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1.
Brief Bioinform ; 23(2)2022 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-35152278

RESUMO

The application of machine intelligence in biological sciences has led to the development of several automated tools, thus enabling rapid drug discovery. Adding to this development is the ongoing COVID-19 pandemic, due to which researchers working in the field of artificial intelligence have acquired an active interest in finding machine learning-guided solutions for diseases like mucormycosis, which has emerged as an important post-COVID-19 fungal complication, especially in immunocompromised patients. On these lines, we have proposed a temporal convolutional network-based binary classification approach to discover new antifungal molecules in the proteome of plants and animals to accelerate the development of antifungal medications. Although these biomolecules, known as antifungal peptides (AFPs), are part of an organism's intrinsic host defense mechanism, their identification and discovery by traditional biochemical procedures is arduous. Also, the absence of a large dataset on AFPs is also a considerable impediment in building a robust automated classifier. To this end, we have employed the transfer learning technique to pre-train our model on antibacterial peptides. Subsequently, we have built a classifier that predicts AFPs with accuracy and precision of 94%. Our classifier outperforms several state-of-the-art models by a considerable margin. The results of its performance were proven as statistically significant using the Kruskal-Wallis H test, followed by a post hoc analysis performed using the Tukey honestly significant difference (HSD) test. Furthermore, we identified potent AFPs in representative animal (Histatin) and plant (Snakin) proteins using our model. We also built and deployed a web app that is freely available at https://tcn-afppred.anvil.app/ for the identification of AFPs in protein sequences.


Assuntos
Antifúngicos/química , Peptídeos Antimicrobianos/química , Aprendizado Profundo , Descoberta de Drogas/métodos , Redes Neurais de Computação , Algoritmos , Antifúngicos/farmacologia , Peptídeos Antimicrobianos/farmacologia , Inteligência Artificial , Bases de Dados Factuais , Humanos , Curva ROC , Reprodutibilidade dos Testes , Software , Fluxo de Trabalho
2.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34670278

RESUMO

Fungal infections or mycosis cause a wide range of diseases in humans and animals. The incidences of community acquired; nosocomial fungal infections have increased dramatically after the emergence of COVID-19 pandemic. The increase in number of patients with immunodeficiency / immunosuppression related diseases, resistance to existing antifungal compounds and availability of limited therapeutic options has triggered the search for alternative antifungal molecules. In this direction, antifungal peptides (AFPs) have received a lot of interest as an alternative to currently available antifungal drugs. Although the AFPs are produced by diverse population of living organisms, identifying effective AFPs from natural sources is time-consuming and expensive. Therefore, there is a need to develop a robust in silico model capable of identifying novel AFPs in protein sequences. In this paper, we propose Deep-AFPpred, a deep learning classifier that can identify AFPs in protein sequences. We developed Deep-AFPpred using the concept of transfer learning with 1DCNN-BiLSTM deep learning algorithm. The findings reveal that Deep-AFPpred beats other state-of-the-art AFP classifiers by a wide margin and achieved approximately 96% and 94% precision on validation and test data, respectively. Based on the proposed approach, an online prediction server is created and made publicly available at https://afppred.anvil.app/. Using this server, one can identify novel AFPs in protein sequences and the results are provided as a report that includes predicted peptides, their physicochemical properties and motifs. By utilizing this model, we identified AFPs in different proteins, which can be chemically synthesized in lab and experimentally validated for their antifungal activity.


Assuntos
Antifúngicos/química , Tratamento Farmacológico da COVID-19 , COVID-19 , Mucormicose , Pandemias/prevenção & controle , Peptídeos/química , SARS-CoV-2 , Antifúngicos/uso terapêutico , COVID-19/epidemiologia , COVID-19/microbiologia , Humanos , Mucormicose/tratamento farmacológico , Mucormicose/epidemiologia
3.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34750606

RESUMO

Due to the rapid emergence of multi-drug resistant (MDR) bacteria, existing antibiotics are becoming ineffective. So, researchers are looking for alternatives in the form of antibacterial peptides (ABPs) based medicines. The discovery of novel ABPs using wet-lab experiments is time-consuming and expensive. Many machine learning models have been proposed to search for new ABPs, but there is still scope to develop a robust model that has high accuracy and precision. In this work, we present StaBle-ABPpred, a stacked ensemble technique-based deep learning classifier that uses bidirectional long-short term memory (biLSTM) and attention mechanism at base-level and an ensemble of random forest, gradient boosting and logistic regression at meta-level to classify peptides as antibacterial or otherwise. The performance of our model has been compared with several state-of-the-art classifiers, and results were subjected to analysis of variance (ANOVA) test and its post hoc analysis, which proves that our model performs better than existing classifiers. Furthermore, a web app has been developed and deployed at https://stable-abppred.anvil.app to identify novel ABPs in protein sequences. Using this app, we identified novel ABPs in all the proteins of the Streptococcus phage T12 genome. These ABPs have shown amino acid similarities with experimentally tested antimicrobial peptides (AMPs) of other organisms. Hence, they could be chemically synthesized and experimentally validated for their activity against different bacteria. The model and app developed in this work can be further utilized to explore the protein diversity for identifying novel ABPs with broad-spectrum activity, especially against MDR bacterial pathogens.


Assuntos
Antibacterianos , Peptídeos , Sequência de Aminoácidos , Antibacterianos/farmacologia , Aprendizado de Máquina , Peptídeos/química , Proteínas
4.
Arch Microbiol ; 206(7): 302, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38874634

RESUMO

Host-generated antimicrobial peptides (AMPs) play a pivotal role in defense against bacterial pathogens. AMPs kill invading bacteria majorly by disrupting the bacterial cell walls. AMPs are actively synthesized and released into the lumen of the gastrointestinal tract to limit colonization of enteric pathogens like Salmonella typhimurium (S. typhimurium). However, S. typhimurium has evolved several resistance mechanisms to defend AMPs. The multicomponent SapABCDF uptake transporter is one such system that helps in resisting AMPs. In the current study, we analyzed the role of S. typhimurium SapA against stress survival and virulence of this bacterium. ∆sapA mutant strain showed hypersensitivity to AMPs, like melittin and mastoparan. Further, ∆sapA mutant showed more than 22 folds (p = 0.019) hypersensitivity to neutrophils as compared to the WT strain of S. typhimurium. In addition, ∆sapA strain showed defective survival in mice. In conclusion, the results of the current study suggest that the SapA is essential for survival against AMPs and virulence of S. typhimurium.


Assuntos
Neutrófilos , Salmonella typhimurium , Animais , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/patogenicidade , Salmonella typhimurium/genética , Camundongos , Neutrófilos/imunologia , Neutrófilos/microbiologia , Virulência , Peptídeos Antimicrobianos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Feminino , Camundongos Endogâmicos BALB C , Infecções por Salmonella/microbiologia , Peptídeos Catiônicos Antimicrobianos/farmacologia
5.
Brief Bioinform ; 22(6)2021 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-34259329

RESUMO

With advancements in genomics, there has been substantial reduction in the cost and time of genome sequencing and has resulted in lot of data in genome databases. Antimicrobial host defense proteins provide protection against invading microbes. But confirming the antimicrobial function of host proteins by wet-lab experiments is expensive and time consuming. Therefore, there is a need to develop an in silico tool to identify the antimicrobial function of proteins. In the current study, we developed a model AniAMPpred by considering all the available antimicrobial peptides (AMPs) of length $\in $[10 200] from the animal kingdom. The model utilizes a support vector machine algorithm with deep learning-based features and identifies probable antimicrobial proteins (PAPs) in the genome of animals. The results show that our proposed model outperforms other state-of-the-art classifiers, has very high confidence in its predictions, is not biased and can classify both AMPs and non-AMPs for a diverse peptide length with high accuracy. By utilizing AniAMPpred, we identified 436 PAPs in the genome of Helobdella robusta. To further confirm the functional activity of PAPs, we performed BLAST analysis against known AMPs. On detailed analysis of five selected PAPs, we could observe their similarity with antimicrobial proteins of several animal species. Thus, our proposed model can help the researchers identify PAPs in the genome of animals and provide insight into the functional identity of different proteins. An online prediction server is also developed based on the proposed approach, which is freely accessible at https://aniamppred.anvil.app/.


Assuntos
Peptídeos Antimicrobianos/química , Peptídeos Antimicrobianos/farmacologia , Inteligência Artificial , Biologia Computacional/métodos , Descoberta de Drogas/métodos , Algoritmos , Animais , Bases de Dados Genéticas , Genoma , Genômica/métodos , Aprendizado de Máquina , Filogenia , Curva ROC , Reprodutibilidade dos Testes , Navegador , Fluxo de Trabalho
6.
Brief Bioinform ; 22(5)2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-33784381

RESUMO

The overuse of antibiotics has led to emergence of antimicrobial resistance, and as a result, antibacterial peptides (ABPs) are receiving significant attention as an alternative. Identification of effective ABPs in lab from natural sources is a cost-intensive and time-consuming process. Therefore, there is a need for the development of in silico models, which can identify novel ABPs in protein sequences for chemical synthesis and testing. In this study, we propose a deep learning classifier named Deep-ABPpred that can identify ABPs in protein sequences. We developed Deep-ABPpred using bidirectional long short-term memory algorithm with amino acid level features from word2vec. The results show that Deep-ABPpred outperforms other state-of-the-art ABP classifiers on both test and independent datasets. Our proposed model achieved the precision of approximately 97 and 94% on test dataset and independent dataset, respectively. The high precision suggests applicability of Deep-ABPpred in proposing novel ABPs for synthesis and experimentation. By utilizing Deep-ABPpred, we identified ABPs in the tail protein sequences of Streptococcus bacteriophages, chemically synthesized identified peptides in lab and tested their activity in vitro. These ABPs showed potent antibacterial activity against selected Gram-positive and Gram-negative bacteria, which confirms the capability of Deep-ABPpred in identifying novel ABPs in protein sequences. Based on the proposed approach, an online prediction server is also developed, which is freely accessible at https://abppred.anvil.app/. This web server takes the protein sequence as input and provides ABPs with high probability (>0.95) as output.


Assuntos
Antibacterianos/química , Antibacterianos/farmacologia , Aprendizado Profundo , Peptídeos/química , Peptídeos/farmacologia , Sequência de Aminoácidos , Antibacterianos/síntese química , Biologia Computacional/métodos , Farmacorresistência Bacteriana/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Peptídeos/síntese química , Fagos de Streptococcus/química , Proteínas da Cauda Viral/química
7.
J Assoc Physicians India ; 71(12): 56-61, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38736055

RESUMO

INTRODUCTION: Hypertension (HTN) remains one of the most important risk factors for cardiovascular (CV) diseases and a leading cause of mortality worldwide. Despite improvement in detection and treatment, poor blood pressure (BP) control rates are observed globally. The situation in India is alarming with only 22.5% of patients maintaining their BP under control. Initiating early and effective treatment for HTN helps control BP within normal limits and reduces associated health risks. In India, currently, there are no guidelines on the choice of dual combination treatment that can be considered an initial treatment for newly diagnosed HTN patients to achieve effective BP control and reduce CV risks. OBJECTIVE: To provide consensus recommendations for preferred initial combinations in newly diagnosed Indian patients with HTN. METHODOLOGY: A core group of 100 experts with HTN expertise conceptualized and formulated the four key questions based on answerability, effectiveness, potential for translation to clinical practice, novelty, and potential impact on the healthcare burden. A mix of Delphi and Child Health and Nutrition Research Initiative (CHNRI) methods was adopted for acceptance or refusal of recommendations. Likert scale 1-9 was used for scoring. A score of ≥7 was considered "statement accepted," >6.50 "near to acceptance" and <6.50 "not accepted." A vote of ≥7 by at least two-thirds of the experts (66.66%) was mandatory for acceptance of the recommendation. CONCLUSION: Combination therapy could be necessary for a majority of newly diagnosed Indian patients for effective BP control. It can manage HTN with better clinical outcomes. Based on mean rating scores from experts, telmisartan plus amlodipine can be considered the preferred initial combination in the management of newly diagnosed Indian patients with HTN to achieve better BP control and improve CV outcomes.


Assuntos
Anlodipino , Anti-Hipertensivos , Hipertensão , Telmisartan , Humanos , Hipertensão/tratamento farmacológico , Anlodipino/administração & dosagem , Anlodipino/uso terapêutico , Índia , Telmisartan/administração & dosagem , Anti-Hipertensivos/uso terapêutico , Anti-Hipertensivos/administração & dosagem , Consenso , Combinação de Medicamentos , Benzimidazóis/administração & dosagem , Benzimidazóis/uso terapêutico , Quimioterapia Combinada , Benzoatos/administração & dosagem , Benzoatos/uso terapêutico
8.
Adv Exp Med Biol ; 1345: 165-191, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34582023

RESUMO

Biomaterials science encompasses elements of medicine, biology, chemistry, materials, and tissue engineering. They are engineered to interact with biological systems to treat, augment, repair, or replace lost tissue function. The choice of biomaterial depends on the procedure being performed, the severity of the patient's condition, and the surgeon's preference. Prostheses made from natural-derived biomaterials are often derived from decellularized extracellular matrix (ECM) of animal (xenograft) or human (allograft) origin. Advantages of using ECM include their resemblance in morphology and three-dimensional structures with that of tissue to be replaced. Due to this, scientists all over are now focusing on naturally derived biomaterials which have been shown to possess several advantages compared to synthetic ones, owing to their biocompatibility, biodegradability, and remodeling properties. Advantages of a naturally derived biomaterial enhance their application for replacement or restoration of damaged organs/tissues. They adequately support cell adhesion, migration, proliferation, and differentiation. Naturally derived biomaterials can induce extracellular matrix formation and tissue repair when implanted into a defect by enhancing attachment and migration of cells from surrounding environment. In the current chapter, we will focus on the natural and synthetic dermal matrix development and all of the progress in this field.


Assuntos
Engenharia Tecidual , Alicerces Teciduais , Animais , Materiais Biocompatíveis , Adesão Celular , Matriz Extracelular , Humanos
9.
Microb Pathog ; 140: 103949, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31875517

RESUMO

Peste des petits ruminant (PPR), a highly contagious viral disease of small ruminants, is characterized by erosive stomatitis and pneumo-enteritis. However, its neurovirulence potential as observed with other morbilliviruses has not been fully investigated. The present study describes the neuropathological alterations induced by PPR virus through apoptotic pathway. A total number of 12 carcasses of local breed goat kids of either sex were received for postmortem examination. The clinical history was described as symptoms of mucopurulent nasal discharge, high to low grade fever, erosive stomatitis, dyspnoea and profuse watery diarrhoea followed by mortality of 35 goat kids within a week. The pathoanatomical lesions and immunohistochemical demonstration of PPRV antigen in lungs, intestine, spleen and lymph nodes confirmed PPR disease in goats. Grossly, five brain specimens showed moderate to severe leptomeningeal congestion during necropsy. Microscopically, brain sections showed leptomeningitis and nonsuppurative encephalitis characterized by vascular congestion, haemorrhages in the parenchyma, perivascular cuffing with mild to moderate mononuclear cells (mainly lymphocytes and few macrophages), focal to diffuse microgliosis, neuronal degeneration, satellitosis and neuronophagia. Immunolabelling of viral antigen was observed in the cytoplasm of neurons and glial cells. The RT-PCR amplification of N gene fragment also confirmed the presence of PPRV in the brain. The strong immunoreactivity of Caspase-3, Caspase-8 and comparatively lower expression of caspase-9 along with the absence of any reactivity for Apaf-1 antigen in the brain sections indicated the role of caspase dependent extrinsic pathway in inducing neuropathological changes. The presence of apoptotic neurons in the brain by TUNEL assay further confirmed the apoptosis and strong immunoreactivity of iNOS in neurons which suggested the generation of oxidative stress, that might have induced the apoptosis. The overall findings confirm the neurovirulence potential of PPR virus, via the extrinsic pathway of apoptosis, in natural cases of PPR disease in goat kids.


Assuntos
Caspases/metabolismo , Doenças das Cabras/enzimologia , Peste dos Pequenos Ruminantes/enzimologia , Animais , Apoptose , Encéfalo/enzimologia , Encéfalo/patologia , Encéfalo/virologia , Caspases/genética , Feminino , Doenças das Cabras/patologia , Doenças das Cabras/fisiopatologia , Doenças das Cabras/virologia , Cabras , Pulmão/enzimologia , Pulmão/patologia , Pulmão/virologia , Masculino , Neuropatologia , Peste dos Pequenos Ruminantes/patologia , Peste dos Pequenos Ruminantes/fisiopatologia , Peste dos Pequenos Ruminantes/virologia , Vírus da Peste dos Pequenos Ruminantes/fisiologia , Baço/enzimologia , Baço/patologia , Baço/virologia
10.
Arch Virol ; 163(9): 2359-2368, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29736673

RESUMO

Canine parvovirus (CPV) is the leading viral cause of enteritis in dogs and occurs mainly in 6- to 8-week-old pups. Rapid diagnosis of CPV under field conditions is now possible due to commercially available immunochromatographic (IC) assays. However, these commercial kits are somewhat expensive because they utilize a minimum of two monoclonal antibodies (mAbs) targeting different epitopes as capture and detector antibodies. Using only a single mAb for both capture and detection purpose may reduce the sensitivity of the assay. In the present study, efforts were made to develop an economical assay that can be utilized for diagnosis of CPV under Indian conditions with a high level of confidence. Rabbit polyclonal antibodies (pAbs) generated against recombinant truncated VP2 proteins of CPV were used as capture antibodies because they can be produced economically, while a commercial anti-CPV mAb was used as the detector antibody. The detection limit of the test strip was 6.6×105 TCID50/ml, and it specifically detected CPV-2, CPV-2a and CPV-2b while displaying no cross-reactivity with other common canine enteric pathogens. The relative sensitivity/specificity of pAb based strip test was 71%/92% and 71%/100% in relation to the hemagglutination test and a commercial IC kit, respectively, with substantial agreement. In addition, two commercially available mAbs targeting different epitopes were also used for development of another IC assay, which showed sensitivity, and specificity of 82%/87% and 90%/98% in relation to the hemagglutination test and commercial kit. Hence, the present strip test based on a combination of mAb and pAb provides an acceptable alternative for onsite and cost-effective diagnosis of CPV infection.


Assuntos
Doenças do Cão/virologia , Ouro/química , Imunoensaio/métodos , Nanopartículas Metálicas/química , Infecções por Parvoviridae/diagnóstico , Parvovirus Canino/isolamento & purificação , Animais , Anticorpos Monoclonais/análise , Anticorpos Antivirais/sangue , Doenças do Cão/sangue , Doenças do Cão/diagnóstico , Cães , Imunoensaio/instrumentação , Masculino , Infecções por Parvoviridae/sangue , Infecções por Parvoviridae/virologia , Parvovirus Canino/genética , Parvovirus Canino/imunologia , Coelhos , Sensibilidade e Especificidade
11.
Artigo em Inglês | MEDLINE | ID: mdl-28346717

RESUMO

Antimicrobial peptides (AMPs) from cuticular extracts of worker ants of Trichomyrmex criniceps (Mayr, Hymenoptera: Formicidae) were isolated and evaluated for their antimicrobial activity. Eight peptides ranging in mass from 804.42 to 1541.04 Da were characterized using a combination of analytical and bioinformatics approach. All the eight peptides were novel with no similarity to any of the AMPs archived in the Antimicrobial Peptide Database. Two of the eight novel peptides, the smallest and the largest by mass were named Crinicepsin-1 and Crinicepsin-2 and were chemically synthesized by solid phase peptide synthesis. The two synthetic peptides had antibacterial and weak hemolytic activity.


Assuntos
Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Formigas/química , Proteínas de Insetos/farmacologia , Oligopeptídeos/farmacologia , Animais , Antibacterianos/síntese química , Antibacterianos/isolamento & purificação , Peptídeos Catiônicos Antimicrobianos/síntese química , Peptídeos Catiônicos Antimicrobianos/isolamento & purificação , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Hemólise , Humanos , Proteínas de Insetos/síntese química , Proteínas de Insetos/isolamento & purificação , Oligopeptídeos/síntese química , Oligopeptídeos/isolamento & purificação , Extratos de Tecidos/química
12.
Indian Heart J ; 65(3): 286-8, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23809383

RESUMO

The last two decades have witnessed vast advances in the field of cardiac intervention, particularly with regard to nonsurgical closure of structural heart diseases including para prosthetic valvular leaks. The use of imaging techniques to guide even well-established procedures enhances the efficiency and safety of these procedures. The present case report aims to highlight the role of three dimensional transesophageal echocardiography in pre, intra and post operative management of patients with mitral para prosthetic valvular regurgitation.


Assuntos
Ecocardiografia Tridimensional/métodos , Ecocardiografia Transesofagiana/métodos , Implante de Prótese de Valva Cardíaca/efeitos adversos , Insuficiência da Valva Mitral/cirurgia , Hemorragia Pós-Operatória/diagnóstico por imagem , Hemorragia Pós-Operatória/terapia , Deiscência da Ferida Operatória/cirurgia , Adulto , Humanos , Masculino , Valva Mitral/diagnóstico por imagem , Valva Mitral/cirurgia , Dispositivo para Oclusão Septal , Ultrassonografia de Intervenção
13.
Artigo em Inglês | MEDLINE | ID: mdl-37115837

RESUMO

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.

14.
Artigo em Inglês | MEDLINE | ID: mdl-37018101

RESUMO

Low hemolytic therapeutic peptides have gained an edge over small molecule-based medicines. However, finding low hemolytic peptides in laboratory is time-consuming, costly and necessitates the use of mammalian red blood cells. Therefore, wet-lab researchers often perform in-silico prediction to select low hemolytic peptides before proceeding with in-vitro testing. The in-silico tools available for this purpose have following limitations: (i) They do not provide predictions for peptides having N/C terminal modifications. (ii) Data is food for AI; however, datasets used to create existing tools do not contain peptide data generated over past eight years. (iii) Performance of available tools is also low. Therefore, a novel framework has been proposed in current work. Proposed framework utilizes recent dataset and uses ensemble learning technique to combine the decisions produced by bidirectional long short-term memory, bidirectional temporal convolutional network, and 1-dimensional convolutional neural network deep learning algorithms. Deep learning algorithms are capable of extracting features themselves from data. However, instead of relying solely on deep learning-based features (DLF), handcrafted features (HCF) were also provided so that deep learning algorithms can learn features that are missing from HCF, and a better feature vector can be constructed by concatenating HCF and DLF. Additionally, ablation studies were carried out to understand the roles of an ensemble algorithm, HCF, and DLF in the proposed framework. Ablation studies found that the ensemble algorithm, HCF and DLF are crucial components of proposed framework, and there is a decrease in performance on eliminating any of them. Mean value of performance metrics, namely Acc, Sn, Pr, Fs, Sp, Ba, and Mcc obtained by proposed framework for test data is ≈ 87, 85, 86, 86, 88, 87, and 73, respectively. To aid scientific community, model developed from proposed framework has been deployed as a web server at https://endl-hemolyt.anvil.app/.

15.
Vaccines (Basel) ; 11(4)2023 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-37112793

RESUMO

Hyalomma anatolicum is the principal vector for Theileria annulata, T. equi, and T. Lestoquardi in animals and the Crimean-Congo hemorrhagic fever virus in humans. Due to the gradual loss of efficacy of the available acaricides against field tick populations, the development of phytoacaricides and vaccines has been considered the two most critical components of the integrated tick management strategies. In the present study, in order to induce both cellular and humoral immune responses in the host against H. anatolicum, two multi-epitopic peptides (MEPs), i.e., VT1 and VT2, were designed. The immune-stimulating potential of the constructs was determined by in silicoinvestigation on allergenicity (non-allergen, antigenic (0.46 and 1.0046)), physicochemical properties (instability index 27.18 and 35.46), as well as the interaction of constructs with TLRs by docking and molecular dynamics analysis. The immunization efficacy of the MEPs mixed with 8% MontanideTM gel 01 PR against H. anatolicum larvae was determined as 93.3% and 96.9% in VT1- and VT2-immunized rabbits, respectively. Against adults, the efficacy was 89.9% and 86.4% in VT1- and VT2-immunized rabbits, respectively. A significant (p < 0.001) reduction in the anti-inflammatory cytokine (IL-4) and significantly higher IgG response was observed in a VT1-immunized group of rabbits as compared with the response observed in the control group. However, in the case of the VT2-immunized rabbits, an elevated anti-VT2 IgG and pro-inflammatory cytokine (IL-2) (>30 fold) along with a decreased level of anti-inflammatory cytokine IL-4 (0.75 times) was noted. The efficacy of MEP and its potential immune stimulatory responses indicate that it might be useful for tick management.

16.
Poult Sci ; 102(6): 102679, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37116285

RESUMO

An immunization experiment was conducted in specific pathogen-free chickens with the inactivated Newcastle disease virus (NDV) vaccine encapsulated in the poly-(lactic-co-glycolic) acid (PLGA) nanoparticles (NP) to evaluate its immunogenicity and protective efficacy. The NDV vaccine was prepared by inactivating one virulent Indian strain of NDV belonging to Genotype VII by using beta-propiolactone. PLGA nanoparticles encapsulating inactivated NDV were prepared by the solvent evaporation method. Scanning electron microscopy and zeta sizer analysis revealed that the (PLGA+NDV) NP were spherical, with an average size of 300 nm, having a zeta potential of -6 mV. The encapsulation efficiency and loading efficiency were 72% and 2.4%, respectively. On immunization trial in chicken, the (PLGA+NDV) NP induced significantly (P < 0.0001) higher levels of HI and IgY antibodies with the peak HI titer of 28 and higher expression of IL-4 mRNA. The consistency of higher antibody levels suggests slow and pulsatile release of the antigens from the (PLGA+NDV) NP. The nano-NDV vaccine also induced cell mediated immunity with higher expression of IFN-γ indicating strong Th1 mediated immune responses in contrast to the commercial oil adjuvanted inactivated NDV vaccine. Further, the (PLGA+NDV) NP afforded 100% protection against the virulent NDV challenge. Our results suggested that PLGA NP have adjuvant potential on induction of humoral as well as Th1 biased cell mediated immune responses and also enhanced protective efficacy of the inactivated NDV vaccine. This study provides an insight for development of PLGA NP based inactivated NDV vaccine using the same genotype circulating in the field as well as for other avian diseases at exigencies.


Assuntos
Nanopartículas , Doença de Newcastle , Vacinas Virais , Animais , Vírus da Doença de Newcastle , Doença de Newcastle/prevenção & controle , Galinhas , Vacinas de Produtos Inativados , Glicóis , Adjuvantes Imunológicos , Imunidade Celular
17.
IEEE J Biomed Health Inform ; 26(10): 5067-5074, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-34822333

RESUMO

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- α 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.


Assuntos
Inteligência Artificial , COVID-19 , Animais , Antivirais/química , Antivirais/farmacologia , Antivirais/uso terapêutico , Humanos , Interferons , Pandemias , Peptídeos/química , Peptídeos/farmacologia , Peptídeos/uso terapêutico
18.
Indian Heart J ; 62(4): 324-9, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-21280473

RESUMO

BACKGROUND: Recently, a concept of multi-drug treatment of all individuals in the form of a polypill, irrespective of their risk factor profile, has been proposed with a view to provide an effective means for prevention of cardiovascular disease (CVD). While the rationale, benefits and ethicality of such an approach continue to remain a matter ofdebate, it is not known what proportion of asymptomatic adult population does actually require pharmacological therapy for primary prevention of CVD according to the existing guidelines. METHODS: 1927 consecutive office executives, free of any CVD, undergoing routine health check-up at a tertiary care centre in North-India during the year 2005 were included in the study. For all subjects, information was collected based on their case-records comprising of comprehensive clinical evaluation and the results of biochemical investigations. Requirement of treatment with three anti-atherosclerotic drugs- aspirin, statin and an anti-hypertensive agent was estimated as per the current guidelines. RESULTS: Mean age of the subjects was 45.2 +/- 10.3 years and 71.6% were males. Diabetes was present in 14.3%, hypertension in 46.3% and dyslipidemia in 76.0%. Metabolic syndrome was diagnosed in 47.5% subjects. According to the currently accepted guidelines, 47.0% of all the individuals were candidates for at least one of the three aforementioned drugs--22.9% needed only one drug, 17.8% needed only two drugs and 6.3% needed all the three drugs. Requirement of the treatment was much higher in the highest age-tertile (>50 years of age) with 78.0% needing at least one medication, 45.1% needing at least two medications and 12.6% needing all the three drugs (p value < 0.001). Of the different drugs, aspirin was the most commonly required medicine (38.3% of all) and a combination of aspirin and statin was the most commonly required two-drug combination. CONCLUSIONS: The present study shows that, in spite of high prevalence of CV risk factors, a majority of office-executives who are free of CVD do not require multi-drug therapy for primary prevention of CVD as per the current recommendations. Though a greater proportion of the individuals > 50 years of age require drug therapy, even among them, a triple-drug combination is warranted only in a small proportion of subjects. When needed, a combination of statin and aspirin is the most commonly required combination.


Assuntos
Anti-Hipertensivos/administração & dosagem , Aspirina/administração & dosagem , Doenças Cardiovasculares/prevenção & controle , Inibidores de Hidroximetilglutaril-CoA Redutases/administração & dosagem , Prevenção Primária , Adulto , Análise de Variância , Doenças Cardiovasculares/epidemiologia , Distribuição de Qui-Quadrado , Comorbidade , Quimioterapia Combinada , Feminino , Humanos , Índia/epidemiologia , Masculino , Pessoa de Meia-Idade , Prevalência , Estudos Retrospectivos , Fatores de Risco
20.
J Tissue Eng Regen Med ; 14(12): 1763-1778, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32931632

RESUMO

Bioengineered scaffolds derived from the decellularized extracellular matrix (ECM) obtained from discarded animal organs and tissues are attractive candidates for regenerative medicine applications. Tailoring these scaffolds with stem cells enhances their regeneration potential making them a suitable platform for regenerating damaged tissues. Thus, the study was designed to investigate the potential of mesenchymal stem cells tailored acellular bubaline diaphragm and aortic ECM for the repair of full-thickness abdominal wall defects in a rabbit model. Tissues obtained from bubaline diaphragm and aorta were decellularized and bioengineered by seeding with rabbit bone marrow derived mesenchymal stem cells (r-BMSC). Full-thickness abdominal wall defects of 3 cm × 4 cm size were created in a rabbit model and repaired using five different prostheses, namely, polypropylene sheet, nonseeded diaphragm ECM, nonseeded aorta ECM, r-BMSC bioengineered diaphragm ECM, and r-BMSC bioengineered aorta ECM. Results from the study revealed that biological scaffolds are superior in comparison to synthetic polymer mesh for regeneration in terms of collagen deposition, maturation, neovascularization, and lack of any significant (P > 0.05) adhesions with the abdominal viscera. Seeding with r-BMSC significantly increased (P < 0.05) the collagen deposition and biomechanical strength of the scaffolds. The bioengineered r-BMSC seeded acellular bubaline diaphragm showed even superior biomechanical strength as compared to synthetic polymer mesh. Tailoring of the scaffolds with the r-BMSC also resulted in significant reduction (P < 0.01) in antibody and cell mediated immune reactions to the xenogeneic scaffolds in rabbit model.


Assuntos
Parede Abdominal/patologia , Aorta/fisiologia , Bioengenharia , Diafragma/fisiologia , Células-Tronco Mesenquimais/citologia , Regeneração/fisiologia , Alicerces Teciduais/química , Adipogenia , Animais , Fenômenos Biomecânicos , Búfalos , Bovinos , Linhagem da Célula , Condrogênese , Colágeno/metabolismo , DNA/metabolismo , Matriz Extracelular/metabolismo , Implantes Experimentais , Osteogênese , Coelhos , Dodecilsulfato de Sódio , Aderências Teciduais/patologia , Água
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