Editor's Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to authors, or important in this field. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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Article
An Open-Source COVID-19 CT Dataset with Automatic Lung Tissue Classification for Radiomics
Bioengineering 2021, 8(2), 26; https://doi.org/10.3390/bioengineering8020026 - 16 Feb 2021
Cited by 3
Abstract
The coronavirus disease 19 (COVID-19) pandemic is having a dramatic impact on society and healthcare systems. In this complex scenario, lung computerized tomography (CT) may play an important prognostic role. However, datasets released so far present limitations that hamper the development of tools [...] Read more.
The coronavirus disease 19 (COVID-19) pandemic is having a dramatic impact on society and healthcare systems. In this complex scenario, lung computerized tomography (CT) may play an important prognostic role. However, datasets released so far present limitations that hamper the development of tools for quantitative analysis. In this paper, we present an open-source lung CT dataset comprising information on 50 COVID-19-positive patients. The CT volumes are provided along with (i) an automatic threshold-based annotation obtained with a Gaussian mixture model (GMM) and (ii) a scoring provided by an expert radiologist. This score was found to significantly correlate with the presence of ground glass opacities and the consolidation found with GMM. The dataset is freely available in an ITK-based file format under the CC BY-NC 4.0 license. The code for GMM fitting is publicly available, as well. We believe that our dataset will provide a unique opportunity for researchers working in the field of medical image analysis, and hope that its release will lay the foundations for the successfully implementation of algorithms to support clinicians in facing the COVID-19 pandemic. Full article
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Article
CRISPR/Cas9-Based Lateral Flow and Fluorescence Diagnostics
Bioengineering 2021, 8(2), 23; https://doi.org/10.3390/bioengineering8020023 - 12 Feb 2021
Cited by 2
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. We integrated commercially available reagents into a CRISPR/Cas9-based lateral flow assay that [...] Read more.
Clustered regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. We integrated commercially available reagents into a CRISPR/Cas9-based lateral flow assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences with single-base specificity. This approach requires minimal equipment and represents a simplified platform for field-based deployment. We also developed a rapid, multiplex fluorescence CRISPR/Cas9 nuclease cleavage assay capable of detecting and differentiating SARS-CoV-2, influenza A and B, and respiratory syncytial virus in a single reaction. Our findings provide proof-of-principle for CRISPR/Cas9 point-of-care diagnosis as well as a scalable fluorescent platform for identifying respiratory viral pathogens with overlapping symptomology. Full article
(This article belongs to the Special Issue CRISPR-Cas: Discovery, Function and Application)
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Article
Characterization of Gelatin Hydrogels Cross-Linked with Microbial Transglutaminase as Engineered Skeletal Muscle Substrates
Bioengineering 2021, 8(1), 6; https://doi.org/10.3390/bioengineering8010006 - 06 Jan 2021
Cited by 6
Abstract
Engineered in vitro models of skeletal muscle are essential for efficiently screening drug safety and efficacy. However, conventional culture substrates poorly replicate physical features of native muscle and do not support long-term culture, which limits tissue maturity. Micromolded gelatin hydrogels cross-linked with microbial [...] Read more.
Engineered in vitro models of skeletal muscle are essential for efficiently screening drug safety and efficacy. However, conventional culture substrates poorly replicate physical features of native muscle and do not support long-term culture, which limits tissue maturity. Micromolded gelatin hydrogels cross-linked with microbial transglutaminase (gelatin-MTG hydrogels) have previously been shown to induce C21C2 myotube alignment and improve culture longevity. However, several properties of gelatin-MTG hydrogels have not been systematically characterized, such as changes in elastic modulus during incubation in culture-like conditions and their ability to support sarcomere maturation. In this study, various gelatin-MTG hydrogels were fabricated and incubated in ambient or culture-like conditions. Elastic modulus, mass, and transmittance were measured over a one- or two-week period. Compared to hydrogels in phosphate buffered saline (PBS) or ambient air, hydrogels in Dulbecco’s Modified Eagle Medium (DMEM) and 5% CO2 demonstrated the most stable elastic modulus. A subset of gelatin-MTG hydrogels was micromolded and seeded with C2C12 or primary chick myoblasts, which aligned and fused into multinucleated myotubes with relatively mature sarcomeres. These data are important for fabricating gelatin-MTG hydrogels with predictable and stable mechanical properties and highlight their advantages as culture substrates for engineering relatively mature and stable muscle tissues. Full article
(This article belongs to the Special Issue Advances in Skeletal Muscle Tissue Engineering)
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Review

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Review
Advantages of Additive Manufacturing for Biomedical Applications of Polyhydroxyalkanoates
Bioengineering 2021, 8(2), 29; https://doi.org/10.3390/bioengineering8020029 - 23 Feb 2021
Cited by 4
Abstract
In recent years, biopolymers have been attracting the attention of researchers and specialists from different fields, including biotechnology, material science, engineering, and medicine. The reason is the possibility of combining sustainability with scientific and technological progress. This is an extremely broad research topic, [...] Read more.
In recent years, biopolymers have been attracting the attention of researchers and specialists from different fields, including biotechnology, material science, engineering, and medicine. The reason is the possibility of combining sustainability with scientific and technological progress. This is an extremely broad research topic, and a distinction has to be made among different classes and types of biopolymers. Polyhydroxyalkanoate (PHA) is a particular family of polyesters, synthetized by microorganisms under unbalanced growth conditions, making them both bio-based and biodegradable polymers with a thermoplastic behavior. Recently, PHAs were used more intensively in biomedical applications because of their tunable mechanical properties, cytocompatibility, adhesion for cells, and controllable biodegradability. Similarly, the 3D-printing technologies show increasing potential in this particular field of application, due to their advantages in tailor-made design, rapid prototyping, and manufacturing of complex structures. In this review, first, the synthesis and the production of PHAs are described, and different production techniques of medical implants are compared. Then, an overview is given on the most recent and relevant medical applications of PHA for drug delivery, vessel stenting, and tissue engineering. A special focus is reserved for the innovations brought by the introduction of additive manufacturing in this field, as compared to the traditional techniques. All of these advances are expected to have important scientific and commercial applications in the near future. Full article
(This article belongs to the Special Issue Biocomposite Inks for 3D Printing)
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Review
High-Throughput Screening Platforms in the Discovery of Novel Drugs for Neurodegenerative Diseases
Bioengineering 2021, 8(2), 30; https://doi.org/10.3390/bioengineering8020030 - 23 Feb 2021
Cited by 35
Abstract
Neurodegenerative diseases (NDDs) are incurable and debilitating conditions that result in progressive degeneration and/or death of nerve cells in the central nervous system (CNS). Identification of viable therapeutic targets and new treatments for CNS disorders and in particular, for NDDs is a major [...] Read more.
Neurodegenerative diseases (NDDs) are incurable and debilitating conditions that result in progressive degeneration and/or death of nerve cells in the central nervous system (CNS). Identification of viable therapeutic targets and new treatments for CNS disorders and in particular, for NDDs is a major challenge in the field of drug discovery. These difficulties can be attributed to the diversity of cells involved, extreme complexity of the neural circuits, the limited capacity for tissue regeneration, and our incomplete understanding of the underlying pathological processes. Drug discovery is a complex and multidisciplinary process. The screening attrition rate in current drug discovery protocols mean that only one viable drug may arise from millions of screened compounds resulting in the need to improve discovery technologies and protocols to address the multiple causes of attrition. This has identified the need to screen larger libraries where the use of efficient high-throughput screening (HTS) becomes key in the discovery process. HTS can investigate hundreds of thousands of compounds per day. However, if fewer compounds could be screened without compromising the probability of success, the cost and time would be largely reduced. To that end, recent advances in computer-aided design, in silico libraries, and molecular docking software combined with the upscaling of cell-based platforms have evolved to improve screening efficiency with higher predictability and clinical applicability. We review, here, the increasing role of HTS in contemporary drug discovery processes, in particular for NDDs, and evaluate the criteria underlying its successful application. We also discuss the requirement of HTS for novel NDD therapies and examine the major current challenges in validating new drug targets and developing new treatments for NDDs. Full article
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Review
Natural Biomaterials and Their Use as Bioinks for Printing Tissues
Bioengineering 2021, 8(2), 27; https://doi.org/10.3390/bioengineering8020027 - 20 Feb 2021
Cited by 10
Abstract
The most prevalent form of bioprinting—extrusion bioprinting—can generate structures from a diverse range of materials and viscosities. It can create personalized tissues that aid in drug testing and cancer research when used in combination with natural bioinks. This paper reviews natural bioinks and [...] Read more.
The most prevalent form of bioprinting—extrusion bioprinting—can generate structures from a diverse range of materials and viscosities. It can create personalized tissues that aid in drug testing and cancer research when used in combination with natural bioinks. This paper reviews natural bioinks and their properties and functions in hard and soft tissue engineering applications. It discusses agarose, alginate, cellulose, chitosan, collagen, decellularized extracellular matrix, dextran, fibrin, gelatin, gellan gum, hyaluronic acid, Matrigel, and silk. Multi-component bioinks are considered as a way to address the shortfalls of individual biomaterials. The mechanical, rheological, and cross-linking properties along with the cytocompatibility, cell viability, and printability of the bioinks are detailed as well. Future avenues for research into natural bioinks are then presented. Full article
(This article belongs to the Special Issue 3D Bioprinting for Tissue Engineering and Regenerative Medicine)
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Review
Collagen Mimetic Peptides
Bioengineering 2021, 8(1), 5; https://doi.org/10.3390/bioengineering8010005 - 05 Jan 2021
Cited by 3
Abstract
Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in [...] Read more.
Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix—the building block of collagen—and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs—their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies. Full article
(This article belongs to the Special Issue Biomedical Applications of Collagen)
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Review
Collagen Structure-Function Mapping Informs Applications for Regenerative Medicine
Bioengineering 2021, 8(1), 3; https://doi.org/10.3390/bioengineering8010003 - 29 Dec 2020
Cited by 7
Abstract
Type I collagen, the predominant protein of vertebrates, assembles into fibrils that orchestrate the form and function of bone, tendon, skin, and other tissues. Collagen plays roles in hemostasis, wound healing, angiogenesis, and biomineralization, and its dysfunction contributes to fibrosis, atherosclerosis, cancer metastasis, [...] Read more.
Type I collagen, the predominant protein of vertebrates, assembles into fibrils that orchestrate the form and function of bone, tendon, skin, and other tissues. Collagen plays roles in hemostasis, wound healing, angiogenesis, and biomineralization, and its dysfunction contributes to fibrosis, atherosclerosis, cancer metastasis, and brittle bone disease. To elucidate the type I collagen structure-function relationship, we constructed a type I collagen fibril interactome, including its functional sites and disease-associated mutations. When projected onto an X-ray diffraction model of the native collagen microfibril, data revealed a matrix interaction domain that assumes structural roles including collagen assembly, crosslinking, proteoglycan (PG) binding, and mineralization, and the cell interaction domain supporting dynamic aspects of collagen biology such as hemostasis, tissue remodeling, and cell adhesion. Our type III collagen interactome corroborates this model. We propose that in quiescent tissues, the fibril projects a structural face; however, tissue injury releases blood into the collagenous stroma, triggering exposure of the fibrils’ cell and ligand binding sites crucial for tissue remodeling and regeneration. Applications of our research include discovery of anti-fibrotic antibodies and elucidating their interactions with collagen, and using insights from our angiogenesis studies and collagen structure-function model to inform the design of super-angiogenic collagens and collagen mimetics. Full article
(This article belongs to the Special Issue Biomedical Applications of Collagen)
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Review
Electrospun Fiber Scaffolds for Engineering Glial Cell Behavior to Promote Neural Regeneration
Bioengineering 2021, 8(1), 4; https://doi.org/10.3390/bioengineering8010004 - 29 Dec 2020
Cited by 5
Abstract
Electrospinning is a fabrication technique used to produce nano- or micro- diameter fibers to generate biocompatible, biodegradable scaffolds for tissue engineering applications. Electrospun fiber scaffolds are advantageous for neural regeneration because they mimic the structure of the nervous system extracellular matrix and provide [...] Read more.
Electrospinning is a fabrication technique used to produce nano- or micro- diameter fibers to generate biocompatible, biodegradable scaffolds for tissue engineering applications. Electrospun fiber scaffolds are advantageous for neural regeneration because they mimic the structure of the nervous system extracellular matrix and provide contact guidance for regenerating axons. Glia are non-neuronal regulatory cells that maintain homeostasis in the healthy nervous system and regulate regeneration in the injured nervous system. Electrospun fiber scaffolds offer a wide range of characteristics, such as fiber alignment, diameter, surface nanotopography, and surface chemistry that can be engineered to achieve a desired glial cell response to injury. Further, electrospun fibers can be loaded with drugs, nucleic acids, or proteins to provide the local, sustained release of such therapeutics to alter glial cell phenotype to better support regeneration. This review provides the first comprehensive overview of how electrospun fiber alignment, diameter, surface nanotopography, surface functionalization, and therapeutic delivery affect Schwann cells in the peripheral nervous system and astrocytes, oligodendrocytes, and microglia in the central nervous system both in vitro and in vivo. The information presented can be used to design and optimize electrospun fiber scaffolds to target glial cell response to mitigate nervous system injury and improve regeneration. Full article
(This article belongs to the Special Issue Electrospinning for Tissue Engineering)
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Review
Spinal Deformities and Advancement in Corrective Orthoses
Bioengineering 2021, 8(1), 2; https://doi.org/10.3390/bioengineering8010002 - 25 Dec 2020
Cited by 3
Abstract
Spinal deformity is an abnormality in the spinal curves and can seriously affect the activities of daily life. The conventional way to treat spinal deformities, such as scoliosis, kyphosis, and spondylolisthesis, is to use spinal orthoses (braces). Braces have been used for centuries [...] Read more.
Spinal deformity is an abnormality in the spinal curves and can seriously affect the activities of daily life. The conventional way to treat spinal deformities, such as scoliosis, kyphosis, and spondylolisthesis, is to use spinal orthoses (braces). Braces have been used for centuries to apply corrective forces to the spine to treat spinal deformities or to stabilize the spine during postoperative rehabilitation. Braces have not modernized with advancements in technology, and very few braces are equipped with smart sensory design and active actuation. There is a need to enable the orthotists, ergonomics practitioners, and developers to incorporate new technologies into the passive field of bracing. This article presents a review of the conventional passive braces and highlights the advancements in spinal orthoses in terms of improved sensory designs, active actuation mechanisms, and new construction methods (CAD/CAM, three-dimensional (3D) printing). This review includes 26 spinal orthoses, comprised of passive rigid/soft braces, active dynamics braces, and torso training devices for the rehabilitation of the spine. Full article
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