Review
Biochemistry & Molecular Biology
Jing Li, Yu Lin, Qianzi Tang, Mingzhou Li
Summary: Recent advances in Hi-C technology and data processing approaches have enabled construction of diploid Hi-C contact maps, accelerating novel discoveries in haplotype-resolved 3D genome studies. Studies have revealed the role of allele biased chromatin conformation in transcriptional regulation and resolved important biological questions related to nuclear functions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Physics, Multidisciplinary
Guang Shi, D. Thirumalai
Summary: Researchers have developed a method (HIPPS) based on polymer physics characteristics of chromosomes and the maximum entropy principles, which allows for calculating three-dimensional chromosome structures solely from Hi-C contact maps. Despite population heterogeneity, HIPPS method accurately captures the overall organization of chromosome structures even in a highly heterogeneous cell population.
Article
Engineering, Mechanical
Fahmi Zairi, Abderrahman Tamoud, Amar Mesbah, Fahed Zairi
Summary: This work proposes a fully three-dimensional model of the human intervertebral disc within an analytical framework, aiming to create patient-specific models that are time and cost-efficient. The model considers deformation-induced damage and hydration effects on disc mechanics, and introduces special functions to generate versatile and anatomically accurate disc geometries. It explicitly incorporates the complex collagen fibrillar networks throughout the disc.
INTERNATIONAL JOURNAL OF MECHANICAL SCIENCES
(2022)
Article
Engineering, Civil
Shengchu Wang, Xianbo Jiang
Summary: In this paper, a three-dimensional universal cooperative localizer (3D UCL) is proposed for vehicular ad-hoc networks (VANETs), and a 3D geographical information enhanced UCL (3D GIE-UCL) is developed by combining 3D UCL with a NLOS identification mechanism assisted by geographical information. Both 3D UCL and 3D GIE-UCL show significant improvement in positioning performance after the application of acceleration techniques.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2021)
Article
Computer Science, Information Systems
Siguo Bi, Juntao Cui, Wei Ni, Yi Jiang, Shui Yu, Xin Wang
Summary: This paper presents a new algorithm for locating multiple IoT devices in a 3-D space. It solves the problem of negligible distance measurement noises and corrupted measurements caused by additive noises and nonlight-of-sight propagation while preserving the rank-3 constraints. Simulation results indicate that the proposed algorithm outperforms existing SDR-based alternatives in terms of accuracy, complexity, and robustness to irregular topology and poor connectivity.
IEEE INTERNET OF THINGS JOURNAL
(2022)
Article
Multidisciplinary Sciences
Morena Miciaccia, Benny Danilo Belviso, Mariaclara Iaselli, Gino Cingolani, Savina Ferorelli, Marianna Cappellari, Paola Loguercio Polosa, Maria Grazia Perrone, Rocco Caliandro, Antonio Scilimati
Summary: The structure of human cyclooxygenase-1 (hCOX-1) has been reported, providing detailed information about the enzyme's active site and key residues involved in inhibitor/substrate binding and catalytic activity. By comparing hCOX-1 crystal structure with ovine COX-1 and human COX-2 structures, differences and similarities are discussed, with emphasis on the motifs responsible for the diversification of these enzymes.
SCIENTIFIC REPORTS
(2021)
Article
Environmental Sciences
Wei Zhang, Yuanxi Yang, Anmin Zeng, Yangyin Xu
Summary: This paper proposes a GNSS/5G integrated positioning scheme based on D2D communication, which improves the positioning accuracy by collaborating and sharing position and measurement information. The DBSCAN and PF algorithms are used to further optimize the position accuracy of cooperative and requesting nodes. Numerical results show that this algorithm is more effective in reducing positioning deviation and improving positioning accuracy compared to non-integrated methods.
Article
Neurosciences
Kuang-Yi Ma, Xin-Yu Cai, Xin-Tai Wang, Zhao-Xiang Wang, Wan-Meng Huang, Zhi-Ying Wu, Zhou-Yan Feng, Ying Shen
Summary: The cerebellum is believed to be a processor of complex movements and plays a role in cognitive and emotional behaviors. This study investigated the output of the cerebellar interposed nucleus to thalamic nuclei and found heterogeneity in recipient zones in the thalamus, suggesting differential control of thalamo-cortical networks by the cerebellum.
NEUROSCIENCE BULLETIN
(2021)
Article
Computer Science, Information Systems
Issei Makino, Nobuhiko Miki
Summary: Accurate performance measurement is crucial for private wireless networks in the industrial IoT, especially in indoor environments. A cost-effective and portable 3D positioning device developed from open-source hardware is implemented to accurately measure the RSSI using low carrier frequency system, enabling assessment of different cellular network-based positioning methods.
Article
Chemistry, Analytical
Mohamed Khalaf-Allah
Summary: The study introduces direct method (DM) and particle filter (PF) algorithms to address the three-anchor time-of-arrival (ToA) based three-dimensional (3D) positioning problem. These algorithms aim to balance accuracy and computational cost by estimating the 3D position of anchor nodes (ANs) in different ways.
Article
Computer Science, Information Systems
Chengkai Tang, Jiaqi Liu, Yi Zhang, Xingxing Zhu, Lingling Zhang
Summary: This research presents a three-dimensional faster cooperative positioning algorithm based on factor graphs, which improves the computing speed of cooperative positioning significantly by independently calculating the positioning data of each node coordinate axis, achieving better positioning performance than traditional methods.
Article
Mechanics
Christiana Mavroyiakoumou, Silas Alben
Summary: We developed a model and numerical method to study the large-amplitude flutter of rectangular membranes shedding a trailing vortex-sheet wake in a 3-D inviscid fluid flow. By computing stability thresholds and large-amplitude dynamics, we found that the 3-D dynamics naturally forms four groups based on the conditions at the leading and trailing edges, similar to the results in the 2-D case.
JOURNAL OF FLUID MECHANICS
(2022)
Article
Engineering, Electrical & Electronic
Zexia He, Tao Liu
Summary: The paper introduces a low-cost, high integration level six-axis force sensor with a 3D capacitor structure and cross-shape shear force sensing cell to improve sensitivity and reduce crosstalk. The prototype sensor was experimentally validated and compared with a commercial six-axis force sensor, showing promising characteristics in linearity, hysteresis, and time drift.
SENSORS AND ACTUATORS A-PHYSICAL
(2021)
Article
Construction & Building Technology
Xiaomei Zhao, Shuo Li, Zhan Zhao, Honggang Li, Adrian Pitts
Summary: This paper proposes a low-cost indoor occupancy information extraction system that utilizes a single RGB camera to estimate the positions and trajectories of indoor occupants. By using an inverse proportional model to estimate the distance between a human head and the camera and associating the 3D coordinates of human heads with human IDs, the system successfully calculates accurate 3D positions and trajectories of indoor occupants.
Article
Engineering, Electrical & Electronic
Jian Chen, Fan Yu, Jiaxin Yu, Lin Lin
Summary: This article presents a three-dimensional pen-like positioning system based on high-precision 3D ultrasonic positioning method, achieving millimeter-level accuracy in a working area of 2m x 1.5m x 1.5m. The system utilizes a high-precision time-of-flight detection method based on dynamic threshold and average zero-crossing detection for real-time performance improvement. Experimental verification shows that the system has high positioning accuracy.
IEEE SENSORS JOURNAL
(2021)
Correction
Biochemistry & Molecular Biology
S. W. Botchway, S. Farooq, A. Sajid, I. K. Robinson, M. Yusuf
CHROMOSOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Archana Bhartiya, Darren Batey, Silvia Cipiccia, Xiaowen Shi, Christoph Rau, Stanley Botchway, Mohammed Yusuf, Ian K. Robinson
Summary: This study used hard X-ray ptychography to extract the individual masses of all 46 chromosomes of metaphase human B and T cells, producing 'X-ray karyotypes' to determine the effect of low-level X-ray irradiation on genetic material. The experiments were conducted at the I-13 beamline of Diamond Light Source in the UK using phase-sensitive X-ray ptychography method.
CHROMOSOME RESEARCH
(2021)
Article
Materials Science, Multidisciplinary
Fei Yang, Xianping Liu, Peiming Wang, Shunfeng Wang, Ian Robinson, Bo Chen
Summary: Hardened tricalcium silicate (C3S) pastes cured for different times were studied using SBFSEM to analyze their three-dimensional spatial structures and morphological characteristics. Results showed the high reactivity of C3S with water and the complex process of pore network formation. SBFSEM was proven to be applicable in the field of cement-based materials through quantitative analysis compared with traditional methods.
MATERIALS CHARACTERIZATION
(2021)
Article
Biochemistry & Molecular Biology
Archana Bhartiya, Ian Robinson, Mohammed Yusuf, Stanley W. Botchway
Summary: This paper introduces a method combining DAPI, FLIM, and M-FISH techniques to understand the nanometer structure of all 46 chromosomes in the nucleus covering the entire human genome at the single cell level. This approach enables the study and observation of structural differences in chromosomes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Materials Science, Multidisciplinary
H. Miao, G. Fabbris, R. J. Koch, D. G. Mazzone, C. S. Nelson, R. Acevedo-Esteves, G. D. Gu, Y. Li, T. Yilimaz, K. Kaznatcheev, E. Vescovo, M. Oda, T. Kurosawa, N. Momono, T. Assefa, I. K. Robinson, E. S. Bozin, J. M. Tranquada, P. D. Johnson, M. P. M. Dean
Summary: This study demonstrates that CDW correlations in La2-xSrxCuO4 persist up to a doping of at least x=0.21, with strong changes through the superconducting transition. Despite changes in Fermi surface topology and electronic transport at the critical doping value of x(c)approximate to 0.19, there is no obvious discontinuity, prompting a reconsideration of the role of CDW correlations in the high-temperature cuprate phase diagram.
NPJ QUANTUM MATERIALS
(2021)
Correction
Biochemistry & Molecular Biology
Archana Bhartiya, Darren Batey, Silvia Cipiccia, Xiaowen Shi, Christoph Rau, Stanley Botchway, Mohammed Yusuf, Ian K. Robinson
CHROMOSOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Atiqa Sajid, El-Nasir Lalani, Bo Chen, Teruo Hashimoto, Darren K. Griffin, Archana Bhartiya, George Thompson, Ian K. Robinson, Mohammed Yusuf
Summary: Three-dimensional ultra-structural imaging is a crucial tool for understanding the organizational structure of individual chromosomes during the cell cycle. By using SBFSEM to analyze human genome at prophase, researchers were able to segment, reconstruct, and extract quantitative 3D structural information about chromosomes. The study revealed that each chromosome in prophase can be identified with its homolog and classified based on their spatial positioning.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Instruments & Instrumentation
Jorg Schwenke, Mohammed Yusuf, Laura A. Shemilt, Ulrich Wagner, Atiqa Sajid, Graeme R. Morrison, Fucai Zhang, Aaron Parsons, Christoph Rau, Ian K. Robinson
Summary: This study used X-ray ptychography to evaluate the masses of human cell nuclei by quantitatively measuring unique phase shift information, demonstrating the effectiveness of a modified ptychographic algorithm in reconstructing weak scattering samples.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Chemistry, Multidisciplinary
Xiang Liu, Xinwei Zhou, Qiang Liu, Jiecheng Diao, Chen Zhao, Luxi Li, Yuzi Liu, Wenqian Xu, Amine Daali, Ross Harder, Ian K. Robinson, Mouad Dahbi, Jones Alami, Guohua Chen, Gui-Liang Xu, Khalil Amine
Summary: This study reveals the mechanism of how a poly(3,4-ethylenedioxythiophene) coating regulates the high-temperature operational tolerance of cathodes, preventing multiple degradation pathways from occurring.
ADVANCED MATERIALS
(2022)
Article
Physics, Multidisciplinary
Longlong Wu, Yao Shen, Andi M. Barbour, Wei Wang, Dharmalingam Prabhakaran, Andrew T. Boothroyd, Claudio Mazzoli, John M. Tranquada, Ian K. Robinson, Mark P. Dean
Summary: The study reveals that the spatial distribution of spin-ordered stripes in LSNO exhibits anisotropy, with correlation lengths strongly coupled in different directions in space. Fluctuations in the real space amplitude signal, rather than the phase or position, suggest that the observed slow dynamics of the stripe domains in LSNO are attributed to thermal fluctuations of the SO domain boundaries.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Min Gyu Kim, Andi Barbour, Wen Hu, Stuart B. Wilkins, Ian K. Robinson, Mark P. M. Dean, Junjie Yang, Choongjae Won, Sang-Wook Cheong, Claudio Mazzoli, Valery Kiryukhin
Summary: Magnetic domains in antiferromagnetic materials are crucial for understanding magnetism and its applications. In this study, videos of fluctuating antiferromagnetic domains in Ni2MnTeO6 were obtained using coherent x-ray diffraction. The findings highlight the potential significance of dynamic domain imaging in phase transition studies and magnetic device research.
Article
Chemistry, Multidisciplinary
Ana F. Suzana, Sizhan Liu, Jiecheng Diao, Longlong Wu, Tadesse A. Assefa, Milinda Abeykoon, Ross Harder, Wonsuk Cha, Emil S. Bozin, Ian K. Robinson
Summary: When synthesized under certain conditions, barium titanate (BTO) nanoparticles show a non-thermodynamic cubic structure and have an enhanced dielectric constant. These nanoparticles are widely used in thin-layer capacitors. Characterization methods, including X-ray refinement and the Williamson-Hall approach, reveal the presence of notable strain associated with the cubic phase. However, X-ray pair distribution function measurements indicate a lower symmetry local structure.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Review
Chemistry, Physical
Ralf F. F. Ziesche, Thomas M. M. Heenan, Pooja Kumari, Jarrod Williams, Weiqun Li, Matthew E. E. Curd, Timothy L. L. Burnett, Ian Robinson, Dan J. L. Brett, Matthias J. J. Ehrhardt, Paul D. D. Quinn, Layla B. B. Mehdi, Philip J. J. Withers, Melanie M. M. Britton, Nigel D. D. Browning, Paul R. R. Shearing
Summary: The demand for low carbon energy storage has emphasized the importance of imaging techniques in characterizing electrode microstructures, determining key parameters for battery manufacture, operation, degradation, and failure in both next generation lithium batteries and other novel battery systems. This review summarizes recent progress and highlights in magnetic resonance, neutron, X-ray, focused ion beam, scanning and transmission electron microscopy. Two major trends are identified: the use of multi-modal microscopy in a correlative fashion, providing contrast modes across length and time scales, and the application of machine learning to guide data collection and analysis, recognizing the role of these tools in evaluating large data streams from increasingly sophisticated imaging experiments.
ADVANCED ENERGY MATERIALS
(2023)
Article
Chemistry, Physical
Longlong Wu, Seongmin Bak, Youngho Shin, Yong S. Chu, Shinjae Yoo, Ian K. Robinson, Xiaojing Huang
Summary: Multimodal hard X-ray scanning probe microscopy combines ptychography with X-ray fluorescence (XRF) microscopy to study functional materials, providing both structural and chemical information. A machine learning model is developed to enhance spatial resolution by decoupling the effect of X-ray probe from the XRF signal, showing superior performance compared to traditional scanning XRF methods. The proposed method can be widely applied in functional materials and biological imaging with XRF microscopy and related applications.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Wei Wang, Junjie Li, Lijun Wu, Jennifer Sears, Fuhao Ji, Xiaozhe Shen, Alex H. Reid, Jing Tao, Ian K. Robinson, Yimei Zhu, Mark P. M. Dean
Summary: This study investigates the interplay between charge order and lattice distortions in magnetite using ultrafast electron diffraction, and explains the mechanism of the Verwey transition through transient structural evolution.