Some last thoughts on compositional data analysis

One of the disadvantages of old age is that there is more past than future: this,however, may be turned into an advantage if the wealth of experience and, hopefully,wisdom gained in the past can be reflected upon and throw some light on possiblefuture trends. To an extent, then, this talk is necessarily personal, certainly nostalgic,but also self critical and inquisitive about our understanding of the discipline ofstatistics. A number of almost philosophical themes will run through the talk: searchfor appropriate modelling in relation to the real problem envisaged, emphasis onsensible balances between simplicity and complexity, the relative roles of theory andpractice, the nature of communication of inferential ideas to the statistical layman, theinter-related roles of teaching, consultation and research. A list of keywords might be:identification of sample space and its mathematical structure, choices betweentransform and stay, the role of parametric modelling, the role of a sample spacemetric, the underused hypothesis lattice, the nature of compositional change,particularly in relation to the modelling of processes. While the main theme will berelevance to compositional data analysis we shall point to substantial implications forgeneral multivariate analysis arising from experience of the development ofcompositional data analysis…

Compositions in life science data

The aim of this talk is to convince the reader that there are a lot of interesting statisticalproblems in presentday life science data analysis which seem ultimately connected withcompositional statistics.Key words: SAGE, cDNA microarrays, (1D-)NMR, virus quasispecies

Experimental design on the simplex

Optimum experimental designs depend on the design criterion, the model andthe design region. The talk will consider the design of experiments for regressionmodels in which there is a single response with the explanatory variables lying ina simplex. One example is experiments on various compositions of glass such asthose considered by Martin, Bursnall, and Stillman (2001).Because of the highly symmetric nature of the simplex, the class of models thatare of interest, typically Scheff´e polynomials (Scheff´e 1958) are rather differentfrom those of standard regression analysis. The optimum designs are also ratherdifferent, inheriting a high degree of symmetry from the models.In the talk I will hope to discuss a variety of modes for such experiments. ThenI will discuss constrained mixture experiments, when not all the simplex is availablefor experimentation. Other important aspects include mixture experimentswith extra non-mixture factors and the blocking of mixture experiments.Much of the material is in Chapter 16 of Atkinson, Donev, and Tobias (2007).If time and my research allows, I would hope to finish with a few comments ondesign when the responses, rather than the explanatory variables, lie in a simplex.ReferencesAtkinson, A. C., A. N. Donev, and R. D. Tobias (2007). Optimum ExperimentalDesigns, with SAS. Oxford: Oxford University Press.Martin, R. J., M. C. Bursnall, and E. C. Stillman (2001). Further results onoptimal and efficient designs for constrained mixture experiments. In A. C.Atkinson, B. Bogacka, and A. Zhigljavsky (Eds.), Optimal Design 2000,pp. 225–239. Dordrecht: Kluwer.Scheff´e, H. (1958). Experiments with mixtures. Journal of the Royal StatisticalSociety, Ser. B 20, 344–360.1

Pre-play communication and credibility: A test of Aumann's conjecture

The effectiveness of pre-play communication in achieving efficientoutcomes has long been a subject of controversy. In some environments,cheap talk may help to achieve coordination. However, Aumannconjectures that, in a variant of the Stag Hunt game, a signal forefficient play is not self-enforcing and concludes that an "agreementto play [the efficient outcome] conveys no information about what theplayers will do." Harsanyi and Selten (1988) cite this example as anillustration of risk-dominance vs. payoff-dominance. Farrell and Rabin(1996) agree with the logic, but suspect that cheap talk willnonetheless achieve efficiency. The conjecture is tested with one-waycommunication. When the sender first chooses a signal and then anaction, there is impressive coordination: a 94% probability for thepotentially efficient (but risky) play, given a signal for efficientplay. Without communication, efforts to achieve efficiency wereunsuccessful, as the proportion of B moves is only 35%. I also test ahypothesis that the order of the action and the signal affects theresults, finding that the decision order is indeed important. WhileAumann s conjecture is behaviorally disconfirmed when the signal isdetermined initially, the signal s credibility seems to be much moresuspect when the sender is known to have first chosen an action, andthe results are not statistically distinguishable from those whenthere is no signal. Some applications and issues in communication andcoordination are discussed.

Communication, coordination and efficiency in evolutionary one-population models

We analyze the role of commitment in pre-play communication for ensuringefficient evolutionarily stable outcomes in coordination games. All players are a priori identical as they are drawn from the same population. In games where efficient outcomes can be reached by players coordinating on the same action we find commitment to be necessary to enforce efficiency. In games where efficienct outcomes only result from play of different actions, communication without commitment is most effective although efficiency can no longer be guaranteed. Only when there are many messages then inefficient outcomes are negligible as their basins of attraction become very small.

A Importância da Diáspora na Política Externa de Cabo Verde

Com a globalização, a emigração tem-se tornado cada vez mais um assunto que desperta muito interesse, por parte dos estudiosos. A emigração tem ganhado um forte cunho nas Relações Internacionais, já que com a alteração do Sistema internacional, o Estado deixou de ser o único actor da cena internacional. Por isso desperta muito o interesse em aprofundar os estudos sobre a emigração que é um fenómeno que tem acontecido no sistema internacional há várias décadas. Após a segunda guerra mundial e com a globalização tem-se verificado muita emigração de sul para norte, em busca de melhores condições de vida. Hoje em dia é comum quando se fala da emigração falar-se da diáspora que é um termo usado para designar a dispersão dos Judeus “exilados/expulsos” da sua terra de origem Palestina. Mas vários investigadores têm usado este termo para caracterizar a emigração cabo-verdiana para várias partes do mundo. E sem fugir à regra, Cabo Verde é um exemplo de fuga de sul para norte. Os cabo-verdianos emigram para norte à procura de melhores condições de vida. E hoje, já não se fala nos emigrantes cabo-verdianos, mas sim na diáspora cabo-verdiana. Por isso pretende-se com essa dissertação procurar fazer um estudo, para saber qual a importância da Diáspora na política externa de Cabo Verde.

Crescimento Económico em Cabo Verde e seu Impacto na Sustentabilidade Ambiental

Para que o crescimento económico seja efetivo, importa registar de igual modo o crescimento real nas outras vertentes que sustentam o próprio crescimento, assim é cada vez mais importante introduzir variáveis ambientais e sociais quando se procede à análise efetiva do crescimento económico. O “crescimento económico é um indicador que revela o bem-estar económico de um país”, (Bürgenmeier, 2005, p.16-17). Só se pode falar da sustentabilidade ao nível do crescimento económico, se efetivamente os recursos forem devidamente racionalizados, mas é igualmente muito importante ter em conta a reutilização de recursos, sobretudo quando são escassos ou quando representam riscos sérios para o ambiente como também para a economia, entre outros. O protocolo do Quioto, a Convenção Quadro sobre as Mudanças Climáticas e os Objetivos Do Milénio (ODM), são apenas alguns exemplos de programas cujos objetivos visam essencialmente disciplinar a emissão de dióxido de carbono (CO2). Um dos objetivos é o de tentar “educar” o mundo global para os problemas que decorrem do uso abusivo e descontrolado de recursos, principalmente aqueles que podem pôr em causa a sustentabilidade do planeta terra. Cabo Verde (CV) é um dos poucos países ao nível do continente africano, e único na sua sub-região, que tem cumprido com os objetivos dos projetos acima listados. Essas conquistas têm permitido que este país conduza as suas políticas de desenvolvimento, balizadas em contextos das melhores práticas mundialmente aceites. Têm sido canalizados investimentos em infraestruturas de elevado valor acrescentado para a captação e exploração de energias verdes. A presente dissertação tem como objetivos: identificar os eventuais impactos ambientais em Cabo Verde que poderão decorrer do crescimento e desenvolvimento económico; sugerir melhorias ao nível da sustentabilidade. Conclui-se, por meio de inquéritos conduzidos por nós, que os Cabo-verdianos se mostram dispostos a colaborar financeiramente para a proteção ambiental em Cabo Verde.

The State of the Judiciary, 2009

Thank you for inviting me again this year to talk with you about the condition of Iowa’s judicial branch. As your partner in government, we look forward to working with you on issues affecting the administration of justice. If I could capture the condition of our courts, indeed the condition of our state, in a few words, it would be: “We live in challenging times.” No one knows the true meaning of this phrase better than those Iowans hit by natural disasters. But my focus today is, of course, on the courts. Ensuring the delivery of equal, affordable and accessible justice is always challenging work, but it will be especially so this year and the next in light of the State’s budget problems. Given the magnitude of this challenge, it is even more imperative that we work together in the spirit of unity, candor and cooperation. And I address you today in this spirit. We are deeply concerned, as you are, about the present financial situation and its effect on individual Iowans. Naturally, we are particularly troubled about its impact on the delivery of justice to our citizens. Even in good economic times, the administration of justice is difficult to fulfill given the sheer volume and complexity of problems Iowans bring to their courthouses. Because of the effects of the nation’s economic downturn, people will need access to justice now more than ever. We already see this happening. The number of mortgage foreclosure cases in Iowa rose 14% in the past year. Debt collection cases increased 20% in the same time. An increase in these types of cases is predictable in tough economic times, but other types of problems may escalate as well. Some experts fear that a recession may also give rise to more crime, child abuse, domestic violence, and substance abuse. Naturally, for the sake of the people who may be harmed by these problems, we hope they do not occur. If they do, however, these matters will demand our immediate attention.

LRF-mediated Dll4 repression in erythroblasts is necessary for hematopoietic stem cell maintenance.

Hematopoietic stem cells (HSCs) are the most primitive cells in the hematopoietic system and are under tight regulation for self-renewal and differentiation. Notch signals are essential for the emergence of definitive hematopoiesis in mouse embryos and are critical regulators of lymphoid lineage fate determination. However, it remains unclear how Notch regulates the balance between HSC self-renewal and differentiation in the adult bone marrow (BM). Here we report a novel mechanism that prevents HSCs from undergoing premature lymphoid differentiation in BM. Using a series of in vivo mouse models and functional HSC assays, we show that leukemia/lymphoma related factor (LRF) is necessary for HSC maintenance by functioning as an erythroid-specific repressor of Delta-like 4 (Dll4) expression. Lrf deletion in erythroblasts promoted up-regulation of Dll4 in erythroblasts, sensitizing HSCs to T-cell instructive signals in the BM. Our study reveals novel cross-talk between HSCs and erythroblasts, and sheds a new light on the regulatory mechanisms regulating the balance between HSC self-renewal and differentiation.

Homeostatic and circadian contribution to EEG and molecular state variables of sleep regulation.

STUDY OBJECTIVES: Besides their well-established role in circadian rhythms, our findings that the forebrain expression of the clock-genes Per2 and Dbp increases and decreases, respectively, in relation to time spent awake suggest they also play a role in the homeostatic aspect of sleep regulation. Here, we determined whether time of day modulates the effects of elevated sleep pressure on clock-gene expression. Time of day effects were assessed also for recognized electrophysiological (EEG delta power) and molecular (Homer1a) markers of sleep homeostasis. DESIGN: EEG and qPCR data were obtained for baseline and recovery from 6-h sleep deprivation starting at ZT0, -6, -12, or -18. SETTING: Mouse sleep laboratory. PARTICIPANTS: Male mice. INTERVENTIONS: Sleep deprivation. RESULTS: The sleep-deprivation induced changes in Per2 and Dbp expression importantly varied with time of day, such that Per2 could even decrease during sleep deprivations occurring at the decreasing phase in baseline. Dbp showed similar, albeit opposite dynamics. These unexpected results could be reliably predicted assuming that these transcripts behave according to a driven damped harmonic oscillator. As expected, the sleep-wake distribution accounted for a large degree of the changes in EEG delta power and Homer1a. Nevertheless, the sleep deprivation-induced increase in delta power varied also with time of day with higher than expected levels when recovery sleep started at dark onset. CONCLUSIONS: Per2 and delta power are widely used as exclusive state variables of the circadian and homeostatic process, respectively. Our findings demonstrate a considerable cross-talk between these two processes. As Per2 in the brain responds to both sleep loss and time of day, this molecule is well positioned to keep track of and to anticipate homeostatic sleep need. CITATION: Curie T; Mongrain V; Dorsaz S; Mang GM; Emmenegger Y; Franken P. Homeostatic and circadian contribution to EEG and molecular state variables of sleep regulation. SLEEP 2013;36(3):311-323.

La resiliència

El present treball és un aprofundiment teòric sobre la resiliència, un concepte transgressor en les ciències socials que invita a tenir una nova visió de les situacions concretes, a un canvi de perspectiva que ens guia a refermar maneres d’intervenció diferents. Precisament, perquè ens porta a canviar la nostra mirada vers les persones i sobre la vida. Aquest projecte s’emmarca en els orígens del concepte, en quin moment es troba avui dia, aquelles teories explicatives i una aportació sobre la seva visió pràctica; tenint present en tot moment tant la dimensió individual com la dimensió comunitària del mateix. La resiliència, reconeix el valor de la imperfecció de l’espècia humana. No és una resposta immediata a l’adversitat sinó un procés que està en constant construcció, canvi i/o evolució en el transcurs del temps. No és un concepte absolut ni total, sinó que està lligat als conceptes dinàmics i complexos de desenvolupament i creixement humà i va més enllà de l’actitud passiva de resistir qualsevol cop; implica l’actitud proactiva d’aprendre/reapendre a viure i construir/reconstruir la vida.

Preservació digital al núvol

Ara que ja ningú qüestiona les publicacions digitals, l'accés obert o els repositoris de tipus institucional o temàtic, cal co-mençar a treballar en els temes de preservació. Som responsables d'assegurar l'accés i l'ús futurs dels documents digitals, hagin nascut en format digital o siguin fruit dels projectes de digitalització. En aquest article es parla sobre la preservació digital i els tipus de continguts, així com els conceptes, tipologies, costos i usos de l'anomenat «núvol». També es mostra un exemple de núvol privat, la preservació de tesis doctorals del TDX i es comenta una experiència de núvol públic, el DuraCloud.

Sistemes encastats en temps real

Resum En l’actualitat, els sistemes electrònics de processament de dades són cada cop més significatius dins del sector industrial. Són moltes les necessitats que sorgeixen en el món dels sistemes d’autentificació, de l’electrònica aeronàutica, d’equips d’emmagatzemament de dades, de telecomunicacions, etc. Aquestes necessitats tecnològiques exigeixen ser controlades per un sistema fiable, robust, totalment dependent amb els esdeveniments externs i que compleixi correctament les restriccions temporals imposades per tal de que realitzi el seu propòsit d’una manera eficient. Aquí és on entren en joc els sistemes encastats en temps real, els quals ofereixen una gran fiabilitat, disponibilitat, una ràpida resposta als esdeveniments externs del sistema, una alta garantia de funcionament i una àmplia possibilitat d’aplicacions. Aquest projecte està pensat per a fer una introducció al món dels sistemes encastats, com també explicar el funcionament del sistema operatiu en temps real FreeRTOS; el qual utilitza com a mètode de programació l’ús de tasques independents entre elles. Donarem una visió de les seves característiques de funcionament, com organitza tasques mitjançant un scheduler i uns exemples per a poder dissenyar-hi aplicacions.

Whose DNA is this? How relevant a question? (a note for forensic scientists).

This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during the analysis of a stain, relevant from the point of view of a Court of Justice? This question relates to skeptical views previously voiced by commentators mainly in the judicial area, but is avoided by a large majority of forensic scientists. Notwithstanding, the pivotal role of this question has recently been evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly that a huge gap still exists between questions lawyers are actually interested in, and the answers that scientists deliver to Courts in written reports or during oral testimony. Participants in the justice system, namely lawyers and jurors on the one hand and forensic geneticists on the other, unfortunately talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases. This paper intends to emphasize the actuality of this topic and suggest beneficial ways ahead towards a more reasoned use of forensic DNA in criminal proceedings.

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

BACKGROUND: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.