Novel quantum chaotic dynamics in cold atoms

We discuss recent experimental and theoretical investigations of quantum dynamics in periodically kicked chaotic systems. These investigations are centred on a modified version of the classic ?-kicked rotor, as realized using laser-cooled caesium atoms. Dramatic phenomena, principally quantum accelerator modes, have been observed and these have inspired novel theoretical approaches to quantum chaos. The latter work has, in turn, prompted further experiments and the combined experimental and theoretical effort continues to lead to exciting advances in this field

A GPU-based real time trigger for rare kaon decays at NA62

Abstract This thesis reports a study for a new real-time trigger for the NA62 experiment based on Graphical Processing Units (GPUs). The NA62 experiment was devised to study with unprecedented precision the ultra-rare decay K+ → π+ ν anti-ν, a process mediated by Flavour-Changing Neutral Currents (FCNC) whose exceptional theoretical cleanliness provides a unique probe to test the Standard Model. The use of a high-rate kaon beam will result in an event rate of about 15 MHz, so high that it will be impossible to store data on disk without an efficient selection. The experiment therefore devised three trigger levels, allowing to reduce the data rate fed to the readout PC farm down to ∼10 kHz. For this thesis I developed an online trigger algorithm that uses data fed by the RICH (Ring Imaging CHerenkov counter) detector in real-time to allow a rejection of the dominant background K+ → π+ π 0 based on kinematical constraints. As a starting point for the development of this algorithm, I verified the feasibility of such a trigger through Montecarlo simulations. I measured the reconstruction resolution, achieved by the RICH detector alone, of the kinematical variables used for the event selection. After that, I analysed the background rejection power and the signal efficiency of several kinematical constraints, and I designed an actual trigger algorithm. The necessity of running the algorithm in real-time, with a maximum latency of 1 ms per event, drove the choice of exploiting the parallel computing power of GPUs. A parallelized algorithm was therefore developed, that can fit up to 4 Cherenkov rings per event. Moreover, a large number of events are processed concurrently. No parallelized and seedless multi-ring fitting algorithm existed before. The developed algorithm consists of a pattern recognition stage, to assign the hits to up to 4 ring candidates, and of a robust single-ring fit routine. The program was tested on GPUs, and its performance and execution latency proved to be compatible with the requirements. This work proves that alternative trigger designs are possible for the NA62 experiment, and represents a starting point for the introduction of flexible GPU-based real-time triggers in High Energy Physics. Sommario La mia tesi costituisce uno studio per un algoritmo di trigger in tempo reale basato su GPU (Graphical Processing Units) per l’esperimento NA62. NA62 è un esperimento progettato per misurare con precisione il decadimento ultra raro K+ → π+ ν anti-ν, un canale mediato da correnti neutre flavour-changing estremamente sensibile all’eventuale presenza di nuova fisica. L’elevato rate di eventi rivelati, dell’ordine di 15 MHz, non permetterà una archiviazione su disco dei dati non moderata da severi criteri di selezione. Sono perciò necessari dei livelli di trigger che consentano di ridurre il rate di eventi salvati fino a circa una decina di kHz. L’algoritmo sviluppato si basa sull’uso del rivelatore RICH (Ring Imaging CHerenkov counter). Le informazioni primitive inviate dal RICH vengono valutate in tempo reale, per produrre una decisione di trigger basata prevalentemente su considerazioni di cinematica. In una prima fase ho verificato, tramite simulazione Montecarlo, la fattibilità e significatività di tale progetto. Ho dapprima misurato la risoluzione sulla ricostruzione di alcune quantità cinematiche ricavate utilizzando unicamente il rivelatore RICH, poiché per un trigger di primo livello in tempo reale non sarà possibile mettere in relazione dati forniti da rivelatori diversi. Ho studiato poi fino a che livello fosse possibile separare il segnale dal fondo, misurando l’efficienza di reiezione e l’accettanza per il segnale al variare di alcuni parametri di selezione. Data la necessità di eseguire il programma in tempo reale, con una latenza massima di 1 ms per evento, si è deciso di sfruttare il potere computazionale parallelo proprio delle GPU (processori grafici ad elevato parallelismo). E’ stato quindi sviluppato un algoritmo in grado di eseguire simultaneamente non solo le istruzioni relative ad eventi diversi, ma anche i fit di fino a 4 anelli Cherenkov diversi appartenenti allo stesso evento. Nessun algoritmo parallelo e seedless di questo tipo esisteva in letteratura. L’algoritmo implementato è composto di due parti: una iniziale di riconoscimento di pattern, che estrae il numero di anelli presenti nella matrice ed identifica gli hit appartenenti a ciascuno di essi, ed una di fit dei singoli cerchi. Il programma è stato testato su GPU, ed efficienza e tempi di esecuzione risultano compatibili con le richieste. Questo lavoro apre la possibilità di implementare trigger alternativi e flessibili per NA62 e rappresenta un primo esempio prototipale dell’uso di GPU in tempo reale

An integrated view of data quality in Earth observation

Data quality is a difficult notion to define precisely, and different communities have different views and understandings of the subject. This causes confusion, a lack of harmonization of data across communities and omission of vital quality information. For some existing data infrastructures, data quality standards cannot address the problem adequately and cannot fulfil all user needs or cover all concepts of data quality. In this study, we discuss some philosophical issues on data quality. We identify actual user needs on data quality, review existing standards and specifications on data quality, and propose an integrated model for data quality in the field of Earth observation (EO). We also propose a practical mechanism for applying the integrated quality information model to a large number of datasets through metadata inheritance. While our data quality management approach is in the domain of EO, we believe that the ideas and methodologies for data quality management can be applied to wider domains and disciplines to facilitate quality-enabled scientific research

Modulation of the Akt/Ras/Raf/MEK/ERK pathway by A3 adenosine receptor

Downstream A3 receptor signalling plays an important role in the regulation of cell death and proliferation. Therefore, it is important to determine the molecular pathways involved through A3 receptor stimulation. The phosphatidylinositide-3-OH kinase (PI3K)/Akt and the Raf/mitogen-activated protein kinase (MAPK/ERK) kinase (MEK)/mitogen-activated protein kinase (MAPK) pathways have central roles in the regulation of cell survival and proliferation. The crosstalk between these two pathways has also been investigated. The focus of this review centres on downstream mediators of A3 adenosine receptor signalling

Statistical design of personalized medicine interventions: The Clarification of Optimal Anticoagulation through Genetics (COAG) trial

<p>Abstract</p> <p>Background</p> <p>There is currently much interest in pharmacogenetics: determining variation in genes that regulate drug effects, with a particular emphasis on improving drug safety and efficacy. The ability to determine such variation motivates the application of personalized drug therapies that utilize a patient's genetic makeup to determine a safe and effective drug at the correct dose. To ascertain whether a genotype-guided drug therapy improves patient care, a personalized medicine intervention may be evaluated within the framework of a randomized controlled trial. The statistical design of this type of personalized medicine intervention requires special considerations: the distribution of relevant allelic variants in the study population; and whether the pharmacogenetic intervention is equally effective across subpopulations defined by allelic variants.</p> <p>Methods</p> <p>The statistical design of the Clarification of Optimal Anticoagulation through Genetics (COAG) trial serves as an illustrative example of a personalized medicine intervention that uses each subject's genotype information. The COAG trial is a multicenter, double blind, randomized clinical trial that will compare two approaches to initiation of warfarin therapy: genotype-guided dosing, the initiation of warfarin therapy based on algorithms using clinical information and genotypes for polymorphisms in <it>CYP2C9 </it>and <it>VKORC1</it>; and clinical-guided dosing, the initiation of warfarin therapy based on algorithms using only clinical information.</p> <p>Results</p> <p>We determine an absolute minimum detectable difference of 5.49% based on an assumed 60% population prevalence of zero or multiple genetic variants in either <it>CYP2C9 </it>or <it>VKORC1 </it>and an assumed 15% relative effectiveness of genotype-guided warfarin initiation for those with zero or multiple genetic variants. Thus we calculate a sample size of 1238 to achieve a power level of 80% for the primary outcome. We show that reasonable departures from these assumptions may decrease statistical power to 65%.</p> <p>Conclusions</p> <p>In a personalized medicine intervention, the minimum detectable difference used in sample size calculations is not a known quantity, but rather an unknown quantity that depends on the genetic makeup of the subjects enrolled. Given the possible sensitivity of sample size and power calculations to these key assumptions, we recommend that they be monitored during the conduct of a personalized medicine intervention.</p> <p>Trial Registration</p> <p>clinicaltrials.gov: NCT00839657</p

Altered intercellular communication in lung fibroblast cultures from patients with idiopathic pulmonary fibrosis

RATIONALE: Gap junctions are membrane channels formed by an array of connexins which links adjacent cells realizing an electro- metabolic synapse. Connexin-mediated communication is crucial in the regulation of cell growth, differentiation, and development. The activation and proliferation of phenotypically altered fibroblasts are central events in the pathogenesis of idiopathic pulmonary fibrosis. We sought to evaluate the role of connexin-43, the most abundant gap-junction subunit in the human lung, in the pathogenesis of this condition. METHODS: We investigated the transcription and protein expression of connexin-43 and the gap-junctional intercellular communication (GJIC) in 5 primary lung fibroblast lines derived from normal subjects (NF) and from 3 histologically proven IPF patients (FF). RESULTS: Here we show that connexin-43 mRNA was significantly reduced in FF as demonstrated by standard and quantitative RT-PCR. GJIC was functionally evaluated by means of flow-cytometry. In order to demonstrate that dye spreading was taking place through gap junctions, we used carbenoxolone as a pharmacological gap-junction blocker. Carbenoxolone specifically blocked GJIC in our system in a concentration dependent manner. FF showed a significantly reduced homologous GJIC compared to NF. Similarly, GJIC was significantly impaired in FF when a heterologous NF line was used as dye donor, suggesting a complete defect in GJIC of FF. CONCLUSION: These results suggest a novel alteration in primary lung fibroblasts from IPF patients. The reduced Cx43 expression and the associated alteration in cell-to-cell communication may justify some of the known pathological characteristic of this devastating disease that still represents a challenge to the medical practice

C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older.

Inflammation is believed to play a role in prostate cancer (PCa) etiology, but it is unclear whether inflammatory markers C-reactive protein (CRP) and interleukin-6 (IL-6) associate with PCa risk in older men. Using Cox regression, we assessed the relationship between baseline concentrations of CRP and IL-6 and the subsequent PCa risk in the Cardiovascular Health Study, a population-based cohort study of mostly European American men of ages >64 years (n = 2,234; mean follow-up = 8.7 years; 215 incident PCa cases). We also tested associations between CRP and IL-6 tagSNPs and PCa risk, focusing on SNPs that are known to associate with circulating CRP and/or IL-6. Neither CRP nor IL-6 blood concentrations was associated with PCa risk. The C allele of IL-6 SNP rs1800795 (-174), a known functional variant, was associated with increased risk in a dominant model (HR = 1.44; 95% CI = 1.03-2.01; p = 0.03), but was not statistically significant after accounting for multiple tests (permutation p = 0.21). Our results suggest that circulating CRP and IL-6 do not influence PCa risk. SNPs at the CRP locus are not associated with PCa risk in this cohort, while the association between rs1800795 and PCa risk warrants further investigation

Workflow in Clinical Trial Sites & Its Association with Near Miss Events for Data Quality: Ethnographic, Workflow & Systems Simulation

10.1371/journal.pone.0039671PLoS ONE76

Social Algorithms

This article concerns the review of a special class of swarm intelligence based algorithms for solving optimization problems and these algorithms can be referred to as social algorithms. Social algorithms use multiple agents and the social interactions to design rules for algorithms so as to mimic certain successful characteristics of the social/biological systems such as ants, bees, bats, birds and animals.Comment: Encyclopedia of Complexity and Systems Science, 201