Control Strategy Identification via Trap Spaces in Boolean Networks

The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables, force the system to evolve to a desired state. This work presents a new approach for finding control strategies in biological systems modeled by Boolean networks. In this context, we explore the properties of trap spaces, subspaces of the state space which the dynamics cannot leave. Trap spaces for biological networks can often be efficiently computed, and provide useful approximations of attraction basins. Our approach provides control strategies for a target phenotype that are based on interventions that allow the control to be eventually released. Moreover, our method can incorporate information about the attractors to find new control strategies that would escape usual percolation-based methods. We show the applicability of our approach to two cell fate decision models.Comment: 16 pages, 2 figure

Temporal Reprogramming of Boolean Networks

International audienceCellular reprogramming, a technique that opens huge opportunities in modern and regenerative medicine, heavily relies on identifying key genes to perturb. Most of computational methods focus on finding mutations to apply to the initial state in order to control which attractor the cell will reach. However, it has been shown, and is proved in this article, that waiting between the perturbations and using the transient dynamics of the system allow new reprogramming strategies. To identify these temporal perturbations, we consider a qualitative model of regulatory networks, and rely on Petri nets to model their dynamics and the putative perturbations. Our method establishes a complete characterization of temporal perturbations, whether permanent (mutations) or only temporary, to achieve the existential or inevitable reachability of an arbitrary state of the system. We apply a prototype implementation on small models from the literature and show that we are able to derive temporal perturbations to achieve trans-differentiation

Comparative results between hysteroscopic and transvaginal ultrasonographic findings in public service

Objective: To evaluate findings of transvaginal ultrasonography and video hysteroscopies in women from a reference center in Aracaju-SE, comparing the results among themselves and as biopsies performed. Method: Retrospective observational study with 361 women aged 20 to 81 years submitted to diagnostic hysteroscopy and ultrasonography, attended at the Center for Integral Attention to Women's Health (CAISM), where the age, origin, indication of hysteroscopy, ultrasonographic diagnosis, hysteroscopic and histopathological. Results: The studied population of 361 patients with average age of 46.61 years and standard deviation of 11.8. The most frequent ultrasonographic and hysteroscopic findings were for endometrial polyp with 50.69% (183) and 47.09% (170), respectively. Biopsies were performed in 250 patients, with 42.8% of them being the most frequent endometrial polyp (107). Among ultrasonographic and hysteroscopic findings, there was a significant association for the diagnosis of endometrial polyp (p-0.001), endometrial thickening (p-0.001) and submucous myoma (p-0.001). Comparing anatomopathological and hysteroscopic findings, there was a significant association between submucosal myoma and endometrial polyp (p-0.002 and p-0.001, respectively). There was no significant association for the diagnosis of endometrial thickening (p-0.382) and submucosal myoma (p-0.075) when comparing biopsies and ultrasonography, but seen for endometrial polyp (p-0.049). Conclusion: A main indication for hysteroscopy and the main result of anatomopathological examination for endometrial polyp. There was a significant association for the results of polyp, endometrial thickening and myoma when comparing hysteroscopy and ultrasonography, and in the comparison between this examination and biopsy there is only a significant association for polyp.Objetivo: Avaliar achados de ultrassonografia transvaginal e vídeo histeroscopias em mulheres oriundas de um centro de referência em Aracaju-SE, comparando os resultados entre si e com as biópsias realizadas. Método: Estudo observacional de caráter retrospectivo com 361 mulheres de 20 a 81 anos, submetidas à histeroscopia diagnóstica e ultrassonografia, atendidas no Centro de Atenção Integral a Saúde da Mulher (CAISM) onde avaliou-se idade, procedência, indicação da histeroscopia, diagnóstico ultrassonográfico, histeroscópico e histopatológico. Resultado: A população estudada foi de 361 pacientes com média de idade de 46,61 anos e desvio padrão de 11,8. O achado ultrassonográfico e histeroscópico mais frequentes foi pólipo endometrial com 50,69% (183) e 47,09% (170), respectivamente. Foram realizadas biópsias em 250 pacientes, tendo como achado mais frequente pólipo endometrial 42,80% (107). Entre os achados ultrassonográficos e histeroscópicos houve associação significativa para o diagnóstico de pólipo endometrial (p-0,001), espessamento endometrial (p-0,001) e mioma submucoso (p-0,001). Comparando-se os achados anatomopatológicos e histeroscópicos houve associação significativa para mioma submucoso e pólipo endometrial (p-0,002 e p-0,001, respectivamente). Não houve associação significativa para o diagnóstico de espessamento endometrial (p-0,382) e mioma submucoso (p-0,075) ao comparar-se biópsias e ultrassonografias, mas houve para pólipo endometrial (p-0,049). Conclusão: A principal indicação para histeroscopia e o principal resultado do exame anatomopatológico foi pólipo endometrial. Houve associação significativa para os resultados de pólipo, espessamento endometrial e mioma quando comparadas histeroscopia e ultrassonografia, sendo que na comparação entre este exame e biópsia só houve associação significativa para pólipo.Aracaju, S