Necrotic enteritis (NE) is an important intestinal infectious disease of commercial poultry flocks caused by Clostridium perfringens. Using an experimental model of NE involving co-infection with C. perfringens and Eimeria maxima, transcriptome profiling and functional genomics approaches were applied to identify the genetic mechanisms that might regulate the host response to this disease. Micr...

Within the multibody systems literature, few attempts have been made to use automatic differentiation for solving forward multibody dynamics and evaluating its computational efficiency. The most relevant implementations are found in the sensitivity analysis field, but they rarely address automatic differentiation issues in depth. This paper presents a thorough analysis of automatic differentiat...

The C++ package ADOL-C described here facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C, C++, Fortran, or any other language that can be linked with C. The numerical values of derivative vectors are obtained free of truncation errors at a smal...

Many scientific applications benefit from the accurate and efficient computation of derivatives. Automatically generating these derivative computations from an applications source code offers a competitive alternative to other approaches, such as less accurate numerical approximations or labor-intensive analytical implementations. ADIC2 is a source transformation tool for generating code for co...

There are several AD tools available, which all implement different strategies for the reverse mode of AD. The major strategies are primal value taping (implemented e.g. by ADOL-c) and Jacobi taping (implemented e.g. by adept and dco/c++). Especially for Jacobi taping, recent advances by using expression templates make this approach very attractive for large scale software. The current implemen...

Using a model from a chromatographic separation process in chemical engineering, we demonstrate that large, sparse Jacobians of fairly complex structures can be computed accurately and efficiently by using automatic differentiation (AD) in combination with a four-step procedure involving matrix compression and de-compression. For the detection of sparsity pattern (step 1), we employ a new opera...

The resolution of genes that determine resistance to disease is described using chicken lines maintained at the Avian Disease and Oncology Laboratory (ADOL). This description includes a summary 1) of existing selected and inbred lines differing for resistance to viral-induced tumors, i.e., Marek's disease (MD) and lymphoid leukosis (LL), and of the use of inbred and line crosses to define relev...

We propose two efficient automatic differentiation (AD) schemes to compute incrementally Taylor series and System Jacobian for solving differential-algebraic equations (DAEs) by Taylor series. Our schemes are based on topological ordering of a DAE’s computational graph and then partitioning the topologically sorted nodes using structural information obtained from the DAE. Solving a DAE by Taylo...

Atopic dermatitis (AD) is a chronic, relapsing, inflammatory systemic condition. Recently, dupilumab has been reimbursed by Italian Medicines Agency (AIFA) for the treatment of adolescents (according to AIFA registry criteria) and adults with severe AD. Furthermore, it authorized European in children The objective this analysis was estimate incremental cost-effectiveness ratio (ICER) versus cur...