Food Microbiology Laboratory Overview of food analysis

Introduction to microorganisms and foodborne diseases. Activities in a Food Microbiology Laboratory.

Search of symmetric composition methods of symmetric integrators

Composition methods are useful when solving Ordinary Differential Equations (ODEs) as they increase the order of accuracy of a given basic numerical integration scheme. We will focus on sy-mmetric composition methods involving some basic second order symmetric integrator with different step sizes [17]. The introduction of symmetries into these methods simplifies the order conditions and reduces the number of unknowns. Several authors have worked in the search of the coefficients of these type of methods: the best method of order 8 has 17 stages [24], methods of order 8 and 15 stages were given in [29, 39, 40], 10-order methods of 31, 33 and 35 stages have been also found [24, 34]. In this work some techniques that we have built to obtain 10-order symmetric composition methods of symmetric integrators of s = 31 stages (16 order conditions) are explored. Given some starting coefficients that satisfy the simplest five order conditions, the process followed to obtain the coefficients that satisfy the sixteen order conditions is provided.

Ecologically relevant characteristics of flow-regime of Rufiji Basin in Tanzania (an ensemble of ecohydrological clues to infer associeted ramifications on dtream and ecosystem)

Disserta����o de Mestrado, Ecohidrologia - Erasmus Mundus, Faculdade de Ci��ncias e Tecnologia, Universidade do Algarve, 2014

Double Hybrid Functionals and the ��-System Bond Length Alternation Challenge: Rivaling Accuracy of Post-HF Methods

Predicting accurate bond length alternations (BLAs) in long conjugated oligomers has been a significant challenge for electronic-structure methods for many decades, made particularly important by the close relationships between BLA and the rich optoelectronic properties of ��-delocalized systems. Here, we test the accuracy of recently developed, and increasingly popular, double hybrid (DH) functionals, positioned at the top of Jacobs Ladder of DFT methods of increasing sophistication, computational cost, and accuracy, due to incorporation of MP2 correlation energy. Our test systems comprise oligomeric series of polyacetylene, polymethineimine, and polysilaacetylene up to six units long. MP2 calculations reveal a pronounced shift in BLAs between the 6-31G(d) basis set used in many studies of BLA to date and the larger cc-pVTZ basis set, but only modest shifts between cc-pVTZ and aug-cc-pVQZ results. We hence perform new reference CCSD(T)/cc-pVTZ calculations for all three series of oligomers against which we assess the performance of several families of DH functionals based on BLYP, PBE, and TPSS, along with lower-rung relatives including global- and range-separated hybrids. Our results show that DH functionals systematically improve the accuracy of BLAs relative to single hybrid functionals. xDH-PBE0 (N4 scaling using SOS-MP2) emerges as a DH functional rivaling the BLA accuracy of SCS-MP2 (N5 scaling), which was found to offer the best compromise between computational cost and accuracy the last time the BLA accuracy of DFT- and wave function-based methods was systematically investigated. Interestingly, xDH-PBE0 (XYG3), which differs to other DHs in that its MP2 term uses PBE0 (B3LYP) orbitals that are not self-consistent with the DH functional, is an outlier of trends of decreasing average BLA errors with increasing fractions of MP2 correlation and HF exchange.

Application of survival analysis to determine the persimmon cv. 'Rama-forte' sensory shelf-life.

2014

AN ASSESSMENT OF FLOW REGIME MAPS AND A NUMERICAL HEAT TRANSFER CORRELATION FOR THE STRATIFIED/ANNULAR REGIME OF SHEAR-DRIVEN INTERNAL CONDENSING FLOWS

Several modern-day cooling applications require the incorporation of mini/micro-channel shear-driven flow condensers. There are several design challenges that need to be overcome in order to meet those requirements. The difficulty in developing effective design tools for shear-driven flow condensers is exacerbated due to the lack of a bridge between the physics-based modelling of condensing flows and the current, popular approach based on semi-empirical heat transfer correlations. One of the primary contributors of this disconnect is a lack of understanding caused by the fact that typical heat transfer correlations eliminate the dependence of the heat transfer coefficient on the method of cooling employed on the condenser surface when it may very well not be the case. This is in direct contrast to direct physics-based modeling approaches where the thermal boundary conditions have a direct and huge impact on the heat transfer coefficient values. Typical heat transfer correlations instead introduce vapor quality as one of the variables on which the value of the heat transfer coefficient depends. This study shows how, under certain conditions, a heat transfer correlation from direct physics-based modeling can be equivalent to typical engineering heat transfer correlations without making the same apriori assumptions. Another huge factor that raises doubts on the validity of the heat-transfer correlations is the opacity associated with the application of flow regime maps for internal condensing flows. It is well known that flow regimes influence heat transfer rates strongly. However, several heat transfer correlations ignore flow regimes entirely and present a single heat transfer correlation for all flow regimes. This is believed to be inaccurate since one would expect significant differences in the heat transfer correlations for different flow regimes. Several other studies present a heat transfer correlation for a particular flow regime - however, they ignore the method by which extents of the flow regime is established. This thesis provides a definitive answer (in the context of stratified/annular flows) to: (i) whether a heat transfer correlation can always be independent of the thermal boundary condition and represented as a function of vapor quality, and (ii) whether a heat transfer correlation can be independently obtained for a flow regime without knowing the flow regime boundary (even if the flow regime boundary is represented through a separate and independent correlation). To obtain the results required to arrive at an answer to these questions, this study uses two numerical simulation tools - the approximate but highly efficient Quasi-1D simulation tool and the exact but more expensive 2D Steady Simulation tool. Using these tools and the approximate values of flow regime transitions, a deeper understanding of the current state of knowledge in flow regime maps and heat transfer correlations in shear-driven internal condensing flows is obtained. The ideas presented here can be extended for other flow regimes of shear-driven flows as well. Analogous correlations can also be obtained for internal condensers in the gravity-driven and mixed-driven configuration.

Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp

High quality, pure DNA is required for ensuring reliable and reproducible results in molecular diagnosis applications. A number of in-house and commercial methods are available for the extraction and purification of genomic DNA from faecal material, each one offering a specific combination of performance, cost-effectiveness, and easiness of use that should be conveniently evaluated in function of the pathogen of interest. In this comparative study the marketed kits QIAamp DNA stool mini (Qiagen), SpeedTools DNA extraction (Biotools), DNAExtract-VK (Vacunek), PowerFecal DNA isolation (MoBio), and Wizard magnetic DNA purification system (Promega Corporation) were assessed for their efficacy in obtaining DNA of the most relevant enteric protozoan parasites associated to gastrointestinal disease globally. A panel of 113 stool specimens of clinically confirmed patients with cryptosporidiosis (n = 29), giardiasis (n = 47) and amoebiasis by Entamoeba histolytica (n = 3) or E. dispar (n = 10) and apparently healthy subjects (n = 24) were used for this purpose. Stool samples were aliquoted in five sub-samples and individually processed by each extraction method evaluated. Purified DNA samples were subsequently tested in PCR-based assays routinely used in our laboratory. The five compared methods yielded amplifiable amounts of DNA of the pathogens tested, although performance differences were observed among them depending on the parasite and the infection burden. Methods combining chemical, enzymatic and/or mechanical lysis procedures at temperatures of at least 56 ��C were proven more efficient for the release of DNA from Cryptosporidium oocysts.

Effects of flow regulation in the life-cycles of a mediterranean cyprinid species, the Iberian chub (Squalius carolitertii Doadrio, 1987)

Streamflow is considered a driver of inter and intra���specific life���history differences among freshwater fish. Therefore, dams and related flow regulation, can have deleterious impacts on their life���cycles. The main objective of this study is to assess the effects of flow regulation on the growth and reproduction of a non���migratory fish species. During one year, samples were collected from two populations of Iberian chub, inhabiting rivers with non���regulated and regulated flow regimes. Flow regulation for water derivation promoted changes in chub���s condition, duration of gonad maturation and spawning, fecundity and oocyte size. However, this non���migratory species was less responsive to streamflow regulation than a migratory species analysed. Findings from this study are important to understand changes imposed by regulated rivers on fish and can be used as guidelines for flow requirements implementations; RESUMO: O caudal �� um dos fatores respons��veis pelo funcionamento dos ciclos de vida das esp��cies pisc��colas dulciaqu��colas. As barragens, e a regulariza����o de caudal associada, podem ter impactes nos ciclos de vida destas esp��cies. O objetivo deste estudo prende���se com a avalia����o dos efeitos da regulariza����o de caudal no crescimento e reprodu����o de uma esp��cie pisc��cola n��o���migradora. A an��lise de amostras recolhidas em popula����es de escalo do Norte provenientes de dois rios de caudal regularizado e n��o regularizado, identificaram impactes significativos a n��vel da condi����o corporal, da matura����o das g��nadas e desova, da fecundidade e da dimens��o dos o��citos. Esta esp��cie n��o���migradora parece ser menos responsiva �� artificializa����o do caudal que uma esp��cie migradora previamente analisada. Estes resultados permitem compreender as altera����es impostas pela regulariza����o do caudal e podem ser usados em programas de reabilita����o fluvial.

Development of machine learning methods for multi-modal biomarkers detection and integration

In medicine, innovation depends on a better knowledge of the human body mechanism, which represents a complex system of multi-scale constituents. Unraveling the complexity underneath diseases proves to be challenging. A deep understanding of the inner workings comes with dealing with many heterogeneous information. Exploring the molecular status and the organization of genes, proteins, metabolites provides insights on what is driving a disease, from aggressiveness to curability. Molecular constituents, however, are only the building blocks of the human body and cannot currently tell the whole story of diseases. This is why nowadays attention is growing towards the contemporary exploitation of multi-scale information. Holistic methods are then drawing interest to address the problem of integrating heterogeneous data. The heterogeneity may derive from the diversity across data types and from the diversity within diseases. Here, four studies conducted data integration using customly designed workflows that implement novel methods and views to tackle the heterogeneous characterization of diseases. The first study devoted to determine shared gene regulatory signatures for onco-hematology and it showed partial co-regulation across blood-related diseases. The second study focused on Acute Myeloid Leukemia and refined the unsupervised integration of genomic alterations, which turned out to better resemble clinical practice. In the third study, network integration for artherosclerosis demonstrated, as a proof of concept, the impact of network intelligibility when it comes to model heterogeneous data, which showed to accelerate the identification of new potential pharmaceutical targets. Lastly, the fourth study introduced a new method to integrate multiple data types in a unique latent heterogeneous-representation that facilitated the selection of important data types to predict the tumour stage of invasive ductal carcinoma. The results of these four studies laid the groundwork to ease the detection of new biomarkers ultimately beneficial to medical practice and to the ever-growing field of Personalized Medicine.

Neural Machine Translation in the Field of Law. Analysis and Evaluation against Human Reference of NMT Raw Outputs of an Atto Costitutivo of S.r.l. from Italian into German.

Artificial Intelligence (AI) is gaining ever more ground in every sphere of human life, to the point that it is now even used to pass sentences in courts. The use of AI in the field of Law is however deemed quite controversial, as it could provide more objectivity yet entail an abuse of power as well, given that bias in algorithms behind AI may cause lack of accuracy. As a product of AI, machine translation is being increasingly used in the field of Law too in order to translate laws, judgements, contracts, etc. between different languages and different legal systems. In the legal setting of Company Law, accuracy of the content and suitability of terminology play a crucial role within a translation task, as any addition or omission of content or mistranslation of terms could entail legal consequences for companies. The purpose of the present study is to first assess which neural machine translation system between DeepL and ModernMT produces a more suitable translation from Italian into German of the atto costitutivo of an Italian s.r.l. in terms of accuracy of the content and correctness of terminology, and then to assess which translation proves to be closer to a human reference translation. In order to achieve the above-mentioned aims, two human and automatic evaluations are carried out based on the MQM taxonomy and the BLEU metric. Results of both evaluations show an overall better performance delivered by ModernMT in terms of content accuracy, suitability of terminology, and closeness to a human translation. As emerged from the MQM-based evaluation, its accuracy and terminology errors account for just 8.43% (as opposed to DeepL���s 9.22%), while it obtains an overall BLEU score of 29.14 (against DeepL���s 27.02). The overall performances however show that machines still face barriers in overcoming semantic complexity, tackling polysemy, and choosing domain-specific terminology, which suggests that the discrepancy with human translation may still be remarkable.

Compara����o entre m��todos de avalia����o do risco de desenvolvimento de les��es musculoesquel��ticas nas extremidades distais dos membros superiores: um estudo em trabalhos de montagem manual

Disserta����o de mestrado em Engenharia Humana

Strategiaty�� maatalouselementtiliiketoiminnan ohjaamisessa

Diplomity��n tavoitteena oli selvitt���� Lujabetoni Oy:n maatalouselementtiliiketoiminnan markkinan��kym��t, kilpailijat toimialalla ja toiminnan rationalisointi niin, ett�� tulevien vuosien investoinnit ja resurssit kohdistettaisiin parhaalla mahdollisella tavalla eri tehdasyksik��iden kesken. Ty��n teoriaosassa esitettiin strategiaty��n osa-alueet ja k��ytetyt strategisen analyysin menetelm��t. Ty��n k��yt��nn��nosassa strategisten analyysimenetelmien avulla pystyttiin m����ritt��m����n liiketoiminnan makroymp��rist��, toimiala- eli kilpailuymp��rist�� ja toimintaymp��rist��. Makroymp��rist��n kuvauksessa annettiin perustiedot Suomen maataloudesta, k��siteltiin rahoitustukip����t��stietoja ja arvioitiin toimialan elinkaaren vaihetta l��hinn�� Maa- ja mets��talousministeri��st�� sek�� useammasta tutkimuslaitoksesta saatujen tietojen pohjalta. Toimialaymp��rist��n kuvauksessa k��siteltiin maatalouselementtiliiketoiminnan kilpailijat. Toimintaymp��rist��n kuvauksessa keskeisimm��ll�� sijalla oli liiketoiminnan analysointi tehtaittain ja tuotteittain. N��iden suorituskyky�� vertailtiin tuottavuus- ja kannattavuuslaskelmien avulla. Tuotteiden joukosta pyrittiin l��yt��m����n tappiolliset ja huonomenekkiset tuotteet. Kuljetuskustannuksia ja logistiikkaa mietittiin eri tehtaiden n��k��kulmista ja pyrittiin l��yt��m����n paras optimi tuotteiden valmistuksen sijainnille. Saatujen tulosten perusteella annettiin toimenpide-ehdotuksia liiketoiminnan kehitt��miseksi ja ohjaamiseksi.

Analyse de r��seau pi��ton et gestion scolaire: sinuosit��, centricit�� et transport optimal r��gularis��

Que ce soit d'un point de vue, urbanistique, social, ou encore de la gouvernance, l'��volution des villes est un d��fi majeur de nos soci��t��s contemporaines. En offrant la possibilit�� d'analyser des configurations spatiales et sociales existantes ou en tentant de simuler celles �� venir, les syst��mes d'information g��ographique sont devenus incontournables dans la gestion et dans la planification urbaine. En cinq ans la population de la ville de Lausanne est pass��e de 134'700 �� 140'570 habitants, alors que les effectifs de l'��cole publique ont cr�� de 12'200 �� 13'500 ��l��ves. Cet accroissement d��mographique associ�� �� un vaste processus d'harmonisation de la scolarit�� obligatoire en Suisse ont amen�� le Service des ��coles �� mettre en place et �� d��velopper en collaboration avec l'universit�� de Lausanne des solutions SIG �� m��me de r��pondre �� diff��rentes probl��matiques spatiales. ��tablies en 1989, les limites des ��tablissements scolaires (bassins de recrutement) ont d�� ��tre red��finies afin de les r��adapter aux r��alit��s d'un paysage urbain et politique en pleine mutation. Dans un contexte de mobilit�� et de durabilit��, un syst��me d'attribution de subventions pour les transports publics bas�� sur la distance domicile-��cole et sur l'��ge des ��coliers, a ��t�� con��u. La r��alisation de ces projets a n��cessit�� la construction de bases de donn��es g��ographiques ainsi que l'��laboration de nouvelles m��thodes d'analyses expos��es dans ce travail. Cette th��se s'est ainsi faite selon une dialectique permanente entre recherches th��oriques et n��cessit��s pratiques. La premi��re partie de ce travail porte sur l'analyse du r��seau pi��ton de la ville. La morphologie du r��seau est investigu��e au travers d'approches multi-��chelles du concept de centralit��. La premi��re conception, nomm��e sinuo-centralit�� ("straightness centrality"), stipule qu'��tre central c'est ��tre reli�� aux autres en ligne droite. La deuxi��me, sans doute plus intuitive, est intitul��e centricit�� ("closeness centrality") et exprime le fait qu'��tre central c'est ��tre proche des autres (fig. 1, II). Les m��thodes d��velopp��es ont pour but d'��valuer la connectivit�� et la marchabilit�� du r��seau, tout en sugg��rant de possibles am��liorations (cr��ation de raccourcis pi��tons). Le troisi��me et dernier volet th��orique expose et d��veloppe un algorithme de transport optimal r��gularis��. En minimisant la distance domicile-��cole et en respectant la taille des ��coles, l'algorithme permet de r��aliser des sc��narios d'enclassement. L'impl��mentation des multiplicateurs de Lagrange offre une visualisation du "co��t spatial" des infrastructures scolaires et des lieux de r��sidence des ��coliers. La deuxi��me partie de cette th��se retrace les aspects principaux de trois projets r��alis��s dans le cadre de la gestion scolaire. �� savoir : la conception d'un syst��me d'attribution de subventions pour les transports publics, la red��finition de la carte scolaire, ou encore la simulation des flux d'��l��ves se rendant �� l'��cole �� pied. *** May it be from an urbanistic, a social or from a governance point of view, the evolution of cities is a major challenge in our contemporary societies. By giving the opportunity to analyse spatial and social configurations or attempting to simulate future ones, geographic information systems cannot be overlooked in urban planning and management. In five years, the population of the city of Lausanne has grown from 134'700 to 140'570 inhabitants while the numbers in public schools have increased from 12'200 to 13'500 students. Associated to a considerable harmonisation process of compulsory schooling in Switzerland, this demographic rise has driven schooling services, in collaboration with the University of Lausanne, to set up and develop GIS capable of tackling various spatial issues. Established in 1989, the school districts had to be altered so that they might fit the reality of a continuously changing urban and political landscape. In a context of mobility and durability, an attribution system for public transport subventions based on the distance between residence and school and on the age of the students was designed. The implementation of these projects required the built of geographical databases as well as the elaboration of new analysis methods exposed in this thesis. The first part of this work focuses on the analysis of the city's pedestrian network. Its morphology is investigated through multi-scale approaches of the concept of centrality. The first conception, named the straightness centrality, stipulates that being central is being connected to the others in a straight line. The second, undoubtedly more intuitive, is called closeness centrality and expresses the fact that being central is being close to the others. The goal of the methods developed is to evaluate the connectivity and walkability of the network along with suggesting possible improvements (creation of pedestrian shortcuts).The third and final theoretical section exposes and develops an algorithm of regularised optimal transport. By minimising home to school distances and by respecting school capacity, the algorithm enables the production of student allocation scheme. The implementation of the Lagrange multipliers offers a visualisation of the spatial cost associated to the schooling infrastructures and to the student home locations. The second part of this thesis recounts the principal aspects of three projects fulfilled in the context of school management. It focuses namely on the built of an attribution system for public transport subventions, a school redistricting process and on simulating student pedestrian flows.