22 papers · ranked by Valyu relevance
Shijia Zhu, Naoto Kubota, Shidan Wang, Tao Wang + 2 more
In spot-based spatial transcriptomics, spots that are of the same size and printed at the fixed location cannot precisely capture the actual randomly located single cells, therefore failing to profile the transcriptome at the single-cell level. The current studies primarily focused on enhancing the spot resolution in…
Shijia Zhu, Naoto Kubota, Shidan Wang, Tao Wang + 2 more
'Yujin Hoshida'] In spot-based spatial transcriptomics, spots that are of the same size and printed at the fixed location cannot precisely capture the actual randomly located single cells, therefore failing to profile the transcriptome at the single-cell level. The current studies primarily focused on enhancing the…
Stavros P. Hadjisolomou, George El-Haddad
Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented…
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin + 1 more
Spatial transcriptomics (ST) has emerged as a powerful technology for bridging histology imaging with gene expression profiling. However, its application has been limited by low throughput and the need for specialized experimental facilities. Prior works sought to predict ST from wholeslide histology images to…
Abdalla Elbialy
Spatial transcriptomics technologies face a fundamental trade-off between transcriptomic breadth and spatial resolution, with widely-used platforms like 10x Visium capturing multiple cells per spot, limiting single-cell insights. Current computational deconvolution methods attempt to address this limitation but…
Chenxin Flora Jiang, Yuxin Yin, Paul Robson, Yuanhao James Li + 2 more
Spatial transcriptomics has transformed our ability to explore gene expression within its tissue context, enabling us to dissect subtle yet biologically significant variations in situ. While numerous computational methods have been proposed for detecting Spatially Varying Genes (SVGs) expression by modeling each…
Eugene Novikov, Emmanuel Barillot
Background Although DNA microarray technologies are very powerful for the simultaneous quantitative characterization of thousands of genes, the quality of the obtained experimental data is often far from ideal. The measured microarrays images represent a regular collection of spots, and the intensity of light at each…
Zijian Niu, Aoife O’Farrell, Jingxin Li, Sam Reffsin + 4 more
Single-molecule RNA fluorescence in situ hybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis…
Shan Yu, Wei Vivian Li
Spatially resolved transcriptomics technologies have opened new avenues for understanding gene expression heterogeneity in spatial contexts. However, existing methods for identifying spatially variable genes often focus solely on statistical significance, limiting their ability to capture continuous expression patterns…
Authors not listed
Quantitative analysis of small extracellular vesicles (sEVs) at single-particle resolution remains challenging due to their nanoscale dimensions and compositional heterogeneity. Existing methods often rely on specialized and costly instrumentation, limiting accessibility for many researchers and necessitates extensive…
Souvik Seal, Brian Neelon
Advances in spatial omics enable measurement of genes (spatial transcriptomics) and peptides, lipids, or N-glycans (mass spectrometry imaging) across thousands of locations within a tissue. While detecting spatially variable molecules is a well-studied problem, robust methods for identifying spatially varying…
Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 31 state-of-the-art methods, categorizing SVGs into three types: overall…
Authors not listed
Dried blood spots (DBS) offer a practical and relatively non-invasive method for sample collection. Here, we evaluate the feasibility of applying ¹H NMR spectroscopy to metabolomic analysis of DBS. Various solvent suppression techniques and extraction protocols were tested using aqueous and methanolic solvents.…
Nnamdi Ekwe-Ekwe, Adam Barker
— Cloud computing is becoming an almost ubiquitous part of the computing landscape. For many companies today, moving their entire infrastructure and workloads to the cloud reduces complexity, time to deployment, and saves money. Spot Instances, a subset of Amazon's cloud computing infrastructure (EC2), expands on this.…
Authors not listed
A thorough understanding of drug pharmacokinetics and target interaction within complex biological environments is critical for successful drug discovery. Quantitative matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI; qMSI) presents a promising avenue for such investigations. While…
Martin Kutzschbach, Johannes Glodny
This study introduces a new approach for in-situ Rb-Sr dating that utilizes rapid line scans instead of static spot ablation, enabling the creation of two-dimensional 87Rb/86Sr and 87Sr/86Sr isotope ratio and Rb-Sr age maps. The data acquisition is conducted utilizing an ICP-MS/MS instrument with N2O as the reaction…
Zhiqiang Ma, Steven Pomerville, Mingyang Di, Armineh Nourbakhsh
In this paper we present SPot, an automated tool for detecting operating segments and their related performance indicators from earnings reports. Due to their company-specific nature, operating segments cannot be detected using taxonomy-based approaches. Instead, we train a Bidirectional RNN classifier that can…
Authors not listed
Introduction: Blood microsampling (BµS) devices collect less than 100 µL of blood, offering a less invasive and more cost-effective alternative to venipuncture. However, its metabolomic comparability to conventional samples remains unclear, and standardized BµS metabolomic workflows are lacking. Objectives: This study…
Kaushi S. T. Kanankege, Julio Alvarez, Lin Zhang, Andres M. Perez
Spatiotemporal visualization and analytical tools (SATs) are increasingly being applied to risk-based surveillance/monitoring of adverse health events affecting humans, animals, and ecosystems. Different disciplines use diverse SATs to address similar research questions. The juxtaposition of these diverse techniques…
Sweta Ojha, P. Travis Thompson, Christian D. Powell, Hunter N.B. Moseley + 1 more
Per- and polyfluoroalkyl substances (PFAS) contamination in water sources near potential PFAS users is well known. Therefore, it is useful for PFAS stakeholders to visualize hot-spot areas and bring attention to the water systems that are near to those areas. Towards this end, we extracted information about PFAS…
Ian Oesterle, Manuel Pristner, Sabrina Berger, Mingxun Wang + 3 more
Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than…
Mohammad Javad Kharazifard, Kurosh Holakouie-Naieni, Mohammad Ali Mansournia
'Mohammad Ali Mansournia'] Multilevel analysis which was primarily introduced to deal with hierarchical data was later applied extensively for research in other fields of science and not only for nested data, but also for repeated measurements or clustered trials. This method of statistical analysis was applied in…