermia. While treating cancer with hyperthermia, accurately assessing the amount of absorbed heat required to eliminate the cancer tissue is a major challenge. Measuring the temperature of all tissue points is practically impossible, making inverse analysis a valuable tool for accessing the heat source within the tissue by using the target temperature of the treated tissue.
INTERNATIONAL JOURNAL OF THERMAL SCIENCES
(2023)
Article
Biochemical Research Methods
Juan Camilo Arboleda-Rivera, Gloria Machado-Rodriguez, Boris A. Rodriguez, Jayson Gutierrez
Summary: Systems biology has rapidly developed with advances in high-performance computing and sophisticated mathematical modeling, allowing for mechanistic understanding and accurate prediction of complex biological processes like cell differentiation and embryogenesis. The field focuses on understanding how cells process external signals and translate them into coherent responses, with recent studies highlighting the crucial role of gene regulatory networks in decoding morphogen information for spatial pattern formation.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Engineering, Geological
Alireza Shahbazi, Romain Chesnaux, Ali Saeidi
Summary: A new method is developed to evaluate the inflow rate to an underground tunnel excavated in a fractured rock mass, combining analytical and numerical tools. The method uses analytical formulas based on Darcy's and Cubic laws, considering discontinuities as main pathways for groundwater flow to calculate effective parameters for groundwater inflow rate.
ENGINEERING GEOLOGY
(2021)
Article
Biodiversity Conservation
Qiang Zhang, Jian-Fei Ye, Chi-Toan Le, Dennis Mwithukia Njenga, Narindra Romer Rabarijaona, Wyckliffe Omondi Omollo, Li-Min Lu, Bing Liu, Zhi-Duan Chen
Summary: The study aims to investigate the distribution patterns and formation of plant diversity in Kenya, as well as the impact of climatic fluctuations and orogeny on them. The results show that the phylogenetic turnover of the Kenyan flora exhibits a non-monotonic pattern along a latitudinal gradient and is strongly influenced by volcanic and coastal areas.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Chemistry, Physical
Yi-Rong Liu, Shuai Jiang, Teng Huang, Fan Zhang
Summary: Atmospheric aerosols have a significant impact on climate change, and the mechanism of aerosol nucleation is still not fully understood. We have developed a hybrid calculation protocol that combines experimental data and computational methods to explore the formation mechanism of acid-base clusters. This protocol accurately explores the configuration space of complex clusters and improves our understanding of aerosol nucleation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ryan S. Kingsbury, Andrew S. Rosen, Ayush S. Gupta, Jason M. Munro, Shyue Ping Ong, Anubhav Jain, Shyam Dwaraknath, Matthew K. Horton, Kristin A. Persson
Summary: Computational materials discovery relies on large databases of properties, and while it is now possible to use more accurate methods for high-throughput calculations, recalculating the entire database is not practical. Therefore, a general procedure is proposed to combine high-fidelity calculations with low-fidelity calculations. Experimental results from the Materials Project database show that this method improves solid and aqueous phase stability predictions.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Wei Su, Xue-Qin Xie, Xiao-Wei Liu, Dong Gao, Cai-Yi Ma, Hasan Zulfiqar, Hui Yang, Hao Lin, Xiao-Long Yu, Yan-Wen Li
Summary: A novel predictor, iRNA-ac4C, was developed to identify ac4C sites in human mRNA using three feature extraction methods. The results showed promising generalization capabilities.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Immunology
Laura Matarazzo, Paulo J. G. Bettencourt
Summary: The success of mRNA-based vaccines against COVID-19 has sparked interest in mRNA technology for vaccinology. Since 2020, there has been a significant increase in the development of mRNA vaccines, with improvements in formulation design, delivery methods, and manufacturing processes. However, challenges such as high raw material costs, lack of standardization, and delivery optimization remain. mRNA technology holds promise for addressing emerging infectious diseases and hard-to-treat diseases such as malaria, tuberculosis, and HIV/AIDS.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Thermodynamics
Donggyun Ku, Minje Choi, Nakyoung Yoo, Seungheon Shin, Seungjae Lee
Summary: This study investigates the optimal routing of electric vehicles by utilizing 3D spatial information data and considering the slope of each link in the route, resulting in improved energy efficiency. By assigning routes to optimize battery efficiency, the proposed approach achieved an energy efficiency improvement of 7.84 km/kWh at an average speed of 70 km/h, demonstrating its effectiveness in achieving the goal of green transportation.
Article
Multidisciplinary Sciences
Giorgio Palma, Umberto Iemma
Summary: The main objective of this paper is to derive and validate a metacontinuum model for phase gradient-based metasurfaces. The model considers the thermal and viscous dissipation effects by introducing a complex-valued speed of sound. The results show that the metacontinuum model provides accurate predictions of the acoustic properties of the examined metasurface samples, outperforming the equivalent impedance model in some circumstances.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Giorgio Palma, Umberto Iemma
Summary: The objective of this study is to derive and validate a metacontinuum model for phase gradient-based metasurfaces. This model defines the metasurface in terms of anisotropic inertia and bulk modulus, and takes into account thermal and viscous dissipation effects by introducing a complex-valued speed of sound. Experimental results show that the metacontinuum model provides reliable predictions for the acoustic properties of metasurface samples, with accuracy comparable to the equivalent impedance model and even outperforming it in some cases.
SCIENTIFIC REPORTS
(2023)
Editorial Material
Biochemistry & Molecular Biology
John D. Laver, Howard D. Lipshitz
Article
Biochemistry & Molecular Biology
Yung-Chia Ariel Chen, Evelyn Stuwe, Yicheng Luo, Maria Ninova, Adrien Le Thomas, Ekaterina Rozhavskaya, Sisi Li, Sivani Vempati, John D. Laver, Dinshaw J. Patel, Craig A. Smibert, Howard D. Lipshitz, Katalin Fejes Toth, Alexei A. Aravin
Article
Biochemistry & Molecular Biology
Hong Na, John D. Laver, Jouhyun Jeon, Fateh Singh, Kristin Ancevicius, Yujie Fan, Wen Xi Cao, Kun Nie, Zhenglin Yang, Hua Luo, Miranda Wang, Olivia Rissland, J. Timothy Westwood, Philip M. Kim, Craig A. Smibert, Howard D. Lipshitz, Sachdev S. Sidhu
Article
Genetics & Heredity
Hua Luo, Xiao Li, Julie M. Claycomb, Howard D. Lipshitz
G3-GENES GENOMES GENETICS
(2016)
Editorial Material
Biochemical Research Methods
Howard D. Lipshitz, Julie M. Claycomb, Craig A. Smibert
Review
Developmental Biology
Nadine L. Vastenhouw, Wen Xi Cao, Howard D. Lipshitz
Article
Genetics & Heredity
Kym M. Boycott, Philippe M. Campeau, Heather E. Howley, Paul Pavlidis, Sanja Rogic, Christine Oriel, Jason N. Berman, Robert M. Hamilton, Geoffrey G. Hicks, Howard D. Lipshitz, Jean-Yves Masson, Eric A. Shoubridge, Anne Junker, Michel R. Leroux, Christopher R. McMaster, Jaques L. Michaud, Stuart E. Turvey, David Dyment, A. Micheil Innes, Clara D. van Karnebeek, Anna Lehman, Ronald D. Cohn, Ian M. MacDonald, Richard A. Rachubinski, Patrick Frosk, Anthony Vandersteen, Richard W. Wozniak, Izabella A. Pena, Xiao-Yan Wen, Thierry Lacaze-Masmonteil, Catharine Rankin, Philip Hieter
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Lucia Bruzzone, Camilla Arguelles, Matthieu Sanial, Samia Miled, Giorgia Alvisi, Marina Goncalves-Antunes, Fairouz Qasrawi, Robert A. Holmgren, Craig C. Smibert, Howard D. Lipshitz, Graciela L. Boccaccio, Anne Plessis, Isabelle Becam
Article
Cell Biology
John D. Laver, Jimmy Ly, Allison K. Winn, Angelo Karaiskakis, Sichun Lin, Kun Nie, Giulia Benic, Nima Jaberi-Lashkari, Wen Xi Cao, Alireza Khademi, J. Timothy Westwood, Sachdev S. Sidhu, Quaid Morris, Stephane Angers, Craig A. Smibert, Howard D. Lipshitz
Article
Cell Biology
Wen Xi Cao, Sarah Kabelitz, Meera Gupta, Eyan Yeung, Sichun Lin, Christiane Rammelt, Christian Ihling, Filip Pekovic, Timothy C. H. Low, Najeeb U. Siddiqui, Matthew H. K. Cheng, Stephane Angers, Craig A. Smibert, Martin Wuehr, Elmar Wahle, Howard D. Lipshitz
Editorial Material
Genetics & Heredity
Howard D. Lipshitz
Article
Genetics & Heredity
Sabine Mohr, Andrew Kenny, Simon T. Y. Lam, Miles B. Morgan, Craig A. Smibert, Howard D. Lipshitz, Paul M. Macdonald
Summary: The localization of oskar mRNA involves transport from nurse cells to the oocyte and subsequent posterior localization within the oocyte. Mutations affecting the SL2a stem-loop structure alter the binding of RNA transport factors like Egalitarian, impacting both transport and cortical anchoring. Staufen proteins are shown to play a role in inhibiting anchoring activity and promoting posterior localization.
Article
Genetics & Heredity
Wen Xi Cao, Angelo Karaiskakis, Sichun Lin, Stephane Angers, Howard D. Lipshitz
Summary: During the maternal-to-zygotic transition, a subset of maternally supplied gene products is cleared, allowing activation of zygotic gene expression. In Drosophila embryos, the protein SMG translationally represses maternal mRNAs, and a protein named Bard is required for the degradation of SMG, thus regulating the orderly progression through the maternal-to-zygotic transition.
Editorial Material
Genetics & Heredity
Valerie Wood, Paul W. Sternberg, Howard D. Lipshitz
Article
Biotechnology & Applied Microbiology
Olivia S. Rissland, Alexander O. Subtelny, Miranda Wang, Andrew Lugowski, Beth Nicholson, John D. Laver, Sachdev S. Sidhu, Craig A. Smibert, Howard D. Lipshitz, David P. Bartel
