Article
Biochemical Research Methods
Min Yang, Bo Qiu, Guo-You He, Jian-Yuan Zhou, Hao-Jie Yu, Yu-Ying Zhang, Yan-Shang Li, Tai-Song Li, Jin-Cheng Guo, Xue-Cang Li, Jian-Jun Xie
Summary: eccDB is a comprehensive database that integrates available resources for extrachromosomal circular DNA (eccDNA) data. It allows storing, browsing, searching, and analyzing eccDNAs from multiple species, providing regulatory and epigenetic information on eccDNAs. The database focuses on analyzing intrachromosomal and interchromosomal interactions to predict transcriptional regulatory functions of eccDNAs. Additionally, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of eccDNAs among different species. In conclusion, eccDB offers web-based analytical tools and serves as a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNAs.
Article
Oncology
Sara M. Tolaney, Elizabeth Garrett-Mayer, Julia White, Victoria S. Blinder, Jared C. Foster, Laleh Amiri-Kordestani, E. Shelley Hwang, Judith M. Bliss, Eileen Rakovitch, Jane Perlmutter, Patricia A. Spears, Elizabeth Frank, Nadine M. Tung, Anthony D. Elias, David Cameron, Neelima Denduluri, Ana F. Best, Angelo DiLeo, Lawrence Baizer, Lynn Pearson Butler, Elena Schwartz, Eric P. Winer, Larissa A. Korde
Summary: This study assessed the adherence of primary efficacy end points in adjuvant breast cancer trials to standardized definitions. Simulation modeling revealed the impact of excluding second nonbreast primary cancers on outcomes, leading to the recommendation of adding invasive breast cancer-free survival as an additional end point.
JOURNAL OF CLINICAL ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hongying Zhao, Xiangzhe Yin, Haotian Xu, Kailai Liu, Wangyang Liu, Lixia Wang, Caiyu Zhang, Lin Bo, Xicheng Lan, Shihua Lin, Ke Feng, Shangwei Ning, Yunpeng Zhang, Li Wang
Summary: The updated LncTarD 2.0 database is a comprehensive resource for studying the regulatory mechanisms of lncRNA in human diseases, and provides various tools for analysis and visualization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Neha Kalmankar, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
Summary: This article introduces DSDBASE2.0, a comprehensive database on disulphide crosslinks that provides free access to relevant information and computational tools. The database also offers several useful features, such as searching for multiple disulphide bond-containing loops and obtaining three-dimensional models of disulphide-rich small proteins.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Biochemistry & Molecular Biology
Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
Summary: The EVLncRNAs database is a comprehensive collection of experimentally validated functional lncRNAs, with information on diseases, interactions, and structures, all checked against known retractions and fake articles for reliability.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Computer Science, Interdisciplinary Applications
Ryan T. Bailey, Pardis Hosseini
Summary: In this paper, the SWAT-MODFLOW-Salt model is introduced, which simulates the fate and transport of major salt ions in watershed systems, with a focus on irrigated stream-aquifer systems. The model accounts for water and salt mass storage and movement in different components, and was applied to a managed region in Colorado to study the impact of soil salinity on crop yield.
ENVIRONMENTAL MODELLING & SOFTWARE
(2023)
Article
Dermatology
Oznur Erbay Dalli, Yasemin Yildirim, Gulbahar CaliSkan, Nermin Kelebek Girgin
Summary: The study demonstrated that the Turkish version of the tool for evaluating nurses' evidence-based knowledge about pressure ulcers has acceptable reliability and validity properties.
JOURNAL OF TISSUE VIABILITY
(2022)
Article
Genetics & Heredity
Margaret M. C. Lam, Ryan R. Wick, Louise M. Judd, Kathryn E. Holt, Kelly L. Wyres
Summary: This study focused on the outer polysaccharide capsule and lipopolysaccharide antigens of Klebsiella pneumoniae and related taxa. The researchers developed a tool called Kaptive 2.0 to rapidly identify and type these antigens. They updated the gene reference database and enhanced the typing capability. By analyzing a large dataset of public genomes, they discovered differences in antigen distribution among species, sampling niches, and clones.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Bailing Zhou, Baohua Ji, Congcong Shen, Xia Zhang, Xue Yu, Pingping Huang, Ru Yu, Hongmei Zhang, Xianghua Dou, Qingshuai Chen, Qiangcheng Zeng, Xiaoxin Wang, Zanxia Cao, Guodong Hu, Shicai Xu, Huiying Zhao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
Summary: Long noncoding RNAs (lncRNAs) play crucial roles in various biological processes and diseases. The EVLncRNAs database, with its latest update, has expanded significantly by incorporating a wide range of information and functional classifications, as well as improving the web interface.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Chemistry, Applied
Martin A. Hubbe
Summary: This review article advocates for a rigorous approach to adsorption studies to improve the experience of researchers and the practical value of published work. It discusses mistakes related to experimental conditions, modeling of results, and the mindset of investigators, emphasizing the importance of obtaining meaningful results and following research strategies accurately. Adsorption experiments can serve as a valuable training ground for researchers to hone their skills and increase the societal value of their work.
SEPARATION AND PURIFICATION REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Chenchen Feng, Chao Song, Shuang Song, Guorui Zhang, Mingxue Yin, Yuexin Zhang, Fengcui Qian, Qiuyu Wang, Maozu Guo, Chunquan Li
Summary: KnockTF 2.0 is a comprehensive database that provides gene expression profile datasets and (epi)genetic annotations, including T(co)F knockdown/knockout data from multiple species, which can contribute to the study of gene function in diseases and biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xun Wang, Yang Li, Mengqi He, Xiangren Kong, Peng Jiang, Xi Liu, Lihong Diao, Xinlei Zhang, Honglei Li, Xinping Ling, Simin Xia, Zhongyang Liu, Yuan Liu, Chun-Ping Cui, Yan Wang, Liujun Tang, Lingqiang Zhang, Fuchu He, Dong Li
Summary: As a crucial post-translational modification, protein ubiquitination is tightly regulated by the balance between ubiquitin ligases and deubiquitinases. UbiBrowser 2.0 provides a tool to predict and explore a large number of E3/deubiquitinase-substrate interactions in 39 organisms, with new features and an improved user interface.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Chemistry, Medicinal
Biswajita Pradhan, Prajna Paramita Bhuyan, Jang-Seu Ki
Summary: Cancer is a widespread disease that causes high death rates. Traditional cancer treatments have shown inefficiency due to drug resistance and negative side effects, leading to an increased focus on bioactive phytochemicals. Polysaccharides derived from marine algal species, especially ulvan from green seaweeds, have shown antioxidant and anticancer properties. Understanding the mechanisms of ulvan's biotherapeutic activities in cancer and immunomodulation is crucial. This review highlights ulvan's anticancer and immunomodulatory effects, along with its pharmacokinetic studies. Ulvan is a potential cancer therapeutic agent that can boost immunity and may be established as an anticancer drug in the future. Additionally, its high nutritional value suggests its potential use as a dietary supplement for cancer patients.
Article
Health Care Sciences & Services
Hein Vincent Stroomberg, S. Benzon Larsen, G. Samso Lanthen, T. Kjaer Nielsen, J. T. Helgstrand, K. Brasso, A. Roder
Summary: This article introduces the Danish Prostate Cancer Registry (DaPCaR) and the Danish Prostate Registry (DanProst), the latter being a comprehensive centralized registry that includes all men who have undergone histological evaluation of the prostate tissue. DanProst is built on the assessment data from the Danish National Registry for Pathology and integrates data from multiple national registries.
JOURNAL OF MEDICAL SYSTEMS
(2023)
Article
Oncology
Yu Jiaze, Hou Sinan, Yang Minjie, Zhou Yongjie, Du Nan, Wang Liangwen, Zhang Wen, Luo Jianjun, Yan Zhiping
Summary: This study found that RCL1 is commonly down-regulated in hepatocellular carcinoma (HCC). Lower expression of RCL1 is associated with higher tumor stage, higher AFP level, vascular invasion, and poor prognosis. RCL1 expression has a significant correlation with immune cells infiltration in HCC, especially myeloid-derived suppressor cell (MDSC). Rcl1 inhibits the growth and metastasis of HCC cells and regulates cell cycle progression, suggesting it may serve as a novel tumor suppressor in HCC.
CANCER CELL INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Alberto Santos, Ana R. Colaco, Annelaura B. Nielsen, Lili Niu, Maximilian Strauss, Philipp E. Geyer, Fabian Coscia, Nicolai J. Wewer Albrechtsen, Filip Mundt, Lars Juhl Jensen, Matthias Mann
Summary: A knowledge graph platform integrates proteomics with other omics data and biomedical databases, providing support for precision medicine. The Clinical Knowledge Graph (CKG) is a flexible data model that can accommodate a large number of nodes and relationships, accelerating the analysis and interpretation of proteomics data. By incorporating CKG, clinical decision-making can be informed and proteomics data can be enriched.
NATURE BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Felix Teufel, Jose Juan Almagro Armenteros, Alexander Rosenberg Johansen, Magnus Halldor Gislason, Silas Irby Pihl, Konstantinos D. Tsirigos, Ole Winther, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
Summary: Signal peptides are short amino acid sequences that regulate protein secretion and translocation. SignalP 6.0, a machine learning model, is introduced to detect all types of signal peptides, including those applicable to metagenomic data.
NATURE BIOTECHNOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Cristina Leal Rodriguez, Benjamin Skov Kaas-Hansen, Robert Eriksson, Jorge Hernansanz Biel, Kirstine G. Belling, Stig Ejdrup Andersen, Soren Brunak
Summary: This study aimed to investigate potential drug-drug interactions and their associated adverse outcomes in Danish hospital prescriptions, and identify patient types that are more affected. The results showed that certain drug combinations may lead to adverse outcomes, including increased mortality rates. Therefore, caution should be exercised to avoid these unsafe drug combinations during prescribing.
PHARMACOEPIDEMIOLOGY AND DRUG SAFETY
(2022)
Article
Public, Environmental & Occupational Health
Benjamin Skov Kaas-Hansen, Cristina Leal Rodriguez, Davide Placido, Hans-Christian Thorsen-Meyer, Anna Pors Nielsen, Nicolas Derian, Soren Brunak, Stig Ejdrup Andersen
Summary: The study aimed to identify predictors of receiving inappropriate doses of renal risk drugs. Using data from Danish National Patient Register and in-hospital data, artificial neural network and linear logistic ridge regression models were trained to predict the risk of five outcomes. Results showed that neural network models had better predictive power and the main prediction drivers were drug usage and diagnosis of chronic kidney failure.
CLINICAL EPIDEMIOLOGY
(2022)
Article
Microbiology
Haris Zafeiropoulos, Savvas Paragkamian, Stelios Ninidakis, Georgios A. Pavlopoulos, Lars Juhl Jensen, Evangelos Pafilis
Summary: PREGO is a comprehensive knowledge base that provides associations between what, where, and who through text mining and data integration techniques, assisting researchers in designing and interpreting experiments and their results.
Article
Hematology
Peter Bruun-Rasmussen, Per Kragh Andersen, Karina Banasik, Soren Brunak, Par Ingemar Johansson
Summary: This study used large real-world data to emulate hypothetical randomized trials and found that transfusing fresher red blood cell (RBC) units can reduce recipient mortality and the risk of thromboembolism or death.
Article
Oncology
Inna M. Chen, Julia S. Johansen, Susann Theile, Jessica X. Hjaltelin, Sif Novitski, Soren Brunak, Jane P. Hasselby, Gro L. Willemoe, Torben Lorentzen, Kasper Madsen, Benny Jensen, Eva E. Wilken, Poul Geertsen, Claus Behrens, Christian Nolsoe, Kirstine L. Hermann, Inge Marie Svane, Dorte Nielsen
Summary: This study evaluated the clinical benefit of nivolumab in combination with stereotactic body radiotherapy (SBRT) with or without ipilimumab in patients with refractory metastatic pancreatic cancer. The results demonstrated clinically meaningful antitumor activity and favorable safety profiles in patients receiving nivolumab combined with ipilimumab and SBRT.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Letter
Public, Environmental & Occupational Health
Benjamin Skov Kaas-Hansen, Cristina Leal Rodriguez, Davide Placido, Hans-Christian Thorsen-Meyer, Anna Pors Nielsen, Nicolas Derian, Soren Brunak, Stig Ejdrup Andersen
CLINICAL EPIDEMIOLOGY
(2022)
Article
Computer Science, Information Systems
Christian Kim Eschen, Karina Banasik, Alex Horby Christensen, Piotr Jaroslaw Chmura, Frants Pedersen, Lars Kober, Thomas Engstrom, Anders Bjorholm Dahl, Soren Brunak, Henning Bundgaard
Summary: This study proposes a deep learning-based approach for classifying the left and right coronary arteries in CAG videos. Through training with manually labeled videos and conducting extensive experiments, the effectiveness of deep learning in accurately curating CAG videos is demonstrated.
Article
Anesthesiology
Gitte K. Vesterlund, Hans-Christian Thorsen-Meyer, Morten H. Moller, Soren Brunak, Thomas Strom, Anders Perner, Benjamin S. Kaas-Hansen
Summary: This study aimed to describe abnormal serum levels of magnesium, phosphate, and zinc in Danish ICU patients and assess their associations with outcomes. The results showed that most ICU patients had low serum levels of magnesium, phosphate, or zinc, and some received supplementation. However, the associations between serum levels and clinical outcomes were inconclusive due to insufficient data.
ACTA ANAESTHESIOLOGICA SCANDINAVICA
(2023)
Article
Cardiac & Cardiovascular Systems
Hildur M. Aegisdottir, Rosa B. Thorolfsdottir, Gardar Sveinbjornsson, Olafur A. Stefansson, Bjarni Gunnarsson, Vinicius Tragante, Gudmar Thorleifsson, Lilja Stefansdottir, Thorgeir E. Thorgeirsson, Egil Ferkingstad, Patrick Sulem, Gudmundur Norddahl, Gudrun Rutsdottir, Karina Banasik, Alex Hoerby Christensen, Christina Mikkelsen, Ole Birger Pedersen, Soren Brunak, Mie Topholm Bruun, Christian Erikstrup, Rikke Louise Jacobsen, Kaspar Rene Nielsen, Erik Sorensen, Michael L. Frigge, Kristjan E. Hjorleifsson, Erna Ivarsdottir, Anna Helgadottir, Solveig Gretarsdottir, Valgerdur Steinthorsdottir, Asmundur Oddsson, Hannes P. Eggertsson, Gisli H. Halldorsson, David A. Jones, Jeffrey L. Anderson, Kirk U. Knowlton, Lincoln D. Nadauld, D. B. D. S. Genomic Consortium DBDS Genomic Consortium, Magnus Haraldsson, Gudmundur Thorgeirsson, Henning Bundgaard, David O. Arnar, Unnur Thorsteinsdottir, Daniel F. Gudbjartsson, Sisse R. Ostrowsk, Hilma Holm, Kari Stefansson
Summary: This study investigates the genetics of syncope and provides insight into its pathophysiology and prognostic implications. The results show that syncope has a distinct genetic architecture involving neural regulatory processes and a complex relationship with heart rate and blood pressure regulation. There is also a shared genetic background with poor cardiovascular health. Thorough assessment is important for individuals presenting with syncope.
EUROPEAN HEART JOURNAL
(2023)
Review
Medicine, General & Internal
Asa Johansson, Ole A. Andreassen, Soren Brunak, Paul W. Franks, Harald Hedman, Ruth J. F. Loos, Benjamin Meder, Erik Melen, Craig E. Wheelock, Bo Jacobsson
Summary: Complex diseases result from a combination of genetic, lifestyle, and environmental factors and include common noncommunicable diseases. Precision medicine, using genomic and molecular data, has been successful for certain diseases but faces challenges due to heterogeneity and high number of risk factors in complex diseases. Subclassifying patients based on molecular or phenotypic data holds promise for improving diagnosis, treatment, and prognosis.
JOURNAL OF INTERNAL MEDICINE
(2023)
Article
Biology
Peter Bruun-Rasmussen, Morten Hanefeld Dziegiel, Karina Banasik, Par Ingemar Johansson, Soren Brunak
Summary: This study found associations between the ABO and RhD blood group systems and susceptibility to various diseases, including tongue cancer, monocytic leukemia, cervical cancer, osteoarthrosis, asthma, as well as HIV and hepatitis B infection. Additionally, marginal evidence of associations between blood groups and age at first diagnosis was found.
Article
Clinical Neurology
Siri A. Vulpius, Sebastian Werge, Isabella Friis Jorgensen, Troels Siggaard, Jorge Hernansanz Biel, Gitte M. Knudsen, Soren Brunak, Lars H. Pinborg
Summary: This study demonstrates that text mining of clinical notes can improve the accuracy of epilepsy diagnosis and classification of different epilepsy types for patients. It suggests that combining population-based health registries with electronic health records can be crucial for future precision medicine development for epilepsy patients.
Article
Computer Science, Artificial Intelligence
Victorine P. Muse, Alejandro Aguayo-Orozco, Sedrah B. Balaganeshan, Soren Brunak
Summary: We found differences in mortality, age, and sex in relation to reference intervals (RIs) for laboratory tests in a population-wide data of nearly 2 million hospital patients in Denmark, which included over 300 million measurements. A low-parameter mathematical wave-based modification method was developed to adjust for dietary and environment influences throughout the year. The resulting mathematical fit improved the association rates between re-classified abnormal laboratory tests, patient diagnoses, and mortality. This study highlights the need for seasonally modified RIs and presents an approach that could reduce over- and underdiagnosis, impacting physician-patient interactions and electronic health record research as a whole.