Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Minzhe Guo, Michael P. Morley, Cheng Jiang, Yixin Wu, Guangyuan Li, Yina Du, Shuyang Zhao, Andrew Wagner, Adnan Cihan Cakar, Michal A. Kouril, Kang Jin, Nathan C. Gaddis, Joseph A. M. Kitzmiller, Kathleen Stewart, Maria C. Basil, Susan M. A. Lin, Yun Ying, Apoorva P. Babu, Kathryn A. Wikenheiser-Brokamp, Kyu Shik N. Mun, Anjaparavanda P. S. Naren, Geremy S. Clair, Joshua N. J. Adkins, Gloria S. L. Pryhuber, Ravi S. Misra, Bruce J. Aronow, Timothy L. E. Tickle, Nathan A. Salomonis, Xin Sun, Edward E. Morrisey, Jeffrey A. Whitsett, Yan Xu
Summary: The authors developed a computational pipeline called LungMAP CellRef for efficient and automated cell-type annotation of normal and disease human and mouse lung single-cell datasets. Accurate cell-type identification is a key step in single-cell data analysis.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Fang Ye, Guodong Zhang, E. Weigao, Haide Chen, Chengxuan Yu, Lei Yang, Yuting Fu, Jiaqi Li, Sulei Fu, Zhongyi Sun, Lijiang Fei, Qile Guo, Jingjing Wang, Yanyu Xiao, Xinru Wang, Peijing Zhang, Lifeng Ma, Dapeng Ge, Suhong Xu, Juan Caballero-Perez, Alfredo Cruz-Ramirez, Yincong Zhou, Ming Chen, Ji-Feng Fei, Xiaoping Han, Guoji Guo
Summary: This study developed a new method of single-cell sequencing to analyze the perturbation patterns of cell type-related gene expression in neotenic and metamorphosed axolotls. By analyzing gene expression of over 1 million single cells, the first adult axolotl cell landscape was constructed. Comparison of single-cell transcriptomes between tissues of neotenic and metamorphosed axolotls revealed the heterogeneity of non-immune parenchymal cells in different tissues and identified their regulatory network.
NATURE COMMUNICATIONS
(2022)
Article
Mechanics
Ebrahim Kadivar, Thanh-Hoang Phan, Warn-Gyu Park, Ould el Moctar
Summary: This study investigated the dynamics of a laser-induced single cavitation bubble near a rigid cylindrical rod, revealing the formation of a mushroom-shaped bubble near the rod at smaller relative wall distances. The results showed significant differences in bubble collapse dynamics near the cylindrical rod compared to solid flat plates.
Article
Multidisciplinary Sciences
Allen W. Lynch, Myles Brown, Clifford A. Meyer
Summary: In this study, the authors propose a method that can effectively analyze batch-confounded chromatin and gene expression states by separating technical and biological effects. The cell state atlases constructed through single-cell RNA-seq and ATAC-seq analysis are powerful tools for studying perturbation effects on complex cell systems. Comparing these atlases can provide new insights into cell state and trajectory alterations.
NATURE COMMUNICATIONS
(2023)
Article
Nanoscience & Nanotechnology
Shaofei Shen, Fangjuan Zhang, Yali Zhang, Yi Li, Yanbing Niu, Long Pang, Jinyi Wang
Summary: A multiconcentration gradient generator was constructed to investigate the effect of different drug concentration gradients on cells. The results showed that chemotherapy drugs inhibited the growth of cancer cells, and hepatoma cells exhibited higher drug resistance. This device provides a simple and reliable platform for studying optimal dosages at the single-cell level and screening chemotherapy regimens.
MICROSYSTEMS & NANOENGINEERING
(2023)
Article
Chemistry, Physical
Samragni Banerjee, Alexander Yu. Sokolov
Summary: An efficient implementation of second- and third-order single-reference ADC theory is presented for calculating electron attachment and ionization energies and spectra. The new program features spin adaptation, density fitting, and vectorized and parallel tensor contractions for closed-shell systems. Results show good agreement with experimental and theoretical simulations for TEMPO radical and two DNA base pairs.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Cell Biology
Riasat Azim, Shulin Wang
Summary: The recent development of high throughput single-cell RNA sequencing allows detailed study of entire transcriptomes and characterization of cell subtypes. Cancer epigenetics can be induced by individual molecules, system dysfunction, and gene coupling effects. Integration of network perturbation theory and significant analysis can be utilized to develop cell-specific networks and identify gene associations based on molecular expressions at single-cell resolution, potentially benefiting personalized drug design and therapeutics.
Article
Multidisciplinary Sciences
Yuxuan Hu, Tao Peng, Lin Gao, Kai Tan
Summary: Single-cell technology allows for unprecedented resolution in studying signal transduction in complex tissues. CytoTalk, an algorithm using single-cell transcriptomic data, constructs cell type-specific signaling networks with improved accuracy compared to existing algorithms. Comparative analysis across tissues and developmental stages reveals increased plasticity of signaling networks, with CytoTalk facilitating de novo construction and comparative analysis of signal transduction pathways.
Article
Optics
Dandan Wen, Kai Pan, Jiajun Meng, Xuanguang Wu, Xuyue Guo, Peng Li, Sheng Liu, Dong Li, Bingyan Wei, Xin Xie, Dexing Yang, Jianlin Zhao, Kenneth B. Crozier
Summary: This study demonstrates a method to generate an array of CVBs using a single optical element, which significantly increases the number of polarization channels compared to previous methods and solves the issue of unequal intensity distributions. Furthermore, it allows for control of CVB orders and polarization rotation, enhancing the flexibility of vector field control.
LASER & PHOTONICS REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Mark Hills, Ester Falconer, Kieran O'Neill, Ashley D. Sanders, Kerstin Howe, Victor Guryev, Peter M. Lansdorp
Summary: Accurate reference genome sequences are crucial for molecular biology and genomics, and correctly organizing sequenced fragments is key in constructing robust genome references. Strand-seq technology can help build and correct full-length chromosomes without needing overlapping sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Interdisciplinary Applications
Chenglin Zheng, Fei Zhao, Lingyu Zhu, Xi Chen
Summary: A new solution approach is proposed for chemical systems to derive explicit expressions of flexibility index on continuous design variables without solving optimization problems. The method reformulates flexibility index and design problems as an existential quantifier model, and utilizes cylindrical algebraic decomposition method to project the solution space onto design variables, flexibility index and uncertain parameters dimensions. The analytical expressions between design variables and flexibility index can be deduced by the inscribed hyperrectangle checking rule, showing applicability to small- or medium-scaled problems.
COMPUTERS & CHEMICAL ENGINEERING
(2021)
Article
Environmental Sciences
Jingnan Zhang, Hanghang Chang, Xiaohu Li, Baoxuan Jiang, Tao Wei, Xincheng Sun, Dawei Liang
Summary: This study demonstrates the feasibility of using cylindrical single-chamber microbial electrolysis cells (MECs) for high H-2 production rate and efficient wastewater treatment. The researchers successfully addressed the low H-2 recovery and production rate issues by adjusting the MEC components and enriching the anodic biofilms. The results showed a high H-2 production rate and a significant degradation of acetate and butyrate, indicating the potential of this technology for practical applications.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Mathematics, Applied
Qinglan Zhao, Mengran Li, Zhixiong Chen, Baodong Qin, Dong Zheng
Summary: FLIP is a new family of stream ciphers presented at Eurocrypt 2016, aiming to enhance the efficiency of homomorphic encryption frameworks. Recent research has focused on studying the cryptographic properties of Boolean functions restricted to subsets of the space Fn2. This paper presents a unified construction of weightwise perfectly balanced (WPB) Boolean functions based on functions with algebraic degrees that can be any power of 2.
DISCRETE APPLIED MATHEMATICS
(2023)
Article
Mathematics
Jorge Gonzalez-Lorca
Summary: An explicit homomorphism is constructed between the generic Hecke algebra H-n(q) of type A and the degenerate affine Hecke algebra DH(S-n) by using a specific generic element satisfying the quadratic Hecke relation. Through the use of Jucys-Murphy's elements associated with the symmetric group Sn, explicit isomorphisms between H-n(q) and the group algebra of the symmetric group defined over C(q) are obtained. This isomorphism is also compatible with the Hoefsmit's model of irreducible representations of H-n(q) and S-n.
JOURNAL OF ALGEBRA
(2021)
Article
Computer Science, Theory & Methods
Elisabeth Gaar, Melanie Siebenhofer
Summary: The open Vizing conjecture states that the domination number of the Cartesian product graph of two graphs G and H is at least the product of the domination numbers of G and H. Recent research reformulated this conjecture using the graph class g and introduced the concept of SOS-certificates. By solving semidefinite programs (SDPs) and applying clever guessing, they obtained SOS-certificates for specific cases. In this paper, we consider their approach for a specific case and derive the unique reduced Grobner basis of the Vizing ideal, which leads to the minimum degree of an SOS-certificate. We also propose a method to find certificates for general cases, which relies on solving smaller SDPs and does not require guessing. We provide new SOS-certificates for various graph classes using our implemented method in SageMath.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Marcel Morales, Nguyen Thi Dung
Summary: The aim of this paper is to provide an effective pseudopolynomial algorithm on a1, which computes the Apery set and the Frobenius number of S. We also find the Grobner basis of the toric ideal defined by S without using Buchberger's algorithm. As an application, special classes of semigroups generated by generalized arithmetic progressions and generalized almost arithmetic progressions are introduced and studied.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Winfried Bruns, Aldo Conca
Summary: The maximal minors of a matrix of indeterminates are a universal Grobner basis according to a theorem by Bernstein, Sturmfels, and Zelevinsky. However, they are not always a universal SAGBI basis. Experimental findings on their behavior under varying monomial orders and their extension to SAGBI bases have motivated the development of a new implementation of the SAGBI algorithm using a Singular script and Normaliz for combinatorial computations. Compared to other packages, it significantly expands the range of computability.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Remi Prebet, Mohab Safey El Din, Eric Schost
Summary: This paper presents a fundamental problem in effective real algebraic geometry, which is answering connectivity queries in real algebraic sets. This problem has many applications in robotics, particularly in motion planning. The problem is solved by computing roadmaps, which are real algebraic subsets of the set under study, with dimension at most one and a connected intersection with all semi-algebraically connected components. The algorithms for computing roadmaps rely on connectivity properties of selected subsets, assuming boundedness of the set. The paper extends these connectivity statements by removing the boundedness assumption and utilizing generalized polar varieties.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Claudia Fevola, Yelena Mandelshtam
Summary: In this work, the Hirota variety arising from a rational nodal curve is studied, with a specific focus on its irreducible subvariety called the main component. Proving this to be an irreducible component corresponds to solving a weak Schottky problem for rational nodal curves. Computational tools are used to solve this problem up to genus nine.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Jinwang Liu, Dongmei Li, Tao Wu
Summary: This paper investigates the reduction of weakly linear multivariate polynomial matrices to their Smith normal forms, using hierarchical-recursive method and Quillen-Suslin Theorem. The necessary and sufficient conditions for such matrices to be reduced to their Smith normal forms are derived, which can be easily checked by computing the reduced Grobner bases of the relevant polynomial ideals. Based on the new results, an algorithm for reducing weakly linear multivariate polynomial matrices to their Smith normal forms is proposed.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Luca Sodomaco, Ettore Teixeira Turatti
Summary: This paper studies the linear span of singular k-tuples of a specific format tensor and proves that the dimension of this linear span is stable in certain formats.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Adrian Becedas, Kathlen Kohn, Lorenzo Venturello
Summary: We study Voronoi diagrams with respect to polyhedral norms for manifolds and varieties. Upper and lower bounds on the dimensions of Voronoi cells are provided. We also examine the full-dimensional Voronoi cells for algebraic varieties. As an application, the polyhedral Wasserstein distance between discrete probability distributions is considered.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Ilias Kotsireas, Toufik Mansour, Gokhan Yildirim
Summary: We introduce an algorithmic approach based on a generating tree method for enumerating the inversion sequences with various pattern-avoidance restrictions. The algorithm outputs either an accurate description of the succession rules of the generating tree or an ansatz for a given set of patterns. We determine the generating trees for several pattern classes and obtain generating functions and enumerating formulas using the kernel method.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Fatih Temiz, Irfan Siap
Summary: In this study, the structure of cyclic codes over the ring Zq[u]/(u2) which is isomorphic to R = Zq + uZq is determined. The algebraic structure of ideals of the polynomial quotient ring R[x]/(xn - 1) is completely addressed, and an exact formula that enumerates the number of ideals of this ring is presented. Furthermore, the size of some special families of cyclic codes for specific q is determined.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Martin Bratelund
Summary: This article develops new techniques to classify critical configurations for 3D scene reconstruction from images taken by unknown cameras. The paper uses an algebraic approach to study the critical configurations for two projective cameras and shows that all critical configurations lie on quadric surfaces. It also describes the relationship between different reconstructions when unique reconstruction is impossible.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Bernd Sturmfels, Simon Telen, Francois-Xavier Vialard, Max von Renesse
Summary: Entropic regularization is a method used for large-scale linear programming. It involves tracing the intersections of the feasible polytope with scaled toric varieties, starting from the Birch point. This method is compared to log-barrier methods that use reciprocal linear spaces starting from the analytic center. The paper also explores the use of optimal conic couplings and algorithms like iterative scaling in this context.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Alheydis Geiger, Marta Panizzut
Summary: In this article, the recently developed Polymake extension TropicalQuarticCurves and its associated database entry in polyDB dealing with smooth tropical quartic curves are introduced. The algorithms implemented to analyze tropical bitangents and their lifting conditions over real closed valued fields are reported. The authors used the new functions and data to provide a tropical proof of Plucker and Zeuthen's count of real bitangents to smooth quartic curves.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Elena Angelini
Summary: Based on the research of Angelini et al. (2018) and the recent analysis on simultaneous identifiability of pairs of ternary forms by Beorchia and Galuppi (2022), a conjecture was proposed towards a complete classification of all simultaneous Waring identifiable cases: for any d >= 2, the general polynomial vectors consisting of d -1 ternary forms of degree d and a ternary form of degree d + 1, with rank d2+d+2 2 , are identifiable over C. This paper obtains, through a computer-aided procedure inspired by Angelini et al. (2018), that the case d = 4 contradicts the previous conjecture, admitting at least 36 complex simultaneous Waring decompositions (of length 11) instead of 1.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)
Article
Computer Science, Theory & Methods
Marc Haerkoenen, Lisa Nicklasson, Bogdan Raita
Summary: We study linear PDE with constant coefficients and investigate the connection between the constant rank condition and primary decomposition. We also make progress in the study of weak lower semicontinuity of integral functionals defined on sequences of PDE constrained fields when the PDEs do not have constant rank.
JOURNAL OF SYMBOLIC COMPUTATION
(2024)