281 results match your criteria maps query


Deep metric learning-based image retrieval system for chest radiograph and its clinical applications in COVID-19.

Med Image Anal 2021 Feb 7;70:101993. Epub 2021 Feb 7.

Department of Radiology, Massachusetts General Hospital, Boston, MA, United States; MGH & BWH Center for Clinical Data Science, Boston, MA, United States. Electronic address:

In recent years, deep learning-based image analysis methods have been widely applied in computer-aided detection, diagnosis and prognosis, and has shown its value during the public health crisis of the novel coronavirus disease 2019 (COVID-19) pandemic. Chest radiograph (CXR) has been playing a crucial role in COVID-19 patient triaging, diagnosing and monitoring, particularly in the United States. Considering the mixed and unspecific signals in CXR, an image retrieval model of CXR that provides both similar images and associated clinical information can be more clinically meaningful than a direct image diagnostic model. Read More

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February 2021

Deep triplet hashing network for case-based medical image retrieval.

Med Image Anal 2021 04 3;69:101981. Epub 2021 Feb 3.

Department of Computer Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address:

Deep hashing methods have been shown to be the most efficient approximate nearest neighbor search techniques for large-scale image retrieval. However, existing deep hashing methods have a poor small-sample ranking performance for case-based medical image retrieval. The top-ranked images in the returned query results may be as a different class than the query image. Read More

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Partial Boolean Functions with Exact Quantum Query Complexity One.

Entropy (Basel) 2021 Feb 3;23(2). Epub 2021 Feb 3.

Institute of Quantum Computing and Computer Theory, School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.

We provide two sufficient and necessary conditions to characterize any -bit partial Boolean function with exact quantum query complexity 1. Using the first characterization, we present all -bit partial Boolean functions that depend on bits and can be computed exactly by a 1-query quantum algorithm. Due to the second characterization, we construct a function that maps any -bit partial Boolean function to some integer, and if an -bit partial Boolean function depends on bits and can be computed exactly by a 1-query quantum algorithm, then F(f) is non-positive. Read More

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February 2021

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters.

Gigascience 2021 Jan;10(1)

Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.

Background: Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. Read More

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January 2021

BSNet: Bi-Similarity Network for Few-shot Fine-grained Image Classification.

IEEE Trans Image Process 2021 23;30:1318-1331. Epub 2020 Dec 23.

Few-shot learning for fine-grained image classification has gained recent attention in computer vision. Among the approaches for few-shot learning, due to the simplicity and effectiveness, metric-based methods are favorably state-of-the-art on many tasks. Most of the metric-based methods assume a single similarity measure and thus obtain a single feature space. Read More

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December 2020

A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database.

Nucleic Acids Res 2021 01;49(D1):D1496-D1501

USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, USA.

SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Read More

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January 2021

A Bibliometric analysis of folate receptor research.

BMC Cancer 2020 Nov 16;20(1):1109. Epub 2020 Nov 16.

Governors State University, 1 University Parkway, University Park, IL, 60484, USA.

Background: The objective of this study was to conduct a bibliometric analysis of the entire field of folate receptor research. Folate receptor is expressed on a wide variety of cancers and certain immune cells.

Methods: A Web of Science search was performed on folate receptor or folate binding protein (1969-to June 28, 2019). Read More

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November 2020

PNEN: Pyramid Non-Local Enhanced Networks.

IEEE Trans Image Process 2020 Sep 3;PP. Epub 2020 Sep 3.

Existing neural networks proposed for low-level image processing tasks are usually implemented by stacking convolution layers with limited kernel size. Every convolution layer merely involves in context information from a small local neighborhood. More contextual features can be explored as more convolution layers are adopted. Read More

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September 2020

Bibliometric analysis of global research output on antimicrobial resistance in the environment (2000-2019).

Glob Health Res Policy 2020 3;5:37. Epub 2020 Aug 3.

Business Faculty, Al-Balqa Applied University, Amman, Jordan.

Background: Antimicrobial resistance (AMR) is a global health threat that requires a "One Health" approach. Of the One Health triad, the environmental component is the most dynamic and most neglected. Therefore, the objective of the current study was to assess and analyze global research activity on AMR in the environment. Read More

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Dataset for homologous proteins in for SARS-CoV-2/human interactome.

Data Brief 2020 Oct 26;32:106082. Epub 2020 Jul 26.

Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Bitoechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.

Animal modelling for infectious diseases is critical to understand the biology of the pathogens including viruses and to develop therapeutic strategies against it. Herein, we present the sequence homology and expression data analysis of proteins found in that are orthologous to human proteins, reported as components of SARS-CoV-2/Human interactome. The dataset enlists sequence homology, query coverage, domain conservation, OrthoMCL and Ensembl Genome Browser support of 326 proteins in that are potentially orthologous to 417 human proteins reported for their direct physical interactions with 28 proteins encoded by SARS-CoV-2 genome. Read More

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October 2020

CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase.

Bioinformatics 2020 Aug 7. Epub 2020 Aug 7.

Quantitative and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA, USA.

Motivation: Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption. Read More

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CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes.

Gigascience 2020 06;9(6)

Background: DNA methylation microarrays are widely used in clinical epigenetics and are often processed using R packages such as ChAMP or RnBeads by trained bioinformaticians. However, looking at specific genes requires bespoke coding for which wet-lab biologists or clinicians are not trained. This leads to high demands on bioinformaticians, who may lack insight into the specific biological problem. Read More

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Human papillomavirus elevated genetic biomarker signature by statistical algorithm.

J Cell Physiol 2020 12 14;235(12):9922-9932. Epub 2020 Jun 14.

Department of Statistics, MMV, Banaras Hindu University, Varanasi, India.

Head and neck squamous cell carcinoma (HNSCC) is the one of the most frequently found cancers in the world. The aim of the study was to find the genes responsible and enriched pathways associated with HNSCC using bioinformatics and survival analysis methods. A total of 646 patients with HNSCC based on clinical information were considered for the study. Read More

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December 2020

U.S. county-level characteristics to inform equitable COVID-19 response.

medRxiv 2020 Apr 11. Epub 2020 Apr 11.

The spread of Coronavirus Disease 2019 (COVID-19) across the United States confirms that not all Americans are equally at risk of infection, severe disease, or mortality. A range of intersecting biological, demographic, and socioeconomic factors are likely to determine an individual's susceptibility to COVID-19. These factors vary significantly across counties in the United States, and often reflect the structural inequities in our society. Read More

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SG-One: Similarity Guidance Network for One-Shot Semantic Segmentation.

IEEE Trans Cybern 2020 Sep 4;50(9):3855-3865. Epub 2020 Jun 4.

One-shot image semantic segmentation poses a challenging task of recognizing the object regions from unseen categories with only one annotated example as supervision. In this article, we propose a simple yet effective similarity guidance network to tackle the one-shot (SG-One) segmentation problem. We aim at predicting the segmentation mask of a query image with the reference to one densely labeled support image of the same category. Read More

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September 2020

Identification of foam cell biomarkers by microarray analysis.

BMC Cardiovasc Disord 2020 05 6;20(1):211. Epub 2020 May 6.

Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, Jilin Province, China.

Background: Lipid infiltration and inflammatory response run through the occurrence of atherosclerosis. Differentiation into macrophages and foam cell formation are the key steps of AS. Aim of this study was that the differential gene expression between foam cells and macrophages was analyzed to search the key links of foam cell generation, so as to explore the pathogenesis of atherosclerosis and provide targets for the early screening and prevention of coronary artery disease (CAD). Read More

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Interactive effects of gender and sexual orientation on cortical thickness, surface area and gray matter volume: a structural brain MRI study.

Quant Imaging Med Surg 2020 Apr;10(4):835-846

Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.

Background: Testosterone is thought to play a crucial role in sexual differentiation of the brain, and sexual orientation is programmed into our brain structures even when we are still fetuses. Although gender and sexual orientation differences have been shown respectively in many brain structures, the mechanism underlying the sexual differentiation of the brain is still unknown. The study is to investigate the interactive effects of gender and sexual orientation on cerebral structures in homosexual and heterosexual people. Read More

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Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments.

Am J Primatol 2020 07 23;82(7):e23136. Epub 2020 Apr 23.

School of Life Sciences, University of Sussex, Brighton, UK.

The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. Read More

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Integrated querying and version control of context-specific biological networks.

Database (Oxford) 2020 01;2020

Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.

Motivation: Biomolecular data stored in public databases is increasingly specialized to organisms, context/pathology and tissue type, potentially resulting in significant overhead for analyses. These networks are often specializations of generic interaction sets, presenting opportunities for reducing storage and computational cost. Therefore, it is desirable to develop effective compression and storage techniques, along with efficient algorithms and a flexible query interface capable of operating on compressed data structures. Read More

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January 2020

Temporal event searches based on event maps and relationships.

Appl Soft Comput 2019 Dec 25;85:105750. Epub 2019 Sep 25.

School of Science and Technology, The Open University of Hong Kong, Hong Kong.

To satisfy a user's need to find and understand the whole picture of an event effectively and efficiently, in this paper we formalize the problem of temporal event searches and propose a framework of event relationship analysis for search events based on user queries. We define three kinds of event relationships: temporal, content dependence, and event reference, that can be used to identify to what extent a component event is dependent on another in the evolution of a target event (i.e. Read More

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December 2019

Rapid action of mechanism investigation of Yixin Ningshen tablet in treating depression by combinatorial use of systems biology and bioinformatics tools.

J Ethnopharmacol 2020 Jul 7;257:112827. Epub 2020 Apr 7.

Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai, 201203, China. Electronic address:

Ethnopharmacological Relevance: Yixin Ningshen tablet is a CFDA-approved TCM formula for treating depression clinically. However, little is known about its active compounds and related potential target proteins, so far, no researches have been performed to investigate its mechanism of action for the treatment of depression.

Aim Of The Study: Here we develop an original bioinformatics pipeline composed of text mining tools, database querying and systems biology combinatorial analysis, which is applied to rapidly explore the mechanism of action of Yixin Ningshen tablet in treating depression. Read More

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A theory of learning to infer.

Psychol Rev 2020 04;127(3):412-441

Department of Psychology, Harvard University.

Bayesian theories of cognition assume that people can integrate probabilities rationally. However, several empirical findings contradict this proposition: human probabilistic inferences are prone to systematic deviations from optimality. Puzzlingly, these deviations sometimes go in opposite directions. Read More

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Advanced Interoperability Techniques: Structure Mapping Service in CrowdHEALTH Project.

Acta Inform Med 2020 Mar;28(1):52-57

ATOS, Madrid, Spain.

Introduction: Due to healthcare information systems interoperability issues, health-related events may be missed. Numerous techniques based on medical standards and technologies have been recommended to address this challenge. Nevertheless, these techniques do not follow a holistic approach. Read More

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Genetic screens in isogenic mammalian cell lines without single cell cloning.

Nat Commun 2020 02 6;11(1):752. Epub 2020 Feb 6.

Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA.

Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs of mammalian cells, however, is labor-intensive, time-consuming, and, in some cell types, essentially impossible. Here, we present an approach to create isogenic pairs of cells that avoids single cell cloning, and screen these pairs with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. Read More

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February 2020

Kohdista: an efficient method to index and query possible Rmap alignments.

Algorithms Mol Biol 2019 12;14:25. Epub 2019 Dec 12.

3Computer & Information Science & Engineering, University of Florida, Gainesville, FL USA.

Background: Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-layout-consensus approach using raw optical map data, which are referred to as Rmaps. Due to the high error-rate of Rmap data, finding the overlap between Rmaps remains challenging. Read More

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December 2019

Gauging classical and quantum integrability through out-of-time-ordered correlators.

Phys Rev E 2019 Oct;100(4-1):042201

Departamento de Física "J. J. Giambiagi" and IFIBA, FCEyN, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina.

Out-of-time-ordered correlators (OTOCs) have been proposed as a probe of chaos in quantum mechanics, on the basis of their short-time exponential growth found in some particular setups. However, it has been seen that this behavior is not universal. Therefore, we query other quantum chaos manifestations arising from the OTOCs, and we thus study their long-time behavior in systems of completely different nature: quantum maps, which are the simplest chaotic one-body system, and spin chains, which are many-body systems without a classical limit. Read More

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October 2019

Evaluation of Skin Response After Erbium:Yttrium- Aluminum-Garnet Laser Irradiation: A Network Analysis Approach.

J Lasers Med Sci 2019 6;10(3):194-199. Epub 2019 Jul 6.

Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Application of laser in medicine and cosmetic purposes has raised grossly in recent years. There are contradictory finding about its side effects. In this research critical differentially expressed proteins after irradiation erbium:yttrium-aluminum-garnet (Er:YAG) laser on skin are investigated. Read More

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Rapid Discovery of Potential Drugs for Osteonecrosis of Femoral Head Based on Gene Expression Omnibus Database and Connectivity Map.

Orthop Surg 2019 Dec 6;11(6):1209-1219. Epub 2019 Nov 6.

Department of Orthopedics, The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.

Objective: To use Gene Expression Omnibus (GEO) database coupled with Connectivity Map (CMap) databases to screen potential therapeutic drugs for osteonecrosis of femoral head (ONFH) rapidly.

Methods: Raw genetic data with accession number GSE74089 that contained eight hip articular cartilage specimens from four ONFH patients and four healthy controls were obtained from the Gene Expression Omnibus (GEO) database and were then integrated using R to identify differentially expressed genes (DEGs). Subsequently, to identify several potential small molecular compounds that were most strongly negatively correlated with ONFH, a search query of DEGs was explored by using CMap. Read More

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December 2019

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.

Database (Oxford) 2019 01;2019

Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.

Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Read More

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January 2019