Effect of inulin on the growth and metabolism of a probiotic strain of Lactobacillus rhamnosus in co-culture with Streptococcus thermophilus

Metabolic studies are very important to improve quality of functional dairy products. For this purpose, the behaviors of pure cultures of Streptococcus thermophilus (St) and Lactobacillus rhamnosus (Lr) as well a co-culture of them (St-Lr) were investigated during skim milk fermentation, and the inulin effect as prebiotic was assessed. Lr was able to metabolize 6 g/100 g more galactose than St and St-Lr. Final lactic acid production by Lr was higher (9.8 g/L) compared to St (9.1 g/L) and St-Lr (9.1 g/L). Acetic acid concentration varied from 0.8 g/L (St-Lr) to 1.5 g/L (Lr) and that of ethanol from only 0.2 g/L (St-Lr) to 0.4 g/L (Lr), which suggests the occurrence in Lr of a NADH oxidase activity and citrate co-metabolization via pyruvate, both dissipating a part of the reducing power. Diacetyl and acetoin accumulated at the highest levels (18.4 and 0.8 mg/L, respectively) with St-Lr, which suggests possible synergistic interactions between these microorganisms as well as the Lr capability of co-metabolizing citrate in the presence of lactose. Inulin stimulated both biomass growth and levels of all end-products, as the likely result of fructose release from its partial hydrolysis and subsequent metabolization as an additional carbon and energy source. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.

Co-metabolic models of Streptococcus thermophilus in co-culture with Lactobacillus bulgaricus or Lactobacillus acidophilus

To shed light on the interactions occurring in fermented milks when using co-cultures of Streptococcus thermophilus with Lactobacillus bulgaricus (StLb) or Lactobacillus acidophilus (StLa), a new co-metabolic model was proposed and checked either in the presence of Inulin as a prebiotic or not. For this purpose, the experimental data of concentrations of substrates and fermented products were utilized in balances of carbon, reduction degree and ATP. S. thermophilus exhibited always quicker growth compared to the other two microorganisms, while the percentage of lactose fermented to lactic acid, that of galactose metabolized, and the levels of diacetyl and acetoin formed strongly depended on the type of co-culture and the presence of inulin. The StLb co-culture led to higher acetoin and lower diacetyl levels compared to StLa, probably because of more reducing conditions or limited acetoin dehydrogenation. Inulin addition to StLa suppressed acetoin accumulation and hindered that of diacetyl, suggesting catabolite repression of alpha-acetolactate synthase expression in S. thermophilus. Both co-cultures showed the highest ATP requirements for biomass growth and maintenance at the beginning of fermentation, consistently with the high energy demand of enzyme induction during lag phase. Inulin reduced these requirements making biomass synthesis and maintenance less energy-consuming. Only a fraction of galactose was released from lactose, consistently with the galactose-positive phenotype of most dairy strains. The galactose fraction metabolized without inulin was about twice that in its presence, which suggests inhibition of the galactose transport system of S. thermophilus by fructose released from partial inulin hydrolysis. (C) 2012 Elsevier B.V. All rights reserved.

Influence of milk type and addition of passion fruit peel powder on fermentation kinetics, texture profile and bacterial viability in probiotic yoghurts

The effect of the addition of passion fruit peel powder (PFPP) on the fermentation kinetics and texture parameters, post-acidification and bacteria counts of probiotic yoghurts made with two milk types were evaluated during 28 days of storage at 4 degrees C. Milks were fermented by Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (CY340), and one strain of probiotic bacteria: Lactobacillus acidophilus (L10 and NCFM), Bifidobacterium animalis subsp. lactis (8104 and HN019). The addition of PFPP reduced significantly fermentation time of skim milk co-fermented by the strains L10, NCFM and HN019. At the end of 28-day shelf-life, counts of B. lactis Bl04 were about 1 Log CFU mL(-1) higher in whole yoghurt fermented with PFPP regarding its control but, in general, the addition of PFPP had less influence on counts than the milk type itself. The titratable acidity in yoghurts with PFPP was significantly higher than in their respective controls, and in skim yoghurts higher than in the whole ones. The PFPP increased firmness, consistency (except for the NCFM strain of L acidophilus) and cohesiveness of all skim yoghurts. The results point out the suitability of using passion fruit by-product in the formulation of both skim and whole probiotic yoghurts. (C) 2012 Elsevier Ltd. All rights reserved.

Potential Respiration in Oxyrrhis marina and Rhodomonas salina

Máster en Oceanografía

Algorithms for network design and routing problems

In this thesis we study three combinatorial optimization problems belonging to the classes of Network Design and Vehicle Routing problems that are strongly linked in the context of the design and management of transportation networks: the Non-Bifurcated Capacitated Network Design Problem (NBP), the Period Vehicle Routing Problem (PVRP) and the Pickup and Delivery Problem with Time Windows (PDPTW). These problems are NP-hard and contain as special cases some well known difficult problems such as the Traveling Salesman Problem and the Steiner Tree Problem. Moreover, they model the core structure of many practical problems arising in logistics and telecommunications. The NBP is the problem of designing the optimum network to satisfy a given set of traffic demands. Given a set of nodes, a set of potential links and a set of point-to-point demands called commodities, the objective is to select the links to install and dimension their capacities so that all the demands can be routed between their respective endpoints, and the sum of link fixed costs and commodity routing costs is minimized. The problem is called non- bifurcated because the solution network must allow each demand to follow a single path, i.e., the flow of each demand cannot be splitted. Although this is the case in many real applications, the NBP has received significantly less attention in the literature than other capacitated network design problems that allow bifurcation. We describe an exact algorithm for the NBP that is based on solving by an integer programming solver a formulation of the problem strengthened by simple valid inequalities and four new heuristic algorithms. One of these heuristics is an adaptive memory metaheuristic, based on partial enumeration, that could be applied to a wider class of structured combinatorial optimization problems. In the PVRP a fleet of vehicles of identical capacity must be used to service a set of customers over a planning period of several days. Each customer specifies a service frequency, a set of allowable day-combinations and a quantity of product that the customer must receive every time he is visited. For example, a customer may require to be visited twice during a 5-day period imposing that these visits take place on Monday-Thursday or Monday-Friday or Tuesday-Friday. The problem consists in simultaneously assigning a day- combination to each customer and in designing the vehicle routes for each day so that each customer is visited the required number of times, the number of routes on each day does not exceed the number of vehicles available, and the total cost of the routes over the period is minimized. We also consider a tactical variant of this problem, called Tactical Planning Vehicle Routing Problem, where customers require to be visited on a specific day of the period but a penalty cost, called service cost, can be paid to postpone the visit to a later day than that required. At our knowledge all the algorithms proposed in the literature for the PVRP are heuristics. In this thesis we present for the first time an exact algorithm for the PVRP that is based on different relaxations of a set partitioning-like formulation. The effectiveness of the proposed algorithm is tested on a set of instances from the literature and on a new set of instances. Finally, the PDPTW is to service a set of transportation requests using a fleet of identical vehicles of limited capacity located at a central depot. Each request specifies a pickup location and a delivery location and requires that a given quantity of load is transported from the pickup location to the delivery location. Moreover, each location can be visited only within an associated time window. Each vehicle can perform at most one route and the problem is to satisfy all the requests using the available vehicles so that each request is serviced by a single vehicle, the load on each vehicle does not exceed the capacity, and all locations are visited according to their time window. We formulate the PDPTW as a set partitioning-like problem with additional cuts and we propose an exact algorithm based on different relaxations of the mathematical formulation and a branch-and-cut-and-price algorithm. The new algorithm is tested on two classes of problems from the literature and compared with a recent branch-and-cut-and-price algorithm from the literature.

Volumenpackungen nach SAE J1100

We present new algorithms to approximate the discrete volume of a polyhedral geometry using boxes defined by the US standard SAE J1100. This problem is NP-hard and has its main application in the car design process. The algorithms produce maximum weighted independent sets on a so-called conflict graph for a discretisation of the geometry. We present a framework to eliminate a large portion of the vertices of a graph without affecting the quality of the optimal solution. Using this framework we are also able to define the conflict graph without the use of a discretisation. For the solution of the maximum weighted independent set problem we designed an enumeration scheme which uses the restrictions of the SAE J1100 standard for an efficient upper bound computation. We evaluate the packing algorithms according to the solution quality compared to manually derived results. Finally, we compare our enumeration scheme to several other exact algorithms in terms of their runtime. Grid-based packings either tend to be not tight or have intersections between boxes. We therefore present an algorithm which can compute box packings with arbitrary placements and fixed orientations. In this algorithm we make use of approximate Minkowski Sums, computed by uniting many axis-oriented equal boxes. We developed an algorithm which computes the union of equal axis-oriented boxes efficiently. This algorithm also maintains the Minkowski Sums throughout the packing process. We also extend these algorithms for packing arbitrary objects in fixed orientations.

Two-Dimensional Bin Packing Problem with Guillotine Restrictions

This thesis, after presenting recent advances obtained for the two-dimensional bin packing problem, focuses on the case where guillotine restrictions are imposed. A mathematical characterization of non-guillotine patterns is provided and the relation between the solution value of the two-dimensional problem with guillotine restrictions and the two-dimensional problem unrestricted is being studied from a worst-case perspective. Finally it presents a new heuristic algorithm, for the two-dimensional problem with guillotine restrictions, based on partial enumeration, and computationally evaluates its performance on a large set of instances from the literature. Computational experiments show that the algorithm is able to produce proven optimal solutions for a large number of problems, and gives a tight approximation of the optimum in the remaining cases.

Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB)

A variety of conformationally constrained aspartate and glutamate analogues inhibit the glutamate transporter 1 (GLT-1, also known as EAAT2). To expand the search for such analogues, a virtual library of aliphatic aspartate and glutamate analogues was generated starting from the chemical universe database GDB-11, which contains 26.4 million possible molecules up to 11 atoms of C, N, O, F, resulting in 101026 aspartate analogues and 151285 glutamate analogues. Virtual screening was realized by high-throughput docking to the glutamate binding site of the glutamate transporter homologue from Pyrococcus horikoshii (PDB code: 1XFH ) using Autodock. Norbornane-type aspartate analogues were selected from the top-scoring virtual hits and synthesized. Testing and optimization led to the identification of (1R*,2R*,3S*,4R*,6R*)-2-amino-6-phenethyl-bicyclo[2.2.1]heptane-2,3-dicarboxylic acid as a new inhibitor of GLT-1 with IC(50) = 1.4 ?M against GLT-1 and no inhibition of the related transporter EAAC1. The systematic diversification of known ligands by enumeration with help of GDB followed by virtual screening, synthesis, and testing as exemplified here provides a general strategy for drug discovery.

Comparison of real-time PCR assays for detection, quantification, and differentiation of campylobacter jejuni and campylobacter coli in broiler neck skin samples

We tested the use of multiplex real-time PCR for detection and quantification of Campylobacter jejuni and Campylobacter coli on broiler carcass neck skin samples collected during 2008 from slaughterhouses in Switzerland. Results from an established TaqMan assay based on two different targets (hipO and ceuE for C. jejuni and C. coli, respectively) were corroborated with data from a newly developed assay based on a single-nucleotide polymorphism in the fusA gene, which allows differentiation between C. jejuni and C. coli. Both multiplex real-time PCRs were applied simultaneously for direct detection, differentiation, and quantification of Campylobacter from 351 neck skin samples and compared with culture methods. There was good correlation in detection and enumeration between real-time PCR results and quantitative culture, with real-time PCR being more sensitive. Overall, 251 (71.5%) of the samples were PCR positive for Campylobacter, with 211 (60.1%) in the hipO-ceuE assays, 244 (69.5%) in the fusA assay, and 204 (58.1%) of them being positive in both PCR assays. Thus, the fusA assay was similarly sensitive to the enrichment culture (72.4% positive); however, it is faster and allows for quantification. In addition, real-time PCR allowed for species differentiation; roughly 60% of positive samples contained C. jejuni, less than 10% C. coli, and more than 30% contained both species. Real-time PCR proved to be a suitable method for direct detection, quantification, and differentiation of Campylobacter from carcasses, and could permit time-efficient surveillance of these zoonotic agents.

Differentiation in Male and Female Speech Styles

From the moment of their birth, a person's life is determined by their sex. Ms. Goroshko wants to know why this difference is so striking, why society is so concerned to sustain it, and how it is able to persist even when certain national or behavioural stereotypes are erased between people. She is convinced of the existence of not only social, but biological differences between men and women, and set herself the task, in a manuscript totalling 126 pages, written in Ukrainian and including extensive illustrations, of analysing these distinctions as they are manifested in language. She points out that, even before 1900, certain stylistic differences between the ways that men and women speak had been noted. Since then it has become possible, for instance in the case of Japanese, to point to examples of male and female sub-languages. In general, one can single out the following characteristics. Males tend to write with less fluency, to refer to events in a verb-phrase, to be time-oriented, to involve themselves more in their references to events, to locate events in their personal sphere of activity, and to refer less to others. Therefore, concludes Ms Goroshko, the male is shown to be more active, more ego-involved in what he does, and less concerned about others. Women, in contrast, were more fluent, referred to events in a noun-phrase, were less time-oriented, tended to be less involved in their event-references, locate events within their interactive community and refer more to others. They spent much more time discussing personal and domestic subjects, relationship problems, family, health and reproductive matters, weight, food and clothing, men, and other women. As regards discourse strategies, Ms Goroshko notes the following. Men more often begin a conversation, they make more utterances, these utterances are longer, they make more assertions, speak less carefully, generally determine the topic of conversation, speak more impersonally, use more vulgar expressions, and use fewer diminutives and more imperatives. Women's speech strategies, apart from being the opposite of those enumerated above, also contain more euphemisms, polite forms, apologies, laughter and crying. All of the above leads Ms. Goroshko to conclude that the differences between male and female speech forms are more striking than the similarities. Furthermore she is convinced that the biological divergence between the sexes is what generates the verbal divergence, and that social factors can only intensify or diminish the differentiation in verbal behaviour established by the sex of a person. Bearing all this in mind, Ms Goroshko set out to construct a grammar of male and female styles of speaking within Russian. One of her most important research tools was a certain type of free association test. She took a list comprising twelve stimuli (to love, to have, to speak, to fuck, a man, a woman, a child, the sky, a prayer, green, beautiful) and gave it to a group of participants specially selected, according to a preliminary psychological testing, for the high levels of masculinity or femininity they displayed. Preliminary responses revealed that the female reactions were more diverse than the male ones, there were more sentences and word combinations in the female reactions, men gave more negative responses to the stimulus and sometimes didn't want to react at all, women reacted more to adjectives and men to nouns, and that, surprisingly, women coloured more negatively their reactions to the words man, to love and a child (Ms. Goroshko is inclined to attribute this to the present economic situation in Russia). Another test performed by Ms. Goroshko was the so-called "defective text" developed by A.A. Brudny. All participants were distributed with packets of complete sentences, which had been taken from a text and then mixed at random. The task was to reconstruct the original text. There were three types of test, the first descriptive, the second narrative, and the third logical. Ms. Goroshko created computer programmes to analyse the results. She found that none of the reconstructed texts was coincident with the original, differing both from the original text and amongst themselves and that there were many more disparities in the male than the female texts. In the descriptive and logical texts the differences manifested themselves more clearly in the male texts, and in the narrative texts in the female texts. The widest dispersal of values was observed at the outset, while the female text ending was practically coincident with the original (in contrast to the male ending). The greatest differences in text reconstruction for both males and females were registered in the middle of the texts. Women, Ms. Goroshko claims, were more sensitive to the semantic structure of the texts, since they assembled the narrative text much more accurately than the other two, while the men assembled more accurately the logical text. Texts written by women were assembled more accurately by women and texts by men by men. On the basis of computer analysis, Ms. Goroshko found that female speech was substantially more emotional. It was expressed by various means, hyperbole, metaphor, comparisons, epithets, ways of enumeration, and with the aid of interjections, rhetorical questions, exclamations. The level of literacy was higher for female speech, and there were fewer mistakes in grammar and spelling in female texts. The last stage of Ms Goroshko's research concerned the social stereotypes of beliefs about men and women in Russian society today. A large number of respondents were asked questions such as "What merits must a woman possess?", "What are male vices and virtues?", etc. After statistical manipulation, an image of modern man and woman, as it exists in the minds of modern Russian men and women, emerged. Ms. Goroshko believes that her findings are significant not only within the field of linguistics. She has already successfully worked on anonymous texts and been able to decide on the sex of the author and consequently believes that in the future her research may even be of benefit to forensic science.

Language Construction of Reality in the German Tabloid Press/on Materials of BILD Newspaper/

From the moment of their birth, a person's life is determined by their sex. Goroshko wanted to find out why this difference is so striking, why society is so determined to sustain it, and how it can persist even when certain national or behavioural stereotypes are erased. She believes there are both social and biological differences between men and women, and set out to analyse these distinctions as they are manifested in language. Certain general characteristics can be identified. Males tend to write with less fluency, to refer to events in a verb phrase, to be time-oriented, to involve themselves more in their references to events, to locate events in their personal sphere of activity, and to refer less to others. Goroshko therefore concludes that the male is more active, more ego-involved in what he does and less concerned about others. Women were more fluent, referred to events in a noun-phrase, were less time-oriented, tended to be less involved in their event references, located events within their interactive community, and referred more to others. They spent much more time discussing personal and domestic subjects, relationship problems, family, health and reproductive matters, weight, food and clothing, men, and other women. Computer analysis showed that female speech was substantially more emotional, using hyperbole, metaphor, comparisons, epithets, ways of enumeration, interjections, rhetorical questions and exclamations. The level of literacy was higher in female speech, and women made fewer grammatical and spelling mistakes in written texts. Goroshko believes that her findings have relevance beyond the linguistic field. When working on anonymous texts she has been able to decide on the sex of the author and so believes that her research may even be of benefit to forensic science.

Higher frequency of chromosomal aberrations in ovarian endometriosis compared to extragonadal endometriosis: A possible link to endometrioid adenocarcinoma

Endometriosis may progress to invasive endometrioid adenocarcinoma, particularly in the ovary. Up to now, little is known of the molecular mechanisms possibly involved in the malignant transformation of endometriosis. Therefore, in this study, extragonadal endometriosis (n = 10), ovarian endometriosis without malignancy (n = 10), ovarian endometriosis with direct transition into endometrioid adenocarcinoma (n = 8), and normal endometrium (n = 12) were investigated for numerical chromosomal aberrations by fluorescence in situ hybridization using centromere enumeration probes. The proportions of cells with aneusomies were semiquantitatively assessed. Trisomies 1 and 7, and monosomies 9 and 17 were found in endometriosis, ovarian endometrioid adenocarcinoma, and normal endometrium. The proportions of aneusomic cells were significantly higher in ovarian endometrioid carcinoma compared with ovarian endometriosis (P < 0.001), and in ovarian endometriosis compared with extragonadal endometriosis and normal endometrium (P < 0.001). The data provide new evidence of a common lineage of endometriosis and ovarian endometrioid carcinoma. The higher frequency of chromosomal aberrations in endometrioid carcinoma than in endometriosis may reflect an expansion of aberrant cell clones already present in endometriosis during the progression to cancer. The higher frequency of chromosomal aberrations in ovarian endometriosis than in extragonadal endometriosis suggests a role of the ovarian stromal milieu in the induction of genetic changes, which may eventually lead to invasive cancer.

Enumerating constrained elementary flux vectors of metabolic networks

The concept of elementary vector is generalised to the case where the steady-state space of the metabolic network is not a flux cone but is a general polyhedron due to further inhomogeneous constraints on the flows through some of the reactions. On one hand, this allows to selectively enumerate elementary modes which satisfy certain optimality criteria and this can yield a large computational gain compared with full enumeration. On the other hand, in contrast to the single optimum found by executing a linear program, this enables a comprehensive description of the set of alternate optima often encountered in flux balance analysis. The concepts are illustrated on a metabolic network model of human cardiac mitochondria.

Online distribution management framework by incorporating wind generation

In distribution system operations, dispatchers at control center closely monitor system operating limits to ensure system reliability and adequacy. This reliability is partly due to the provision of remote controllable tie and sectionalizing switches. While the stochastic nature of wind generation can impact the level of wind energy penetration in the network, an estimate of the output from wind on hourly basis can be extremely useful. Under any operating conditions, the switching actions require human intervention and can be an extremely stressful task. Currently, handling a set of switching combinations with the uncertainty of distributed wind generation as part of the decision variables has been nonexistent. This thesis proposes a three-fold online management framework: (1) prediction of wind speed, (2) estimation of wind generation capacity, and (3) enumeration of feasible switching combinations. The proposed methodology is evaluated on 29-node test system with 8 remote controllable switches and two wind farms of 18MW and 9MW nameplate capacities respectively for generating the sequence of system reconfiguration states during normal and emergency conditions.

Multinomial goodness-of-fit: large sample tests with survey design correction and exact tests for small samples

I introduce the new mgof command to compute distributional tests for discrete (categorical, multinomial) variables. The command supports largesample tests for complex survey designs and exact tests for small samples as well as classic large-sample x2-approximation tests based on Pearson’s X2, the likelihood ratio, or any other statistic from the power-divergence family (Cressie and Read, 1984, Journal of the Royal Statistical Society, Series B (Methodological) 46: 440–464). The complex survey correction is based on the approach by Rao and Scott (1981, Journal of the American Statistical Association 76: 221–230) and parallels the survey design correction used for independence tests in svy: tabulate. mgof computes the exact tests by using Monte Carlo methods or exhaustive enumeration. mgof also provides an exact one-sample Kolmogorov–Smirnov test for discrete data.