Memristive Control of Plasmon-Mediated Nonlinear Photoluminescence in Au Nanowires.

Nonlinear photoluminescence (N-PL) is a broadband photon emission arising from a nonequilibrium heated electron distribution generated at the surface of metallic nanostructures by ultrafast pulsed laser illumination. N-PL is sensitive to surface morphology, local electromagnetic field strength, and electronic band structure, making it relevant to probe optically excited nanoscale plasmonic systems. It also has been key to accessing the complex multiscale time dynamics ruling electron thermalization. Here, we show that plasmon-mediated N-PL emitted by a gold nanowire can be modified by an electrical architecture featuring a nanogap. Upon voltage activation, we observe that N-PL becomes dependent on the electrical transport dynamics and can thus be locally modulated. This finding brings an electrical leverage to externally control the photoluminescence generated from metal nanostructures and constitutes an asset for the development of emerging nanoscale interface devices managing photons and electrons.

A Retrospective Analysis of BCR-ABL1 Kinase Domain Mutations in the Frontline Drug Intolerant or Resistant Chronic Myeloid Leukemia Patients: An Indian Experience from a High-End Referral Laboratory.

Atreye MajumdarSambit K. MohantyObjective This article identifies and evaluates the frequency of mutations in the BCR-ABL1 kinase domain (KD) of chronic myeloid leukemia (CML) patients who showed suboptimal response to their current tyrosine kinase inhibitor (TKI) regime and assesses their clinical value in further treatment decisions. Materials and Methods Peripheral and/or bone marrow were collected from 791 CML patients. Ribonucleic acid was extracted, reverse transcribed, and Sanger sequencing method was utilized to detect single-nucleotide variants (SNVs) in BCR-ABL1 KD. Results Thirty-eight different SNVs were identified in 29.8% ( n = 236/791) patients. T315I, E255K, and M244V were among the most frequent mutations detected. In addition, one patient harbored a novel L298P mutation. A subset of patients from the abovementioned harbored compound mutations (13.3%, n = 33/236). Follow-up data was available in 28 patients that demonstrated the efficacy of TKIs in correlation with mutation analysis and BCR-ABL1 quantitation. Molecular response was attained in 50% patients following an appropriate TKI shift. A dismal survival rate of 40% was observed in T315I-harboring patients on follow-up. Conclusion This study shows the incidence and pattern of mutations in one of the largest sets of Indian CML patients. In addition, our findings strengthen the prognostic value of KD mutation analysis among strategies to overcome TKI resistance.

Antitubercular activity of 2-mercaptobenzothiazole derivatives targeting Mycobacterium tuberculosis type II NADH dehydrogenase.

Mycobacterium tuberculosis (Mtb) type II NADH dehydrogenase (NDH-2) transports electrons into the mycobacterial respiratory pathway at the cost of reduction of NADH to NAD+ and is an attractive drug target. Herein, we have synthesised a series of 2-mercaptobenzothiazoles (C1-C14) and evaluated their anti-tubercular potential as Mtb NDH-2 inhibitors. The synthesised compounds C1-C14 were evaluated for MIC90 and ATP depletion against Mtb H37Ra, M. bovis, and Mtb H37Rv mc2 6230. Compounds C3, C4, and C11 were found to be the active molecules in the series and were further evaluated for their MIC90 against Mtb-resistant strains and for their bactericidal potential against Mtb H37Rv mc26230. The Peredox-mCherry-expressing Mtb strain was used to examine whether C3, C4, and C11 possess NDH-2 inhibitory potential. Furthermore, cytotoxicity analysis against HepG2 displayed a safety index (SI) of >10 for C3 and C4. To get an insight into the mode of interaction at NDH-2, we have performed computational analysis of our active compounds.

Cytochrome bd oxidase: an emerging anti-tubercular drug target.

Cytochrome bd (cyt-bd) oxidase, one of the two terminal oxidases in the Mycobacterium tuberculosis (Mtb) oxidative phosphorylation pathway, plays an indispensable role in maintaining the functionality of the metabolic pathway under stressful conditions. However, the absence of this oxidase in eukaryotic cells allows researchers to select it as a potential drug target for the synthesis of anti-tubercular (anti-TB) molecules. Cyt-bd inhibitors have often been combined with cytochrome bcc/aa3 super-complex inhibitors in anti-TB drug regimens to achieve a desired bactericidal response. The functional redundancy between both the terminal oxidases is responsible for this. The cryo-EM structure of cyt-bd oxidase from Mtb (PDB ID: 7NKZ) further accelerated the research to identify its inhibitor. Herein, we have summarized the reported anti-TB cyt-bd inhibitors, insight into the rationale behind targeting cyt-bd oxidase, and an outline of the architecture of Mtb cyt-bd oxidase.

DNA topoisomerases as a drug target in Leishmaniasis: Structural and mechanistic insights.

Leishmaniasis, caused by a protozoan parasite, is among humanity's costliest banes, owing to the high mortality and morbidity ratio in poverty-stricken areas. To date, no vaccine is available for the complete cure of the disease. Current chemotherapy is expensive, has undesirable side effects, and faces drug resistance limitations and toxicity concerns. The substantial differences in homology between leishmanial DNA topoisomerase IB compared with the human counterparts provided a new lead in the study of the structural determinants that can be targeted. Several research groups explored this molecular target, trying to fill the therapeutic gap, and came forward with various anti-leishmanial scaffolds. This article is a comprehensive review of knowledge about topoisomerases as an anti-leishmanial drug target and their inhibitors collected over the years. In addition to information on molecular targets and reported scaffolds, the review details the structure-activity relationship of described compounds with leishmanial Topoisomerase IB. Moreover, the work also includes information about the structure of the inhibitors, showing common interacting residues with leishmanial topoisomerases that drive their mode of action towards them. Finally, in search of topoisomerase inhibitors at the stage of clinical trials, we have listed all the drugs that have been in clinical trials against leishmaniasis.

Shape Expressions (ShEx) schemas for the FHIR R5 specification.

This work continues along a visionary path of using Semantic Web standards such as RDF and ShEx to make healthcare data easier to integrate for research and leading-edge patient care. The work extends the ability to use ShEx schemas to validate FHIR RDF data, thereby enhancing the semantic web ecosystem for working with FHIR and non-FHIR data using the same ShEx validation framework. It updates FHIR's ShEx schemas to fix outstanding issues and reflect changes in the definition of FHIR RDF. In addition, it experiments with expressing FHIRPath constraints (which are not captured in the XML or JSON schemas) in ShEx schemas. These extended ShEx schemas were incorporated into the FHIR R5 specification and used to successfully validate FHIR R5 examples that are included with the FHIR specification, revealing several errors in the examples.

Design, synthesis, and biological evaluation of 3,3'-diindolylmethane N-linked glycoconjugate as a leishmanial topoisomerase IB inhibitor with reduced cytotoxicity.

Leishmaniasis, one of the neglected diseases, ranks second to malaria in the cause of parasitic mortality and morbidity. The present chemotherapeutic regimen faces the limitations of drug resistance and toxicity concerns, raising a great need to develop new chemotherapeutic leads that are orally administrable, potent, non-toxic, and cost-effective. Several research groups came forward to fill this therapeutic gap with new classes of active compounds against leishmaniasis, one such being 3,3'-diindolylmethane (DIM) derivatives. We tried to link this concept with another promising approach of glycoconjugation to study how glycosylated groups work differently from non-glycosylated ones. In the present study, a series of 3,3'-DIM derivatives have been synthesized and screened for their anti-leishmanial potency on Leishmania donovani promastigotes. Next, we synthesized the ß-N,N' glycoside of potent compound 3d using indole-indoline conversion, Fischer-type glycosylation, 2,3-dichloro-5,6-dicyano-1,4-benzoquionone (DDQ) oxidation, and molecular iodine catalyzed coupling with a suitable aldehyde in reasonable overall yield. The biological evaluation revealed that glycosides had reduced cytotoxic effects on the J774A.1 macrophage cell line. The enzyme inhibition study confirms that the glycoside derivatives have significant inhibitory activity against the leishmanial topoisomerase IB enzyme. Molecular docking further displayed the better binding efficiency of glycoside 13 with the target enzyme, suggesting the involvement of more H-bond interactions in the case of glycosides as compared to free drugs. Therefore, this work helps in proposing the fact that the addition of sugar moieties adds some favorable characteristics to free inhibitors, making it a promising approach for future clinical diagnostic and therapeutic applications, which can prove to be a valuable arsenal in combating such neglected diseases.

Visible light induced regioselective C-3 thiocyanation of imidazoheterocycles through naphthalimide dye based photoredox catalysis.

A visible light induced C-3 thiocyanation of imidazo[1,2-a]pyridines by using a naphthalimide based photoredox catalyst has been reported. Tolerance of electron withdrawing and donating groups at different positions of the imidazo[1,2-a]pyridine ring led to a wide substrate accessibility of this method. This methodology is further reproducible with other heterocycles like benzo[d]imidazo[2,1-b]thiazoles, indoles, azaindoles, and anilines.

Rottlerin renders a selective and highly potent CYP2C8 inhibition to impede EET formation for implication in cancer therapy.

CYP2C8 is a crucial CYP isoform responsible for the metabolism of xenobiotics and endogenous molecules. CYP2C8 converts arachidonic acid to epoxyeicosatrienoic acids (EETs) that cause cancer progression. Rottlerin possess significant anticancer actions. However, information on its CYP inhibitory action is lacking in the literature and therefore, we aimed to explore the same using in silico, in vitro, and in vivo approaches. Rottlerin showed highly potent and selective CYP2C8 inhibition (IC50 < 0.1 µM) compared to negligible inhibition (IC50 > 10 µM) for seven other experimental CYPs in human liver microsomes (HLM) (in vitro) using USFDA recommended index reactions. Mechanistic studies reveal that rottlerin could reversibly (mixed-type) block CYP2C8. Molecular docking (in silico) results indicate a strong interaction could occur between rottlerin and the active site of human CYP2C8. Rottlerin boosted the plasma exposure of repaglinide and paclitaxel (CYP2C8 substrates) by delaying their metabolism using the rat model (in vivo). Multiple-dose treatment of rottlerin with CYP2C8 substrates lowered the CYP2C8 protein expression and up-regulated & down-regulated the mRNA for CYP2C12 & CYP2C11 (rat homologs), respectively, in rat liver tissue. Rottlerin substantially hindered the EET formation in HLM. Overall results of rottlerin on CYP2C8 inhibition and EET formation insinuate further exploration for cancer therapy.

FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model.

BACKGROUND: Knowledge graphs (KGs) play a key role to enable explainable artificial intelligence (AI) applications in healthcare. Constructing clinical knowledge graphs (CKGs) against heterogeneous electronic health records (EHRs) has been desired by the research and healthcare AI communities. From the standardization perspective, community-based standards such as the Fast Healthcare Interoperability Resources (FHIR) and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) are increasingly used to represent and standardize EHR data for clinical data analytics, however, the potential of such a standard on building CKG has not been well investigated. OBJECTIVE: To develop and evaluate methods and tools that expose the OMOP CDM-based clinical data repositories into virtual clinical KGs that are compliant with FHIR Resource Description Framework (RDF) specification. METHODS: We developed a system called FHIR-Ontop-OMOP to generate virtual clinical KGs from the OMOP relational databases. We leveraged an OMOP CDM-based Medical Information Mart for Intensive Care (MIMIC-III) data repository to evaluate the FHIR-Ontop-OMOP system in terms of the faithfulness of data transformation and the conformance of the generated CKGs to the FHIR RDF specification. RESULTS: A beta version of the system has been released. A total of more than 100 data element mappings from 11 OMOP CDM clinical data, health system and vocabulary tables were implemented in the system, covering 11 FHIR resources. The generated virtual CKG from MIMIC-III contains 46,520 instances of FHIR Patient, 716,595 instances of Condition, 1,063,525 instances of Procedure, 24,934,751 instances of MedicationStatement, 365,181,104 instances of Observations, and 4,779,672 instances of CodeableConcept. Patient counts identified by five pairs of SQL (over the MIMIC database) and SPARQL (over the virtual CKG) queries were identical, ensuring the faithfulness of the data transformation. Generated CKG in RDF triples for 100 patients were fully conformant with the FHIR RDF specification. CONCLUSION: The FHIR-Ontop-OMOP system can expose OMOP database as a FHIR-compliant RDF graph. It provides a meaningful use case demonstrating the potentials that can be enabled by the interoperability between FHIR and OMOP CDM. Generated clinical KGs in FHIR RDF provide a semantic foundation to enable explainable AI applications in healthcare.

Rottlerin promotes anti-metastatic events by ameliorating pharmacological parameters of paclitaxel: An in-vivo investigation in the orthotopic mouse model of breast cancer.

Despite substantial breakthroughs in cancer research, there is hardly any specific therapy available to date that can alleviate triple-negative breast cancer (TNBC). Paclitaxel is the first-line chemotherapy option, but its treatment is often associated with early discontinuation of therapy due to the development of resistance and/or precipitation of severe side effects. In the quest to establish a suitable combination therapy with a low dose of paclitaxel, we explored rottlerin (a pure and characterized phytoconstituent from Mallotus philippensis) because of its multifaceted pharmacological actions against cancer. The study was performed to assess the therapeutic effects of rottlerin (5-20 mg/kg) with a low dose of paclitaxel (5 mg/kg) using a highly aggressive mouse mammary carcinoma model. Rottlerin augmented the paclitaxel effect by reducing tumor burden as well as metastatic lung nodules formation. Rottlerin in combination with paclitaxel remarkably altered the expression of vital epithelial-mesenchymal transition (EMT) markers such as E-cadherin, Snail 1, & Vimentin and thus improved the anti-metastatic efficacy of paclitaxel. Significant attenuation of anti-apoptotic protein (Bcl-2) along with amplification of pro-apoptotic (cleaved PARP) marker confers that rottlerin could ameliorate the pro-apoptotic potential of paclitaxel. In this study, a rational combination of rottlerin and paclitaxel treatment curtailed CYP2J2 expression and epoxyeicosatrienoic acids (EETs) levels, responsible for restrain tumor growth and metastasis. Additionally, rottlerin lessened paclitaxel treatment-mediated hematological alterations and prevented paclitaxel treatment-linked key serum biochemical changes related to organ toxicities. These rottlerin treatment-mediated protective changes are closely associated with the lower paclitaxel accumulation in the corresponding tissues. Rottlerin caused significant pharmacokinetic interaction with paclitaxel to boost the plasma level of paclitaxel in a typical mouse model and possibly helpful towards the use of a low dose of paclitaxel in combination. Overall, it can be stated that rottlerin has significant potential to augment the anti-metastatic efficacy of paclitaxel via impeding EMT activation along with attenuating its treatment-associated toxicological alterations. Hence, rottlerin has significant potential to explore further as a suitable neoadjuvant therapy with paclitaxel against TNBC.

Pharmacokinetic Assessment of Rottlerin from Mallotus philippensis Using a Highly Sensitive Liquid Chromatography-Tandem Mass Spectrometry-Based Bioanalytical Method.

Rottlerin is a key bioactive phytoconstituent present in the pericarp of Mallotus philippensis. It shows promising multifaceted pharmacological actions against cancer. However, there is hardly any report for the quantification of rottlerin in the biological matrix and on its pharmacokinetic behavior. Therefore, we aimed in the present study to assess selective in vitro ADME properties and in vivo pharmacokinetics of isolated and characterized rottlerin using a newly developed and validated liquid chromatography-tandem mass spectrometry-based highly sensitive bioanalytical method. The method was found to be simple (mobile phase and analytical column), sensitive (1.9 ng/mL), and rapid (run time of 2.5 min). All the validation parameters were within the acceptable criteria of the United States Food and Drug Administration's bioanalytical method validation guideline. The method was found to be very useful to assess lipophilicity, plasma stability, metabolic stability, plasma protein binding of rottlerin, as well as its oral and intravenous pharmacokinetics in mice. Rottlerin showed a number of drug-like pharmacokinetic properties (in vitro). Moreover, it displayed an excellent half-life (>2 h) and oral bioavailability (>35%) as compared to other members of natural phenolics. The present study is the first-time report of in vitro ADME properties and in vivo preclinical pharmacokinetics of rottlerin. The generated information is very much useful for its further development as a phytotherapeutics toward cancer therapy.

Modal and wavelength conversions in plasmonic nanowires.

We show that plasmonic nanowire-nanoparticle systems can perform nonlinear wavelength and modal conversions and potentially serve as building blocks for signal multiplexing and novel trafficking modalities. When a surface plasmon excited by a pulsed laser beam propagates in a nanowire, it generates a localized broadband nonlinear continuum at the nanowire surface as well as at active locations defined by sites where nanoparticles are absorbed (enhancement sites). The local response may couple to new sets of propagating modes enabling a complex routing of optical signals through modal and spectral conversions. Different aspects influencing the optical signal conversions are presented, including the parameters defining the local formation of the continuum and the subsequent modal routing in the nanowire.

Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data.

BACKGROUND AND OBJECTIVE: Identification and Standardization of data elements used in clinical trials may control and reduce the cost and errors during the operational process, and enable seamless data exchange between the electronic data capture (EDC) systems and Electronic Health Record (EHR) systems. This study presents a methodology to comprehensively capture the clinical trial data element needs. MATERIALS AND METHODS: Case report forms (CRF) for clinical trial data collection were used to approximate the clinical information need, whereby these information needs were then mapped to a semantically equivalent field within an existing FHIR cancer profile. For items without a semantically equivalent field, we considered these items to be information needs that cannot be represented in current standards and proposed extensions to support these needs. RESULTS: We successfully identified 62 discrete items from a preliminary survey of 43 base questions in four CRFs used in colorectal cancer clinical trials, in which 28 items are modeled with FHIR extensions and their associated responses for colorectal cancer. We achieved promising results in the data population of the CRFs with average Precision 98.5 %, Recall 96.2 %, and F-measure 96.8 % for all base questions. We also demonstrated the auto-filled answers in CRFs can be used to discover patient subgroups using a topic modeling approach. CONCLUSION: CRFs can be considered as a proxy for representing information needs for their respective cancer types. Mining the information needs can serve as a valuable resource for expanding existing standards to ensure they can comprehensively represent relevant clinical data without loss of granularity.

Developing a FHIR-based Framework for Phenome Wide Association Studies: A Case Study with A Pan-Cancer Cohort.

Phenome Wide Association Studies (PheWAS) enables phenome-wide scans to discover novel associations between genotype and clinical phenotypes via linking available genomic reports and large-scale Electronic Health Record (EHR). Data heterogeneity from different EHR systems and genetic reports has been a critical challenge that hinders meaningful validation. To address this, we propose an FHIR-based framework to model the PheWAS study in a standard manner. We developed an FHIR-based data model profile to enable the standard representation of data elements from genetic reports and EHR data that are used in the PheWAS study. As a proof-of-concept, we implemented the proposed method using a cohort of 1,595 pan-cancer patients with genetic reports from Foundation Medicine as well as the corresponding lab tests and diagnosis from Mayo EHRs. A PheWAS study is conducted and 81 significant genotype-phenotype associations are identified, in which 36 significant associations for cancers are validated based on a literature review.

Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records.

PURPOSE: The Fast Healthcare Interoperability Resources (FHIR) is emerging as a next-generation standards framework developed by HL7 for exchanging electronic health care data. The modeling capability of FHIR in standardizing cancer data has been gaining increasing attention by the cancer research informatics community. However, few studies have been conducted to examine the capability of FHIR in electronic data capture (EDC) applications for effective cancer clinical trials. The objective of this study was to design, develop, and evaluate an FHIR-based method that enables the automation of the case report forms (CRFs) population for cancer clinical trials using real-world electronic health records (EHRs). MATERIALS AND METHODS: We developed an FHIR-based computational pipeline of EDC with a case study for modeling colorectal cancer trials. We first leveraged an existing FHIR-based cancer profile to represent EHR data of patients with colorectal cancer, and then we used the FHIR Questionnaire and QuestionnaireResponse resources to represent the CRFs and their data population. To test the accuracy of and overall quality of the computational pipeline, we used synoptic reports of 287 Mayo Clinic patients with colorectal cancer from 2013 to 2019 with standard measures of precision, recall, and F1 score. RESULTS: Using the computational pipeline, a total of 1,037 synoptic reports were successfully converted as the instances of the FHIR-based cancer profile. The average accuracy for converting all data elements (excluding tumor perforation) of the cancer profile was 0.99, using 200 randomly selected records. The average F1 score for populating nine questions of the CRFs in a real-world colorectal cancer trial was 0.95, using 100 randomly selected records. CONCLUSION: We demonstrated that it is feasible to populate CRFs with EHR data in an automated manner with satisfactory performance. The outcome of the study provides helpful insight into future directions in implementing FHIR-based EDC applications for modern cancer clinical trials.

Oncological outcome following initiation of treatment for stage III and IV HPV negative oropharyngeal cancers with transoral robotic surgery (TORS).

OBJECTIVE: To report long-term oncological and functional outcome of Transoral Robotic Surgery escalated treatment including radiotherapy or chemoradiotherapy for Stage III-IV HPV negative oropharyngeal malignancies. METHOD: From March 2013 to September 2015, 153 patients with oropharyngeal carcinoma were included in the study. Patients were evaluated for disease free survival, overall survival and post-treatment functional outcomes. RESULTS: 153 patients (96 males and 57 females) underwent TORS for oropharyngeal carcinoma. 142 patients on final histopathology had stage III and IV disease and received adjuvant treatment based on final histopathology. One hundred and sixteen (81.7%) patients were disease free on average follow-up of 48 months with an overall survival of 91.5% at mean follow-up of 48 months. CONCLUSION: TORS can be used to intensify treatment of Stage III/IV oropharyngeal carcinoma and avoid early and late toxicities due to higher doses of upfront RT/CTRT and achieve better oncological outcome.

Sulfonamides Are an Overlooked Class of Electron Donors in Luminogenic Luciferins and Fluorescent Dyes.

Many fluorophores, and all bright light-emitting substrates for firefly luciferase, contain hydroxyl or amine electron donors. Sulfonamides were found to be capable of serving as replacements for these canonical groups. Unlike "caged" carboxamides, sulfonamide donors enable bioluminescence, and sulfonamidyl luciferins, coumarins, rhodols, and rhodamines are fluorescent in water.

Pharmacokinetic evaluation of medicinally important synthetic N,N' diindolylmethane glucoside: Improved synthesis and metabolic stability.

An improved route for the synthesis of N,N'-diindolyl methane (DIM) glycosides has been developed by using Fe/Al pillared clay catalyst. In-silico pharmacokinetics followed by in-vitro studies like aqueous solubility, lipophilicity, P-glycoprotein (P-gp) dependent ATPase activity, permeability, plasma protein binding, RBC partitioning, metabolic stability in different liver microsomes and its in-vitro-in-vivo extrapolation were conducted for the most potent derivative namely NGD16. The compound was found to have low solubility, optimum lipophilicity, no P-gp inhibitory activity, intermediate permeability, high plasma protein binding, low RBC partitioning, acceptable metabolic stability in rat liver microsomes (RLM) as well as human liver microsomes (HLM) with intermediate hepatic extraction ratio.

Directional second-harmonic generation controlled by sub-wavelength facets of an organic mesowire.

Directional harmonic generation is an important property characterizing the ability of nonlinear optical antennas to diffuse the signal in a well-defined region of space. Herein, we show how sub-wavelength facets of an organic molecular mesowire crystal can be utilized to systematically vary the directionality of second-harmonic generation (SHG) in the forward-scattering geometry. We demonstrate this capability on crystalline diamonoanthraquinone (DAAQ) mesowires with sub-wavelength facets. We observed that the radial angles of the SHG emission can be tuned over a range of 130 deg. This angular variation arises due to spatially distributed nonlinear dipoles in the focal volume of the excitation as well as the geometrical cross section and facet orientation of the mesowire. Numerical simulations of the near-field excitation profile corroborate the role of the mesowire geometry in localizing the electric field. In addition to directional SHG from the mesowire, we experimentally observe optical waveguiding of the nonlinear two-photon excited fluorescence (TPEF). Interestingly, we observed that for a given pump excitation, the TPEF signal is isotropic and delocalized, whereas the SHG emission is directional and localized at the location of excitation. All the observed effects have direct implications not only in active nonlinear optical antennas but also in nonlinear signal processing.