Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

The art of building trust via e-communication channels: Post-acquisition integration as a special context

This study discusses the importance of establishing trust in post-acquisition integration context and how the use of e-channels facilitates or inhibits this process. The objective of this study is to analyze how the use of electronic communication channels influences the post-acquisition integration process in terms of trust establishment and overall integration efficiency, developing a framework as a result. Three sub-objectives are introduced: to find out the building blocks of trust in M&A’s, to analyse how the use of e-channels influence the process of trust establishment in post-acquisition integration context, and to define the consequences trust and use of e-channels have for the process. The theoretical background of the study includes literature and theories relating to trust establishment in post-acquisition integration context and how the use of e-channels influences the process of trust development on a general level. The empirical research is conducted as a single case study, based on key informant interviews. The interview data was collected between October 2015 and January 2016. Altogether nine interviews were realised; six with representatives from the acquiring firm and three with target firm members. Thematic analysis was selected as the main method for analysing and processing the qualitative data. This study finds that trust has an essential role in post-acquisition integration context, facilitating the integration process in various different ways. Hence, identifying the different building blocks of trust is important in order for members of the organisations to be better able establish and maintain trust. In today’s international business, the role of electronic communication channels has also increased in importance significantly and it was confirmed that these pose both challenges and possibilities for the development of interpersonal trust. One of the most important underlying factors influencing the trust levels via e-communication channels is the level of user’s comfort in using the different e-channels. Without sufficient and meaningful training, the communication conducted via these channels in inhibited in a number of ways. Hence, understanding the defining characteristics of e-communication together with the risks and opportunities related to the use of these can have far-reaching consequences for the post-acquisition integration process as a whole. The framework based on the findings and existing theory introduces the most central factors influencing the trust establishment together with the positive and negative consequences these have for the integration process. Moreover, organizational level consistency and the existence of shared guidelines on appropriate selection of communication channels according to the nature of the task at hand are seen as important

Asymptotic and structural properties of special cases of the Wright function arising in probability theory

This analysis paper presents previously unknown properties of some special cases of the Wright function whose consideration is necessitated by our work on probability theory and the theory of stochastic processes. Specifically, we establish new asymptotic properties of the particular Wright function 1Ψ1(ρ, k; ρ, 0; x) = X∞ n=0 Γ(k + ρn) Γ(ρn) x n n! (|x| < ∞) when the parameter ρ ∈ (−1, 0)∪(0, ∞) and the argument x is real. In the probability theory applications, which are focused on studies of the Poisson-Tweedie mixtures, the parameter k is a non-negative integer. Several representations involving well-known special functions are given for certain particular values of ρ. The asymptotics of 1Ψ1(ρ, k; ρ, 0; x) are obtained under numerous assumptions on the behavior of the arguments k and x when the parameter ρ is both positive and negative. We also provide some integral representations and structural properties involving the ‘reduced’ Wright function 0Ψ1(−−; ρ, 0; x) with ρ ∈ (−1, 0) ∪ (0, ∞), which might be useful for the derivation of new properties of members of the power-variance family of distributions. Some of these imply a reflection principle that connects the functions 0Ψ1(−−;±ρ, 0; ·) and certain Bessel functions. Several asymptotic relationships for both particular cases of this function are also given. A few of these follow under additional constraints from probability theory results which, although previously available, were unknown to analysts.

Insight assessment in psychosis and psychopathological correlates: validation of the Spanish version of the Schedule for Assessment of Insight - Expanded Version

Background and Objectives: Lack of insight is a cardinal feature of psycho­sis. Insight has been found to be a multidimensional concept, including awareness of having a mental illness, ability to relabel psychotic phenomena as abnormal and compliance with treatment., which can be measured with the Schedule for Assessment of Insight (SAI-E). The aim of this study was to validate the Spanish version of SAI-E. Methods: The SAI-E was translated into Spanish and back-translated into English, which was deemed appropriate by the original scale author. Next, the Spanish version of the SAI-E was administered to 39 patients with schizophrenia or schizoaffective disorder (DSM-IV criteria) from a North Peruvian psychiatric hospital. The Positive and Negative Syndrome Scale for Schizophrenia (PANSS) and the Scale of Unawareness of Mental Disorder (SUMD) were also administered. Specifically, internal consistency and convergent validity were assessed. Results: Internal consistency between the 11 items of the SAI-E was found to be good to excellent (α = 0.942). Compliance items did not contribute to internal consistency (A = 0.417, B = 572). Inter-rater reliability was excellent (ICC = 0.99). Regarding concurrent validity, the SAI-E total score correlated negatively with the lack of insight and judgement item of the PANNS (r = -0.91, p <0.01) and positively with the SUMD total score (r = 0.92, p <0.001). Conclusions: The Spanish version of the SAI-E scale was demonstrated to have both excellent reliability and external validity in our sample of South American Spanish-speaking patients with schizophrenia spectrum disorders.

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189 +/- 58 operational taxonomic units (OTUs) but dropped to 27 +/- 12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

'Enhanced Direct and Indirect Genetic Algorithm Approaches for a Mall Layout and Tenant Selection Problem'

During our earlier research, it was recognised that in order to be successful with an indirect genetic algorithm approach using a decoder, the decoder has to strike a balance between being an optimiser in its own right and finding feasible solutions. Previously this balance was achieved manually. Here we extend this by presenting an automated approach where the genetic algorithm itself, simultaneously to solving the problem, sets weights to balance the components out. Subsequently we were able to solve a complex and non-linear scheduling problem better than with a standard direct genetic algorithm implementation.

Datasets, features, learning, and models in visual recognition

Visual recognition is a fundamental research topic in computer vision. This dissertation explores datasets, features, learning, and models used for visual recognition. In order to train visual models and evaluate different recognition algorithms, this dissertation develops an approach to collect object image datasets on web pages using an analysis of text around the image and of image appearance. This method exploits established online knowledge resources (Wikipedia pages for text; Flickr and Caltech data sets for images). The resources provide rich text and object appearance information. This dissertation describes results on two datasets. The first is Berg’s collection of 10 animal categories; on this dataset, we significantly outperform previous approaches. On an additional set of 5 categories, experimental results show the effectiveness of the method. Images are represented as features for visual recognition. This dissertation introduces a text-based image feature and demonstrates that it consistently improves performance on hard object classification problems. The feature is built using an auxiliary dataset of images annotated with tags, downloaded from the Internet. Image tags are noisy. The method obtains the text features of an unannotated image from the tags of its k-nearest neighbors in this auxiliary collection. A visual classifier presented with an object viewed under novel circumstances (say, a new viewing direction) must rely on its visual examples. This text feature may not change, because the auxiliary dataset likely contains a similar picture. While the tags associated with images are noisy, they are more stable when appearance changes. The performance of this feature is tested using PASCAL VOC 2006 and 2007 datasets. This feature performs well; it consistently improves the performance of visual object classifiers, and is particularly effective when the training dataset is small. With more and more collected training data, computational cost becomes a bottleneck, especially when training sophisticated classifiers such as kernelized SVM. This dissertation proposes a fast training algorithm called Stochastic Intersection Kernel Machine (SIKMA). This proposed training method will be useful for many vision problems, as it can produce a kernel classifier that is more accurate than a linear classifier, and can be trained on tens of thousands of examples in two minutes. It processes training examples one by one in a sequence, so memory cost is no longer the bottleneck to process large scale datasets. This dissertation applies this approach to train classifiers of Flickr groups with many group training examples. The resulting Flickr group prediction scores can be used to measure image similarity between two images. Experimental results on the Corel dataset and a PASCAL VOC dataset show the learned Flickr features perform better on image matching, retrieval, and classification than conventional visual features. Visual models are usually trained to best separate positive and negative training examples. However, when recognizing a large number of object categories, there may not be enough training examples for most objects, due to the intrinsic long-tailed distribution of objects in the real world. This dissertation proposes an approach to use comparative object similarity. The key insight is that, given a set of object categories which are similar and a set of categories which are dissimilar, a good object model should respond more strongly to examples from similar categories than to examples from dissimilar categories. This dissertation develops a regularized kernel machine algorithm to use this category dependent similarity regularization. Experiments on hundreds of categories show that our method can make significant improvement for categories with few or even no positive examples.

Do simple ventilation and gas exchange measurements predict early successful weaning from respiratory support in unselected general intensive care patients?

Background. The value of respiratory variables as weaning predictors in the intensive care unit (ICU) is controversial. We evaluated the ability of tidal volume (Vtexp), respiratory rate ( f ), minute volume (MVexp), rapid shallow breathing index ( f/Vt), inspired–expired oxygen concentration difference [(I–E)O2], and end-tidal carbon dioxide concentration (PE′CO2) at the end of a weaning trial to predict early weaning outcomes. Methods. Seventy-three patients who required .24 h of mechanical ventilation were studied. A controlled pressure support weaning trial was undertaken until 5 cm H2O continuous positive airway pressure or predefined criteria were reached. The ability of data from the last 5 min of the trial to predict whether a predefined endpoint indicating discontinuation of ventilator support within the next 24 h was evaluated. Results. Pre-test probability for achieving the outcome was 44% in the cohort (n¼32). Non-achievers were older, had higher APACHE II and organ failure scores before the trial, and higher baseline arterial H+ concentrations. The Vt, MV, f, and f/Vt had no predictive power using a range of cut-off values or from receiver operating characteristic (ROC) analysis. The [I–E]O2 and PE′CO2 had weak discriminatory power [areaunder the ROC curve: [I–E]O2 0.64 (P¼0.03); PE′CO2 0.63 (P¼0.05)]. Using best cut-off values for [I–E]O2 of 5.6% and PE′CO2 of 5.1 kPa, positive and negative likelihood ratios were 2 and 0.5, respectively, which only changed the pre- to post-test probability by about 20%. Conclusions. In unselected ICU patients, respiratory variables predict early weaning from mechanical ventilation poorly.

Language use and language attitudes in Malawian universities

This study aims to investigate patterns of language use and language attitudes amongst students in Malawian universities. This will highlight whether language issues affect Malawians’ ability to engage with tertiary education. It has been claimed that ineffective language policies in developing countries restrict people’s ability to access systems such as education. As a result, this has a negative impact on their own, and their country's, development. Specifically, Malawi frequently has the lowest rates of university enrolment worldwide and is consistently ranked amongst the world’s poorest countries. Recent language policy changes within Malawi have brought the issue of language use within education to the fore, with increased debate over whether English or indigenous languages are suitable for use in education. Through targeting university students across Malawi’s universities using semistructured interviews, data was collected to illustrate aspects of the sociolinguistic situation within Malawian universities. The results reveal that both English and indigenous languages are used within the university environment, while also suggesting that issues do arise from language use within university. While students recognise both positive and negative aspects of using each language, they are generally more favourable towards the use of English as a medium of instruction within university

Children's mental representations of attachment: associations with attachment security and parent-child narrative quality

The goal of this study was to examine the antecedents and correlates of children’s mental representations of attachment at 5 years (Attachment Story Completion Task, Bretherton, Ridgeway, & Cassidy, 1990; MacArthur Story Stem Battery, Bretherton, Oppenheim, Buchsbaum, Emde, & the MacArthur Narrative Group, 1990). Predictors included children’s attachment security with mothers and fathers assessed via the Attachment Q-Set (AQS, Waters, 1987) at 3 years, and parent-child narrative quality regarding positive and negative events at 5 years. Participants included 71 children and their mothers and fathers. Structural equation models (SEM) indicated that children’s attachment security exerted a significant indirect effect on children’s mental representations through parent-child narrative quality. Specifically, children’s attachment security with fathers was related to their mental representations via father-child reminiscing about positive events, and children’s attachment security with mothers was related to their mental representations via mother-child reminiscing about negative events. Results are discussed in terms of the development and implications of attachment relationships within the family context.

Enhanced Direct and Indirect Genetic Algorithm Approaches for a Mall Layout and Tenant Selection Problem

During our earlier research, it was recognised that in order to be successful with an indirect genetic algorithm approach using a decoder, the decoder has to strike a balance between being an optimiser in its own right and finding feasible solutions. Previously this balance was achieved manually. Here we extend this by presenting an automated approach where the genetic algorithm itself, simultaneously to solving the problem, sets weights to balance the components out. Subsequently we were able to solve a complex and non-linear scheduling problem better than with a standard direct genetic algorithm implementation.

Video lectures and online activities to engage students in a flipped classroom

In recent years there have been several proposals for alternative pedagogical practices. Most of these proposals are based in the, so called, “active learning”, in opposition to the common “passive learning”, which is centered on transmission of information inside classrooms as well as recognized as teacher-centered procedure. In an active learning pedagogical structure, students have a more participative role in the overall learning/teaching process, being encouraged to face new learning challenges like, for instance, solving problems and developing projects, in an autonomous approach trying to make them, consequently, able to build their own knowledge. The flipped or “inverted” classroom is one of these active learning pedagogical methodologies that emphasizes a learner-centered instruction. According to this approach, the first contact that students have with the content on a particular curriculum subject is not transmitted by the lecturer in the classroom, this teaching strategy requires students to assess and analyze the specific subject before attending to class, therefore the informational component from the lecture is the homework, and class time is dedicated to exercises and assignments, always with support from the instructor, who acts as a facilitator, helping students when needed and offering supplementary explanation as required. The main objective of this paper is to discuss and explore how the use of different types of instructional videos and online activities may be implemented in the flipped classroom procedure (as means of incorporating new content and teaching new competencies) and to describe students’ perceptions of this approach within a course in a Higher Education Institution (HEI), presenting some positive and negative features of this pedagogical practice.

'Enhanced Direct and Indirect Genetic Algorithm Approaches for a Mall Layout and Tenant Selection Problem'

During our earlier research, it was recognised that in order to be successful with an indirect genetic algorithm approach using a decoder, the decoder has to strike a balance between being an optimiser in its own right and finding feasible solutions. Previously this balance was achieved manually. Here we extend this by presenting an automated approach where the genetic algorithm itself, simultaneously to solving the problem, sets weights to balance the components out. Subsequently we were able to solve a complex and non-linear scheduling problem better than with a standard direct genetic algorithm implementation.

Types of embedded ties in buyer-supplier relationships and their combined effects on innovation performance

[EN] Purpose of the paper - This research analyzes the impact of three types of embedded ties, namely, specialized complementary resources, idiosyncratic investments, and knowledge sharing, on the innovation capacity of the firms. We also study the particularities of the Machine-Tool industry. Theoretical background – Our evaluation of the embedded buyer-supplier ties is based on the potential sources of relational rents proposed by Dyer and Sing (1998). We also draw on Uzzi and Lancaster (2003), Noordhoff et al. (2011), among others, to discuss the positive and negative aspects of embedded ties. Design/Methodology/Approach ‐ Using data from a survey of 202 European machine-tool firms acting as buyers and sellers, we propose and evaluate a Structural Equation model. Findings ‐ Only knowledge-sharing routines exert a significant positive effect on product innovation performance. Neither an increase in the idiosyncratic investments nor in complementary resources and capabilities enhance innovation performance. Also, knowledge-sharing routines mediate in the effect from idiosyncratic investments on innovation performance. Research Limitations. ‐ The machine tool industry has unique characteristics that make this generalization difficult. Also, there is considerable difficulty associated with testing more deeply the interrelations among these embedded ties in the long run. It is plausible to understand that these interrelations operate within a gradual process. Originality/Value/Contribution of Paper ‐ This research contributes to a better understanding of the role of embedded ties on innovativeness. To the best of our knowledge, there is no previous international empirical research analyzing the mediation effects among specialized complementary resources, idiosyncratic investments and knowledge sharing, and their effects on the innovation capacity of firms.