CAR: A MATLAB Package to Compute Correspondence Analysis with Rotations

Correspondence analysis (CA) is a popular method that can be used to analyse relationships between categorical variables. Like principal component analysis, CA solutions can be rotated both orthogonally and obliquely to simple structure without affecting the total amount of explained inertia. We describe a MATLAB package for computing CA. The package includes orthogonal and oblique rotation of axes. It is designed not only for advanced users of MATLAB but also for beginners. Analysis can be done using a user-friendly interface, or by using command lines. We illustrate the use of CAR with one example.

Expectations and Bubbles in Asset Pricing Experiments

We present results on expectation formation in a controlled experimental environment. In each period subjects are asked to predict the next price of a risky asset. The realized market price is derived from an unknown market equilibrium equation with feedback from individual forecasts. In most experiments prices deviate from the benchmark fundamental and bubbles emerge endogenously. These bubbles are inconsistent with rational expectations and seem to be driven by trend chasing behavior or “positive feedback expectations” of the participants. We also analyze individual predictions of participants and find that participants within a group tend to coordinate on a common prediction strategy

CAR:A MATLAB Package to Compute Correspondence Analysis with Rotations

Correspondence analysis (CA) is a popular method that can be used to analyse relationships between categorical variables. Like principal component analysis, CA solutions can be rotated both orthogonally and obliquely to simple structure without affecting the total amount of explained inertia. We describe a MATLAB package for computing CA. The package includes orthogonal and oblique rotation of axes. It is designed not only for advanced users of MATLAB but also for beginners. Analysis can be done using a user-friendly interface, or by using command lines. We illustrate the use of CAR with one example

Modifications to the Cauchy–Born rule: Applications in the deformation of single-walled carbon nanotubes

AbstractThis paper presents a study of the Cauchy–Born (CB) rule as applied to the deformation analysis of single-walled carbon nanotubes (SWNTs) that are modeled as 2-dimensional manifolds. The C–C bond vectors in the SWNT are assumed to deform according to the local deformation gradient as per the CB rule or a modified version thereof. Aspects of the CB rule related to spatial inhomogeneity of the deformation gradient at the atomic scale are investigated in the context of a specific class of extension–twist deformation problems. Analytic expressions are derived for the deformed bond lengths using the standard CB rule as well as modified versions of the standard CB rule. Since the deformation map is conveniently prescribed in this work, it is possible to compare the performance of these deformation rules with the exact solution (i.e. the exact analytic expression for the deformed bond vectors) given directly by the deformation map. This approach provides insights into the CB rule and its possible modifications for use in more complicated deformations where an explicit deformation map is not available. Specifically, it is concluded that in the case of inhomogeneous deformations at the atomic scale for which the CB rule is only approximate (as demonstrated in Section 1 of this paper), the mean value theorem in calculus can be used as a guide to modify the CB rule and construct a more rigorous and accurate atomistic–continuum connection. The deformed bond lengths are used to formulate an enriched continuum hyperelastic strain energy density function based on interatomic potentials (the multi-body Tersoff–Brenner [Tersoff, J., 1988. New empirical approach for the structure and energy of covalent systems. Phys. Rev. B 37, 6991–7000; Brenner, D.W., 1990. Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Phys. Rev. B 42, 9458–9471] empirical interatomic potential for carbon-carbon bonds is used in this work). The deformation map (and hence the deformation gradient, the bond vectors and the continuum strain energy density) contains certain parameters, some of which are imposed and others determined as a result of energy minimization in the standard variational formulation. Numerical results for kinematic coupling and binding energy per atom are presented in the case of imposed extension and twist deformations on representative chiral, zig-zag and armchair nanotubes using the CB rule and its modifications. These results are compared with the exact solution based on the deformation map which serves as a basis for evaluating the efficacy of these deformation rules. The ideas presented in this paper can also be directly extended to other lattices

Patients with Biallelic BRCA1/2 Inactivation respond to Olaparib treatment across Histologic tumor types

Purpose: To assess the efficacy of olaparib, a PARP inhibitor (PARPi) in patients with tumors with BRCA1/2 mutations, regardless of histologic tumor type. Patients and Methods: Patients with treatment-refractory BRCA1/2-mutated cancer were included for treatment with offlabel olaparib 300 mg twice daily until disease progression or unacceptable toxicity. In Drug Rediscovery Protocol (DRUP), patients with treatment-refractory solid malignancies receive offlabel drugs based on tumor molecular profiles while whole-genome sequencing (WGS) is performed on baseline tumor biopsies. The primary endpoint was clinical benefit (CB; defined as objective response or stable disease ≥ 16 weeks according to RECIST 1.1). Per protocol patients were enrolled using a Simon-like two-stage model. Results: Twenty-four evaluable patients with nine different tumor types harboring BRCA1/2 mutations were included, 58% had CB from treatment with olaparib. CB was observed in patients with complete loss of function (LoF) of BRCA1/2, while 73% of patients with biallelic BRCA LoF had CB. In 17 patients with and seven without current labeled indication, 10 and four patients had CB, respectively. Treatment resistance in four patients with biallelic loss might be explained by an additional oncogenic driver which was discovered by WGS, including Wnt pathway activation, FGFR amplification, and CDKN2A loss, in three tumor types. Conclusions: These data indicate that using PARPis is a promising treatment strategy for patients with non-BRCA-associated histologies harboring biallelic BRCA LoF. WGS allows to accurately detect complete LoF of BRCA and homologous repair deficiency (HRD) signature as well as oncogenic drivers that may contribute to resistance, using a single assay

Patients with Rare Cancers in the Drug Rediscovery Protocol (DRUP) Benefit from Genomics-Guided Treatment

Purpose: Patients with rare cancers (incidence less than 6 cases per 100,000 persons per year) commonly have less treatment opportunities and are understudied at the level of genomic targets. We hypothesized that patients with rare cancer benefit from approved anticancer drugs outside their label similar to common cancers. Experimental Design: In the Drug Rediscovery Protocol (DRUP), patients with therapy-refractory metastatic cancers harboring an actionable molecular profile are matched to FDA/European Medicines Agency–approved targeted therapy or immunotherapy. Patients are enrolled in parallel cohorts based on the histologic tumor type, molecular profile and study drug. Primary endpoint is clinical benefit (complete response, partial response, stable disease ≥ 16 weeks). Results: Of 1,145 submitted cases, 500 patients, including 164 patients with rare cancers, started one of the 25 available drugs and were evaluable for treatment outcome. The overall clinical benefit rate was 33% in both the rare cancer and nonrare cancer subgroup. Inactivating alterations of CDKN2A and activating BRAF aberrations were overrepresented in patients with rare cancer compared with nonrare cancers, resulting in more matches to CDK4/6 inhibitors (14% vs. 4%; P ≤ 0.001) or BRAF inhibitors (9% vs. 1%; P ≤ 0.001). Patients with rare cancer treated with small-molecule inhibitors targeting BRAF experienced higher rates of clinical benefit (75%) than the nonrare cancer subgroup. Conclusions: Comprehensive molecular testing in patients with rare cancers may identify treatment opportunities and clinical benefit similar to patients with common cancers. Our findings highlight the importance of access to broad molecular diagnostics to ensure equal treatment opportunities for all patients with cancer