Assessment of novel prognostic biomarkers to predict pathological complete response in patients with non-metastatic triple-negative breast cancer using a window of opportunity design.

Background: Triple-negative breast cancer (TNBC) includes approximately 20% of all breast cancer and is characterized by its aggressive nature, high recurrence rates, and visceral metastasis. Pathological complete response (pCR) is an established surrogate endpoint for survival. The window of opportunity studies provide valuable information on the disease biology prior to definitive treatment. Objectives: To study the association of dynamic change in pathological, imagining, and genomic biomarkers that can prognosticate pCR. The study aims to develop a composite prognostic score. Design: Clinical, interventional, and prognostic biomarker study using the novel window of opportunity design. Methods: The study aims to enroll 80 treatment-naïve, pathologically confirmed TNBC patients, administering a single dose of paclitaxel and carboplatin during the window period before neoadjuvant chemotherapy (NACT). Tumor tissue will be obtained through a tru-cut biopsy, and positron emission tomography and computed tomography scans will be performed for each patient at two time points aiming to evaluate biomarker alterations. This will be followed by the administration of standard dose-dense NACT containing anthracyclines and taxanes, with the study culminating in surgery to assess pCR. Results: The study would develop a composite prognostic risk score derived from the dynamic change in the Ki-67, tumor-infiltrating lymphocytes, Standardized Uptake Value (SUV max), Standardized Uptake Value for lean body mass (SUL max), and gene expression level pre- and post-intervention during the window period prior to the start of definitive treatment. This outcome will aid in categorizing the disease biology into risk categories. Trial registration: The current study is approved by the Institutional Ethics Committee [Ethics: Protocol. no. JIP/IEC/2020/019]. This study was registered with ClinicalTrials.gov [CTRI Registration: CTRI/2022/06/043109]. Conclusion: The validated biomarker score will help to personalize NACT protocols in patients in TNBC planned for definitive treatment.

Precision in action: unveiling predictive biomarkers for enhanced TNBC treatment We are investigating new ways to predict how well a particular treatment will work in patients with a specific type of breast cancer called triple-negative breast cancer. The study goal is to find biomarkers that change in response to drugs to predict the complete elimination of cancer in patients before it spreads to other parts of the body. To do this, we are using a special research approach called a 'window of opportunity design.' This information could be valuable in personalizing and improving cancer treatments.

Pyrolysis behavior, kinetics, and thermodynamics of waste pharmaceutical blisters under CO2 atmosphere.

The disastrous impact of COVID-19 pandemic has caused a significantly increased production and use of pharmaceutical drugs, which is accompanied by the rapid generation of waste pharmaceutical blisters (WPBs). Nonetheless, its treatment has not gained appropriate attentions and a perceptible process development was not achieved. In this study, the WPBs pyrolysis in CO2 atmosphere was conducted as well as the thermodynamics and kinetics were investigated. The thermogravimetric analysis revealed that the WPBs decomposition could be divided into two stages of 25 - 365 °C and 365 - 900 °C with mass loss of 56.5 - 60.5 wt% and 22.5 - 25.9 wt%, respectively. Fourier-transform infrared spectroscopy analysis indicated the dechlorination process initiating at ∼300 °C. The simultaneous asymmetric stretching of HCl and stretching vibration of C-Cl bond was detected in the range of 2600 - 3250 cm-1 and 660 - 750 cm-1, respectively. The dechlorination reactions were almost complete at ∼520 °C and minor peaks (2900 -3100 cm-1) due to C-H vibrations were observed. Gas chromatography-mass spectrometry analysis indicated that the evolved products included alkanes, benzene, olefin, as well as HCl. The cycloalkenes content significantly increased during the second conversion stage, implying the addition reactions between alkanes and olefins. The apparent activation energy was calculated using three model-free methods and the values from Flynn-Wall-Ozawa model increased from 142.0 to 255.8 kJ·mol-1 with an average value of 147.4 kJ·mol-1. The methods of Coats-Redfern as well as Malek were applied to determine the reaction mechanism. The one-dimensional diffusion model was more reliable to describe the WPBs pyrolysis. This study will represent a significant reference case for the thermochemical conversion of multilayer packing waste and facing the increasing demand for the medical waste recycling.

Citrus limetta fruit waste management by liquefaction using hydrogen-donor solvent.

The liquefaction of Citrus limetta fruit waste (both pulp and peel) in a hydrogen-donor solvent has not been reported in the literature and authors considered the same as the objective of this work. Thus, results on waste management of this potential fruit wastes by liquefaction in hydrogen-donor methanol solvent at 260 °C temperature, residence time of 30 min, and 1 : 2, 1 : 3 and 1 : 4 biomass-to-solvent ratios were reported in this work. The aim was to achieve biofuels of high quantity and quality from this waste, which would otherwise be disposed of without any value addition. A maximum of 12.5 wt% of biocrude yield was found from Citrus limetta peel biomass, which was higher than that from the thermochemical conversion of other citrus fruit waste biomasses. Biocrude having higher heating value (HHV) of 26.76 MJ kg-1 from Citrus limetta pulp, when the feed biomass pulp-to-solvent ratio was 1 : 4, found to be the best outcome of this study. Biocrude and biochar have also been extremely characterized using several advanced techniques such as Gas Chromatography Mass Spectrometry (GC-MS), Fourier Transform Infrared Spectroscopy (FTIR), and Field Emission Scanning Electron Microscopy (FESEM), etc. Finally, the novelty of this work is not only obtaining higher yield of biocrude but also better HHV compared to other similar studies in the literature.

Regurgitation on pressure over the lacrimal sac versus lacrimal irrigation in determining lacrimal obstruction prior to intraocular surgeries.

Purpose: : To determine the diagnostic accuracy of manual regurgitation on pressure over the lacrimal sac (ROPLAS) versus lacrimal irrigation for screening nasolacrimal duct obstruction (NLDO) in adults prior to intraocular surgeries. Methods: This cross-sectional study took place in a tertiary eye care hospital in South Tamil Nadu, India. From January to December 2017 and included consecutive patients who presented for routine cataract surgery. Prospective data collection occurred in 8369 eyes of patients who underwent cataract surgery. All patients underwent ROPLAS testing by an ophthalmologist followed by lacrimal irrigation by trained ophthalmic assistants, rechecked or confirmed in equivocal cases by ophthalmologists who were masked to the ROPLAS status. The primary outcome, the sensitivity, specificity, positive, and negative predictive values to detect lacrimal occlusion by ROPLAS compared with lacrimal irrigation with 95% confidence intervals was estimated. Results: : A total of 8369 eyes underwent cataract surgery during the time periods of the study. ROPLAS and lacrimal irrigation were performed in all eyes. The sensitivity of ROPLAS to diagnose NLDO correctly was 54.5% (95% CI, 44.8%-63.9%) and its specificity was 100% (95% CI, 100%-100%). The positive and negative predictive values were 75.3% (95% CI, 65.6%-83.0%) and 99.4% (95% CI, 99.2%-99.5%), respectively. Conclusion: : We found that ROPLAS when used alone had very low sensitivity and low positive predictive value in detecting NLDO prior to cataract surgery as compared with lacrimal irrigation. Hence, we recommend performing ROPLAS and lacrimal irrigation in every patient as part of the routine preoperative workup prior to cataract surgery.

Dehydrogenation and dehydration of formic acid over orthorhombic molybdenum carbide.

The dehydrogenation and dehydration of formic acid is investigated on the ß-Mo2C (100) catalyst surface using time independent density functional theory. The energetics of the two mechanisms are calculated, and the thermochemistry and kinetics are discussed using the transition state theory. Subsequently, microkinetic modelling of the system is conducted, considering the batch reactor model. The potential energy landscape of the reaction shows a thermodynamically favourable cleavage of H-COOH to form CO; however, the kinetics show that the dehydrogenation mechanism is faster and CO2 is continuously formed. The effect of HCOOH adsorption on the surface is also analysed, in a temperature-programmed desorption, with the conversion proceeding at under 350 K and desorption of CO2 is observed with a selectivity of about 100 %, in line with the experimental reports.

Study of Conversion of Bio-oil Model Compounds in Supercritical Water Using Density Functional Theory.

It is well known that supercritical water is a favourable medium for biomass conversion followed by its hydrodeoxygenation (HDO). Moreover, the actual kinetics and mechanism of reaction occurring in the supercritical water are not yet completely understood, either by experimental or computational approaches. Within the framework of DFT, the major challenge is non-availability of models to simulate supercritical phase. In this study, the authors manually define the descriptors of a solvation model to describe an implicit supercritical phase. In order to examine the suitability of supercritical water for thermal and hydrotreatment of bio-oil model compounds, nine different reactions involving conversion of furfural, tetrahydrofuran, xylose, phenol, guaiacol, ferulic acid, acetic acid, 2-hydroxybenzaldehyde and hydroxyacetone have been considered. Further these reactions are also studied in gas and liquid phase to compare results of different phases, including supercritical water. It was found that while HDO of aromatic compounds like phenol and 2-hydroxybenzaldehyde was favourable in the supercritical phase, smaller molecules like acetic acid and hydroxyacetone did not show much advantage in the supercritical phase over gas and liquid phase. It was also found that the thermochemical parameter - Gibbs free energy change (ΔG) was equally influenced by the solvation effect and the effect of temperature-pressure under supercritical conditions. In several instances, the two effects were found to offset each other in the supercritical phase.

DFT study on dibenzofuran conversion to cyclohexane and benzene in gas, water and methanol solvents.

Hydrodeoxygenation (HDO) of dibenzofuran is studied using density functional theory (DFT) with SMD implicit solvation model to give products like benzene and cyclohexane. Water and methanol are used as solvents, and gas-phase calculations are also performed for comparison. HDO is proposed via two major route- 1) saturation of phenyl rings followed by deoxygenation, 2) cleavage of C-O bond for oxy -removal followed by ring saturation. First, thermochemical parameters like Gibbs free energy change and enthalpy change are calculated at varying temperature in gas, water and methanol. Then, the solvation free energy is calculated for methanol and water to determine the ease of separation of products from the solvents. Finally, a Single Point Energy calculation is performed in the gas phase. It is found that water is the best solvent among three mediums and offers a significant advantage in some reactions such as the conversion of dibenzofuran to 1,2,3,4,4a,9b-hexahydrodibenzo[b,d]furan, 2-cyclohexyl phenol to bicyclo-hexan-2-ol and biphenyl to cyclohexyl benzene. Water is also found to be a better medium for separation of all the intermediates and products from the solvent over methanol. The effect of temperature was also studied, and it was found that the increase in temperature is unfavourable in all mediums for almost all reactions.

First-principles study on the gas-phase decomposition of bio-oil oxygenated compounds over the palladium catalyst surface.

Unprocessed bio-oils derived from the thermochemical conversion of lignocellulosic biomass suffer from low energy density primarily due to the presence of high amounts of oxygen functional groups. Therefore, the elimination of oxygen atoms over a suitable catalyst surface is viewed as one of the appropriate mechanisms for elevating the quality of bio-oils. Here, in this computational study, three oxygenated bio-oil model compounds, namely, 2-butenal, butan-2,3-diol, and butan-2,3-dione were considered as the representative compounds of the oxygenated catalogue of bio-oils. The decomposition mechanisms of these model compounds along with microkinetic modelling were studied over a palladium catalyst surface to produce low or no oxygen-containing products under the density functional theory (DFT) framework. Propene and methane were observed as the major products in the decomposition processes of 2-butenal and butan-2,3-dione, respectively. Butan-2,3-diol showed no major products due to high barriers. The increase in temperature was observed to be beneficial for improving the reaction rate constants; however, in many cases, the elevation of temperature shifted the equilibrium towards the reactants. CO acted as one of the major inhibitors due to the decarbonylation reaction of aldehydes.

DFT investigation on thermochemical analyses of conversion of xylose to linear alkanes in aqueous phase.

Xylose is an integral part of hemicellulose fraction of lignocellulosic biomass. Its abundance in the lignocellulose makes it a desirable component for converting into various value-added compounds. In this study, conversion of xylose to four linear alkanes has been discussed by five different schemes including their thermochemistry under the framework of density functional theory. Main products are butane, pentane, octane and tridecane whereas the intermediate products include furfural, tetrahydrofuran, pentane-1,5-diol, etc. The simulations have been performed at B3LYP/6-31 + g(d,p) and M06-2X/6-31 + g(d,p) level of theories in aqueous phase using SMD solvation model. Thermochemical parameters (ΔG, ΔH and Keq) are obtained at a wide range of temperature, i.e. 298-698 K. Single point energy change (ΔE) of all the conversion steps has also been calculated at M05-2X/6-311++g(3df,2p) level of theory in the aqueous phase. It is observed that temperature plays a vital role in the formation of products. At high temperature, only scheme RS 1 (i.e. xylose to butane) can proceed to produce butane. The absolute difference between two functionals, B3LYP and M06-2X, was found to be small (<2 kcal/mol) for ring opening reactions making both the functionals suitable for a qualitative study. For saturation of cyclic compounds, a large difference (>10 kcal/mol) was observed between the two functionals making higher accuracy method more suitable for them. For all other reactions, use of M06-2X can be preferred.

Molecular modeling approach to elucidate gas phase hydrodeoxygenation of guaiacol over a Pd(111) catalyst within DFT framework.

Excessive amounts of oxy-functional groups in unprocessed bio-oil vitiate its quality as fuel; therefore, it has to be channelized to upgrading processes, and catalytic hydrodeoxygenation is one of the most suitable routes for the upgrading of crude bio-oil. In this computational work, catalytic hydrodeoxygenation (HDO) of guaiacol, which is an important phenolic compound of crude bio-oil, has been carried out using density functional theory (DFT) over a Pd(111) catalyst. The Pd(111) catalyst surface does not endorse direct eliminations of functional groups of guaiacol; however, it is found to perform excellently in stepwise dehydrogenation reactions of oxy-functionals of guaiacol according to present DFT results. The catechol product, formed through dehydrogenation of the methoxy group, followed by elimination of CH2 and association of the hydrogen atom, has been identified as one of the major products. The overall reaction rate is controlled by scission of CH2 from 2-methylene-oxy-phenol with an activation energy demand of 23.06 kcal mol-1. Further, the kinetic analysis of each reaction step involved in HDO of guaiacol over the Pd(111) catalyst surface has also been carried out at atmospheric pressure and at a wide range of temperatures from 473 to 673 K, with temperature intervals of 50 K. In the kinetic analysis part, various kinetic parameters, such as forward and reverse reaction rate constants, Arrhenius constants, and equilibrium rate constants, are reported. The kinetic modeling of the dominating reaction steps has revealed that even a lower temperature of 473 K provides a favorable reaction environment; and the temperature increment further improves the reaction favorability.

Publisher Correction: Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Quantum chemical study on gas phase pyrolysis of p-isopropenylphenol.

In the pyrolysis of Sphagnum moss species, p-isopropenylphenol (p-IPP) is a major product which has been considered in this density functional theory based computational study for its conversion to various products such as benzene, phenol, 4-propenylphenol, indan-5-ol, 4-propylcyclohexanone, 4-cyclopropylphenol, etc. In order to achieve these products, eight different reaction schemes are performed using B3LYP/6-311 + g (d,p) level of theory. Further, thermodynamic properties such as reaction free energies and reaction enthalpies associated with these eight reaction schemes are developed in the temperature range of 298-898 K. The reaction schemes that include partial hydrogenation of the aromatic carbon followed by elimination of functional groups are found to demand low activation energy. The production of benzene from p-IPP with isopropenylbenzene as an intermediate product requiring only 19.83 kcal/mol of activation energy is the rate limiting reaction step. Indan-5-ol produced from p-IPP is validated with the literature results and found excellent agreement between two results. Furthermore, the temperature is found to have phenomenal effect in each reaction scheme.

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.

The rpoB gene encodes the ß subunit of RNA polymerase holoenzyme in Mycobacterium leprae (M. leprae). Missense mutations in the rpoB gene were identified as etiological factors for rifampin resistance in leprosy. In the present study, we identified mutations corresponding to rifampin resistance in relapsed leprosy cases from three hospitals in southern India which treat leprosy patients. DNA was extracted from skin biopsies of 35 relapse/multidrug therapy non-respondent leprosy cases, and PCR was performed to amplify the 276 bp rifampin resistance-determining region of the rpoB gene. PCR products were sequenced, and mutations were identified in four out of the 35 cases at codon positions D441Y, D441V, S437L and H476R. The structural and functional effects of these mutations were assessed in the context of three-dimensional comparative models of wild-type and mutant M. leprae RNA polymerase holoenzyme (RNAP), based on the recently solved crystal structures of RNAP of Mycobacterium tuberculosis, containing a synthetic nucleic acid scaffold and rifampin. The resistance mutations were observed to alter the hydrogen-bonding and hydrophobic interactions of rifampin and the 5' ribonucleotide of the growing RNA transcript. This study demonstrates that rifampin-resistant strains of M. leprae among leprosy patients in southern India are likely to arise from mutations that affect the drug-binding site and stability of RNAP.

Computational Study on Ring Saturation of 2-Hydroxybenzaldehyde Using Density Functional Theory.

Bio-oil produced from pyrolysis of lignocellulosic biomass consists of several hundreds of oxygenated compounds resulting in a very low quality with poor characteristics of low stability, low pH, low stability, low heating value, high viscosity, and so on. Therefore, to use bio-oil as fuel for vehicles, it needs to be upgraded using a promising channel. On the other hand, raw bio-oil can also be a good source of many specialty chemicals, e.g., 5-HMF, levulinic acid, cyclohexanone, phenol, etc. In this study, 2-hydroxybenzaldehyde, a bio-oil component that represents the phenolic fraction of bio-oil, is considered as a model compound and its ring saturation is carried out to produce cyclohexane and cyclohexanone along with various other intermediate products using density functional theory. The geometry optimization, vibrational frequency, and intrinsic reaction coordinate calculations are carried out at the B3LYP/6-311+g(d,p) level of theory. Furthermore, a single point energy calculation is performed at each structure at the M06-2X/6-311+g(3df,2p)//B3LYP/6-311+g(d,p) level of theory to accurately predict the energy requirements. According to bond dissociation energy calculations, the dehydrogenation of formyl group of 2-hydroxybenzaldehyde is the least energy demanding bond cleavage. The production of cyclohexane has a lower energy of activation than the production of cyclohexanone.

Molecular simulations of palladium catalysed hydrodeoxygenation of 2-hydroxybenzaldehyde using density functional theory.

The catalytic conversion of 2-hydroxybenzaldehyde (2-HB) is carried out numerically over a Pd(111) surface using density functional theory. The palladium catalyst surface is designed using a 12 atom monolayer and verified with the adsorption of phenol, benzene, anisole, guaiacol, and vanillin; it is found that the adsorption energies along with the adsorption configurations of phenol and benzene are in excellent agreement with the literature. The conversion of 2-HB over the Pd(111) catalyst surface is performed using four reaction schemes: (i) dehydrogenation of the formyl group followed by elimination of CO and association of hydrogen with 2-hydroxyphenyl to produce phenol, (ii) direct elimination of CHO from 2-HB followed by elimination of hydrogen from adsorbed CHO and association of hydrogen with 2-hydroxyphenyl to produce phenol, (iii) direct dehydroxylation of 2-HB followed by association of a hydrogen atom with 2-formylphenyl to produce benzaldehyde, and (iv) dehydrogenation of the hydroxyl group of 2-HB followed by elimination of an oxygen atom and association of a hydrogen atom with 2-formylphenyl to produce benzaldehyde. Along with the reaction mechanisms and their barrier heights, all reaction steps are considered for kinetic modelling in the temperature range 498-698 K with 50 K intervals. The rate constants, pre-exponential factors, and equilibrium constants of all elementary reaction steps are evaluated for each temperature. Kinetic analyses of the catalytic conversion of 2-HB over the Pd(111) surface suggests the production of phenol as an intermediate, instead of benzaldehyde, via dehydrogenation of the formyl group of 2-HB as a first elementary reaction step because of its low activation barrier and the high rate constant of the rate controlling step. Furthermore, the equilibrium constants of the rate controlling step in the production of phenol from 2-HB over the Pd(111) surface report a major fraction of the product in the product mixture even at a low temperature of 498 K.

Platinum catalyzed hydrodeoxygenation of guaiacol in illumination of cresol production: a density functional theory study.

The unprocessed bio-oil obtained by the pyrolysis of lignocellulosic biomass comprises hundreds of oxy-components which vitiate its quality in terms of low heating value, low stability, low pH, etc. Therefore, it has to be upgraded prior to its use as transportation fuel. In this work, guaiacol, a promising compound of the phenolic fraction of unprocessed bio-oil, is considered as a model component for studying its hydrodeoxygenation over a Pt3 catalyst cluster. The production of catechol, 3-methylcatechol, m-cresol and o-cresol from guaiacol over a Pt3 cluster is numerically investigated using density functional theory. Further, the kinetic parameters are obtained over a wide range of temperature, i.e. 473-673 K at an interval of 50 K. Briefly, results indicate that O─H and C─H bond scissions determine the reaction rates of 'guaiacol to catechol' and 'catechol to 3-methylcatechol' reactions with activation energies of 30.32 and 41.3 kcal mol-1, respectively. On the other hand, C─O bond scissions determine the rates of 3-methylcatechol to m- and o-cresol production reactions, respectively. The kinetics of all reactions indicate that ln k versus 1/T plots are linear over the entire range of temperature considered herein.

Structural analysis of the Leptospiral sphingomyelinases: in silico and experimental evaluation of Sph2 as an Mg-dependent sphingomyelinase.

BACKGROUND: Leptospiral sphingomyelinases are candidate virulence factors present only in pathogenic Leptospira spp. Leptospira interrogans serovar Lai encodes Sph1, Sph2, Sph3, Sph4 and SphH. Except for Sph4, they all possess the exo-endo-phosphatase domain that groups them under the DNase I superfamily. METHODS, RESULTS AND CONCLUSIONS: Modeling of exo-endo-phosphatase domains reveals high-level structural similarity of Sph2 with the crystal structure of SmcL and BC SMase sphingomyelinases from Listeria ivanovii and Bacillus cereus, respectively. A ß-hairpin loop, essential for host cell membrane interaction, is absent in leptospiral sphingomyelinases. Instead, several aromatic amino acids were oriented outward from the surface of these molecules and formed clusters of hydrophobic regions that possibly enables the anchoring of these molecules into the host cell membrane, as demonstrated in Sph2 and Sph3. Sph2 is unique and possesses the Mg(++)-binding Glu53 residue in the metal-binding site and two His residues (His151 and His286) in the catalytic site. We demonstrate experimentally the Mg(++)-dependent hemolysis of erythrocytes by rSph2 and its ability to cleave sphingomyelin to ceramide. Anti-Sph2 antibodies neutralized the hemolytic activity of Sph2. In conclusion, we provide evidence showing that Sph2 is a Mg(++)-dependent hemolysin with both sphingomyelinase and hemolytic activities.