NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.

The automatic recognition of chemical names and their corresponding database identifiers in biomedical text is an important first step for many downstream text-mining applications. The task is even more challenging when considering the identification of these entities in the article's full text and, furthermore, the identification of candidate substances for that article's metadata [Medical Subject Heading (MeSH) article indexing]. The National Library of Medicine (NLM)-Chem track at BioCreative VII aimed to foster the development of algorithms that can predict with high quality the chemical entities in the biomedical literature and further identify the chemical substances that are candidates for article indexing. As a result of this challenge, the NLM-Chem track produced two comprehensive, manually curated corpora annotated with chemical entities and indexed with chemical substances: the chemical identification corpus and the chemical indexing corpus. The NLM-Chem BioCreative VII (NLM-Chem-BC7) Chemical Identification corpus consists of 204 full-text PubMed Central (PMC) articles, fully annotated for chemical entities by 12 NLM indexers for both span (i.e. named entity recognition) and normalization (i.e. entity linking) using MeSH. This resource was used for the training and testing of the Chemical Identification task to evaluate the accuracy of algorithms in predicting chemicals mentioned in recently published full-text articles. The NLM-Chem-BC7 Chemical Indexing corpus consists of 1333 recently published PMC articles, equipped with chemical substance indexing by manual experts at the NLM. This resource was used for the evaluation of the Chemical Indexing task, which evaluated the accuracy of algorithms in predicting the chemicals that should be indexed, i.e. appear in the listing of MeSH terms for the document. This set was further enriched after the challenge in two ways: (i) 11 NLM indexers manually verified each of the candidate terms appearing in the prediction results of the challenge participants, but not in the MeSH indexing, and the chemical indexing terms appearing in the MeSH indexing list, but not in the prediction results, and (ii) the challenge organizers algorithmically merged the chemical entity annotations in the full text for all predicted chemical entities and used a statistical approach to keep those with the highest degree of confidence. As a result, the NLM-Chem-BC7 Chemical Indexing corpus is a gold-standard corpus for chemical indexing of journal articles and a silver-standard corpus for chemical entity identification in full-text journal articles. Together, these resources are currently the most comprehensive resources for chemical entity recognition, and we demonstrate improvements in the chemical entity recognition algorithms. We detail the characteristics of these novel resources and make them available for the community. Database URL: https://ftp.ncbi.nlm.nih.gov/pub/lu/NLM-Chem-BC7-corpus/.

Hyaluronan Hydrogels for a Biomimetic Spongiosa Layer of Tissue Engineered Heart Valve Scaffolds.

Advanced tissue engineered heart valves must be constructed from multiple materials to better mimic the heterogeneity found in the native valve. The trilayered structure of aortic valves provides the ability to open and close consistently over a full human lifetime, with each layer performing specific mechanical functions. The middle spongiosa layer consists primarily of proteoglycans and glycosaminoglycans, providing lubrication and dampening functions as the valve leaflet flexes open and closed. In this study, hyaluronan hydrogels were tuned to perform the mechanical functions of the spongiosa layer, provide a biomimetic scaffold in which valve cells were encapsulated in 3D for tissue engineering applications, and gain insight into how valve cells maintain hyaluronan homeostasis within heart valves. Expression of the HAS1 isoform of hyaluronan synthase was significantly higher in hyaluronan hydrogels compared to blank-slate poly(ethylene glycol) diacrylate (PEGDA) hydrogels. Hyaluronidase and matrix metalloproteinase enzyme activity was similar between hyaluronan and PEGDA hydrogels, even though these scaffold materials were each specifically susceptible to degradation by different enzyme types. KIAA1199 was expressed by valve cells and may play a role in the regulation of hyaluronan in heart valves. Cross-linked hyaluronan hydrogels maintained healthy phenotype of valve cells in 3D culture and were tuned to approximate the mechanical properties of the valve spongiosa layer. Therefore, hyaluronan can be used as an appropriate material for the spongiosa layer of a proposed laminate tissue engineered heart valve scaffold.

Electrospun Polyurethane and Hydrogel Composite Scaffolds as Biomechanical Mimics for Aortic Valve Tissue Engineering.

In this study, a composite scaffold consisting of an electrospun polyurethane and poly(ethylene glycol) hydrogel was investigated for aortic valve tissue engineering. This multilayered approach permitted the fabrication of a scaffold that met the desired mechanical requirements while enabling the 3D culture of cells. The scaffold was tuned to mimic the tensile strength, anisotropy, and extensibility of the natural aortic valve through design of the electrospun polyurethane mesh layer. Valve interstitial cells were encapsulated inside the hydrogel portion of the scaffold around the electrospun mesh, creating a composite scaffold approximately 200 µm thick. The stiffness of the electrospun fibers caused the encapsulated cells to exhibit an activated phenotype that resulted in fibrotic remodeling of the scaffold in a heterogeneous manner. Remodeling was further explored by culturing the scaffolds in both a mechanically constrained state and in a bent state. The constrained scaffolds demonstrated strong fibrotic remodeling with cells aligning in the direction of the mechanical constraint. Bent scaffolds demonstrated that applied mechanical forces could influence cell behavior. Cells seeded on the outside curve of the bend exhibited an activated, fibrotic response, while cells seeded on the inside curve of the bend were a quiescent phenotype, demonstrating potential control over the fibrotic behavior of cells. Overall, these results indicate that this polyurethane/hydrogel scaffold mimics the structural and functional heterogeneity of native valves and warrants further investigation to be used as a model for understanding fibrotic valve disease.