The complexity of Drosophila innate immunity

Metazoans rely on efficient mechanisms to oppose infections caused by pathogens. The immediate and first-line defense mechanism(s) in metazoans, referred to as the innate immune system, is initiated upon recognition of microbial intruders by germline encoded receptors and is executed by a set of rapid effector mechanisms. Adaptive immunity is restricted to vertebrate species and it is controlled and assisted by the innate immune system. Interestingly, most of the basic signaling cascades that regulate the primeval innate defense mechanism(s) have been well conserved during evolution, for instance between humans and the fruit fly, Drosophila melanogaster. Being devoid of adaptive signaling and effector systems, Drosophila has become an established model system for studying pristine innate immune cascades and reactions. In general, an immune response is evoked when microorganisms pass the fruit fly’s physical barriers (e.g. cuticle, epithelial lining of gut and trachea), and it is mainly executed in the hemolymph, the equivalent of the mammalian blood. Innate immunity in the fruit fly consists of a phenoloxidase (PO) response, a cellular response (hemocytes), an antiviral response, and the NF-κB dependent production of antimicrobial peptides referred to as the humoral response. The JAK/STAT and Jun kinase signaling cascades are also implicated in the defence against pathogens.

Severus Snape : The Complexity and Unconventional Heroism of Severus Snape in the Harry Potter Books

Being an evildoer and being evil is not always the same thing; author J.K Rowling’s character Professor Severus Snape from the Harry Potter series is balancing on that very line. Although being unfair and mean to the protagonist Harry Potter all through the series, Professor Snape is revealed as a hero in the seventh book Harry Potter and the Deathly Hallows (2007). This essay focuses on some of the complex psychological reasons as to why Snape acts the way he does towards Harry and why many readers consider him to be just as great a hero as the protagonist. It argues that his difficult upbringing is the cause of his complexity and the series of books are analyzed from a structuralist perspective, using A.J Greimas’ actantial model and Frank Kermode’s theories about endings and plot twists. Snape’s hate for Harry’s father, caused by years of bullying, is examined as well as his love for Harry’s mother. This essay also discusses in what ways Snape’s change of allegiance, brought on by his eternal love for Harry’s mother, is a great aid in defeating the Dark Lord.

On the extension complexity of combinatorial polytopes

In this paper we extend recent results of Fiorini et al. on the extension complexity of the cut polytope and related polyhedra. We first describe a lifting argument to show exponential extension complexity for a number of NP-complete problems including subset-sum and three dimensional matching. We then obtain a relationship between the extension complexity of the cut polytope of a graph and that of its graph minors. Using this we are able to show exponential extension complexity for the cut polytope of a large number of graphs, including those used in quantum information and suspensions of cubic planar graphs.

Influence of pharmacotherapy complexity on compliance with the therapeutic objectives for HIV+ patients on antiretroviral treatment concomitant with therapy for dyslipidemia: INCOFAR Project

Objectives: To analyze the relationship between pharmacotherapeutical complexity and compliance of therapeutic objectives in HIV+ patients on antiretroviral treatment and concomitant dyslipidemia therapy. Materials and methods: A retrospective observational study including HIV patients on stable antiretroviral treatment during the past 6 months, and dyslipidemia treatment between January and December, 2013. The complexity index was calculated with the tool developed by McDonald et al. Other variables analyzed were: age, gender, risk factor of HIV, smoking, alcoholism and drugs, psychiatric disorders, adherence to antiretroviral treatment and lipid lowering drugs, and clinical parameters (HIV viral load, CD4 count, plasma levels of total cholesterol, LDL, HDL, and triglycerides). In order to determine the predictive factors associated with the compliance of therapeutic objectives, univariate analysis was conducted through logistical regression, followed by a multivariate analysis. Results: The study included 89 patients; 56.8% of them met the therapeutic objectives for dyslipidemia. The complexity index was significantly higher (p = 0.02) in those patients who did not reach the objective values (median 51.8 vs. 38.9). Adherence to lipid lowering treatment was significantly associated with compliance of the therapeutic objectives established for dyslipidemia treatment. A 67.0% of patients met the objectives for their antiretroviral treatment; however, the complexity index was not significantly higher (p = 0.06) in those patients who did not meet said objectives. Conclusions: Pharmacotherapeutical complexity represents a key factor in terms of achieving health objectives in HIV+ patients on treatment for dyslipidemia.

Algol 68 Dialect Conversion -- a Syntactic Approach

A syntax directed package for converting Revised Algol 68 programs into Algol 68-R form, (where possible) is being developed at Nottingham. The package makes use of J.M. Foster's Syntax Improving Device (SID) [1]. The experience gained has underlined the value of a syntactic approach to problems of this sort. A far wider range of constructs can be translated than would ever be possible by using ad hoc methods. In many respects the difficulties encountered are those of conventional compiler writing, but some intriguing new problems arise when, as in this case, the source language and target language differ relatively little in philosophy and appearance.

An experiment on the parameter uncertainty of hydrological models with different levels of complexity in a climate change context

La possibilité d’estimer l’impact du changement climatique en cours sur le comportement hydrologique des hydro-systèmes est une nécessité pour anticiper les adaptations inévitables et nécessaires que doivent envisager nos sociétés. Dans ce contexte, ce projet doctoral présente une étude sur l’évaluation de la sensibilité des projections hydrologiques futures à : (i) La non-robustesse de l’identification des paramètres des modèles hydrologiques, (ii) l’utilisation de plusieurs jeux de paramètres équifinaux et (iii) l’utilisation de différentes structures de modèles hydrologiques. Pour quantifier l’impact de la première source d’incertitude sur les sorties des modèles, quatre sous-périodes climatiquement contrastées sont tout d’abord identifiées au sein des chroniques observées. Les modèles sont calés sur chacune de ces quatre périodes et les sorties engendrées sont analysées en calage et en validation en suivant les quatre configurations du Different Splitsample Tests (Klemeš, 1986;Wilby, 2005; Seiller et al. (2012);Refsgaard et al. (2014)). Afin d’étudier la seconde source d’incertitude liée à la structure du modèle, l’équifinalité des jeux de paramètres est ensuite prise en compte en considérant pour chaque type de calage les sorties associées à des jeux de paramètres équifinaux. Enfin, pour évaluer la troisième source d’incertitude, cinq modèles hydrologiques de différents niveaux de complexité sont appliqués (GR4J, MORDOR, HSAMI, SWAT et HYDROTEL) sur le bassin versant québécois de la rivière Au Saumon. Les trois sources d’incertitude sont évaluées à la fois dans conditions climatiques observées passées et dans les conditions climatiques futures. Les résultats montrent que, en tenant compte de la méthode d’évaluation suivie dans ce doctorat, l’utilisation de différents niveaux de complexité des modèles hydrologiques est la principale source de variabilité dans les projections de débits dans des conditions climatiques futures. Ceci est suivi par le manque de robustesse de l’identification des paramètres. Les projections hydrologiques générées par un ensemble de jeux de paramètres équifinaux sont proches de celles associées au jeu de paramètres optimal. Par conséquent, plus d’efforts devraient être investis dans l’amélioration de la robustesse des modèles pour les études d’impact sur le changement climatique, notamment en développant les structures des modèles plus appropriés et en proposant des procédures de calage qui augmentent leur robustesse. Ces travaux permettent d’apporter une réponse détaillée sur notre capacité à réaliser un diagnostic des impacts des changements climatiques sur les ressources hydriques du bassin Au Saumon et de proposer une démarche méthodologique originale d’analyse pouvant être directement appliquée ou adaptée à d’autres contextes hydro-climatiques.

The Borel Complexity of Isomorphism for Some First Order Theories

In this work we consider several instances of the following problem: "how complicated can the isomorphism relation for countable models be?"' Using the Borel reducibility framework, we investigate this question with regard to the space of countable models of particular complete first-order theories. We also investigate to what extent this complexity is mirrored in the number of back-and-forth inequivalent models of the theory. We consider this question for two large and related classes of theories. First, we consider o-minimal theories, showing that if T is o-minimal, then the isomorphism relation is either Borel complete or Borel. Further, if it is Borel, we characterize exactly which values can occur, and when they occur. In all cases Borel completeness implies lambda-Borel completeness for all lambda. Second, we consider colored linear orders, which are (complete theories of) a linear order expanded by countably many unary predicates. We discover the same characterization as with o-minimal theories, taking the same values, with the exception that all finite values are possible except two. We characterize exactly when each possibility occurs, which is similar to the o-minimal case. Additionally, we extend Schirrman's theorem, showing that if the language is finite, then T is countably categorical or Borel complete. As before, in all cases Borel completeness implies lambda-Borel completeness for all lambda.

Transactions and schema evolution in a persistent object-oriented programming system

Applications are subject of a continuous evolution process with a profound impact on their underlining data model, hence requiring frequent updates in the applications' class structure and database structure as well. This twofold problem, schema evolution and instance adaptation, usually known as database evolution, is addressed in this thesis. Additionally, we address concurrency and error recovery problems with a novel meta-model and its aspect-oriented implementation. Modern object-oriented databases provide features that help programmers deal with object persistence, as well as all related problems such as database evolution, concurrency and error handling. In most systems there are transparent mechanisms to address these problems, nonetheless the database evolution problem still requires some human intervention, which consumes much of programmers' and database administrators' work effort. Earlier research works have demonstrated that aspect-oriented programming (AOP) techniques enable the development of flexible and pluggable systems. In these earlier works, the schema evolution and the instance adaptation problems were addressed as database management concerns. However, none of this research was focused on orthogonal persistent systems. We argue that AOP techniques are well suited to address these problems in orthogonal persistent systems. Regarding the concurrency and error recovery, earlier research showed that only syntactic obliviousness between the base program and aspects is possible. Our meta-model and framework follow an aspect-oriented approach focused on the object-oriented orthogonal persistent context. The proposed meta-model is characterized by its simplicity in order to achieve efficient and transparent database evolution mechanisms. Our meta-model supports multiple versions of a class structure by applying a class versioning strategy. Thus, enabling bidirectional application compatibility among versions of each class structure. That is to say, the database structure can be updated because earlier applications continue to work, as well as later applications that have only known the updated class structure. The specific characteristics of orthogonal persistent systems, as well as a metadata enrichment strategy within the application's source code, complete the inception of the meta-model and have motivated our research work. To test the feasibility of the approach, a prototype was developed. Our prototype is a framework that mediates the interaction between applications and the database, providing them with orthogonal persistence mechanisms. These mechanisms are introduced into applications as an {\it aspect} in the aspect-oriented sense. Objects do not require the extension of any super class, the implementation of an interface nor contain a particular annotation. Parametric type classes are also correctly handled by our framework. However, classes that belong to the programming environment must not be handled as versionable due to restrictions imposed by the Java Virtual Machine. Regarding concurrency support, the framework provides the applications with a multithreaded environment which supports database transactions and error recovery. The framework keeps applications oblivious to the database evolution problem, as well as persistence. Programmers can update the applications' class structure because the framework will produce a new version for it at the database metadata layer. Using our XML based pointcut/advice constructs, the framework's instance adaptation mechanism is extended, hence keeping the framework also oblivious to this problem. The potential developing gains provided by the prototype were benchmarked. In our case study, the results confirm that mechanisms' transparency has positive repercussions on the programmer's productivity, simplifying the entire evolution process at application and database levels. The meta-model itself also was benchmarked in terms of complexity and agility. Compared with other meta-models, it requires less meta-object modifications in each schema evolution step. Other types of tests were carried out in order to validate prototype and meta-model robustness. In order to perform these tests, we used an OO7 small size database due to its data model complexity. Since the developed prototype offers some features that were not observed in other known systems, performance benchmarks were not possible. However, the developed benchmark is now available to perform future performance comparisons with equivalent systems. In order to test our approach in a real world scenario, we developed a proof-of-concept application. This application was developed without any persistence mechanisms. Using our framework and minor changes applied to the application's source code, we added these mechanisms. Furthermore, we tested the application in a schema evolution scenario. This real world experience using our framework showed that applications remains oblivious to persistence and database evolution. In this case study, our framework proved to be a useful tool for programmers and database administrators. Performance issues and the single Java Virtual Machine concurrent model are the major limitations found in the framework.

Processing of hierarchical syntactic strusture in music

Hierarchical structure with nested nonlocal dependencies is a key feature of human language and can be identified theoretically in most pieces of tonal music. However, previous studies have argued against the perception of such structures in music. Here, we show processing of nonlocal dependencies in music. We presented chorales by J. S. Bach and modified versions inwhich the hierarchical structure was rendered irregular whereas the local structure was kept intact. Brain electric responses differed between regular and irregular hierarchical structures, in both musicians and nonmusicians. This finding indicates that, when listening to music, humans apply cognitive processes that are capable of dealing with longdistance dependencies resulting from hierarchically organized syntactic structures. Our results reveal that a brain mechanism fundamental for syntactic processing is engaged during the perception of music, indicating that processing of hierarchical structure with nested nonlocal dependencies is not just a key component of human language, but a multidomain capacity of human cognition.

THE RELATIVE SIGNIFICANCE OF SYNTACTIC KNOWLEDGE AND VOCABULARY KNOWLEDGE IN SECOND LANGUAGE LISTENING COMPREHENSION

The main purpose of the current study was to examine the role of vocabulary knowledge (VK) and syntactic knowledge (SK) in L2 listening comprehension, as well as their relative significance. Unlike previous studies, the current project employed assessment tasks to measure aural and proceduralized VK and SK. In terms of VK, to avoid under-representing the construct, measures of both breadth (VB) and depth (VD) were included. Additionally, the current study examined the role of VK and SK by accounting for individual differences in two important cognitive factors in L2 listening: metacognitive knowledge (MK) and working memory (WM). Also, to explore the role of VK and SK more fully, the current study accounted for the negative impact of anxiety on WM and L2 listening. The study was carried out in an English as a Foreign Language (EFL) context, and participants were 263 Iranian learners at a wide range of English proficiency from lower-intermediate to advanced. Participants took a battery of ten linguistic, cognitive and affective measures. Then, the collected data were subjected to several preliminary analyses, but structural equation modeling (SEM) was then used as the primary analysis method to answer the study research questions. Results of the preliminary analyses revealed that MK and WM were significant predictors of L2 listening ability; thus, they were kept in the main SEM analyses. The significant role of WM was only observed when the negative effect of anxiety on WM was accounted for. Preliminary analyses also showed that VB and VD were not distinct measures of VK. However, the results also showed that if VB and VD were considered separate, VD was a better predictor of L2 listening success. The main analyses of the current study revealed a significant role for both VK and SK in explaining success in L2 listening comprehension, which differs from findings from previous empirical studies. However, SEM analysis did not reveal a statistically significant difference in terms of the predictive power of the two linguistic factors. Descriptive results of the SEM analysis, along with results from regression analysis, indicated to a more significant role for VK.

Rangeland profitability in the northern Gulf region of Queensland: understanding beef business complexity and the subsequent impact on land resource management and environmental outcomes

The farm-gate value of extensive beef production from the northern Gulf region of Queensland, Australia, is ~$150 million annually. Poor profitability and declining equity are common issues for most beef businesses in the region. The beef industry relies primarily on native pasture systems and studies continue to report a decline in the condition and productivity of important land types in the region. Governments and Natural Resource Management groups are investing significant resources to restore landscape health and productivity. Fundamental community expectations also include broader environmental outcomes such as reducing beef industry greenhouse gas emissions. Whole-of-business analysis results are presented from 18 extensive beef businesses (producers) to highlight the complex social and economic drivers of management decisions that impact on the natural resource and environment. Business analysis activities also focussed on improving enterprise performance. Profitability, herd performance and greenhouse emission benchmarks are documented and discussed.

Characterization of the effect of nitrogen deficiency on above-ground plant phenotypes in relation to root complexity in maize

Nitrogen (N) is an essential plant nutrient in maize production, and if considering only natural sources, is often the limiting factor world-wide in terms of a plant’s grain yield. For this reason, many farmers around the world supplement available soil N with synthetic man-made forms. Years of over-application of N fertilizer have led to increased N in groundwater and streams due to leaching and run-off from agricultural sites. In the Midwest Corn Belt much of this excess N eventually makes its way to the Gulf of Mexico leading to eutrophication (increase of phytoplankton) and a hypoxic (reduced oxygen) dead zone. Growing concerns about these types of problems and desire for greater input use efficiency have led to demand for crops with improved N use efficiency (NUE) to allow reduced N fertilizer application rates and subsequently lower N pollution. It is well known that roots are responsible for N uptake by plants, but it is relatively unknown how root architecture affects this ability. This research was conducted to better understand the influence of root complexity (RC) in maize on a plant’s response to N stress as well as the influence of RC on other above-ground plant traits. Thirty-one above-ground plant traits were measured for 64 recombinant inbred lines (RILs) from the intermated B73 & Mo17 (IBM) population and their backcrosses (BCs) to either parent, B73 and Mo17, under normal (182 kg N ha-1) and N deficient (0 kg N ha-1) conditions. The RILs were selected based on results from an earlier experiment by Novais et al. (2011) which screened 232 RILs from the IBM to obtain their root complexity measurements. The 64 selected RILs were comprised of 31 of the lowest complexity RILs (RC1) and 33 of the highest complexity RILs (RC2) in terms of root architecture (characterized as fractal dimensions). The use of the parental BCs classifies the experiment as Design III, an experimental design developed by Comstock and Robinson (1952) which allows for estimation of dominance significance and level. Of the 31 traits measured, 12 were whole plant traits chosen due to their documented response to N stress. The other 19 traits were ear traits commonly measured for their influence on yield. Results showed that genotypes from RC1 and RC2 significantly differ for several above-ground phenotypes. We also observed a difference in the number and magnitude of N treatment responses between the two RC classes. Differences in phenotypic trait correlations and their change in response to N were also observed between the RC classes. RC did not seem to have a strong correlation with calculated NUE (ΔYield/ΔN). Quantitative genetic analysis utilizing the Design III experimental design revealed significant dominance effects acting on several traits as well as changes in significance and dominance level between N treatments. Several QTL were mapped for 26 of the 31 traits and significant N effects were observed across the majority of the genome for some N stress indicative traits (e.g. stay-green). This research and related projects are essential to a better understanding of plant N uptake and metabolism. Understanding these processes is a necessary step in the progress towards the goal of breeding for better NUE crops.

Safety and complexity: the inter-departmental threats to patient safety in the operating department

Purpose: Current thinking about ‘patient safety’ emphasises the causal relationship between the work environment and the delivery of clinical care. This research draws on the theory of Normal Accidents to extend this analysis and better understand the ‘organisational factors’ that threaten safety. Methods: Ethnographic research methods were used, with observations of the operating department setting for 18 month and interviews with 80 members of hospital staff. The setting for the study was the Operating Department of a large teaching hospital in the North-West of England. Results: The work of the operating department is determined by inter-dependant, ‘tightly coupled’ organisational relationships between hospital departments based upon the timely exchange of information, services and resources required for the delivery of care. Failures within these processes, manifest as ‘breakdowns’ within inter-departmental relationships lead to situations of constraint, rapid change and uncertainty in the work of the operating department that require staff to break with established routines and work with increased time and emotional pressures. This means that staff focus on working quickly, as opposed to working safely. Conclusion: Analysis of safety needs to move beyond a focus on the immediate work environment and individual practice, to consider the more complex and deeply structured organisational systems of hospital activity. For departmental managers the scope for service planning to control for safety may be limited as the structured ‘real world’ situation of service delivery is shaped by inter-department and organisational factors that are perhaps beyond the scope of departmental management.

TcT: Tyrolean Complexity Tool

International audience