MolDy: molecular dynamics simulation made easy.

MOTIVATION: Molecular dynamics (MD) is a computational experiment that is crucial for understanding the structure of biological macro and micro molecules, their folding, and the inter-molecular interactions. Accurate knowledge of these structural features is the cornerstone in drug development and elucidating macromolecules functions. The open-source GROMACS biomolecular MD simulation program is recognized as a reliable and frequently used simulation program for its precision. However, the user requires expertise, and scripting skills to carrying out MD simulations. RESULTS: We have developed an end-to-end interactive MD simulation application, MolDy for Gromacs. This front-end application provides a customizable user interface integrated with the Python and Perl-based logical backend connecting the Linux shell and Gromacs software. The tool performs analysis and provides the user with simulation trajectories and graphical representations of relevant biophysical parameters. The advantages of MolDy are (i) user-friendly, does not requiring the researcher to have prior knowledge of Linux; (ii) easy installation by a single command; (iii) freely available for academic research; (iv) can run with minimum configuration of operating systems; (v) has valid default prefilled parameters for beginners, and at the same time provides scope for modifications for expert users. AVAILABILITY AND IMPLEMENTATION: MolDy is available freely as compressed source code files with user manual for installation and operation on GitHub: https://github.com/AIBResearchMolDy/Moldyv01.git and on https://aibresearch.com/innovations.

A Unique Case of Eight Fetuses in a Single Fetu.

Fetus in fetu is a rare congenital anomaly in which a malformed parasitic twin is found within the body of a living child or adult. In this case report, a 1-day-old child presented with a large firm abdominal mass on the left side of the upper abdomen. Imaging studies misdiagnosed the mass as an intraperitoneal benign dermoid cyst displacing the bowel loops and internal viscera. A surgical resection was performed on 21 days of life, and pathology confirmed eight fetuses inside the cyst.

Nanomedicine for glioblastoma: Progress and future prospects.

Glioblastoma is the most aggressive form of brain tumor, accounting for the highest mortality and morbidity rates. Current treatment for patients with glioblastoma includes maximal safe tumor resection followed by radiation therapy with concomitant temozolomide (TMZ) chemotherapy. The addition of TMZ to the conformal radiation therapy has improved the median survival time only from 12 months to 16 months in patients with glioblastoma. Despite these aggressive treatment strategies, patients' prognosis remains poor. This therapeutic failure is primarily attributed to the blood-brain barrier (BBB) that restricts the transport of TMZ from reaching the tumor site. In recent years, nanomedicine has gained considerable attention among researchers and shown promising developments in clinical applications, including the diagnosis, prognosis, and treatment of glioblastoma tumors. This review sheds light on the morphological and physiological complexity of the BBB. It also explains the development of nanomedicine strategies to enhance the permeability of drug molecules across the BBB.

Skin cancer: understanding the journey of transformation from conventional to advanced treatment approaches.

Skin cancer is a global threat to the healthcare system and is estimated to incline tremendously in the next 20 years, if not diagnosed at an early stage. Even though it is curable at an early stage, novel drug identification, clinical success, and drug resistance is another major challenge. To bridge the gap and bring effective treatment, it is important to understand the etiology of skin carcinoma, the mechanism of cell proliferation, factors affecting cell growth, and the mechanism of drug resistance. The current article focusses on understanding the structural diversity of skin cancers, treatments available till date including phytocompounds, chemotherapy, radiotherapy, photothermal therapy, surgery, combination therapy, molecular targets associated with cancer growth and metastasis, and special emphasis on nanotechnology-based approaches for downregulating the deleterious disease. A detailed analysis with respect to types of nanoparticles and their scope in overcoming multidrug resistance as well as associated clinical trials has been discussed.

A Comprehensive review on Pharmacokinetic Studies of Vaccines: Impact of delivery route, carrier-and its modulation on immune response.

The lack of knowledge about the absorption, distribution, metabolism, and excretion (ADME) of vaccines makes former biopharmaceutical optimization difficult. This was shown during the COVID-19 immunization campaign, where gradual booster doses were introduced.. Thus, understanding vaccine ADME and its effects on immunization effectiveness could result in a more logical vaccine design in terms of formulation, method of administration, and dosing regimens. Herein, we will cover the information available on vaccine pharmacokinetics, impacts of delivery routes and carriers on ADME, utilization and efficiency of nanoparticulate delivery vehicles, impact of dose level and dosing schedule on the therapeutic efficacy of vaccines, intracellular and endosomal trafficking and in vivo fate, perspective on DNA and mRNA vaccines, new generation sequencing and mathematical models to improve cancer vaccination and pharmacology, and the reported toxicological study of COVID-19 vaccines. Altogether, this review will enhance the reader's understanding of the pharmacokinetics of vaccines and methods that can be implied in delivery vehicle design to improve the absorption and distribution of immunizing agents and estimate the appropriate dose to achieve better immunogenic responses and prevent toxicities.

Advanced multifunctional nano-lipid carrier loaded gel for targeted delivery of 5-flurouracil and cannabidiol against non-melanoma skin cancer.

Non-melanoma skin cancer is one of the most common malignancies reported around the globe. Current treatment therapies fail to meet the desired therapeutic efficacy due to high degree of drug resistance. Thus, there is prominent demand in advancing the current conventional therapy to achieve desired therapeutic efficacy. To break the bottleneck, nanoparticles have been used as next generation vehicles that facilitate the efficient interaction with the cancer cells. Here, we developed combined therapy of 5-fluorouracil (5-FU) and cannabidiol (CBD)-loaded nanostructured lipid carrier gel (FU-CBD-NLCs gel). The current investigation has been designed to evaluate the safety and efficacy of developed 5-Flurouracil and cannabidiol loaded combinatorial lipid-based nanocarrier (FU-CBD NLCs) gel for the effective treatment of skin cancer. Initially, confocal microscopy study results showed excellent uptake and deposition at epidermal and the dermal layer. Irritation studies performed by IR camera and HET cam shows FU-CBD NLCs was much more tolerated and less irritant compared to conventional treatment. Furthermore, gamma scintigraphy evaluation shows the skin retention behavior of the formulation. Later, in-ovo tumor remission studies were performed, and it was found that prepared FU-CBD NLCs was able to reduce tumor volume significantly compared to conventional formulation. Thus, obtained results disclosed that permeation and disposition of 5-FU and CBD into different layers of the skin FU-CBD NLCs gel could be more potential carrier than conventional gel. Furthermore, prepared formulation showed greater tumor remission, better survival rate, reduction in tumor number, area, and volume with improved biochemical profile. Thus, prepared gel could serve as a promising formulation approach for the skin cancer treatment.

Advanced targeted drug delivery by bioengineered white blood cell-membrane camouflaged nanoparticulate delivery nanostructures.

Targeted drug delivery has emerged as a pivotal approach within precision medicine, aiming to optimize therapeutic efficacy while minimizing systemic side effects. Leukocyte membrane coated nanoparticles (NPs) have attracted a lot of interest as an effective approach for delivering targeted drugs, capitalizing on the natural attributes of leukocytes to achieve site-specific accumulation, and heightened therapeutic outcomes. An overview of the present state of the targeted medication delivery research is given in this review. Notably, Leukocyte membrane-coated NPs offer inherent advantages such as immune evasion, extended circulation half-life, and precise homing to inflamed or diseased tissues through specific interactions with adhesion molecules. leukocyte membrane-coated NPs hold significant promise in advancing targeted drug delivery for precision medicine. As research progresses, they are anticipated to contribute to improved therapeutic outcomes, enabling personalized and effective treatments for a wide range of diseases and conditions. The review covers the method of preparation, characterization, and biological applications of leucocytic membrane coated NPs. Further, patents related factors, gap of translation from laboratory to clinic, and future prospective were discussed in detail. Overall, the review covers extensive literature to establish leucocytic membrane NPs for targeted drug delivery.

Porous MgNiO2 Chrysanthemum Flower Nanostructure Electrode for Toxic Hg2+ Ion Monitoring in Aquatic Media.

A simple hydrothermal synthesis approach was used to synthesize porous MgNiO2 Chrysanthemum Flowers (CFs) nanostructures and applied as a sensing electrode for quick detection of hazardous mercury (Hg2+ ions). The morphological, structural, and electrochemical properties of MgNiO2 CFs were investigated. The morphological characteristic of MgNiO2 CFs, with a specific surface area of 45.618 m2/g, demonstrated strong electrochemical characteristics, including cations in different oxidation states of Ni3+/Ni2+. Using a three-electrode system for electrochemical detection, the MgNiO2 CFs based electrode revealed a good correlation coefficient (R2) of ~0.9721, a limit of detection (LOD) of ~11.7 µM, a quick response time (10 s), and a sensitivity of 8.22 µA∙µM-1∙cm-2 for Hg2+ ions over a broad linear range of 10-100 µM. Moreover, the selectivity for Hg2+ ions in tap water and drinking water was determined, and a promising stability of 25 days by MgNiO2 CFs electrode was exhibited. The obtained results indicate that the developed MgNiO2 CFs are a promising electrode for detecting hazardous Hg2+ ions in water and have the potential to be commercialized in the future.

Exploring the Remarkable Chemotherapeutic Potential of Polyphenolic Antioxidants in Battling Various Forms of Cancer.

Plant-derived compounds, specifically antioxidants, have played an important role in scavenging the free radicals present under diseased conditions. The persistent generation of free radicals in the body leads to inflammation and can result in even more severe diseases such as cancer. Notably, the antioxidant potential of various plant-derived compounds prevents and deregulates the formation of radicals by initiating their decomposition. There is a vast literature demonstrating antioxidant compounds' anti-inflammatory, anti-diabetic, and anti-cancer potential. This review describes the molecular mechanism of various flavonoids, such as quercetin, kaempferol, naringenin, epicatechin, and epicatechin gallate, against different cancers. Additionally, the pharmaceutical application of these flavonoids against different cancers using nanotechnologies such as polymeric, lipid-based nanoparticles (solid-lipid and liquid-lipid), liposomes, and metallic nanocarriers is addressed. Finally, combination therapies in which these flavonoids are employed along with other anti-cancer agents are described, indicating the effective therapies for the management of various malignancies.

In-Silico Analysis of Phytocompounds of Olea europaea as Potential Anti-Cancer Agents to Target PKM2 Protein.

Globally, cancer is the second leading cause of mortality and morbidity. The growth and development of cancer are extremely complex. It is caused by a variety of pathways and involves various types of enzymes. Pyruvate kinase M2 (PKM2) is an isoform of pyruvate kinase, that catalyses the last steps of glycolysis to produce energy. PKM2 is relatively more expressed in tumour cells where it tends to exist in a dimer form. Various medicinal plants are available that contain a variety of micronutrients to combat against different cancers. The phytocompounds of the olive tree (Olea europaea) leaves play an important role in inhibiting the proliferation of several cancers. In this study, the phytocompounds of olive leaf extract (OLE) were studied using various in silico tools, such as pkCSM software to predict ADMET properties and PASS Online software to predict anticancer activity. However, the molecular docking study provided the binding energies and inhibition constant and confirmed the interaction between PKM2 and the ligands. The dynamic behaviour, conformational changes, and stability between PKM2 and the top three hit compounds (Verbascoside (Ver), Rutin (Rut), and Luteolin_7_O_glucoside (Lut)) are studied by MD simulations.

Culture conversion and six months interim outcomes in retreatment cases of pulmonary MDRTB - a six month interim analysis.

OBJECTIVE: To estimate the time to culture conversion and factors associated with failure to culture conversion, six-month interim outcomes and associated risk factors with poor interim outcomes in multi-drug resistant tuberculosis patients previously treated with second-line drugs. METHODS: The prospective clinical case series study was conducted from March 2016 to January 2017 at the Indus Hospital Tuberculosis Clinic and seven other sites that are part of the hospital's Programmatic Management of Drug Resistant Tuberculosis initiative. All bacteriologically confirmed multi-drug resistant tuberculosis retreatment patients were enrolled. Data was collected on age, gender, site of enrollment, detailed history of previous treatment with anti-tuberculosis drugs, medical history, history of first-line drugs, history of second-line drugs, treatment outcomes, baseline sputum smear microscopy and monthly follow-up sputum smear microscopy and culture results. Data was subjected to univariate and multiple logistic regression analyses, and risk factors for failure to culture conversion were assessed using Cox Proportional Hazards Model. RESULTS: Out of 266 patients, 143(53.8%) were males, the overall largest age group was 5-24 years 97(36.5%), and 250 (94%) patients had previous history of treatment with first-line drugs. Overall, 101(40.1%) patients experienced poor interim outcome. Poor interim outcomes were significantly associated with higher number of drugs on the regimen, (odds ratio: 1.27; 95% confidence interval: 1.03-1.58) and high sputum smear grading (odds ratio: 4.56; 95% confidence interval: 3.30-18.71). Besides, 186(70.3%) patients experienced culture conversion within the initial six months of treatment. CONCLUSIONS: The success rate of re-treatment of multi-drug resistant tuberculosis with conventional regimen was found to be unacceptably low.

Enzyme targeting strategies for prevention and treatment of cancer: Implications for cancer therapy.

Extensive growth of cancer in humans is a major cause of death. Numerous studies are being conducted to improve the early diagnosis, prevention, and treatment of cancer. Recent technological advancements in medical science and research indicate molecular target therapy holds much promise in cancer treatment. In the past, therapeutic and diagnostic targeting of non-glycolytic and glycolytic enzymes in cancer have been successful, and discoveries of biomarker enzymes in cancer hold promise for therapeutic treatments. In this review, we discuss the roles of several cancer-associated enzymes that could potentially act as therapeutic targets, and place special focus on non-glycolytic and glycolytic enzymes. This review indicates that the targeting of metabolic signaling offers a promising means of developing novel anti-cancer therapies.

Treatment outcomes of the drug resistant tuberculosis cases previously exposed to second line anti Tuberculosis drugs in Pakistan: A multi-center cross-sectional study.

OBJECTIVE: To determine the treatment outcomes of the drug-resistant tuberculosis patients who were previously exposed to second line drugs. METHODS: The retrospective study was conducted at eight Programmatic Management of Drug Resistant Tuberculosis (PMDT) sites in Sindh and Balochistan. Data of patients who were previously exposed to second line drugs and re-enrolled in the drug-resistant tuberculosis register at PMDT sites in Sindh and Balochistan between 2008 and 2016 was included for analysis. Data of those still under treatment or transferred to another treatment site was excluded. Association was explored between treatment outcomes and other independent variables, while in order to identify the risk factors associated with poor treatment outcomes univariate and multivariate logistic regression was used. RESULTS: Overall, there were 3645 patients and 288(8%) were previously exposed to second line drugs. Of them, 95(33%) were excluded, and the final sample stood at 193; 99(51.3%) males and 94(48.7%) females. The median age of the sample was 29 years (inter-quartile range: 22-41 years). The mean duration of treatment was 20}11.14 months. Overall success rate of the re-treatment of previously treated patients was 105(54.4%). Observed relapse rate was 9(4.7%).. CONCLUSIONS: The success rate for re-treatment drug-resistant tuberculosis patients was found to be unacceptably low. New drugs and novel regimens should be made widely available.

Candidiasis: Prevalence and resistance profiling in a tertiary care hospital of Pakistan.

OBJECTIVE: To determine Candida colonisation/infection in renal transplant patients and to determine the resistance pattern against antifungal drugs. METHODS: This prospective, observational study was conducted at Al-Sayyed Hospital, Rawalpindi, Pakistan, from January to October 2014, in collaboration with the Microbiology and Public Health Laboratory's, Islamabad campus..The clinical specimens investigated included respiratory tract secretions, blood, urine, high vaginal swab, skin scrapings, and plastic devices samples. RESULTS: Of the 7,850 samples, 164(2.08%) were positive for Candida. Candida albicans were most prevalent as they were found in 114(69%) samples. Besides, 56(34%) of the positive samples were resistant to one or more antifungal agents. Highest resistance was obtained against fluconazole. We found only 5(3.04%) positive samples of Candida glabrata; of them, 3(60%)were resistant. In case of Candida spp, 27(48%) resistance was observed. In Candida albicans, 23(41%) of the samples were found to be resistant. Most of the Candida isolates was recovered from bronchial alveolar lavage. CONCLUSIONS: Although Candida albicans remained the main responsible species for Candida infections, but non-albican Candida species are also emerging.

AN EXPERIENCE OF BRONCHOTOMY AND RESECTIONAL PROCEDURES AFTER FAILED BRONCHOSCOPIC FOERIGN BODY RETRIEVAL.

BACKGROUND: Foreign body bronchus is a surgical emergency and is associated with a high mortality if neglected or complicated. The objective of this study was to analyse the outcome of bronchotomy and resectional procedures after failed bronchoscopic foreign body retrieval. METHODS: This study of 24 cases of bronchotomy and resectional procedures after failed bronchoscopic foreign body retrieval was done from June 2008 to June 2009 and March 2010 to Sep 2013. Patients after failed retrieval of foreign body by bronchoscopy either by ENT specialists or thoracic surgeons underwent bronchotomy or resectional procedures were included in the study. We used the posterolateral thoracotomy approach for the surgical procedures. RESULTS: Bronchotomy and resectional procedures were done in 24 cases. Age of patients ranged from 2 years to 51 years. Most patients were children and right side was mostly involved. Bronchotomy procedures were 10 (41%) and resectional surgeries were 13 (58%). Emergency lobectonies were 3 out of 13 resectional surgeries. Right intermedius bronchus was opened up and incision was extended in the direction of foreign body in 6 cases and left bronchus intermedius was opened in 4 cases. Haemoptysis was the main symptom in late presenters. Range of objects retrieved in our study was from pins, needles to whistles. CONCLUSION: Retention causes endobronchial obstruction with stasis leading to irreversible damaged parenchyma. Foreign body with structural changes require resection, others can be offered bronchotomy which is a safe procedure for retained non retrievable foreign bodies.

Non-linear modeling using fuzzy principal component regression for Vidyaranyapuram sewage treatment plant, Mysore - India.

Fuzzy principal component regression (FPCR) is proposed to model the non-linear process of sewage treatment plant (STP) data matrix. The dimension reduction of voluminous data was done by principal component analysis (PCA). The PCA score values were partitioned by fuzzy-c-means (FCM) clustering, and a Takagi-Sugeno-Kang (TSK) fuzzy model was built based on the FCM functions. The FPCR approach was used to predict the reduction in chemical oxygen demand (COD) and biological oxygen demand (BOD) of treated wastewater of Vidyaranyapuram STP with respect to the relations modeled between fuzzy partitioned PCA scores and target output. The designed FPCR model showed the ability to capture the behavior of non-linear processes of STP. The predicted values of reduction in COD and BOD were analyzed by performing the linear regression analysis. The predicted values for COD and BOD reduction showed positive correlation with the observed data.

Spectrum of pathologies in cases of intestinal obstruction & perforation based on histopathological examination of resected intestine - Report from a third world country.

BACKGROUND AND OBJECTIVE: Cases presenting with intestinal perforation and obstruction constitute a substantial work load on our surgical service. Etiologies vary in underdeveloped and developed countries. Histopathological examination of resected intestine is expected to provide the definite evidence of the underlying etiology- guiding a better health care planning for preventive measures. Our objective was to study the spectrum of histopathological findings in resected intestines from cases of intestinal obstruction and perforation in our local population to document the underlying etiology. METHODS: A total of 120 cases of intestinal resection were included. Detailed gross and microscopic examination with routine stains was performed. Definite evidence of any specific etiology on the basis of morphology was documented. RESULTS: A total of 95 cases with clinical/radiological diagnosis of obstruction (79.2%) and 25 of intestinal, perforation (20.8%) were included. Tuberculous enteritis was the commonest etiology (n=41; 43.1%) in cases of intestinal obstruction followed by malignant tumours (n=30; 31.5%). ischemic infarct/gangrene, post op illeal adhesions, polyps and ulcerative colitis followed. In cases of perforation, Typhoid enteritis (n=15; 60%), was the commonest pathology followed by idiopathic perforation (n=5; 20%), tuberculous enteritis (n=3;12%), carcinoma (4%) and ulcerative coliti (4%). Conclusion : In developing countries infective etiology remains a dominant cause of intestinal obstruction and perforation. Its presentation in younger age leading to intestinal resection demands effective preventive measures in this part of the world to prevent morbidity and mortality.

Fabrication of Tungsten Oxide Nanowalls through HFCVD for Improved Electrochemical Detection of Methylamine.

In this study, well-defined tungsten oxide (WO3) nanowall (NW) thin films were synthesized via a controlled hot filament chemical vapor deposition (HFCVD) technique and applied for electrochemical detection of methylamine toxic substances. Herein, for the thin-film growth by HFCVD, the temperature of tungsten (W) wire was held constant at ~1450 °C and gasification was performed by heating of W wire using varied substrate temperatures ranging from 350 °C to 450 °C. At an optimized growth temperature of 400 °C, well-defined and extremely dense WO3 nanowall-like structures were developed on a Si substrate. Structural, crystallographic, and compositional characterizations confirmed that the deposited WO3 thin films possessed monoclinic crystal structures of high crystal quality. For electrochemical sensing applications, WO3 NW thin film was used as an electrode, and cyclic voltammetry (CV) and linear sweep voltammetry (LSV) were measured with a wide concentration range of 20 µM~1 mM of methylamine. The fabricated electrochemical sensor achieved a sensitivity of ~183.65 µA mM-1 cm-2, a limit of detection (LOD) of ~20 µM and a quick response time of 10 s. Thus, the fabricated electrochemical sensor exhibited promising detection of methylamine with considerable stability and reproducibility.

Microplastic contaminants detection in aquatic environment by hydrophobic cerium oxide nanoparticles.

Microplastics (MPs) poses a significant threat to ecosystems and human health, demanding immediate attention. The reported research work offers an effective and low cost method towards the detection of toxic MPs. In this study, hydrophobic cerium oxide nanoparticles (CeO2 NPs) are synthesized and applied as promising electrode material for the detection of two different types of MPs, i.e. polyethylene (PE) and polypropylene (PP). Through electrochemical analyses, such as cyclic voltammetry (CV) and linear sweep voltammetry (LSV), hydrophobic CeO2 NPs modified glassy carbon electrode (GCE) based sensor demonstrated remarkable sensitivity of ∼0.0343 AmLmg-1cm-2 and detection limit of ∼0.226 mgmL-1, with promising correlation coefficient (R2) towards the detection of PE (∼27-32 µm). Furthermore, hydrophobic CeO2 NPs modified GCE exhibited promising stability and reproducibility towards PE (∼27-32 µm), suggesting the promising potential of hydrophobic CeO2 NPs as electrode materials for an electrochemical microplastics detection.

Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases.

A biomarker is any measurable biological moiety that can be assessed and measured as a potential index of either normal or abnormal pathophysiology or pharmacological responses to some treatment regimen. Every tissue in the body has a distinct biomolecular make-up, which is known as its biomarkers, which possess particular features, viz., the levels or activities (the ability of a gene or protein to carry out a particular body function) of a gene, protein, or other biomolecules. A biomarker refers to some feature that can be objectively quantified by various biochemical samples and evaluates the exposure of an organism to normal or pathological procedures or their response to some drug interventions. An in-depth and comprehensive realization of the significance of these biomarkers becomes quite important for the efficient diagnosis of diseases and for providing the appropriate directions in case of multiple drug choices being presently available, which can benefit any patient. Presently, advancements in omics technologies have opened up new possibilities to obtain novel biomarkers of different types, employing genomic strategies, epigenetics, metabolomics, transcriptomics, lipid-based analysis, protein studies, etc. Particular biomarkers for specific diseases, their prognostic capabilities, and responses to therapeutic paradigms have been applied for screening of various normal healthy, as well as diseased, tissue or serum samples, and act as appreciable tools in pharmacology and therapeutics, etc. In this review, we have summarized various biomarker types, their classification, and monitoring and detection methods and strategies. Various analytical techniques and approaches of biomarkers have also been described along with various clinically applicable biomarker sensing techniques which have been developed in the recent past. A section has also been dedicated to the latest trends in the formulation and designing of nanotechnology-based biomarker sensing and detection developments in this field.