Temporal Stream Logic: Synthesis beyond the Bools

Reactive systems that operate in environments with complex data, such as mobile apps or embedded controllers with many sensors, are difficult to synthesize. Synthesis tools usually fail for such systems because the state space resulting from the discretization of the data is too large. We introduce TSL, a new temporal logic that separates control and data. We provide a CEGAR-based synthesis approach for the construction of implementations that are guaranteed to satisfy a TSL specification for all possible instantiations of the data processing functions. TSL provides an attractive trade-off for synthesis. On the one hand, synthesis from TSL, unlike synthesis from standard temporal logics, is undecidable in general. On the other hand, however, synthesis from TSL is scalable, because it is independent of the complexity of the handled data. Among other benchmarks, we have successfully synthesized a music player Android app and a controller for an autonomous vehicle in the Open Race Car Simulator (TORCS.

Abstract Learning Frameworks for Synthesis

We develop abstract learning frameworks (ALFs) for synthesis that embody the principles of CEGIS (counter-example based inductive synthesis) strategies that have become widely applicable in recent years. Our framework defines a general abstract framework of iterative learning, based on a hypothesis space that captures the synthesized objects, a sample space that forms the space on which induction is performed, and a concept space that abstractly defines the semantics of the learning process. We show that a variety of synthesis algorithms in current literature can be embedded in this general framework. While studying these embeddings, we also generalize some of the synthesis problems these instances are of, resulting in new ways of looking at synthesis problems using learning. We also investigate convergence issues for the general framework, and exhibit three recipes for convergence in finite time. The first two recipes generalize current techniques for convergence used by existing synthesis engines. The third technique is a more involved technique of which we know of no existing instantiation, and we instantiate it to concrete synthesis problems

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

13 p.-7 fig.-1 tab.DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii)sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.This study was supported by the Ministerio de Economía y Competitividad (Grants BFU2008-02372/BMC; BFU2011-22588, BFU2014-53550 and Unidad de Excelencia Maria de Maeztu MDM-2014-0435 to MC; BIO2009-10964 and E-SCIENCE to MO;BFU2010-19597, PNEUMOTALK, and CSD2008-00013, INTERMODS, to GdS; Ramón and Cajal subprogramme RYC-2011-09071 to CM), the Generalitat de Catalunya (Grants 2014-SGR1309 to MC and SGR2009-1348 to MO),Fundación Marcelino Botín (MO) and the European Commission (Cooperation Project SILVER, GA No. 260644 to MC and SCALALIFE Project to MO).Peer reviewe

Cáncer pulmonar: prevención y pesquisa precoz

ResumenEl cáncer pulmonar es el más mortal de todos los cánceres. Debido a que la gran mayoría de los cánceres pulmonares son causados por el hábito de fumar, su erradicación es la mejor estrategia de prevención primaria. El diagnóstico del cáncer pulmonar en etapas tempranas mejora significativamente su pronóstico, por lo que ésta es la mejor estrategia de prevención secundaria. Recientemente se ha reportado que un programa de pesquisa de cáncer pulmonar con escáner de tórax (TAC) reduce la mortalidad por cáncer. El objetivo de esta revisión es, en primer lugar, apelar a la evidencia en cuanto al rendimiento de los programas de pesquisa de cáncer pulmonar en poblaciones de alto riesgo, y en segundo lugar, analizar las distintas estrategias que tiene un médico cuando se enfrenta a un paciente a quien se le ha encontrado incidentalmente un nódulo pulmonar.SummaryLung cancer is a deadly disease. Since this cancer is closely related to tobacco smoke, the best way to avoid this disease is smoking prevention. Unfortunately smoking is a worldwide epidemic and in Chile its prevalence is not decreasing. The second best strategy is an early detection. For the first time there is a report showing that screening with the use of low-dose CT reduces mortality from lung cancer. The prognosis is much better in early stages. The purpose of this publication is to review the evidence about screening of lung cancer, and to analyze the different strategies to deal, in the general practice, with a finding of a lung nodule

Learning Moore Machines from Input-Output Traces

The problem of learning automata from example traces (but no equivalence or membership queries) is fundamental in automata learning theory and practice. In this paper we study this problem for finite state machines with inputs and outputs, and in particular for Moore machines. We develop three algorithms for solving this problem: (1) the PTAP algorithm, which transforms a set of input-output traces into an incomplete Moore machine and then completes the machine with self-loops; (2) the PRPNI algorithm, which uses the well-known RPNI algorithm for automata learning to learn a product of automata encoding a Moore machine; and (3) the MooreMI algorithm, which directly learns a Moore machine using PTAP extended with state merging. We prove that MooreMI has the fundamental identification in the limit property. We also compare the algorithms experimentally in terms of the size of the learned machine and several notions of accuracy, introduced in this paper. Finally, we compare with OSTIA, an algorithm that learns a more general class of transducers, and find that OSTIA generally does not learn a Moore machine, even when fed with a characteristic sample

Outbreak of persistent cutaneous abscesses due to Mycobacterium chelonae after mesotherapy sessions, Lima, Peru

Surtos de micobactérias de crescimento rápido têm sido relatados ocasionalmente. O estudo relata um surto de abscessos cutâneos por Mycobacterium chelonae após sessões de mesoterapia em Lima, Peru. De dezembro de 2004 a janeiro de 2005, 35 pessoas que haviam passado por sessões de mesoterapia apresentaram esses abscessos cutâneos. Treze (37%) desses casos suspeitos concordaram em realizar exames clínicos. Foram realizadas biópsias de punção de pele de lesões suspeitas e examinadas substâncias injetadas durante a mesoterapia. Os casos suspeitos eram predominantemente mulheres jovens e as lesões incluíram nódulos subcutâneos, abscessos e úlceras. Mycobacterium chelonae foi isolada de quatro pacientes e de um frasco de procaína. Em conclusão, é importante considerar a mesoterapia como fonte potencial de infecções de micobactérias de crescimento rápido.Outbreaks of rapidly growing mycobacteria have been occasionally described. The article reports an outbreak of cutaneous abscesses due to Mycobacterium chelonae following mesotherapy in Lima, Peru. From December 2004 through January 2005, 35 subjects who had participated in mesotherapy training sessions presented with persistent cutaneous abscesses. Thirteen (37%) of these suspected cases consented to underwent clinical examination. Skin punch-biopsies were collected from suspicious lesions and substances injected during mesotherapy were analyzed. Suspected cases were mainly young women and lesions included subcutaneous nodules, abscesses and ulcers. Mycobacterium chelonae was isolated from four patients and from a procaine vial. In conclusion, it is important to consider mesotherapy as a potential source of rapidly growing mycobacteria infections