Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria

Experimental benchmark control problem for multi-axial real-time hybrid simulation

Advancing RTHS methods to readily handle multi-dimensional problems has great potential for enabling more advanced testing and synergistically using existing laboratory facilities that have the capacity for such experimentation. However, the high internal coupling between hydraulics actuators and the nonlinear kinematics escalates the complexity of actuator control and boundary condition tracking. To enable researchers in the RTHS community to develop and compare advanced control algorithms, this paper proposes a benchmark control problem for a multi-axial real-time hybrid simulation (maRTHS) and presents its definition and implementation on a steel frame excited by seismic loads at the base. The benchmark problem enables the development and validation of control techniques for tracking both translation and rotation degrees of freedom of a plant that consists of a steel frame, two hydraulic actuators, and a steel coupler with high stiffness that couples the axial displacements of the hydraulic actuators resulting in the required motion of the frame node. In this investigation, the different components of this benchmark were developed, tested, and a set of maRTHS were conducted to demonstrate its feasibility in order to provide a realistic virtual platform. To offer flexibility in the control design process, experimental data for identification purposes, finite element models for the reference structure, numerical, and physical substructure, and plant models with model uncertainties are provided. Also, a sample example of an RTHS design based on a linear quadratic Gaussian controller is included as part of a computational code package, which facilitates the exploration of the tradeoff between robustness and performance of tracking control designs. The goals of this benchmark are to: extend existing control or develop new control techniques; provide a computational tool for investigation of the challenging aspects of maRTHS; encourage a transition to multiple actuator RTHS scenarios; and make available a challenging problem for new researchers to investigate maRTHS approaches. We believe that this benchmark problem will encourage the advancing of the next-generation of controllers for more realistic RTHS methods

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. \ud \ud Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. \ud \ud Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria

Fields of research and quality of systematic reviews developed in Latin America: Scoping review

The purpose of this study is to evaluate the characteristics of systematic reviews reports published by authors affiliated to institutions(s) located in LAC or focused on health research in LAC countries

Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria