Operational semantics of a domain specific language for real time musician–computer interaction

With the advent and availability of powerful personal computing, the computer music research and industry have been focusing on real-time musical interactions between musicians and computers; delegating human-like actions to computers who interact with a musical environment. One common use-case of this kind is Automatic Accompaniment where the system is comprised of a real-time machine listening system that in reaction to recognition of events in a score from a human performer, launches necessary actions for the accompaniment section. While the real-time detection of score events out of live musicians’ performance has been widely addressed in the literature, score accompaniment (or the reactive part of the process) has been rarely discussed. This paper deals with this missing component in the literature from a formal language perspective. We show how language considerations would enable better authoring of time and interaction during programming/composing and how it addresses critical aspects of a musical performance (such as errors) in real-time. We sketch the real-time features required by automatic musical accompaniment seen as a reactive system. We formalize the timing strategies for musical events taking into account the various temporal scales used in music. Various strategies for the handling of synchronization constraints and the handling of errors are presented. We give a formal semantics to model the possible behaviors of the system in terms of Parametric Timed Automata.     

A decision-oriented model to evaluate the effect of land use and agricultural management on herbicide contamination in stream water

Modelling stream water pollution by herbicides in agricultural areas is a critical issue since numerous and incompletely known processes are involved. A decision-oriented model, SACADEAU-Transf, which represents water and pesticide transfer in medium-sized catchments (10–50 km²) is presented. This model aims at evaluating the effect of land use, agricultural practice and landscape on the contamination of stream water in rural catchments. The processes are represented in an easily understandable way with a moderate amount of information, producing semi-quantitative and spatialized outputs. Modelling focuses on the first few months after herbicide application when high levels of contamination are generally observed, by considering transfer through the catchment area via surface and subsurface flow. The surface flow, based on a tree plot network representation of the catchment, is controlled by soil-surface properties and saturated conditions. The subsurface flow based on Topmodel concepts is controlled by the topography. Herbicide transfer is coupled to water transfer by taking into account the main characteristics of the chemicals. The model simulates the daily water and herbicide outflow at the outlets of the farmers' fields as well as from the catchment. Preliminary results on maize herbicide transfer are presented for an agricultural catchment with an area of 17 km² located in north-western France. The relevance of SACADEAU-Transf model is discussed in view of the qualities required for the decision-oriented models developed for improving agro-environmental management.     

Modeling the short-circuit current density of polymer solar cells based on P3HT:PCBM blend

We have investigated the short-circuit current density of organic solar cells based on poly (3-hexylthiophene)(P3HT)/6,6-phenyl C61-butyric acid methyl ester (PCBM) blend. In order to model charge collection efficiencies with respect to short circuit density in such blends, a full optical modeling of the cell is performed. From the distribution of the electromagnetic field, we compute the rate of exciton generation. This exciton generation rate is used as input in the transport equations of holes and electrons. Charge densities at steady state are obtained as solutions are used for computing short-circuit current densities generated in the cell. The dependence of short-circuit current densities versus the thickness of the blend is analyzed and compared with our experimental data and with data extracted from the literature.     

Tyro3 Targeting as a Radiosensitizing Strategy in Bladder Cancer through Cell Cycle Dysregulation

Bladder cancer is a common cancer; it is the tenth most common cancer in the world. Around one fourth of all diagnosed patients have muscle-invasive bladder cancer (MIBC), characterized by advanced tumors and which remains a lethal disease. The standard treatment for MIBC is the bladder removal by surgery. However, bladder-preserving alternatives are emerging by combining chemotherapy, radiotherapy and minimal surgery, aiming to increase the patient’s quality of life. The aim of the study was to improve these treatments by investigating a novel approach where in addition to radiotherapy, a receptor, TYRO3, a member of TAM receptor tyrosine kinase family known to be highly expressed on the bladder cancer cells and involved in the control of cell survival is targeted. For this, we evaluated the influence of TYRO3 expression levels on a colony or cell survival assays, DNA damage, γH2AX foci formation, gene expression profiling and cell cycle regulation, after radiation on different bladder cell models. We found that TYRO3 expression impacts the radiation response via the cell cycle dysregulation with noeffets on the DNA repair. Therefore, targeting TYRO3 is a promising sensitization marker that could be clinically employed in future treatments.     

Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes

Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.     

Labeled TEMPO-Oxidized Mannan Differentiates Binding Profiles within the Collectin Families

Establishing the rapid and accurate diagnosis of sepsis is a key component to the improvement of clinical outcomes. The ability of analytical platforms to rapidly detect pathogen-associated molecular patterns (PAMP) in blood could provide a powerful host-independent biomarker of sepsis. A novel concept was investigated based on the idea that a pre-bound and fluorescent ligand could be released from lectins in contact with high-affinity ligands (such as PAMPs). To create fluorescent ligands with precise avidity, the kinetically followed TEMPO oxidation of yeast mannan and carbodiimide coupling were used. The chemical modifications led to decreases in avidity between mannan and human collectins, such as the mannan-binding lectin (MBL) and human surfactant protein D (SP-D), but not in porcine SP-D. Despite this effect, these fluorescent derivatives were captured by human lectins using highly concentrated solutions. The resulting fluorescent beads were exposed to different solutions, and the results showed that displacements occur in contact with higher affinity ligands, proving that two-stage competition processes can occur in collectin carbohydrate recognition mechanisms. Moreover, the fluorescence loss depends on the discrepancy between the respective avidities of the recognized ligand and the fluorescent mannan. Chemically modulated fluorescent ligands associated with a diversity of collectins may lead to the creation of diagnostic tools suitable for multiplex array assays and the identification of high-avidity ligands.     

PVS#: Streamlined Tacticals for PVS

The semantics of a proof language relies on the representation of the state of a proof after a logical rule has been applied. This information, which is usually meaningless from a logical point of view, is fundamental to describe the control mechanism of the proof search provided by the language. In this paper, we present a monadic datatype to represent the state information of a proof and we illustrate its use in the PVS theorem prover. We show how this representation can be used to design a new set of powerful tacticals for PVS, called PVS#, that have a simpler and clearer semantics compared to the semantics of standard PVS tacticals.     

MyLabStocks: a web‐application to manage molecular biology materials

Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web‐based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user‐defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens‐lyon.fr/redmine/projects/mylabstocks under an open source licence. © 2014 Laboratoire de Biologie Moleculaire de la Cellule CNRS. Yeast published by John Wiley & Sons, Ltd.     

Proteomic analysis of BRCA1-depleted cell line reveals a putative role for replication protein A2 up-regulation in BRCA1 breast tumor development

Purpose : Germline mutations in BRCA1 result in a strong predisposition to breast cancer, with frequent loss of heterozygosity of the remaining wild‐type allele. The development of BRCA1 tumors is likely to depend on additional genetic alterations and gene expression changes which follow growth and DNA repair defects associated with BRCA1 deficiency. The identification of these modifications offers an opportunity to find surrogate markers of BRCA1 tumors. Here, we sought to identify differentially expressed proteins related to BRCA1 depletion. Experimental design : We used isogenic HeLa cells either stably knocked‐down or not for BRCA1 (BRCA1^KD) and compared protein profiles of these cells by DIGE. Results : We detected increased levels of Replication protein A2 (RPA2) in BRCA1^KD cells as compared to control cells. RPA2 is an essential protein required for DNA replication and repair. We further demonstrated that depletion of RPA2 subunit delays growth of BRCA1^KD respect to isogenic control cells. Strikingly, elevated levels of RPA2 were more frequently observed in BRCA1 tumors when triple‐negative tumors from BRCA1 mutation carriers (n=13) and non‐carriers (n=36) were stained in situ for RPA2. Conclusions and clinical relevance : RPA2 up‐regulation may thus be involved in the growth and/or survival of BRCA1 tumor cells and useful in immunohistochemical discrimination of triple‐negative BRCA1 tumors.