Impact of adaptive gastric electrical stimulation on weight, food intake, and food intake rate in dogs.

BACKGROUND: Gastric electrical stimulation (GES) has been studied for decades as a promising treatment for obesity. Stimulation pulses with fixed amplitude and pulse width are usually applied, but these have limitations with regard to overcoming habituation to GES and inter-subject variation. This study aims to analyze the efficacy of an adaptive GES protocol for reducing food intake and maintaining lean weight in dogs. METHODS: Six beagle dogs were implanted with a remotely programmable gastric stimulator. An adaptive protocol was designed to increase the stimulation energy proportionally to the excess of food consumption, with respect to the dogs' maintenance energy requirements. After surgery and habituation to experimental conditions, the dogs went through both a control and a stimulation period of 4 weeks each, in a randomized order. The stimulation parameters were adapted daily. Body weight, food intake, food intake rate, and postprandial cutaneous electrogastrograms (EGG) were recorded to assess the effect of adaptive GES. RESULTS: Adaptive GES decreased food intake and food intake rate (p < 0.05) resulting in weight maintenance. In the absence of GES, the dogs gained weight (p < 0.05). Postprandial EGG dominant frequency was accelerated by GES (p < 0.05). The strategy of adapting the stimulation energy was effective in causing significant mid-term changes. CONCLUSION: Adaptive GES is effective for reducing food intake and maintaining lean weight. The proposed adaptive strategy may offer benefits to counter habituation and adapt to inter-subject variation in clinical use of GES for obesity.

In Vivo Validation of a Less Invasive Gastrostimulator.

Gastrointestinal stimulator implants have recently shown promising results in helping obese patients lose weight. However, to place the implant, the patient currently needs to undergo an invasive surgical procedure. We report a less invasive procedure to stimulate the stomach with a gastrostimulator. After attempting fully endoscopic implantation, we more recently focused on a single incision percutaneous procedure. In both cases, the challenges in electronic design of the implant are largely similar. This article covers the work achieved to meet these and details the in vivo validation of a gastrostimulator aimed to be endoscopically placed and anchored to the stomach.

Deciphering transcriptional regulations coordinating the response to environmental changes.

BACKGROUND: Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless, the prediction of TRNs based on the affinity of transcription factors (TFs) with binding sites (BSs) generally produces an over-estimation of the observable TF/BS relations within the network and therefore many of the predicted relations are spurious. RESULTS: We present LOMBARDE, a bioinformatics method that extracts from a TRN determined from a set of predicted TF/BS affinities a subnetwork explaining a given set of observed co-expressions by choosing the TFs and BSs most likely to be involved in the co-regulation. LOMBARDE solves an optimization problem which selects confident paths within a given TRN that join a putative common regulator with two co-expressed genes via regulatory cascades. To evaluate the method, we used public data of Escherichia coli to produce a regulatory network that explained almost all observed co-expressions while using only 19 % of the input TF/BS affinities but including about 66 % of the independent experimentally validated regulations in the input data. When all known validated TF/BS affinities were integrated into the input data the precision of LOMBARDE increased significantly. The topological characteristics of the subnetwork that was obtained were similar to the characteristics described for known validated TRNs. CONCLUSIONS: LOMBARDE provides a useful modeling scheme for deciphering the regulatory mechanisms that underlie the phenotypic responses of an organism to environmental challenges. The method can become a reliable tool for further research on genome-scale transcriptional regulation studies.

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.

MOTIVATION: The increasing availability of metabolomics data enables to better understand the metabolic processes involved in the immediate response of an organism to environmental changes and stress. The data usually come in the form of a list of metabolites whose concentrations significantly changed under some conditions, and are thus not easy to interpret without being able to precisely visualize how such metabolites are interconnected. RESULTS: We present a method that enables to organize the data from any metabolomics experiment into metabolic stories. Each story corresponds to a possible scenario explaining the flow of matter between the metabolites of interest. These scenarios may then be ranked in different ways depending on which interpretation one wishes to emphasize for the causal link between two affected metabolites: enzyme activation, enzyme inhibition or domino effect on the concentration changes of substrates and products. Equally probable stories under any selected ranking scheme can be further grouped into a single anthology that summarizes, in a unique subnetwork, all equivalently plausible alternative stories. An anthology is simply a union of such stories. We detail an application of the method to the response of yeast to cadmium exposure. We use this system as a proof of concept for our method, and we show that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further show that this response is mostly based on enzyme activation. We also provide a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. We discuss several interpretations for the changes we see, and we suggest hypotheses that could in principle be experimentally tested. Noticeably, our method requires simple input data and could be used in a wide variety of applications. AVAILABILITY AND IMPLEMENTATION: The code for the method presented in this article is available at http://gobbolino.gforge.inria.fr.

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

MOTIVATION: In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal subsets of that are able to produce all the metabolites in T. Such subsets are called the minimal precursor sets of T. The problem is then whether we can enumerate all of them efficiently. RESULTS: We propose a new characterization of precursor sets as the inputs of reaction sets called factories and an efficient algorithm to decide if a set of sources is precursor set of T. We show proofs of hardness for the problems of finding a precursor set of minimum size and of enumerating all minimal precursor sets T. We propose two new algorithms which, despite the hardness of the enumeration problem, allow to enumerate all minimal precursor sets in networks with up to 1000 reactions. AVAILABILITY: Source code and datasets used in our benchmarks are freely available for download at http://sites.google.com/site/pitufosoftware/download. CONTACT: vicente77@gmail.com, pvmilreu@gmail.com or marie-france.sagot@inria.fr.

Unveiling abundance-dependent metabolic phenotypes of microbial communities.

IMPORTANCE: In nature, organisms live in communities and not as isolated species, and their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question. In this work, we provide a novel approach that, only using genomic information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding light of the degrees of metabolic plasticity inherent to the community.

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Endosymbiotic bacteria from different species can live inside cells of the same eukaryotic organism. Metabolic exchanges occur between host and bacteria but also between different endocytobionts. Since a complete genome annotation is available for both, we built the metabolic network of two endosymbiotic bacteria, Sulcia muelleri and Baumannia cicadellinicola, that live inside specific cells of the sharpshooter Homalodisca coagulata and studied the metabolic exchanges involving transfers of carbon atoms between the three. We automatically determined the set of metabolites potentially exogenously acquired (seeds) for both metabolic networks. We show that the number of seeds needed by both bacteria in the carbon metabolism is extremely reduced. Moreover, only three seeds are common to both metabolic networks, indicating that the complementarity of the two metabolisms is not only manifested in the metabolic capabilities of each bacterium, but also by their different use of the same environment. Furthermore, our results show that the carbon metabolism of S. muelleri may be completely independent of the metabolic network of B. cicadellinicola. On the contrary, the carbon metabolism of the latter appears dependent on the metabolism of S. muelleri, at least for two essential amino acids, threonine and lysine. Next, in order to define which subsets of seeds (precursor sets) are sufficient to produce the metabolites involved in a symbiotic function, we used a graph-based method, PITUFO, that we recently developed. Our results highly refine our knowledge about the complementarity between the metabolisms of the two bacteria and their host. We thus indicate seeds that appear obligatory in the synthesis of metabolites are involved in the symbiotic function. Our results suggest both B. cicadellinicola and S. muelleri may be completely independent of the metabolites provided by the co-resident endocytobiont to produce the carbon backbone of the metabolites provided to the symbiotic system (., thr and lys are only exploited by B. cicadellinicola to produce its proteins).

Optimization and assessment of a novel gastric electrode anchoring system designed to be implanted by minimally invasive surgery.

A novel electrode anchoring design and its implantation procedure, aiming for a minimally invasive solution for gastric electrical stimulation, are presented. The system comprises an anchor made of a flexible body embedding two needle-shaped electrodes. The electrodes can easily switch from a parallel position - to pierce the stomach - to a diverging position - enabling them to remain firmly anchored into the muscular layer of the stomach. Key device parameters governing anchoring stability were assessed on a traction test bench, and optimal values were derived. The device was then implanted in six dogs by open surgery to assess its anchoring durability in vivo. Computed tomography images showed that the electrodes remained well placed within the dogs' gastric wall over the entire assessment period (more than one year). Finally, a prototype of a surgical tool for the minimally invasive device placement was manufactured, and the anchoring procedure was tested on a dog cadaver, providing the proof of concept of the minimally invasive implantation procedure. The use of our electrode anchoring system in long-term gastric electrical stimulation is promising in terms of implantation stability (the anchor withstands a force up to 0.81 N), durability (the anchor remains onto the stomach over one year) and minimal invasiveness of the procedure (the diameter of the percutaneous access is smaller than 12 mm). Moreover, the proposed design could have clinical applications in other hollow organs, such as the urinary bladder.

Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways.

Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.

Inductive Powering of Subcutaneous Stimulators: Key Parameters and Their Impact on the Design Methodology.

Inductive powering of implantable medical devices involves numerous factors acting on the system efficiency and safety in adversarial ways. This paper lightens up their role and identifies a procedure enabling the system design. The latter enables the problem to be decoupled into four principal steps: the frequency choice, the magnetic link optimization, the secondary circuit and then finally the primary circuit designs. The methodology has been tested for the powering system of a device requirering a power of 300mW and implanted at a distance of 15 to 30mm from the outside power source. It allowed the identification of the most critical parameters. A satisfying efficiency of 34% was reached at 21mm and tend to validate the proposed design procedure.

Power Strategy in DC/DC Converters to Increase Efficiency of Electrical Stimulators.

Power efficiency is critical for electrical stimulators. Battery life of wearable stimulators and wireless power transmission in implanted systems are common limiting factors. Boost DC/DC converters are typically needed to increase the supply voltage of the output stage. Traditionally, boost DC/DC converters are used with fast control to regulate the supply voltage of the output. However, since stimulators are acting as current sources, such voltage regulation is not needed. Banking on this, this paper presents a DC/DC conversion strategy aiming to increase power efficiency. It compares, in terms of efficiency, the traditional use of boost converters to two alternatives that could be implemented in future hardware designs.

Enumeration of minimal stoichiometric precursor sets in metabolic networks.

BACKGROUND: What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. RESULTS: Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. CONCLUSIONS: The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.

Design and Implementation of a Less Invasive Gastrostimulator.

Gastrointestinal stimulator implants have recently shown positive results in helping obese patients lose weight. However, to place the implant, the patient currently needs to undergo an invasive surgical procedure. Our team is aiming for a less invasive procedure to stimulate the stomach with a gastrostimulator. Attempts covered fully endoscopic implantation and, more recently, we have focussed on a single incision laparoscopic procedure. Whatever the chosen implantation solution, the electronic design of the implant system shares many challenges. This paper covers the work achieved to meet these.

Diabetes gestacional, hipotiroidismo y concentración urinaria de yodo en embarazadas. Yodurias en escolares en Paraguay: Exceso de yodo en la sal y riesgo de hiper e hipotiroidismo / Gestational diabetes, hypothyroidism and iodine urinary concentration in pregnant women. Urinary iodine in schoolage children in Paraguay: Iodine excess in salt and hyper and hypothyroidism risk

The main inclicator of iodine nutritional status of salt for human con-sumption is the urinary concentration of iodine, which is useful in monitoring universal levels in salt. Paraguay has suffered deficiency in salt with highprevalence of goiter in thepopulation reaching48.6%. In 2000, results of the ThyroidMobileproject in Latin America showed a goiter prevalence of 17% but 79.6% of the consumed iodized salt was adequate in paraguayan households (more than 15 ppm of iodine). The average values of iodine urinary concentration in 4487 scholars was 437 µg/L, 30% of the average value was between the ideal of 100 to 199 µg/L and 46.1% were above 300 mg/L, with risk of excess iodine. Urinary concentration of iodine during pregnancy was measure for the first time in Paraguay in 200 women; the average was 484 µg/L but diabetes and hypothyroidism during pregnancy was observe in 50% of them. Objective: Determine iodine concentration in urine of the school population in 17 departments of the country and measure the levels of iodine in urine in 200 pregnant women from 15-37 years of age and their levels of glycaemia, and thyroid TSH. Methods: During the years, 2006 and 2007 were evaluated 4487 school randomized, in a probabilistic sample, 3198 in rural areas and 1,289 in urban areas; casual urine samples was collected to determine iodine content. The urinary concentration of iodine in two hundredpregnant women, concentration of iodine in salt, and levels of glycaemia and TSH were also included in the present study All candidates agreed with the informed consent under the ethics rules. Results: These data showed by comparing the levels of iodine in urine concentration in more than adequate and excessive level but this last was markedly elevated (93.8%). The median level greater than 300 µg/L was observed in 100% of the 4,487 urine samples, while the median urinary iodine levels of300-500 µg/L was 91.3% and above 500 was 9.7%. These levels showed the risk of developing thyroid autoimmune diseases. In 200 pregnancy women the average of urine concentration of iodine was 498 pcg/L, subclinical and clinical hypothyroidism and gestational diabetes was 50% of both. Conclu-sion: To obtain normal median urinary iodine levels is necessary to decrease the amount of iodine in salt. The main recommendation is to insist on adequate monitoring of iodized salt consumption. Also continue surveillance and monitoring in sentinel sites reporting the importance of adequate iodine intake of the population especially in pregnant women that also need to be warm about the diabetes during pregnancy but also a regimen is necessary to keep them within the normal levels of glycemia. The subclinical hypothyroidism has been also studied in the same patients.

El principal indicador del impacto de la yodación de la sal de consumo humano es la concentración urinaria de yodo la cual es útil en el monitoreo de la sal. En la encuesta del año 1988 realizada en el Paraguay, se alcanzó una prevalencia de bocio de 48,6% en la población escolar con un déficit de yodo en la sal, pero el año 2000 en el estudio del proyecto de Tiroides Móvil, se redujo por el método ecográfico a 17%. Ese mismo año la mediana de los niveles urinarios en niños escolares de 6-12 años fue 258 µg/L, considerando que 30% se encontraba entre el valor ideal de 100 a 199 µg/L y 46,1% sobre 300 µg/L, implicando un riesgo de exceso de yodo en dicha población con las posibles consecuencias de aparición tanto de hipo como de hipertiroidismo. El 93% presentó exceso de yodo en la sal y la mediana urinaria fue 437 ug/ mL. Un grupo de embarazadas han sido estudiadas en el Hospital San Pablo por primera vez en el Paraguay para la determinación de la yoduria, yodo en sal, diabetes gestacional, hipotiroidismo en el embarazo y sus valores antropométricos resultando un hipotiroidismo subclínico del 50% y diabetes gestacional del 50%. Objetivo: Determinar las yodurias en la población escolar de 6-12 años pre púber de ambos sexos en 17 departamentos del país y en una submuestra en embarazadas y también niveles de glicemia en el embarazo en un hospital de Asunción. Sujetos y Métodos: En el periodo del 2006-2007 fueron evaluados 4.487 escolares randomizados, en una muestra probabilística, 3.198 en el área rural y 1.289 en el área urbana con muestras en orina casual. El año 2015, doscientas embarazadas fueron estudiadas con muestras de glicemia en ayunas y 2 horas post prandial, dosaje de TSH, yodo en sal de 100 gramos de la sal de consumo en sus hogares y de orina para ver la concentración de yodo en sal y urinaria de yodo. Todos los candidatos fueron estudiados bajo consentimiento autorizado y de acuerdo a normas éticas. Resultados: Al comparar los niveles de yodo en orina en el nivel más que adecuado y el excesivo de la yoduria se vió que éste último nivel estaba marcadamente elevado (93.8%), que la mediana de los niveles mayores a 300 ug/L era del 100% del total de las 4.487 muestras de orina, mientras que la mediana de los niveles de yoduria entre 300-500 µg/L fue de 91,3% y por encima de 500 fue 9.7% lo cual implicó el riesgo de desarrollar enfermedades tiroideas autoinmunes. Las embarazadas presentaron una mediana urinaria de yodo 484 µg/L, diabetes gestacional e hipotiroidismo subclínico en 50%. Conclusión: Para normalizar los niveles de yoduria, es necesario disminuir la cantidad de yodo en la sal. La recomendación es insistir en el monitoreo de la adecuada yodación de las sales de consumo familiar y continuar con la vigilancia y el monitoreo constante en sitios centinelas divulgando la importancia de la adecuada ingesta de yodo a la población. Un régimen dietético a las embarazadas es necesario implementar en el primer trimestre del embarazo.

A note on the complexity of finding and enumerating elementary modes.

In the context of the study into elementary modes of metabolic networks, we prove two complexity results. Enumerating elementary modes containing a specific reaction is hard in an enumeration complexity sense. The decision problem if there exists an elementary mode containing two specific reactions is NP-complete. The complexity of enumerating all elementary modes remains open.

Modes and cuts in metabolic networks: complexity and algorithms.

Constraint-based approaches recently brought new insight into our understanding of metabolism. By making very simple assumptions such as that the system is at steady-state and some reactions are irreversible, and without requiring kinetic parameters, general properties of the system can be derived. A central concept in this methodology is the notion of an elementary mode (EM for short) which represents a minimal functional subsystem. The computation of EMs still forms a limiting step in metabolic studies and several algorithms have been proposed to address this problem leading to increasingly faster methods. However, although a theoretical upper bound on the number of elementary modes that a network may possess has been established, surprisingly, the complexity of this problem has never been systematically studied. In this paper, we give a systematic overview of the complexity of optimisation problems related to modes. We first establish results regarding network consistency. Most consistency problems are easy, i.e., they can be solved in polynomial time. We then establish the complexity of finding and counting elementary modes. We show in particular that finding one elementary mode is easy but that this task becomes hard when a specific EM (i.e. an EM containing some specified reactions) is sought. We then show that counting the number of elementary modes is musical sharpP-complete. We emphasize that the easy problems can be solved using currently existing software packages. We then analyse the complexity of a closely related task which is the computation of so-called minimum reaction cut sets and we show that this problem is hard. We then present two positive results which both allow to avoid computing EMs as a prior to the computation of reaction cuts. The first one is a polynomial approximation algorithm for finding a minimum reaction cut set. The second one is a test for verifying whether a set of reactions constitutes a reaction cut; this test can be readily included in existing algorithms to improve their performance. Finally, we discuss the complexity of other cut-related problems.