A high-mobility, low-cost phenotype defines human effector-memory CD8+ T cells.

T cells move randomly ("random-walk"), a characteristic thought to be integral to their function. Using migration assays and time-lapse microscopy, we found that CD8+ T cells lacking the lymph node homing receptors CCR7 and CD62L migrate more efficiently in transwell assays, and that these same cells are characterized by a high frequency of cells exhibiting random crawling activity under culture conditions mimicking the interstitial/extravascular milieu, but not when examined on endothelial cells. To assess the energy efficiency of cells crawling at a high frequency, we measured mRNA expression of genes key to mitochondrial energy metabolism (peroxisome proliferator-activated receptor gamma coactivator 1beta [PGC-1beta], estrogen-related receptor alpha [ERRalpha], cytochrome C, ATP synthase, and the uncoupling proteins [UCPs] UCP-2 and -3), quantified ATP contents, and performed calorimetric analyses. Together these assays indicated a high energy efficiency of the high crawling frequency CD8+ T-cell population, and identified differentially regulated heat production among nonlymphoid versus lymphoid homing CD8+ T cells.

Homeostatic proliferation and survival of naïve and memory T cells.

The immune system relies on homeostatic mechanisms in order to adapt to the changing requirements encountered during steady-state existence and activation by antigen. For T cells, this involves maintenance of a diverse repertoire of naïve cells, rapid elimination of effector cells after pathogen clearance, and long-term survival of memory cells. The reduction of T-cell counts by either cytotoxic drugs, irradiation, or certain viruses is known to lead to lymphopenia-induced proliferation and restoration of normal T-cell levels. Such expansion is governed by the interaction of TCR with self-peptide/MHC (p/MHC) molecules plus contact with cytokines, especially IL-7. These same ligands, i.e. p/MHC molecules and IL-7, maintain naïve T lymphocytes as resting cells under steady-state T-cell-sufficient conditions. Unlike naïve cells, typical "central" memory T cells rely on a combination of IL-7 and IL-15 for their survival in interphase and for occasional cell division without requiring signals from p/MHC molecules. Other memory T-cell subsets are less quiescent and include naturally occurring activated memory-phenotype cells, memory cells generated during chronic viral infections, and effector memory cells. These subsets of activated memory cells differ from central memory T cells in their requirements for homeostatic proliferation and survival. Thus, the factors controlling T-cell homeostasis can be seen to vary considerably from one subset to another as described in detail in this review.

Working memory load improves early stages of independent visual processing.

Increasing evidence suggests that working memory and perceptual processes are dynamically interrelated due to modulating activity in overlapping brain networks. However, the direct influence of working memory on the spatio-temporal brain dynamics of behaviorally relevant intervening information remains unclear. To investigate this issue, subjects performed a visual proximity grid perception task under three different visual-spatial working memory (VSWM) load conditions. VSWM load was manipulated by asking subjects to memorize the spatial locations of 6 or 3 disks. The grid was always presented between the encoding and recognition of the disk pattern. As a baseline condition, grid stimuli were presented without a VSWM context. VSWM load altered both perceptual performance and neural networks active during intervening grid encoding. Participants performed faster and more accurately on a challenging perceptual task under high VSWM load as compared to the low load and the baseline condition. Visual evoked potential (VEP) analyses identified changes in the configuration of the underlying sources in one particular period occurring 160-190 ms post-stimulus onset. Source analyses further showed an occipito-parietal down-regulation concurrent to the increased involvement of temporal and frontal resources in the high VSWM context. Together, these data suggest that cognitive control mechanisms supporting working memory may selectively enhance concurrent visual processing related to an independent goal. More broadly, our findings are in line with theoretical models implicating the engagement of frontal regions in synchronizing and optimizing mnemonic and perceptual resources towards multiple goals.

Improving globally distributed software development and support processes - A workflow view

We propose a new approach and related indicators for globally distributed software support and development based on a 3-year process improvement project in a globally distributed engineering company. The company develops, delivers and supports a complex software system with tailored hardware components and unique end-customer installations. By applying the domain knowledge from operations management on lead time reduction and its multiple benefits to process performance, the workflows of globally distributed software development and multitier support processes were measured and monitored throughout the company. The results show that the global end-to-end process visibility and centrally managed reporting at all levels of the organization catalyzed a change process toward significantly better performance. Due to the new performance indicators based on lead times and their variation with fixed control procedures, the case company was able to report faster bug-fixing cycle times, improved response times and generally better customer satisfaction in its global operations. In all, lead times to implement new features and to respond to customer issues and requests were reduced by 50%.

Profiling of signal transduction in human memory T cells

Résumé pour un large public: La vaccination a eu un impact énorme sur la santé mondiale. Mais, quel est le principe d'un vaccin? Il est basé sur la 'mémoire immunologique', qui est une particularité exclusive des systèmes immunitaires des organismes évolués. Suite à une infection par un pathogène, des cellules spécialisées de notre système immunitaire (les lymphocytes) le reconnaissent et initient une réaction immunitaire qui a pour but son élimination. Pendant cette réaction se développent aussi des cellules, appelées cellules lymphocytaires mémoire, qui persistent pour longue durée et qui ont la capacité de stimuler une réaction immunitaire très efficace immédiatement après une seconde exposition à ce même pathogène. Ce sont ces cellules mémoires (lymphocytes B et T) qui sont à la base de la 'mémoire immunologique' et qui sont stimulées lors de la vaccination. Chez l'homme, deux populations distinctes des lymphocytes T mémoires ont été identifiées: les cellules centrales (CM) et effectrices (EM) mémoires. Ces populations sont fonctionnellement hétérogènes et exercent des rôles distincts et essentiels dans l'immunité protectrice. Typiquement, les cellules effectrices mémoires sont capables de tuer immédiatement le pathogène tandis que les cellules centrales mémoires sont responsables d'initier une réponse immunitaire complète. Pourtant, les mécanismes biochimiques qui contrôlent les fonctions de ces cellules ont été jusqu'à présent peu étudiés à cause de la faible fréquence de ces cellules et de la quantité limitée de tissus humains disponibles pour les analyses. La compréhension de ces mécanismes est cruciale pour la réalisation de vaccins efficaces et pour le développement de nouveaux médicaments capables de moduler la réponse immunitaire lymphocytaire. Dans cette thèse, nous avons d'abord développé et amélioré une technologie appelée 'protéine array en phase inverse' qui possède un niveau de sensibilité beaucoup plus élevé par rapport aux technologies classiquement utilisées dans l'étude des protéines. Grâce à cette technique, nous avons pu comparer la composition protéique du système de transmission des signaux d'activation des cellules CM et EM humaines. L'analyse de 8 à 13 sujets sains a montré que ces populations des cellules mémoires possèdent un système de signalisation protéique différent. En effet, les cellules EM possèdent, par rapport aux cellules CM, des niveaux réduits d'une protéine régulatrice (appelée c-Cbl) que nous avons démontré comme étant responsable des fonctions spécifiques de ces cellules. En effet, en augmentant artificiellement l'expression de cette protéine régulatrice dans les cellules EM jusqu'au niveau de celui des cellules CM, nous avons induit dans les cellules EM des capacités fonctionnelles caractéristiques des cellules CM. En conclusion, notre étude a identifié, pour la première fois chez l'homme, un mécanisme biochimique qui contrôle les fonctions des populations des cellules mémoires. Résumé en Français: Les cellules mémoires persistent inertes dans l'organisme et produisent des réactions immunitaires rapides et robustes contre les pathogènes précédemment rencontrés. Deux populations distinctes des cellules mémoires ont été identifiées chez l'homme: les cellules centrales (CM) et effectrices (EM) mémoires. Ces populations sont fonctionnellement hétérogènes et exercent des rôles distincts et critiques dans l'immunité protectrice. Les mécanismes biochimiques qui contrôlent leurs fonctions ont été jusqu'à présent peu étudiés, bien que leur compréhension soit cruciale pour le développement des vaccins et des nouveaux traitements/médicaments. Les limites majeures à ces études sont la faible fréquence de ces populations et la quantité limitée de tissus humains disponibles. Dans cette thèse nous avons d'abord développé et amélioré la technologie de 'protéine array en phase inverse' afin d'analyser les molécules de signalisation des cellules mémoires CD4 et CD8 humaines isolées ex vivo. L'excellente sensibilité, la reproductibilité et la linéarité de la détection, ont permis de quantifier des variations d'expression protéiques supérieures à 20% dans un lysat équivalent à 20 cellules. Ensuite, grâce à l'analyse de 8 à 13 sujets sains, nous avons prouvé que les cellules mémoires CD8 ont une composition homogène de leur système de signalisation tandis que les cellules CD4 EM expriment significativement de plus grandes quantités de SLP-76 et des niveaux réduits de c-Cbl, Syk, Fyn et LAT par rapport aux cellules CM. En outre, l'expression réduite du régulateur négatif c-Cbl est corrélée avec l'expression des SLP-76, PI3K et LAT uniquement dans les cellules EM. L'évaluation des propriétés fonctionnelles des cellules mémoires a permis de démontrer que l'expression réduite du c-Cbl dans les cellules EM est associé à une diminution de leur seuil d'activation. En effet, grâce a la technique de transduction cytosolique, nous avons augmenté la quantité de c-Cbl des cellules EM à un niveau comparable à celui des cellules CM et constaté une réduction de la capacité des cellules EM à proliférer et sécréter des cytokines. Ce mécanisme de régulation dépend principalement de l'activité d'ubiquitine ligase de c-Cbl comme démontré par l'impact réduit du mutant enzymatiquement déficient de c-Cbl sur les fonctions de cellules EM. En conclusion, cette thèse identifie c-Cbl comme un régulateur critique des réponses fonctionnelles des populations de cellules T mémoires et fournit, pour la première fois chez l'homme, un mécanisme contrôlant l'hétérogénéité fonctionnelle des ces cellules. De plus, elle valide l'utilisation combinée des 'RPP arrays' et de la transduction cytosolique comme outil puissant d'analyse quantitative et fonctionnel des protéines de signalisation. Summary : Memory cells persist in a quiescent state in the body and mediate rapid and vigorous immune responses toward pathogens previously encountered. Two subsets of memory cells, namely central (CM) and effector (EM) memory cells, have been identified in humans. These subsets display high functional heterogeneity and assert critical and distinct roles in the control of protective immunity. The biochemical mechanisms controlling their functional properties remain so far poorly investigated, although their clarification is crucial for design of effective T-cell vaccine and drug development. Major limitations to these studies lie in the low frequency of memory T cell subsets and the limited amount of human specimen available. In this thesis we first implemented the innovative reverse phase protein array approach to profile 15 signalling components in human CD8 and CD4 memory T cells isolated ex vivo. The high degree of sensitivity, reproducibility and linearity achieved, allowed an excellent quantification of variations in protein expression higher than 20% in as few as 20-cell equivalent per spot. Based on the analysis of 8 to 13 healthy subjects, we showed that CD8 memory cells have a homogeneous composition of their signaling machinery while CD4 EM cells express statistically significant increased amounts of SLP-76 and reduced levels of c- Cbl, Syk, Fyn and LAT as compared to CM cells. Moreover, in EM but not CM cells, reduced expression of negative regulator c-Cbl correlated with the expression of SLP-76, PI3K and LAT. Subsequently, we demonstrated that the higher functional properties and the lower functional threshold of EM cells is associated with reduced expression of c-Cbl. Indeed, by increasing c-Cbl content of EM cells to the same level of CM cells using cytosolic transduction, we impaired their proliferation and cytokine production. This regulatory mechanism was primarily dependent on c-Cbl E3 ubiquitin ligase activity as evidenced by the weaker impact of enzymatically deficient c-Cbl C381A mutant on EM cell functions. Together, these results identify c-Cbl as a critical regulator of the functional responses of memory T cell subsets and provides, for the first time in humans, a mechanism controlling the functional heterogeneity of memory CD4 cells. Moreover it validates the combined use of RPP arrays and cytosolic transduction approaches as a powerful tool to quantitatively analyze signalling proteins and functionally assess their roles.

On solving fair exchange and related distributed problems in Byzantine environments

Abstract The solvability of the problem of fair exchange in a synchronous system subject to Byzantine failures is investigated in this work. The fair exchange problem arises when a group of processes are required to exchange digital items in a fair manner, which means that either each process obtains the item it was expecting or no process obtains any information on, the inputs of others. After introducing a novel specification of fair exchange that clearly separates safety and liveness, we give an overview of the difficulty of solving such a problem in the context of a fully-connected topology. On one hand, we show that no solution to fair exchange exists in the absence of an identified process that every process can trust a priori; on the other, a well-known solution to fair exchange relying on a trusted third party is recalled. These two results lead us to complete our system model with a flexible representation of the notion of trust. We then show that fair exchange is solvable if and only if a connectivity condition, named the reachable majority condition, is satisfied. The necessity of the condition is proven by an impossibility result and its sufficiency by presenting a general solution to fair exchange relying on a set of trusted processes. The focus is then turned towards a specific network topology in order to provide a fully decentralized, yet realistic, solution to fair exchange. The general solution mentioned above is optimized by reducing the computational load assumed by trusted processes as far as possible. Accordingly, our fair exchange protocol relies on trusted tamperproof modules that have limited communication abilities and are only required in key steps of the algorithm. This modular solution is then implemented in the context of a pedagogical application developed for illustrating and apprehending the complexity of fair exchange. This application, which also includes the implementation of a wide range of Byzantine behaviors, allows executions of the algorithm to be set up and monitored through a graphical display. Surprisingly, some of our results on fair exchange seem contradictory with those found in the literature of secure multiparty computation, a problem from the field of modern cryptography, although the two problems have much in common. Both problems are closely related to the notion of trusted third party, but their approaches and descriptions differ greatly. By introducing a common specification framework, a comparison is proposed in order to clarify their differences and the possible origins of the confusion between them. This leads us to introduce the problem of generalized fair computation, a generalization of fair exchange. Finally, a solution to this new problem is given by generalizing our modular solution to fair exchange

A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

Long-lasting stem cell-like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination.

Efficient and persisting immune memory is essential for long-term protection from infectious and malignant diseases. The yellow fever (YF) vaccine is a live attenuated virus that mediates lifelong protection, with recent studies showing that the CD8(+) T cell response is particularly robust. Yet, limited data exist regarding the long-term CD8(+) T cell response, with no studies beyond 5 years after vaccination. We investigated 41 vaccinees, spanning 0.27 to 35 years after vaccination. YF-specific CD8(+) T cells were readily detected in almost all donors (38 of 41), with frequencies decreasing with time. As previously described, effector cells dominated the response early after vaccination. We detected a population of naïve-like YF-specific CD8(+) T cells that was stably maintained for more than 25 years and was capable of self-renewal ex vivo. In-depth analyses of markers and genome-wide mRNA profiling showed that naïve-like YF-specific CD8(+) T cells in vaccinees (i) were distinct from genuine naïve cells in unvaccinated donors, (ii) resembled the recently described stem cell-like memory subset (Tscm), and (iii) among all differentiated subsets, had profiles closest to naïve cells. Our findings reveal that CD8(+) Tscm are efficiently induced by a vaccine in humans, persist for decades, and preserve a naïveness-like profile. These data support YF vaccination as an optimal mechanistic model for the study of long-lasting memory CD8(+) T cells in humans.

Effect of cattle on Salmonella carriage, diversity and antimicrobial resistance in free-ranging wild boar (Sus scrofa) in northeastern Spain

Salmonella is distributed worldwide and is a pathogen of economic and public health importance. As a multi-host pathogen with a long environmental persistence, it is a suitable model for the study of wildlife-livestock interactions. In this work, we aim to explore the spill-over of Salmonella between free-ranging wild boar and livestock in a protected natural area in NE Spain and the presence of antimicrobial resistance. Salmonella prevalence, serotypes and diversity were compared between wild boars, sympatric cattle and wild boars from cattle-free areas. The effect of age, sex, cattle presence and cattle herd size on Salmonella probability of infection in wild boars was explored by means of Generalized Linear Models and a model selection based on the Akaike’s Information Criterion. Prevalence was higher in wild boars co-habiting with cattle (35.67%, CI 95% 28.19–43.70) than in wild boar from cattle-free areas (17.54%, CI 95% 8.74–29.91). Probability of a wild boar being a Salmonella carrier increased with cattle herd size but decreased with the host age. Serotypes Meleagridis, Anatum and Othmarschen were isolated concurrently from cattle and sympatric wild boars. Apart from serotypes shared with cattle, wild boars appear to have their own serotypes, which are also found in wild boars from cattle-free areas (Enteritidis, Mikawasima, 4:b:- and 35:r:z35). Serotype richness (diversity) was higher in wild boars co-habiting with cattle, but evenness was not altered by the introduction of serotypes from cattle. The finding of a S. Mbandaka strain resistant to sulfamethoxazole, streptomycin and chloramphenicol and a S. Enteritidis strain resistant to ciprofloxacin and nalidixic acid in wild boars is cause for public health concern.

A European survey on current practices in epilepsy monitoring units and implications for patients' safety.

OBJECTIVE: This study aimed to survey current practices in European epilepsy monitoring units (EMUs) with emphasis on safety issues. METHODS: A 37-item questionnaire investigating characteristics and organization of EMUs, including measures for prevention and management of seizure-related serious adverse events (SAEs), was distributed to all identified European EMUs plus one located in Israel (N=150). RESULTS: Forty-eight (32%) EMUs, located in 18 countries, completed the questionnaire. Epilepsy monitoring unit beds are 1-2 in 43%, 3-4 in 34%, and 5-6 in 19% of EMUs; staff physicians are 1-2 in 32%, 3-4 in 34%, and 5-6 in 19% of EMUs. Personnel operating in EMUs include epileptologists (in 69% of EMUs), clinical neurophysiologists trained in epilepsy (in 46% of EMUs), child neurologists (in 35% of EMUs), neurology and clinical neurophysiology residents (in 46% and in 8% of EMUs, respectively), and neurologists not trained in epilepsy (in 27% of EMUs). In 20% of EMUs, patients' observation is only intermittent or during the daytime and primarily carried out by neurophysiology technicians and/or nurses (in 71% of EMUs) or by patients' relatives (in 40% of EMUs). Automatic detection systems for seizures are used in 15%, for body movements in 8%, for oxygen desaturation in 33%, and for ECG abnormalities in 17% of EMUs. Protocols for management of acute seizures are lacking in 27%, of status epilepticus in 21%, and of postictal psychoses in 87% of EMUs. Injury prevention consists of bed protections in 96% of EMUs, whereas antisuffocation pillows are employed in 21%, and environmental protections in monitoring rooms and in bathrooms are implemented in 38% and in 25% of EMUs, respectively. The most common SAEs were status epilepticus reported by 79%, injuries by 73%, and postictal psychoses by 67% of EMUs. CONCLUSIONS: All EMUs have faced different types of SAEs. Wide variation in practice patterns and lack of protocols and of precautions to ensure patients' safety might promote the occurrence and severity of SAEs. Our findings highlight the need for standardized and shared protocols for an effective and safe management of patients in EMUs.

Automated monitoring of medical protocols: a secure and distributed architecture

The control of the right application of medical protocols is a key issue in hospital environments. For the automated monitoring of medical protocols, we need a domain-independent language for their representation and a fully, or semi, autonomous system that understands the protocols and supervises their application. In this paper we describe a specification language and a multi-agent system architecture for monitoring medical protocols. We model medical services in hospital environments as specialized domain agents and interpret a medical protocol as a negotiation process between agents. A medical service can be involved in multiple medical protocols, and so specialized domain agents are independent of negotiation processes and autonomous system agents perform monitoring tasks. We present the detailed architecture of the system agents and of an important domain agent, the database broker agent, that is responsible of obtaining relevant information about the clinical history of patients. We also describe how we tackle the problems of privacy, integrity and authentication during the process of exchanging information between agents.

Memory Revisited in Julian Barnes's The Sense of an Ending

An accumulation of years brings with it an accumulation of experiences. The revision of such experiences usually becomes more recurrent after retirement, a transition time from one period of life to another and, as such, a time in which we, human beings, have a tendency to take stock of our lives. This is actually one of the main issues present in Julian Barnes's last novel The Sense of an Ending (2011). When the main protagonist, a retired man quite comfortable and contented with his present life, receives an unexpected inheritance from the mother of a girlfriend from his university years, he is forced to track down a part of his life that he had left at the back of his mind a long time ago. As he explains his story, the protagonist and narrator of the novel raises a number of questions related to the quality and function of memory as one gets into old age. He experiments the unreliability of memory and questions to what extent memory is constructed through the remembered emotions that invaded him over that episode of his life rather than through the events as they actually took place. On the other hand, the act of revisiting and revising that specific episode, brings with it feelings of guilt and remorse as the protagonist realises that his past acts were not as noble as he remembered them to be. However, these acts are part of the past and they cannot be changed; thus, another question that the novel raises is how to account for those actions of which one does not feel proud and, more importantly, how to manage those bad memories as one gets older.

APOE status modulates the changes in network connectivity induced by brain stimulation in non-demented elders.

Behavioral consequences of a brain insult represent an interaction between the injury and the capacity of the rest of the brain to adapt to it. We provide experimental support for the notion that genetic factors play a critical role in such adaptation. We induced a controlled brain disruption using repetitive transcranial magnetic stimulation (rTMS) and show that APOE status determines its impact on distributed brain networks as assessed by functional MRI (fMRI).Twenty non-demented elders exhibiting mild memory dysfunction underwent two fMRI studies during face-name encoding tasks (before and after rTMS). Baseline task performance was associated with activation of a network of brain regions in prefrontal, parietal, medial temporal and visual associative areas. APOE ε4 bearers exhibited this pattern in two separate independent components, whereas ε4-non carriers presented a single partially overlapping network. Following rTMS all subjects showed slight ameliorations in memory performance, regardless of APOE status. However, after rTMS APOE ε4-carriers showed significant changes in brain network activation, expressing strikingly similar spatial configuration as the one observed in the non-carrier group prior to stimulation. Similarly, activity in areas of the default-mode network (DMN) was found in a single component among the ε4-non bearers, whereas among carriers it appeared disaggregated in three distinct spatiotemporal components that changed to an integrated single component after rTMS. Our findings demonstrate that genetic background play a fundamental role in the brain responses to focal insults, conditioning expression of distinct brain networks to sustain similar cognitive performance.

Populating ACT-R's Declarative Memory with Internet Statistics

Decision situations are often characterized by uncertainty: we do not know the values of the different options on all attributes and have to rely on information stored in our memory to decide. Several strategies have been proposed to describe how people make inferences based on knowledge used as cues. The present research shows how declarative memory of ACT-R models could be populated based on internet statistics. This will allow to simulate the performance of decision strategies operating on declarative knowledge based on occurrences and co-occurrences of objects and cues in the environment.