Computing Equilibrium in Matching Markets

Market equilibria of matching markets offer an intuitive and fair solution for matching problems without money with agents who have preferences over the items. Such a matching market can be viewed as a variation of Fisher market, albeit with rather peculiar preferences of agents. These preferences can be described by piece-wise linear concave (PLC) functions, which however, are not separable (due to each agent only asking for one item), are not monotone, and do not satisfy the gross substitute property-- increase in price of an item can result in increased demand for the item. Devanur and Kannan in FOCS 08 showed that market clearing prices can be found in polynomial time in markets with fixed number of items and general PLC preferences. They also consider Fischer markets with fixed number of agents (instead of fixed number of items), and give a polynomial time algorithm for this case if preferences are separable functions of the items, in addition to being PLC functions. Our main result is a polynomial time algorithm for finding market clearing prices in matching markets with fixed number of different agent preferences, despite that the utility corresponding to matching markets is not separable. We also give a simpler algorithm for the case of matching markets with fixed number of different items

Aerodynamic Characterisation of Ramjet Missile through Combined External-internal Computational Fluid Dynamics Simulation

Combined external-internal flow simulation is required for the estimation of aerodynamic forces and moments of high speed air-breathing vehicle design. A wingless, X-tail configuration with asymmetrically placed rectangular air intake is numerically explored for which experimental data is available for different angles of attack. The asymmetrically placed air intakes and protrusions make the flow field highly three-dimensional and existing empirical relations are inadequate for preliminary design. Three dimensional Navier Stokes equations along with SST-kω turbulence model were solved with a commercial CFD solver to analyse the combined external and internal flow field of the configuration at different angles of attack. Estimated aerodynamic coefficients match well with experimental data and estimated drag coefficient are within 8.5 per cent of experimental data. Intake performance parameters were also evaluated for different angles of attack

Carbon Nanotube–Purification and Sorting Protocols

Carbon nanotubes (CNTs) have shown extraordinary mechanical, thermal, electrical, and electronic properties. Electronic properties of CNT are very sensitive to its diameter and chirality, making it metallicor semiconducting, depending upon its chiral vector. The extraordinary properties of CNTs have led to demonstration of several applications but commercial realisation of these devices require consistent qualityof CNTs, and these should be  free of any impurity. For development of electronic devices, CNTs should notjust be pure but also of similar length, diameter, and electronic behaviour. Such demanding requirements need development of elaborate purification and sorting protocols. In this paper,  a brief review of the existing technologies and the research done is presented.Defence Science Journal, 2008, 58(5), pp.591-599, DOI:http://dx.doi.org/10.14429/dsj.58.169

Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of protein-targets.

Docking scores and simulation parameters to study the potency of natural compounds against protein targets in (M) were retrieved through molecular docking and structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding M target proteins. M protein targets were actively involved in translation mechanism, nucleic acid metabolism and membrane integrity. Standard structural screening and stereochemical optimizations were adopted to generate the 3D protein structures and their corresponding ligands prior to molecular docking. Force-field integration and energy minimization were further employed to obtain the proteins in their ideal geometry. Surflex-dock algorithm using Hammerhead scoring functions were used to finally produce the docking scores between each protein and the corresponding ligand(s). The best-docked complexes selected for simulation studies were subjected to topology adjustments, charge neutralizations, solvation and equilibrations (temperature, volume and pressure). The protein-ligand complexes and molecular dynamics parameter files have been provided. The trajectories of the simulated parameters such as density, pressure and temperature were generated with integrated tools of the simulation suite. The datasets can be useful to computational and molecular medicine researchers to find therapeutic leads relevant to the chemical behaviours of a specific class of compounds against biological systems. Structural parameters and energy functions provided a set of standard values that can be utilised to design simulation experiments regarding similar macromolecular interactions

Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer

Circulating tumor DNA (ctDNA) in peripheral blood has been used to predict prognosis and therapeutic response for triple-negative breast cancer (TNBC) patients. However, previous approaches typically use large comprehensive panels of genes commonly mutated across all breast cancers. Given the reduction in sequencing costs and decreased turnaround times associated with panel generation, the objective of this study was to assess the use of custom micro-panels for tracking disease and predicting clinical outcomes for patients with TNBC. Paired tumor-normal samples from patients with TNBC were obtained at diagnosis (T0) and whole exome sequencing (WES) was performed to identify somatic variants associated with individual tumors. Custom micro-panels of 4-6 variants were created for each individual enrolled in the study. Peripheral blood was obtained at baseline, during Cycle 1 Day 3, at time of surgery, and in 3-6 month intervals after surgery to assess variant allele fraction (VAF) at different timepoints during disease course. The VAF was compared to clinical outcomes to evaluate the ability of custom micro-panels to predict pathological response, disease-free intervals, and patient relapse. A cohort of 50 individuals were evaluated for up to 48 months post-diagnosis of TNBC. In total, there were 33 patients who did not achieve pathological complete response (pCR) and seven patients developed clinical relapse. For all patients who developed clinical relapse and had peripheral blood obtained ≤ 6 months prior to relapse (n = 4), the custom ctDNA micro-panels identified molecular relapse at an average of 4.3 months prior to clinical relapse. The custom ctDNA panel results were moderately associated with pCR such that during disease monitoring, only 11% of patients with pCR had a molecular relapse, whereas 47% of patients without pCR had a molecular relapse (Chi-Square; p-value = 0.10). In this study, we show that a custom micro-panel of 4-6 markers can be effectively used to predict outcomes and monitor remission for patients with TNBC. These custom micro-panels show high sensitivity for detecting molecular relapse in advance of clinical relapse. The use of these panels could improve patient outcomes through early detection of relapse with preemptive intervention prior to symptom onset