In this paper, we tell the story of efforts currently underway, on diverse fronts, to build digital knowledge repositories ('knowledge-bases') to support research in the life sciences. If successful, knowledge bases will be part of a new knowledge infrastructure-capable of facilitating ever-more comprehensive, computational models of biological systems. Such an infrastructure would, however, represent a sea-change in the technological management and manipulation of complex data, inducing a generational shift in how questions are asked and answered and results published and circulated. Integrating such knowledge bases into the daily workflow of the lab thus destabilizes a number of well-established habits which biologists rely on to ensure the quality of the knowledge they produce, evaluate, communicate and exploit. As the story we tell here shows, such destabilization introduces a situation of unfamiliarity, one that carries with it epistemic risks. It should elicit-to use Niklas Luhmann's terms-the question of trust: a shared recognition that the reliability of research practices is being risked, but that such a risk is worth taking in view of what may be gained. And yet, the problem of trust is being unexpectedly silenced. How that silencing has come about, why it matters, and what might yet be done forms the heart of this paper.
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http://dx.doi.org/10.1007/s11019-020-09957-0 | DOI Listing |
J Transl Med
January 2025
School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou, 550000, China.
Background: Human kinesin family member 11 (KIF11) plays a vital role in regulating the cell cycle and is implicated in the tumorigenesis and progression of various cancers, but its role in endometrial cancer (EC) is still unclear. Our current research explored the prognostic value, biological function and targeting strategy of KIF11 in EC through approaches including bioinformatics, machine learning and experimental studies.
Methods: The GSE17025 dataset from the GEO database was analyzed via the limma package to identify differentially expressed genes (DEGs) in EC.
Sci Rep
January 2025
Cardiology Department, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China.
Atherosclerosis (AS) is a chronic vascular disease characterized by inflammation of the arterial wall and the formation of cholesterol plaques. Hashimoto's thyroiditis (HT) is an autoimmune disorder marked by chronic inflammation and destruction of thyroid tissue. Although previous studies have identified common risk factors between AS and HT, the specific etiology and pathogenic mechanisms underlying these associations remain unclear.
View Article and Find Full Text PDFPLoS Genet
January 2025
Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
Hox proteins, a sub-group of the homeodomain (HD) transcription factor family, provide positional information for axial patterning in development and evolution. Hox protein functional specificity is reached, at least in part, through interactions with Pbc (Extradenticle (Exd) in Drosophila) and Meis/Prep (Homothorax (Hth) in Drosophila) proteins. Most of our current knowledge of Hox protein specificity stems from the study of anterior and central Hox proteins, identifying the molecular and structural bases for Hox/Pbc/Meis-Prep cooperative action.
View Article and Find Full Text PDFPeerJ
January 2025
Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China.
Purpose: In this study, we aimed to study the role of extracellular proteins as biomarkers associated with newly diagnosed Type 1 diabetes (NT1D) diagnosis and prognosis.
Patients And Methods: We retrieved and analyzed the GSE55098 microarray dataset from the Gene Expression Omnibus (GEO) database. Using R software, we screened out the extracellular protein-differentially expressed genes (EP-DEGs) through several protein-related databases.
J Cell Mol Med
January 2025
Department of Medical Biology, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey.
Chemotherapy is a potent tool against cancer, but drug resistance remains a major obstacle. To combat this, understanding the molecular mechanisms behind resistance in cancer cells and the protein expression changes driving these mechanisms is crucial. Targeting the Ubiquitin-Proteasome System (UPS) has proven effective in treating multiple myeloma and shows promise for solid tumours.
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