Article
Biochemistry & Molecular Biology
Bin Duan, Shaoqi Chen, Xiaohan Chen, Chenyu Zhu, Chen Tang, Shuguang Wang, Yicheng Gao, Shaliu Fu, Qi Liu
Summary: Efficient single-cell assignment is crucial for analyzing single-cell sequencing data, and integrating multiple references can further improve single-cell assignment. The mtSC framework proposed in this study integrates multiple references based on multitask deep metric learning, demonstrating state-of-the-art effectiveness for integrative single-cell assignment with multiple references through evaluation on publicly available benchmark datasets.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Automation & Control Systems
Ignacio J. Sanchez, Agustina D'Jorge, Alejandro C. Limache, Alejandro H. Gonzalez, Antonio Ferramosca
Summary: This paper presents a model predictive controller that can track periodic parametric reference curves. The controller solves the time-parameterization, trajectory planning, and trajectory tracking tasks in a single optimization problem at each sampling time. The optimization problem includes auxiliary state and input trajectories as decision variables, which are effectively followed as planned trajectories. The closed-loop system is designed to guarantee the recursive feasibility of the optimization problem and handle arbitrary changes of reference during execution time. The paper discusses these properties in detail and presents new results on asymptotic average performance. Simulation results demonstrate the benefits of the proposed strategy.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2023)
Editorial Material
Biochemistry & Molecular Biology
Craig D. Kaplan, Karen M. Arndt
Summary: Scientists have been captivated by the complexity of eukaryotic transcription and the numerous proteins involved at each step. In this issue of Cell, Schilbach et al. bring us closer to a complete understanding of transcription at atomic resolution.
Article
Public, Environmental & Occupational Health
Jennifer A. Hutcheon, Jessica Liauw
Summary: The study found that there was little practical difference between using a fetal growth reference or a standard to detect small infants, with both methods showing similar results.
Article
Computer Science, Hardware & Architecture
Yi He, Yuan Zhou, Yajin Zhou, Qi Li, Kun Sun, Yacong Gu, Yong Jiang
Summary: This article investigates the vulnerabilities in system services and resources in Android, particularly the issue of denial-of-service attacks caused by the exhaustion of JNI global references (JGR). Through analysis and tool development, multiple vulnerabilities were discovered in different Android versions, and a new defense method was proposed.
IEEE TRANSACTIONS ON DEPENDABLE AND SECURE COMPUTING
(2022)
Article
Microbiology
Daniel Hakim, Stephen Wandro, Karsten Zengler, Livia S. Zaramela, Brent Nowinski, Austin Swafford, Qiyun Zhu, Se Jin Song, Antonio Gonzalez, Daniel McDonald, Rob Knight
Summary: Assigning taxonomy in microbiome studies is challenging due to the ambiguity of reads overlapping multiple reference genomes. The introduction of genome cover as a metric helps distinguish artifacts from true contaminants. Saturated genome cover is essential for accurate interpretation, especially for low abundance bacteria, and the Zebra filter provides a method to compute and threshold genome cover for reproducible results.
Article
Computer Science, Artificial Intelligence
Yunfeng Zhao, Stuart Ferguson, Huiyu Zhou, Christopher Elliott, Karen Rafferty
Summary: Relative colour constancy is crucial in scientific imaging applications, but achieving consistent colour assessment across different devices is challenging. We propose a colour alignment model that treats camera image formation as a black-box and formulates colour alignment as a three-step process: camera response calibration, response linearisation, and colour matching. The model utilizes a novel balance-of-linear-distances feature and works with non-standard colour references.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2022)
Article
Psychology, Clinical
Barry A. Hong, David E. Pollio, Dana L. Downs, Daniel W. Coyne, Carol S. North
Summary: This article examines the consequences of favoring newer data and references in current publication practices and suggests the need to reconsider the utility of older data and references. Examples from the literature are used to exemplify the value of older data and older references.
PSYCHOLOGICAL MEDICINE
(2022)
Article
Computer Science, Artificial Intelligence
Daniel Carlos Guimaraes Pedronette, Lucas Pascotti Valem, Ricardo da S. Torres
Summary: A novel unsupervised manifold learning method based on ranking references is proposed in this paper, which computes a more effective similarity measure and improves the ranking results of search sessions. Multiple experiments on public datasets show high effectiveness results compared to state-of-the-art approaches.
PATTERN RECOGNITION
(2021)
Article
Biodiversity Conservation
Tiago Shizen Pacheco Toma, Gerhard Ernst Overbeck, Milton de Souza Mendonca, G. Wilson Fernandes
Summary: Restoration and conservation are interconnected as restoration can assist in enhancing, expanding, or linking protected areas. The authors argue that conservation can support restoration by identifying optimal references, which are areas representative of the range of habitats to be restored. Given the high rates of habitat loss and ambitious restoration goals, the availability of suitable references is crucial. However, the utilization and prioritization of these references in conservation efforts are not always optimal. The authors emphasize the need for defining, prioritizing, and protecting optimal references as a strategic approach to effectively address current and future challenges in conservation and restoration.
PERSPECTIVES IN ECOLOGY AND CONSERVATION
(2023)
Article
Biochemical Research Methods
Allan-Hermann Pool, Helen Poldsam, Sisi Chen, Matt Thomson, Yuki Oka
Summary: This study presents an improved approach for mapping single-cell RNA-seq reads using optimized transcriptomic references. It addresses the issue of missing gene expression data in droplet-based scRNA-seq datasets and demonstrates improved cellular profiling resolution. The findings emphasize the importance of optimizing transcriptomic references for scRNA-seq analysis and suggest a reanalysis of previously published datasets and cell atlases.
Article
Physics, Particles & Fields
A. V. Toporensky, O. B. Zaslavskii
Summary: We study general radially moving frames in the background of nonextremal black holes similar to the Schwarzschild metric. We generalize the Lemaitre approach and construct free-falling frames composed of reference particles with arbitrary specific energy, including negative energy. We provide the general formula for the 3-velocity of a freely falling particle with respect to a frame with a specific energy. We investigate the relation between the properties of these frames near a horizon and the Banados-Silk-West effect of indefinite growth of energy of particle collisions. Using our radially moving frames, we also consider the nonradial motion of test particles, including regions near the horizon and singularity. We discuss the properties of the Lemaitre time at horizons depending on the frame and sign of particle energy.
EUROPEAN PHYSICAL JOURNAL C
(2023)
Article
Biochemical Research Methods
Allan-Hermann Pool, Helen Poldsam, Sisi Chen, Matt Thomson, Yuki Oka
Summary: This study identifies the reasons for missing gene expression data in single-cell RNA sequencing and proposes a method to optimize the reference transcriptome. By recovering false intergenic reads, implementing a hybrid pre-mRNA mapping strategy, and resolving gene overlaps, missing gene expression data can be restored. The findings have important implications for improving cellular profiling resolution and discovering missing cell types and marker genes.
Article
Multidisciplinary Sciences
Angel Martin Pendas, Evelio Francisco
Summary: Chemical bonding theory is crucial to chemistry, but existing models have internal and external reference biases that need further exploration. Real space analyses are advocated as reference-less methods, where delocalisation serves as the ultimate root of bonding.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Information Systems
Paulo Martins, Altigran Soares da Silva, Ariel Afonso, Joao Cavalcanti, Edleno de Moura
Summary: R-KwS systems allow naive/informal users to explore and retrieve information from relational databases without knowing schema details or query languages. Lathe is a novel R-KwS system that supports keyword queries referring to the database schema, and it improves query effectiveness through a ranking algorithm and evaluation strategy.
