Browsing by Author "Sonal Saxena"

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An introduction to biomaterials
(Elsevier, 2024) Naveen Kumar; Vineet Kumar; Anil Kumar Gangwar; Sameer Shrivastava; Sonal Saxena; Sangeeta Devi Khangembam; Swapan Kumar Maiti; Rahul Kumar Udehiya; Mamta Mishra; Pawan Diwan Singh Raghuvanshi; Naresh Kumar Singh
A biomaterial can be defined as any material used to make devices to replace a part or a function of the body in a safe, reliable, economic, and physiologically acceptable manner. Some people refer to materials of biological origin, such as wood and bone, as biomaterials, but we refer to such materials as “biological materials.” A variety of devices and materials are used in the treatment of disease or injury. Commonplace examples include sutures, tooth fillings, needles, catheters, bone plates, etc. A biomaterial may be a synthetic material used to replace part of a living system or to function in intimate contact with living tissue. © 2025 Elsevier Inc. All rights reserved.
Artificial Intelligence-Based Model for Predicting the Minimum Inhibitory Concentration of Antibacterial Peptides Against ESKAPEE Pathogens
(Institute of Electrical and Electronics Engineers Inc., 2024) Ritesh Sharma; Sameer Shrivastava; Sanjay Kumar Singh; Abhinav Kumar; Amit Kumar Singh; Sonal Saxena
In response to environmental threats, pathogens make several changes in their genome, leading to antimicrobial resistance (AMR). Due to AMR, the pathogens do not respond to antibiotics. Amongst drug-resistant pathogens, the ESKAPEE group of bacteria poses a major threat to humans, and therefore World Health Organization has given them the highest priority status. Antibacterial peptides (ABPs) are a family of peptides found in nature that play a crucial role in the innate immune systems of organisms. These ABPs offer several advantages over widely used antibiotics. As a result, they have recently received a lot of attention as potential replacements for currently available antibiotics. But it is expensive and time-consuming to identify ABPs from natural sources. Thus, wet lab researchers employ various tools to screen promising ABPs rapidly. However, the main limitation of the existing tools is that they do not provide the minimum inhibitory concentration values against the ESKAPEE pathogens for the identified ABP. To address this, in the current work, we developed ESKAPEE-MICpred, a two-input model that utilizes transfer learning and ensemble learning techniques. The concept of ensemble learning was realized by combining the decisions provided by deep learning algorithms, whereas the concept of transfer learning was realized by utilizing pretrained amino acid embeddings. The proposed model has been deployed as a web server at https://eskapee-micpred.anvil.app/ to aid the scientific community. © 2013 IEEE.
Crosslinking of biomaterials
(Elsevier, 2024) Naveen Kumar; Anil Kumar Gangwar; Vineet Kumar; Dayamon David Mathew; Pawan Diwan Singh Raghuvanshi; Rahul Kumar Udehiya; Naresh Kumar Singh; Sangeeta Devi Khangembam; Sameer Shrivastava; Sonal Saxena; Rukmani Dewangan
Crosslinking of biomaterials is used to improve their properties for a variety of biomedical applications. For example, crosslinking can be used to improve the mechanical strength, stability, and durability of biomaterials. Crosslinking can also be used to control the release of drugs or other molecules from biomaterials. © 2025 Elsevier Inc. All rights reserved.
Decellularization and characterization methods
(Elsevier, 2024) Naveen Kumar; Vineet Kumar; Anil Kumar Gangwar; Sangeeta Devi Khangembam; Naresh Kumar Singh; Pawan Diwan Singh Raghuvanshi; Sameer Shrivastava; Sonal Saxena; Sangeetha P.; Rahul Kumar Udehiya; Dayamon David Mathew
An ideal biomaterial should initiate the minimal immune response possible and allow cellular infiltration while maintaining its structure and performing its intended function. Eventually, it will degrade and promote healthy tissue regeneration rather than fibrous scarring. The physiological similarity of the biomaterials is probably the most important factor governing their ability to obtain approval for use. Native extracellular matrices (ECMs) provoke a more natural healing response than synthetic materials, promoting cellular infiltration, proliferation, and differentiation into structures very similar to those of the uninjured host tissue. As previously discussed, many of the first ECM biomaterials were used in prostheses, providing structural support or mechanical functionality. Consequently, preservation of the original structure and strength while reducing immunogenicity was paramount. The most abundant protein in ECMs is collagen, a fibrous protein that is remarkably preserved across species and, therefore, invokes one of the weakest immune responses of all the proteins. This is, in fact, one reason natural collagen sutures implanted for thousands of years were so effective. Bovine collagen is still one of the most widely used and abundantly available xenogeneic materials used in biomedical applications. Even though it is so well preserved, xenogeneic collagen can still provoke immune reactions in humans who are hypersensitive to it or in extenuating circumstances. Typically, proper cleaning with detergents and terminal sterilization by gamma irradiation or ethylene oxide gas is enough to reduce the immune response to a very minimal level, lower even than synthetic meshes. © 2025 Elsevier Inc. All rights reserved.
Deep-AVPpred: Artificial Intelligence Driven Discovery of Peptide Drugs for Viral Infections
(Institute of Electrical and Electronics Engineers Inc., 2022) Ritesh Sharma; Sameer Shrivastava; Sanjay Kumar Singh; Abhinav Kumar; Amit Kumar Singh; Sonal Saxena
Rapid increase in viral outbreaks has resulted in the spread of viral diseases in diverse species and across geographical boundaries. The zoonotic viral diseases have greatly affected the well-being of humans, and the COVID-19 pandemic is a burning example. The existing antivirals have low efficacy, severe side effects, high toxicity, and limited market availability. As a result, natural substances have been tested for antiviral activity. The host defense molecules like antiviral peptides (AVPs) are present in plants and animals and protect them from invading viruses. However, obtaining AVPs from natural sources for preparing synthetic peptide drugs is expensive and time-consuming. As a result, an in-silico model is required for identifying new AVPs. We proposed Deep-AVPpred, a deep learning classifier for discovering AVPs in protein sequences, which utilises the concept of transfer learning with a deep learning algorithm. The proposed classifier outperformed state-of-The-Art classifiers and achieved approximately 94% and 93% precision on validation and test sets, respectively. The high precision indicates that Deep-AVPpred can be used to propose new AVPs for synthesis and experimentation. By utilising Deep-AVPpred, we identified novel AVPs in human interferons-family proteins. These AVPs can be chemically synthesised and experimentally verified for their antiviral activity against different viruses. The Deep-AVPpred is deployed as a web server and is made freely available at https://deep-Avppred.anvil.app, which can be utilised to predict novel AVPs for developing antiviral compounds for use in human and veterinary medicine. © 2013 IEEE.
Diaphragm-derived extracellular matrix scaffolds and clinical application
(Elsevier, 2024) Vineet Kumar; Naveen Kumar; Anil Kumar Gangwar; Kaarthick D.T.; Harendra Rathore; Swapan Kumar Maiti; Ashok Kumar Sharma; Dayamon David Mathew; Jetty Devarathnam; Sameer Shrivastava; Sonal Saxena; Apra Shahi; Himani Singh; Karam Pal Singh
Collagen is regarded as one of the most useful biomaterial due to its excellent biocompatibility, biodegradability, and weak antigenicity. In cellular grafts, the histocompatibility antigens of the cells cause immunological reaction phenomenon. Less immunogenicity and better tolerance of acellular grafts were observed in rats and rabbits. The need of the readily availability of a nonimmunogenic and nonprosthetic biomaterial that could guide the regeneration of normal tissue is a fascinating possibility. Acellular biological tissues have been proposed to be used as natural biomaterials for tissue repair. Natural biomaterials are composed of extracellular matrix proteins that are conserved and can be served as scaffolds for cell attachment, migration, and proliferation. The acellular matrix can stimulate exact regeneration of missing tissue. © 2025 Elsevier Inc. All rights reserved.
Fish swim bladder-derived tissue scaffolds
(Elsevier, 2024) Remya Vellachi; Naveen Kumar; Ashok Kumar Sharma; Sonal Saxena; Swapan Kumar Maiti; Vineet Kumar; Dayamon David Mathew; Sameer Shrivastava
Organ damage or loss can occur from congenital disorders, cancer, trauma, infection, inflammation, iatrogenic injuries, or other conditions and often necessitates reconstruction or replacement. Depending on the organ and severity of damage, autologous tissues can be used for reconstruction. However, there is unavailability of sufficient tissue and there is a degree of morbidity associated with the harvest procedure. For functional replacement, organ transplants are used for damaged tissues. However, there is a severe shortage of donor organs, which is worsening with the ageing of the population. Both aforementioned approaches rarely replace the entire function of the original organ. Tissues used for reconstruction can lead to complications because of their inherent divergent functional parameters. The replacement of deficient tissues with functionally equivalent tissues would improve the outcome for these patients. Therefore, engineered biological substitutes that can restore and maintain normal tissue function would be useful in tissue and organ replacement applications. © 2025 Elsevier Inc. All rights reserved.
Gall bladder-derived extracellular matrix scaffolds
(Elsevier, 2024) Naveen Kumar; Anil Kumar Gangwar; Sangeeta Devi Khangembam; Poonam Shakya; Ashok Kumar Sharma; Amit Kumar Sachan; Ravi Prakash Goyal; Parvez Ahmed; Kiranjeet Singh; Aswathy Gopinathan; Sonal Saxena; Sameer Shrivastava; Remya Vellachi; Dayamon David Mathew; Swapan Kumar Maiti; Karam Pal Singh
The extracellular matrix (ECM) with adequate bioactive molecules, capable of supporting the growth of cells participating in regeneration, is an ideal graft suitable for wound healing application. The ECM isolated from certain mammalian organs and tissues have been found to have these essential biocomponents that support cell proliferation, migration, and differentiation. These scaffolds are naturally rich in collagen, elastin, glycosaminoglycans, laminin, and fibronectin on which the cells can migrate, attach, and grow. In addition, many of the bioactive degradation products released from the graft at the site of the grafting mimic growth factors required for healing. The ECM is also known to aid angiogenesis by regulating the migration, proliferation, and sustenance of endothelial cells. Intact decellularized allogenic/xenogenic ECM has the necessary requisites to provide for initial requirements of repair and subsequent remodeling. Hence, ECM is correctly termed as nature’s ideal scaffold material. The decellularization specifically removes cellular components that give rise to a residual immunological response. These decellularization techniques include chemical, enzymatic, and mechanical means of removing cellular components, leaving a material composed essentially of ECM components. The decellularized tissues are expected to mimic closely the complex three-dimensional structure and mechanical properties of the native tissues from where it origins. One of the major goals in using natural biodegradable materials is to induce the host, to replace the implanted construct with native tissue. Cholecyst-derived ECM (CEM) recovered from ECM of porcine gall bladder had variable application in the field of regenerative medicine. This CEM found to be a novel acellular proteinaceous biodegradable biomaterial and may have potential applications as scaffolds in heart valve tissue engineering. This matrix is rich in collagen and contains several other macromolecules useful in tissue remodeling. © 2025 Elsevier Inc. All rights reserved.
Natural Biomaterials for Tissue Engineering
(Elsevier, 2024) Naveen Kumar; Sonal Saxena; Vineet Kumar; Anil Kumar Gangwar; Dayamon David Mathew; Sameer Shrivastava; Naresh Kumar Singh
Natural Biomaterials for Tissue Engineering is a comprehensive reference that provides in-depth principles for supporting and enabling knowledge during the tissue production process, focusing on different cell systems. The tissue fabrication process is illustrated with specific examples for more than 30 tissues, which may soon lead to new tissue engineering therapies. The section coverage includes an overall introduction, decellularization protocols specific to each tissue, characterization, materials and methods, cell seeding process, preclinical evaluation in laboratory animals, clinical applications, limitations, conclusion, and future challenges. Readers may turn to this up-to-date coverage for a widespread understanding of regenerative medicine, which will be useful to students and experts alike. © 2025 Elsevier Inc. All rights are reserved including those for text and data mining AI training and similar technologies.
Preface
(Elsevier, 2024) Naveen Kumar; Sonal Saxena; Vineet Kumar; Anil Kumar Gangwar; Dayamon David Mathew; Sameer Shrivastava; Naresh Kumar Singh
[No abstract available]
Rumen-derived extracellular matrix scaffolds and clinical application
(Elsevier, 2024) Ajit Kumar Singh; Naveen Kumar; Pawan Diwan Singh Raghuvanshi; Harendra Rathore; Anil Kumar Gangwar; Sameer Shrivastava; Sonal Saxena; Mohar Singh; Dayamon David Mathew; Karam Pal Singh
The ruminant refers to a mammal having a stomach with four chambers. These include a forestomach, consists of a rumen, a reticulum and an omasum, and a fourth chamber known as an abomasum. Examples of ruminants include mammals belonging to the genus Copra, Bos, Cervus, and Ovis. The rumen underpins much of our agricultural industry. Without this stomach chamber, cows and other ruminants would be much less efficient at turning grass into milk, meat, and wool. A cow’s rumen has a capacity of up to 95 L and contains billions of bacteria and other microbes. These microbes produce the enzymes that digest cellulose into sugars and fatty acids for their hosts to use. A less desirable by-product is the potent greenhouse gas, methane; a single cow can produce up to 280 L of methane a day. Collectively, these organs occupy almost three-fourths of the abdominal cavity, filling virtually all of the left side and extending significantly into the right. The reticulum lies against the diaphragm and is joined to the rumen by a fold of tissue. The rumen is the largest of the forestomachs and is itself sacculated by muscular pillars into what are called the dorsal, ventral, caudodorsal, and caudoventral sacs. In many respects, the reticulum can be considered a “cranioventral sac” of the rumen; for example, ingesta flow freely between these two organs. The reticulum is connected to the spherical omasum by a short tunnel. The abomasum is the ruminant’s true or glandular stomach. © 2025 Elsevier Inc. All rights reserved.
Scaffolds for abdominal wall reconstruction
(Elsevier, 2019) Naveen Kumar; Vineet Kumar; Anil Kumar Gangwar; Sameer Shrivastava; Swapan Kumar Maiti; Khangembam Sangeeta Devi; Sonal Saxena; P.D.S. Raghuvanshi; Naresh Kumar Singh; Ajit Kumar Singh; Karam Pal Singh
The abdominal wall is a layer of skeletal muscles, which protects the vital organs and provides mechanical support to the viscera. Any defect in the abdominal wall, in the form of tear or rupture occurred either due to trauma or congenital defect, may lead to the development of a hernia. A hernia represents protrusion of an organ or tissue through an acquired or natural opening in the abdominal wall like inguinal canal. Revolutionary advances have been developed in the past 20 years with respect to abdominal wall reconstruction (AWR). Innovative surgical approaches and contemporary synthetic and biological prosthetics have been an integral part of the surgical arsenal. Patients with complex abdominal wall defects must be evaluated on a case-by-case basis; interventions can vary from simple coverage and contouring to reconstruction of a dynamic functional abdominal wall. There is a substantial recurrence rate after ventral herniorrhaphy and a higher incidence of surgical-site occurrences (seroma, hematoma formation) and surgical-site infections. Although there is not a successful “one-size-fits-all” approach to AWR, there are treatment modalities, which significantly improve these outcomes. In this regard, selecting the appropriate synthetic or biologic scaffolds for a given clinical scenario is of great interest. © 2019 Elsevier Ltd. All rights reserved.
Scaffolds for bladder tissue engineering
(Elsevier, 2019) Naveen Kumar; Sonal Saxena; Vineet Kumar; Sameer Shrivastava; Anil Kumar Gangwar; Swapan Kumar Maiti; Rukmani Dewangan; Sangeeta Devi Khangembam; P.D.S. Raghuvanshi; Naresh Kumar Singh; Ajit Kumar Singh; Karam Pal Singh
Bladder dysfunction induced by disease or surgical intervention can result in chronic urinary incontinence and increased upper urinary tract pressure leading to irreversible kidney damage. Currently, the treatment of choice in these patients is enterocystoplasty with the aim to increase bladder capacity and lower the storage pressure. However, it fails to restore the emptying function and is associated with complications such as increased mucus production, metabolic disturbances, urolithiasis, infections, and even malignancy. To prevent these, various materials have been tried for reconstruction with only limited success so far. This chapter aims to address the current challenges and opportunities associated with the use of tissue engineering scaffolds for the repair and reconstruction of the functional bladder. © 2019 Elsevier Ltd. All rights reserved.