The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies

An integrated network of Arabidopsis growth regulators and its use for gene prioritization

Elucidating the molecular mechanisms that govern plant growth has been an important topic in plant research, and current advances in large-scale data generation call for computational tools that efficiently combine these different data sources to generate novel hypotheses. In this work, we present a novel, integrated network that combines multiple large-scale data sources to characterize growth regulatory genes in Arabidopsis, one of the main plant model organisms. The contributions of this work are twofold: first, we characterized a set of carefully selected growth regulators with respect to their connectivity patterns in the integrated network, and, subsequently, we explored to which extent these connectivity patterns can be used to suggest new growth regulators. Using a large-scale comparative study, we designed new supervised machine learning methods to prioritize growth regulators. Our results show that these methods significantly improve current state-of-the-art prioritization techniques, and are able to suggest meaningful new growth regulators. In addition, the integrated network is made available to the scientific community, providing a rich data source that will be useful for many biological processes, not necessarily restricted to plant growth

Equid herpesvirus type 1 (EHV-1) disrupt actin cytoskeleton during productive infection in equine leukocytes

Equid herpesvirus type 1 (EHV-1) is a prevalent causative agent of equine diseases worldwide. After primary replication in the respiratory epithelium the virus disseminates systemically through a peripheral blood mononuclear cell (PBMC)-associated viraemia. EHV-1 is the only alphaherpes-virus known so far which is capable of establishing latent infection not only in neurons but also in immune system cells (mainly in lymphocytes and macrophages). Since leukocytes are not the target cells for viral replication but are used to transport EHV-1 to the internal organs, the question remains how the virus avoids the immune response and whether it could potentially be associated with virus-induced cytoskeletal rearrangements. Therefore, the aim of this study was to investigate the progress of EHV-1 replication in leukocytes stimulated by phytohemagglutinin and the impact of EHV-1 infection on the actin cytoskeleton. Using the real-time PCR method we evaluated the quantity of viral DNA from samples collected at indicated time points post infection. In order to examine possible changes in actin cytoskeleton organization due to EHV-1 infection, we performed immunofluorescent staining using TRITC-phalloidin conjugate. The results showed that EHV-1 replicates in leukocytes at a restricted level but with the accompaniment of chromatin degradation. Simultaneously, infection with EHV-1 caused disruption of the actin cytoskeleton; this was particularly apparent in further stages of infection. Disruption of the actin cytoskeleton may lead to the limited release of the virus from the cells, but may be also beneficial for the virus, since at the same time it potentially impairs the immune function of leukocytes

Speciation of neptunium during sorption and diffusion in natural clay

In argillaceous rocks, which are considered as a potential host rock for nuclear waste repositories, sorption and diffusion processes govern the migration behaviour of actinides like neptunium. For the safety analysis of such a repository, a molecular-level understanding of the transport and retardation phenomena of radioactive contaminants in the host rock is mandatory. The speciation of Np during sorption and diffusion in Opalinus Clay was studied at near neutral pH using a combination of spatially resolved synchrotron radiation techniques. During the sorption and diffusion experiments, the interaction of 8 μM Np(V) solutions with the clay lead to the formation of spots at the clay-water interface with increased Np concentrations as determined by μ-XRF. Several of these spots are correlated with areas of increased Fe concentration. Np L3-edge μ-XANES spectra revealed that up to 85% of the initial Np(V) was reduced to Np(IV). Pyrite could be identified by μ-XRD as a redox-active mineral phase responsible for the formation of Np(IV). The analysis of the diffusion profile within the clay matrix after an in-diffusion experiment for two months showed that Np(V) is progressively reduced with diffusion distance, i.e. Np(IV) amounted to ≈12% and ≈26% at 30 μm and 525 μm, respectively

Smooth crack-free targets for nuclear applications produced by molecular plating

Vascon A, Santi S, Isse AA, et al. Smooth crack-free targets for nuclear applications produced by molecular plating. Nuclear Instruments and Methods in Physics Research A. 2013;714:163-175.The production process of smooth and crack-free targets by means of constant current electrolysis in organic media, commonly known as molecular plating, was optimized. Using a Nd salt, i.e., [Nd(NO3)(3)center dot 6H(2)O], as model electrolyte several constant current density electrolysis experiments were carried out to investigate the effects of different parameters, namely the plating solvent (isopropanol and isobutanol mixed together, pyridine, and N,N-dimethylformamide), the electrolyte concentration (0.11, 0.22, 0.44 mM), the applied current density (0.17, 0.3, 0.7, and 1.3 mA/cm(2)), and the surface roughness of the deposition substrates (12 and 24 nm). Different environments (air and Ar) were used to dry the samples and the effects on the produced layers were investigated. The obtained deposits were characterized using gamma-ray spectroscopy for determining Nd deposition yields, X-ray photoelectron spectroscopy for chemical analysis of the produced surfaces, radiographic imaging for surface homogeneity inspection, atomic force microscopy for surface roughness evaluation, and scanning electron microscopy for surface morphology investigation. The results allowed identifying the optimum parameters for the production of smooth and crack-free targets by means of molecular plating. The smoothest layers, which had an average RMS roughness of ca. 20 nm and showed no cracks, were obtained using 0.22 mM [Nd(NO3)(3)center dot 6H(2)O] plated from N,N-dimethylformamide at current densities in the range of 0.3-0.7 mA/cm(2) on the smoothest deposition substrate available. (c) 2013 Elsevier B.V. All rights reserved

Compound A, a selective glucocorticoid receptor modulator, enhances heat shock protein Hsp70 gene promoter activation

Compound A possesses glucocorticoid receptor (GR)-dependent anti-inflammatory properties. Just like classical GR ligands, Compound A can repress NF-kappa B-mediated gene expression. However, the monomeric Compound A-activated GR is unable to trigger glucocorticoid response element-regulated gene expression. The heat shock response potently activates heat shock factor 1 (HSF1), upregulates Hsp70, a known GR chaperone, and also modulates various aspects of inflammation. We found that the selective GR modulator Compound A and heat shock trigger similar cellular effects in A549 lung epithelial cells. With regard to their anti-inflammatory mechanism, heat shock and Compound A are both able to reduce TNF-stimulated I kappa B alpha degradation and NF-kappa B p65 nuclear translocation. We established an interaction between Compound A-activated GR and Hsp70, but remarkably, although the presence of the Hsp70 chaperone as such appears pivotal for the Compound A-mediated inflammatory gene repression, subsequent novel Hsp70 protein synthesis is uncoupled from an observed CpdA-induced Hsp70 mRNA upregulation and hence obsolete in mediating CpdA's anti-inflammatory effect. The lack of a Compound A-induced increase in Hsp70 protein levels in A549 cells is not mediated by a rapid proteasomal degradation of Hsp70 or by a Compound A-induced general block on translation. Similar to heat shock, Compound A can upregulate transcription of Hsp70 genes in various cell lines and BALB/c mice. Interestingly, whereas Compound A-dependent Hsp70 promoter activation is GR-dependent but HSF1-independent, heat shock-induced Hsp70 expression alternatively occurs in a GR-independent and HSF1-dependent manner in A549 lung epithelial cells

Colon cancer-derived myofibroblasts increase endothelial cell migration by glucocorticoid-sensitive secretion of a pro-migratory factor

AbstractAngiogenesis is important in cancer progression and can be influenced by tumor-associated myofibroblasts. We addressed the hypothesis that glucocorticoids indirectly affect angiogenesis by altering the release of pro-angiogenic factors from colon cancer-derived myofibroblasts.Our study shows that glucocorticoids reduced prostanoids, urokinase-type plasminogen activator (uPA) and angiopoietin-like protein-2 (ANGPTL2) levels, but increased angiogenin (ANG) in supernatant from human CT5.3hTERT colon cancer-derived myofibroblasts. Conditioned medium from solvent- (CMS) and dexamethasone (Dex)-treated (CMD) myofibroblasts increased human umbilical vein endothelial cell (HUVEC) proliferation, but did not affect expression of pro-angiogenic factors or tube-like structure formation (by HUVECs or human aortic ECs). In a HUVEC scratch assay CMS-induced acceleration of wound healing was blunted by CMD treatment. Moreover, CMS-induced neovessel growth in mouse aortic rings ex vivo was also blunted using CMD. The latter effect could be ascribed to both Dex-driven reduction of secreted factors and potential residual Dex present in CMD (indicated using a dexamethasone-spiked CMS control). A similar control in the scratch assay, however, revealed that altered levels of factors in the CMD, and not potential residual Dex, were responsible for decreased wound closure.In conclusion, our results suggest that glucocorticoids indirectly alter endothelial cell function during tumor development in vivo

A Global Federated Real-World Data and Analytics Platform for Research

Objective This article describes a scalable, performant, sustainable global network of electronic health record data for biomedical and clinical research. Materials and Methods TriNetX has created a technology platform characterized by a conservative security and governance model that facilitates collaboration and cooperation between industry participants, such as pharmaceutical companies and contract research organizations, and academic and community-based healthcare organizations (HCOs). HCOs participate on the network in return for access to a suite of analytics capabilities, large networks of de-identified data, and more sponsored trial opportunities. Industry participants provide the financial resources to support, expand, and improve the technology platform in return for access to network data, which provides increased efficiencies in clinical trial design and deployment. Results TriNetX is a growing global network, expanding from 55 HCOs and 7 countries in 2017 to over 220 HCOs and 30 countries in 2022. Over 19 000 sponsored clinical trial opportunities have been initiated through the TriNetX network. There have been over 350 peer-reviewed scientific publications based on the network’s data. Conclusions The continued growth of the TriNetX network and its yield of clinical trial collaborations and published studies indicates that this academic-industry structure is a safe, proven, sustainable path for building and maintaining research-centric data networks

Exploring Breast Cancer Systemic Drug Therapy Patterns in Real-World Data

PURPOSE: To explore medications and their administration patterns in real-world patients with breast cancer. METHODS: A retrospective study was performed using TriNetX, a federated network of deidentified, Health Insurance Portability and Accountability Act-compliant data from 21 health care organizations across North America. Patients diagnosed with breast cancer between January 1, 2013, and May 31, 2022, were included. We investigated a rule-based and unsupervised learning algorithm to extract medications and their administration patterns. To group similar administration patterns, we used three features in k-means clustering: total number of administrations, median number of days between administrations, and standard deviation of the days between administrations. We explored the first three lines of therapy for patients classified into six groups on the basis of their stage at diagnosis (early as stages I-III RESULTS: In early-stage HR+/ CONCLUSION: Although there is a general agreement with the NCCN Guidelines, real-world medication data exhibit variability in the medications and their administration patterns