Predicting Prostate Cancer Molecular Subtype With Deep Learning on Histopathologic Images.

Microscopic examination of prostate cancer has failed to reveal a reproducible association between molecular and morphologic features. However, deep-learning algorithms trained on hematoxylin and eosin (H&E)-stained whole slide images (WSI) may outperform the human eye and help to screen for clinically-relevant genomic alterations. We created deep-learning algorithms to identify prostate tumors with underlying ETS-related gene (ERG) fusions or PTEN deletions using the following 4 stages: (1) automated tumor identification, (2) feature representation learning, (3) classification, and (4) explainability map generation. A novel transformer-based hierarchical architecture was trained on a single representative WSI of the dominant tumor nodule from a radical prostatectomy (RP) cohort with known ERG/PTEN status (n = 224 and n = 205, respectively). Two distinct vision transformer-based networks were used for feature extraction, and a distinct transformer-based model was used for classification. The ERG algorithm performance was validated across 3 RP cohorts, including 64 WSI from the pretraining cohort (AUC, 0.91) and 248 and 375 WSI from 2 independent RP cohorts (AUC, 0.86 and 0.89, respectively). In addition, we tested the ERG algorithm performance in 2 needle biopsy cohorts comprised of 179 and 148 WSI (AUC, 0.78 and 0.80, respectively). Focusing on cases with homogeneous (clonal) PTEN status, PTEN algorithm performance was assessed using 50 WSI reserved from the pretraining cohort (AUC, 0.81), 201 and 337 WSI from 2 independent RP cohorts (AUC, 0.72 and 0.80, respectively), and 151 WSI from a needle biopsy cohort (AUC, 0.75). For explainability, the PTEN algorithm was also applied to 19 WSI with heterogeneous (subclonal) PTEN loss, where the percentage tumor area with predicted PTEN loss correlated with that based on immunohistochemistry (r = 0.58, P = .0097). These deep-learning algorithms to predict ERG/PTEN status prove that H&E images can be used to screen for underlying genomic alterations in prostate cancer.

Glyco-conjugated metal-organic framework biosensor for fluorescent detection of bacteria.

Metal-organic frameworks (MOFs) are hybrid materials constructed by the linkage between an inorganic secondary building unit and an organic linker. A number of MOFs are luminescent in nature and can be structurally tuned for desirable geometry, surface functionality, and porosity. Luminescent MOFs have been endorsed for various biosensing applications. Lectins and carbohydrates have been used for the development of simple and convenient biosensing and bioimaging tools. Lectins are mostly present on the surface of microorganisms where they aid in pathogenesis. Due to this, they can be potential targets for a microbial biosensor. The present study, for the first time, explores the usage of a carbohydrate-conjugated FeMOF (Glyco-MOF) bioprobe for the selective determination of Pseudomonas aeruginosa and Escherichia coli. NH2-MIL-53(Fe) MOF was synthesized via a room temperature protocol and separately conjugated with galactose and mannose sugars via glutaraldehyde chemistry. The synthesized bioprobe is validated for structural integrity, luminescent nature, stability, and analyte assay. Electron microscopy studies validated the unhindered MOF's morphology and structural integrity, after bioconjugation. The synthesized bioprobes were able to detect P. aeruginosa and E. coli up to respective detection limits of 202 and 8 CFU/mL, respectively. The bioprobes are selective even in co-presence of possible interferants as well as being environmentally stable.

Liver Phosphoenolpyruvate Carboxykinase-1 Downregulation via siRNA-Functionalized Graphene Oxide Nanosheets Restores Glucose Homeostasis in a Type 2 Diabetes Mellitus In Vivo Model.

Metabolic disorders have been increasing at an alarming rate, and one such example of metabolic disorder is type 2 diabetes mellitus (T2DM). Unregulated gluconeogenesis in T2DM results in increased hepatic glucose output that causes fasting and postprandial hyperglycaemia. Extensive proofs have shown that the downregulation of the key rate-limiting enzyme phosphoenolpyruvate carboxykinase-1 (PCK-1) of gluconeogenesis improved glucose homeostasis in vivo. In the present study, we have synthesized and characterized liver-specific stearic acid conjugated octaarginine (StA-R8) functionalized 4arm-2K-PEGamineylated graphene oxide nanosheets (GPR8) for the delivery of siRNA against PCK-1 in T2DM C57BL/6 mice. We found that a single intravenous administration of siRNA (3 mg/kg BW) conjugated to GPR8 (GPR8:PCK-1siRNA(3 mg/kg BW) conjugate) in an optimized N/P ratio exploited as a therapeutic nanoformulation maintained glucose homeostasis for nearly 4 weeks in the T2DM mice. Efficient silencing of PCK-1 in T2DM liver tissue increased the phosphorylation of serine-256 of FOXO-1, thus showing a marked decrease in hepatic gluconeogenesis. Gluconeogenesis control and consequently glucose output from the liver furthermore partially enhanced liver and muscle insulin sensitivity results in the stimulation of the insulin/AKT-2 signaling pathway which indirectly restored glucose homeostasis in the treated T2DM group. Our therapeutic nanoformulation also improved glycogen storage in the liver and membrane translocation of GLUT4 in the muscle of the treated T2DM group. In conclusion, GPR8:PCK-1siRNA (3 mg/Kg BW) restored glucose homeostasis by controlling the hepatic glucose production and improved peripheral insulin sensitivity as a consequence of reduced hyperglycemia. Thus, the current approach offered an alternative strategy for the therapeutics for T2DM.

Catalytic and highly regenerable aminic organoselenium antioxidants with cytoprotective effects.

Novel N-methylated ebselenamine antioxidants were prepared from the corresponding diselenides with iodomethane. All ebselenamines showed excellent chain-breaking and glutathione peroxidase (GPx)-like activities. They could also inhibit lipid peroxidation much more efficiently than α-tocopherol. They could also mimic the functions of the GPx-enzymes nearly two times better than ebselen in the coupled reductase assay. Also, they were found to scavenge the ROS produced at low concentration (10 µM) with low toxicity effects and could have therapeutic potential against autoxidation. It is anticipated that these compounds could potentially be used against several diseases caused by autoxidation, and thus provide protection from cell death to mammals.

Biscoumarin-pyrimidine conjugates as potent anticancer agents and binding mechanism of hit candidate with human serum albumin.

In our continuing efforts to develop therapeutically active coumarin-based compounds, a series of new C4-C4' biscoumarin-pyrimidine conjugates (1a-l) was synthesized via SN 2 reaction of substituted 4-bromomethyl coumarin with thymine. All compounds were characterized using spectroscopic techniques, that is, attenuated total reflection infrared (ATR-IR), CHN elemental analysis, and 1 H and 13 C NMR (nuclear magnetic resonance). In addition, the structure of compound 1d (1,3-bis[(7-chloro-2-oxo-2H-chromen-4-yl)methyl]-5-methylpyrimidine-2,4(1H,3H)-dione) was established through X-ray crystallography. Compounds 1a-l were screened for in vitro anticancer activity against C6 rat glioma cells. Among the screened compounds, 1,3-bis[(6-chloro-2-oxo-2H-chromen-4-yl)methyl]-5-methylpyrimidine-2,4(1H,3H)-dione (1c) was identified as the best antiproliferative candidate, exhibiting an IC50 value of 4.85 µM. All the compounds (1a-l) were found to be nontoxic toward healthy human embryonic kidney cells (HEK293), indicating their selective nature. In addition, the most active compound (1c) displayed strong binding interactions with the drug carrier protein, human serum albumin, and exhibited good solution stability at biological pH conditions. Fluorescence, UV-visible spectrophotometry and molecular modeling methodologies were employed for studying the interaction mechanism of compound 1c with protein.

Multifunctional Mono-Triazole Derivatives Inhibit Aß42 Aggregation and Cu2+-Mediated Aß42 Aggregation and Protect Against Aß42-Induced Cytotoxicity.

Amyloid beta (Aß) peptide aggregation is considered as one of the key hallmarks of Alzheimer's disease (AD). Moreover, Aß peptide aggregation increases considerably in the presence of metal ions and triggers the generation of reactive oxygen species (ROS), which ultimately leads to oxidative stress and neuronal damage. Based on the 'multitarget-directed ligands' (MTDLs) strategy, we designed, synthesized, and evaluated a novel series of triazole-based compounds for AD treatment via experimental and computational methods. Among the designed MTDLs [4(a-x)], the triazole derivative 4v exhibited the most potent inhibition of self-induced Aß42 aggregation (78.02%) with an IC50 value of 4.578 ± 0.109 µM and also disassembled the preformed Aß42 aggregates significantly. In addition, compound 4v showed excellent metal chelating ability and maintained copper in the redox-dormant state to prevent the generation of ROS in copper-ascorbate redox cycling. Further, 4v significantly inhibited Cu2+-induced Aß42 aggregation and disassembled the Cu2+-induced Aß42 protofibrils as compared to the reference compound clioquinol (CQ). Importantly, 4v did not show cytotoxicity and was able to inhibit the toxicity induced by Aß42 aggregates in SH-SY5Y cells. Molecular docking results confirmed the strong binding of 4v with Aß42 monomer and Aß42 protofibril structure. The experimental and molecular docking results highlighted that 4v is a promising multifunctional lead compound for AD.

Multi-target-directed triazole derivatives as promising agents for the treatment of Alzheimer's disease.

A novel series of triazole-based compounds have been designed, synthesised and evaluated as multi-target-directed ligands (MTDLs) against Alzheimer disease (AD). The triazole-based compounds have been designed to target four major AD hallmarks that include Aß aggregation, metal-induced Aß aggregation, metal dys-homeostasis and oxidative stress. Among the synthesised compounds, 6n having o-CF3 group on the phenyl ring displayed most potent inhibitory activity (96.89% inhibition, IC50 = 8.065 ±â€¯0.129 µM) against Aß42 aggregation, compared to the reference compound curcumin (95.14% inhibition, IC50 = 6.385 ±â€¯0.009 µM). Compound 6n disassembled preformed Aß42 aggregates as effectively as curcumin. Furthermore, 6n displayed metal chelating ability and significantly inhibited Cu2+-induced Aß42 aggregation and disassembled preformed Cu2+-induced Aß42 aggregates. 6n successfully controlled the generation of the reactive oxygen species (ROS) by preventing the copper redox cycle. In addition, 6n did not display cytotoxicity and was able to inhibit toxicity induced by Aß42 aggregates in SH-SY5Y cells. The preferred binding regions and key interactions of 6n with Aß42 monomer and Aß42 protofibril structure was evaluated with molecular docking. Compound 6n binds preferably to the C-terminal region of Aß42 that play a critical role in Aß42 aggregation. The results of the present study highlight a novel triazole-based compound, 6n, as a promising MTDL against AD.

Coumarin tethered cyclic imides as efficacious glucose uptake agents and investigation of hit candidate to probe its binding mechanism with human serum albumin.

A series of novel coumarin-cyclic imide conjugates (1a-1j) were designed and synthesized to evaluate their glucose uptake activity by insulin resistant liver hepatocyte carcinoma (HepG2) cells through 2-NBDG uptake assay. Compounds (1a-1j) were characterised using various analytical methods such as 1H NMR, 13C NMR, IR, GC-MS, elemental and single-crystal X-ray diffraction techniques. Compounds (1a-1j) exhibited 85.21 - 65.80% of glucose uptake and showed low level of cytotoxicity towards human embryonic kidney cells (HEK-293) indicating good selectivity and safety profile. Compound 1f was identified as a hit candidate exhibiting 85.21% of glucose uptake which was comparable with standard antidiabetic drug Metformin (93.25% glucose uptake). Solution stability study under physiological pH conditions ≈ (3.4 - 8.7), indicates that compound 1f is sufficiently stable at varied pH conditions and thereby compatible with bio-physiological environments. Interaction of 1f with human serum albumin (HSA) were also studied which quantifies that compound 1f binds with HSA efficiently through facile binding reaction in solution. Fluorescence, UV-vis spectrophotometry and molecular modeling methodologies were employed for studying the interaction mechanism of compound 1f with protein.

Potential use of ZnO@activated carbon nanocomposites for the adsorptive removal of Cd2+ ions in aqueous solutions.

Nowadays, the pollution in water resources has become a major concern, both environmentally and in perspective of human health. The bioaccumulation of pollutants, especially heavy metal ions through the food chain, poses a hazardous risk to humans and other living organisms. Nanomaterials and their composites have been recognized for their potential to resolve such problems. Herein, ZnO nanoparticles were synthesized and characterized via different microscopic/spectroscopic techniques. ZnO nanoparticles (i.e., 20 to 50 nm) were obtained in high yield via a facile chemical approach. The ratio of ZnO nanoparticles and activated carbon was optimized to achieve enhanced electrostatic interactions for the effective adsorption of cadmium ions (Cd2+). The adsorptive performance of the nanocomposite was further assessed in relation to several key parameters (e.g., contact time, solution pH, and adsorbent/adsorbate dosage). The nanocomposites (1 mg/ml) offered amaximum adsorption capacity of 96.2 mg/g for Cd2+ ions as confirmed through adsorption isotherms for a best interpretation of the adsorption phenomenon. The favourable adsorption capacity of the synthesized ZnO/activated carbon (9:1) nanocomposites supported their use as an efficient sorbent material in practical performance metrics (e.g., partition coefficient of 0.54 mg g-1µM-1) for the adsorption of Cd2+ ions.

Metal organic frameworks MIL-100(Fe) as an efficient adsorptive material for phosphate management.

The excessive discharge of phosphate in water bodies is one of the primary factors causing eutrophication. Therefore, its removal is of significant research interest. The present study deals with the development and performance of highly effective phosphate-adsorbent. Here, we have synthesized MIL-100(Fe) metal-organic frameworks as a facile strategy to effectively remove phosphate from eutropic water samples. The adsorbent was characterized by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis (TGA), Brunauer-Emmett-Teller (BET), scanning electron microscopy (SEM), and wavelength dispersive X-ray fluorescence (WDXRF). The phosphate adsorption performance of MIL-100(Fe) was evaluated with the help of different batch experiments relating to the effect of adsorbent/adsorbate concentrations and the solution pH. The MOF offered a maximum adsorption capacity of 93.6 mg g-1 for phosphate from aqueous solutions with Langmuir isotherm model (R2 = 0.99). MIL-100(Fe) offered an absolute phosphate adsorption performance with a partition co-efficient of 15.98 mg g-1 µM-1 at pH 4 and room temperature conditions. Final experiments with real water samples were also performed to examine the effectiveness of MIL-100(Fe) for phosphate adsorption even in the presence of other ions. These findings support the potential utility of MIL-100(Fe) as nanoadsorbent in phosphate removal for water management.

Phosphoenolpyruvate carboxykinase-1 targeted siRNA promotes wound healing in type 2 diabetic mice by restoring glucose homeostasis.

It is well-accepted that the liver plays a vital role in the metabolism of glucose and its homeostasis. Dysregulated hepatic glucose production and utilization, leads to type 2 diabetes (T2DM). In the current study, RNA sequencing and qRT-PCR analysis of nanoformulation-treated T2DM mice (TGthr group) revealed beneficial crosstalk of PCK-1 silencing with other pathways involved in T2DM. The comparison of precise genetic expression profiles of the different experimental groups showed significantly improved hepatic glucose, fatty acid metabolism and several other T2DM-associated crucial markers after the nanoformulation treatment. As a result of these improvements, we observed a significant acceleration in wound healing and improved insulin signaling in vascular endothelial cells in the TGthr group as compared to the T2DM group. Enhanced phosphorylation of PI3K/Akt pathway proteins in the TGthr group resulted in increased angiogenesis as observed by the increased expression of endothelial cell markers (CD31, CD34) thereby improving endothelial dysfunctions in the TGthr group. Additionally, therapeutic nanoformulation has been observed to improve the inflammatory cytokine profile in the TGthr group. Overall, our results demonstrated that the synthesized therapeutic nanoformulation referred to as GPR8:PCK-1siRNA holds the potential in ameliorating hyperglycemia-associated complications such as delayed wound healing in diabetes.

Bells and Whistles on Fertilizers: Molecular Hands to Hang Nanoporous Foliar Fertilizer Reservoirs.

Porous materials are highly explored platforms for fertilizer delivery. Among porous materials, metal-organic frameworks (MOFs) are an important class of coordination polymers in which metal ions and organic electron donors as linkers are assembled to form crystalline structures with stable nanoporosity. Selected amino acids were inherently found to have the capacity to hold the leaf cuticle. Hence, MOF synthesis was attempted in the presence of amino acids, which can act as surface terminators and can assist as hands to hold to the leaf for a controlled nutrient supply. By serendipity, the amino acids were found to act as modulators, resulting in well-stabilized porous MOF structures with iron metal nodes, which are often noted to be unstable. Thus, the composite, i.e., (MOF@aa) MOF modulated with amino acids, has efficient nutrient-feeding ability through the foliar route when compared to the control.

Predicting prostate cancer grade reclassification on active surveillance using a deep Learning-Based grading algorithm.

Deep learning (DL)-based algorithms to determine prostate cancer (PCa) Grade Group (GG) on biopsy slides have not been validated by comparison to clinical outcomes. We used a DL-based algorithm, AIRAProstate, to re-grade initial prostate biopsies in two independent PCa active surveillance (AS) cohorts. In a cohort initially diagnosed with GG1 PCa using only systematic biopsies (n = 138), upgrading of the initial biopsy to ≥GG2 by AIRAProstate was associated with rapid or extreme grade reclassification on AS (odds ratio 3.3, p = .04), whereas upgrading of the initial biopsy by contemporary uropathologist reviews was not associated with this outcome. In a contemporary validation cohort that underwent prostate magnetic resonance imaging before initial biopsy (n = 169), upgrading of the initial biopsy (all contemporary GG1 by uropathologist grading) by AIRAProstate was associated with grade reclassification on AS (hazard ratio 1.7, p = .03). These results demonstrate the utility of a DL-based grading algorithm in PCa risk stratification for AS.

Synthetically Tunable Suprahybrid Nanoparticle Platform for the Efficacious Delivery of Therapeutics.

The discovery of lipid-hybrid nanosystems has offered potential solutions to various drug delivery and theranostic challenges. However, in many instances, the commonly used lipids and other components in these systems often pose challenges related to their solubility, physicochemical properties, immune compatibility, and limited synthetic tunability. In this work, we introduce a synthetically tunable supramolecular scaffold with amphiphilic characteristics based on the calix[4]arene macrocyclic system. We designed and synthesized two novel calix[4]arene-polyethylene glycol (PEG) conjugates, termed Cal-P1 and Cal-P2, and these were characterized utilizing a wide range of spectroscopic and analytical methods. The rational design of Cal-P1 and Cal-P2 demonstrates their utility in forming stable blended nanospheres with sustained drug release characteristics. The synergistic blending of PLGA and the calixarene scaffold (Cal-P1 and Cal-P2) in constructing long-lasting and controlled-release nanoparticles (NPs), which are optimized for encapsulating Nile Red dye, and their successful internalization and retention in HeLa cancer cells are demonstrated through in vitro assays. The potential of these NPs as sustained therapeutic carriers is investigated in vivo, showing improved retention compared to free dye with negligible toxicity. The successful design and construction of Cal-P1 and Cal-P2 nanosystems represent a new paradigm for addressing drug loading challenges, opening up opportunities for the development of highly efficient, synthetically tunable alternative adjuvants for drug encapsulation and delivery.

Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art.

Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.

Triazole-Peptide Conjugate as a Modulator of Aß-Aggregation, Metal-Mediated Aß-Aggregation, and Cytotoxicity.

Amyloid-ß (Aß) aggregation plays a key role in the pathogenesis of Alzheimer's disease (AD). Along with this, the presence of redox-active metals like Cu2+ further enhances Aß aggregation, oxidative stress, and cellular toxicity. In this study, we have rationally designed, synthesized, and evaluated a series of triazole-peptide conjugates as potential promiscuous ligands capable of targeting different pathological factors of AD. In particular, peptidomimetic DS2 showed the best inhibitory activity against Aß aggregation with an IC50 value of 2.43 ± 0.05 µM. In addition, DS2 disaggregates preformed Aß42 fibrils, chelates metal ions, inhibits metal-mediated Aß aggregation, significantly controls reactive oxygen species production, and reduces oxidative stress. DS2 exhibited very low cytotoxicity and significantly ameliorated the Aß-induced toxicity in differentiated neuroblastoma cells, SH-SY5Y. In addition, alteration in the fibrillary architecture of Aß42 in the absence and presence of DS2 was validated by transmission electron microscopy (TEM) images. To shed light on the inhibitory mechanism of DS2 against Aß aggregation and disassembly of the protofibril structure, molecular dynamics (MD) simulations have been performed. DS2 binds preferentially with the central hydrophobic core (CHC) residues of Aß42 monomer and chains D-E of Aß42 protofibril. The dictionary of secondary structure of proteins analysis indicated a noteworthy increase in the helix content from 38.5 to 61% and, notably, a complete loss of ß-sheet content of Aß42 monomer when DS2 is added to it. DS2 suppressed Aß42 monomer aggregation by preserving helical conformations and was able to reduce the production of aggregation-prone ß-sheet structures, which are consistent with ThT, circular dichroism, and TEM assay that indicate a reduction in the formation of toxic Aß42 aggregated species on the addition of DS2. Moreover, DS2 destabilized the Aß42 protofibril structure by significantly reducing the binding affinity between chains D-E of protofibril, which highlighted the disruption of interchain interactions and subsequent deformation of the protofibril structure. The results of the present study demonstrate that triazole-peptide conjugates may be valuable chemotypes for the development of promising multifunctional AD therapeutic candidates.

Trace elements dyshomeostasis in liver and brain of weanling mice under altered dietary selenium conditions.

BACKGROUND: A balanced diet containing selenium (Se) and other trace elements is essential for normal development and growth. Se has been recognized as an essential trace element; however, its interaction with other elements has not been fully investigated. In the present study, sodium (Na), magnesium (Mg), potassium (K), calcium (Ca), chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn), Se and rubidium (Rb), were analysed in liver and brain regions under altered dietary Se intake in weanling mice to identify major discriminatory elements. METHODS: The study investigated the effects of different levels of Se intake on the elemental composition in liver and brain tissues of weaned mice. After 24 weeks of feeding with Se adequate, deficient, and excess diets, elemental analysis was performed on the harvested tissues using Inductively coupled plasma mass spectrometry (ICP-MS). Statistical analysis that included analysis of covariance (ANCOVA), correlation coefficient analysis, principal component analysis, and partial least squares discriminant analysis were performed. RESULTS: The ANCOVA showed statistically significant changes and correlations among the analysed elements under altered dietary Se status. The multivariate analysis showed differential changes in elements in liver and brain regions. The results suggest that long-term dietary Se alternations lead to dyshomeostasis in trace elements that are required in higher concentrations compared to Se. It was observed that changes in the Fe, Co, and Rb levels were similar in all the tissues studied, whereas the changes in Mg, Cr, and Mn levels were different among the tissues under altered dietary Se status. Additionally, the changes in Rb levels correlated with the dietary Se intake but had no relation with the tissue Se levels. CONCLUSIONS: The findings suggest interactions between Mg, Cr, Mn, Fe, Co, and Se under altered Se status may impact cellular functions during postnatal development. However, the possible biological significance of alterations in Rb levels under different dietary Se paradigms needs to be further explored.

Salmonella typhimurium detection and ablation using OmpD specific aptamer with non-magnetic and magnetic graphene oxide.

Foodborne diseases have increased in the last few years due to the increased consumption of packaged and contaminated food. Major foodborne bacteria cause diseases such as diarrhea, vomiting, and sometimes death. So, there is a need for early detection of foodborne bacteria as pre-existing detection techniques are time-taking and tedious. Aptamer has gained interest due to its high stability, specificity, and sensitivity. Here, aptamer has been developed against Salmonella Typhimurium through the Cell-Selex method, and to further find the reason for specificity and sensitivity, OmpD protein was isolated, and binding studies were done. Single molecular FRET experiment using aptamer and graphene oxide studies has also been done to understand the mechanism of FRET and subsequently used for target bacterial detection. Using this assay, Salmonella Typhimurium can be detected up to 10 CFU/mL. Further, Magnetic Graphene oxide was used to develop an assay to separate and ablate bacteria using 808 nm NIR where temperature increase was more than 60 °C within 30 s and has been shown by plating as well as a confocal live dead assay. Thus, using various techniques, bacteria can be detected and ablated using specific aptamer and Graphene oxide.

Multiepitope glycan based laser assisted fluorescent nanocomposite with dual functionality for sensing and ablation of Pseudomonas aeruginosa.

Pseudomonas aeruginosa (P. aeruginosa) infection is becoming a severe health hazard and needs early diagnosis with high specificity. However, the non-specific binding of a biosensor is a challenge to the current bacterial detection system. For the first time, we chemically synthesized a galactose tripod (GT) as a P. aeruginosa-specific ligand. We conjugated GT to a photothermally active fluorescent nanocomposite (Au@SiO2-TCPP). P. aeruginosa can be detected using Au@SiO2-TCPP-GT, and additionally ablated as well using synergistic photothermal and photodynamic therapy. Molecular dynamics and simulation studies suggested better binding of GT (binding energy = -6.6 kcal mol-1) with P. aeruginosa lectin than that of galactose monopod (GM) (binding energy = -5.9 kcal mol-1). Furthermore, a binding study was extended to target P. aeruginosa, which has a galactose-binding carbohydrate recognition domain receptor. The colorimetric assay confirmed a limit of detection (LOD) of 104 CFU mL-1. We also looked into the photosensitizing property of Au@SiO2-TCPP-GT, which is stimulated by laser light (630 nm) and causes photoablation of bacteria by the formation of singlet oxygen in the surrounding media. The cytocompatibility of Au@SiO2-TCPP-GT was confirmed using cytotoxicity assays on mammalian cell lines. Moreover, Au@SiO2-TCPP-GT also showed non-hemolytic activity. Considering the toxicity analysis and efficacy of the synthesized glycan nanocomposites, these can be utilized for the treatment of P. aeruginosa-infected wounds. Furthermore, the current glycan nanocomposites can be used for bacterial detection and ablation of P. aeruginosa in contaminated food and water samples as well.

Rethinking ImageNet Pre-training for Computational Histopathology.

Transfer learning from ImageNet pretrained weights is widely used when training Deep Learning models on a Histopathology dataset. However, the visual features of the two domains are different. Rather than ImageNet pretrained weights, pre-training on a Histopathology dataset may provide better initialization. To prove this hypothesis, we train two commonly used Deep Learning model architectures - ResNet and DenseNet on a complex Histopathology classification dataset, and compare transfer learning performance with ImageNet pretrained weights. Based on the fine-tuning on three histopathology datasets including two different stains (H&E and IHC), we show that the domain specific pretrained weights are better suited for transfer learning. This is reflected by higher performance, lower training time as well as better feature reuse. Clinical Relevance - The paper establishes merit of using Histopathology domain specific pretrained weights rather than ImageNet pretrained weights.