TumorML: Concept and requirements of an in silico cancer modelling markup language

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification

Determination of the number of atoms trapped in an optical cavity

The number of atoms trapped within the mode of an optical cavity is determined in real time by monitoring the transmission of a weak probe beam. Continuous observation of atom number is accomplished in the strong coupling regime of cavity quantum electrodynamics and functions in concert with a cooling scheme for radial atomic motion. The probe transmission exhibits sudden steps from one plateau to the next in response to the time evolution of the intracavity atom number, from Ngreater than or equal to 3 to N=2-->1-->0 atoms, with some trapping events lasting over 1 s

Cavity QED "By The Numbers"

The number of atoms trapped within the mode of an optical cavity is determined in real time by monitoring the transmission of a weak probe beam. Continuous observation of atom number is accomplished in the strong coupling regime of cavity quantum electrodynamics and functions in concert with a cooling scheme for radial atomic motion. The probe transmission exhibits sudden steps from one plateau to the next in response to the time evolution of the intracavity atom number, from N >= 3 to N = 2 to 1 to 0, with some trapping events lasting over 1 second.Comment: 5 pages, 4 figure

Cavity QED with Single Atoms and Photons

Recent experimental advances in the field of cavity quantum electrodynamics (QED) have opened new possibilities for control of atom-photon interactions. A laser with "one and the same atom" demonstrates the theory of laser operation pressed to its conceptual limit. The generation of single photons on demand and the realization of cavity QED with well defined atomic numbers N = 0, 1, 2,... both represent important steps toward realizing diverse protocols in quantum information science. Coherent manipulation of the atomic state via Raman transitions provides a new tool in cavity QED for in situ monitoring and control of the atom-cavity system. All of these achievements share a common point of departure: the regime of strong coupling. It is thus interesting to consider briefly the history of the strong coupling criterion in cavity QED and to trace out the path that research has taken in the pursuit of this goal

Control of contagious bovine pleuropneumonia: knowledge, attitudes, perceptions and practices in Narok district of Kenya

CBPP is an important transboundary disease in sub-Saharan Africa whose control is urgent. Participatory data collection involving 52 focus group discussions in 37 village clusters and key informant interviews, a cross-sectional study involving 232 households and a post-vaccination follow up involving 203 households was carried out in 2006–2007 in Narok South district of Kenya. This was to investigate knowledge, attitudes, perceptions and practices (KAPP) associated with control of CBPP as well as the adverse post-vaccination reactions in animals in order to advice the control policy. The community perceived trans-boundary CBPP threat to their cattle. They had traditional disease coping mechanisms and were conversant with CBPP prevention and control with 49.8% (95%CI: 42.8–56.7%) giving priority to CBPP control. However, 12.9% (95%CI: 9.0–18.1%) of pastoralists had no knowledge of any prevention method and 10.0% (95%CI: 6.5–14.7%) would not know what to do or would do nothing in the event of an outbreak. Although 43.5% (95%CI: 37.1–50.2%) of pastoralists were treating CBPP cases with antimicrobials, 62.5% (95%CI: 52.1–71.7%) of them doubted the effectiveness of the treatments. Pastoralists perceived vaccination to be the solution to CBPP but vaccination was irregular due to unavailability of the vaccine. Vaccination was mainly to control outbreaks rather than preventive and exhibited adverse post-vaccination reactions among 70.4% (95%CI: 63.6–76.5%) of herds and 3.8% (95%CI: 3.5–4.2%) of animals. Consequently, nearly 25.2% (95%CI: 18.5–33.2%) of pastoralists may resist subsequent vaccinations against CBPP. Pastoralists preferred CBPP vaccination at certain times of the year and that it is combined with other vaccinations. In conclusion, pastoralists were not fully aware of the preventive measures and interventions and post-vaccination reactions may discourage subsequent CBPP vaccinations. Consequently there is need for monitoring and management of post vaccination reactions and awareness creation on CBPP prevention and interventions and their merits and demerits. CBPP vaccine was largely unavailable to the pastoralists and the preference of the pastoralists was for vaccination at specified times and vaccine combinations which makes it necessary to avail the vaccine in conformity with the pastoralists preferences. In addition, planning vaccinations should involve pastoralists and neighbouring countries. As the results cannot be generalized, further studies on CBPP control methods and their effectiveness are recommended

Dynamics of a tunable superfluid junction

We study the population dynamics of a Bose-Einstein condensate in a double-well potential throughout the crossover from Josephson dynamics to hydrodynamics. At barriers higher than the chemical potential, we observe slow oscillations well described by a Josephson model. In the limit of low barriers, the fundamental frequency agrees with a simple hydrodynamic model, but we also observe a second, higher frequency. A full numerical simulation of the Gross-Pitaevskii equation giving the frequencies and amplitudes of the observed modes between these two limits is compared to the data and is used to understand the origin of the higher mode. Implications for trapped matter-wave interferometers are discussed.Comment: 8 pages, 7 figures; v3: Journal reference added, minor changes to tex

Observation of the Vacuum-Rabi Spectrum for One Trapped Atom

The transmission spectrum for one atom strongly coupled to the field of a high-finesse optical resonator is observed to exhibit a clearly resolved vacuum-Rabi splitting characteristic of the normal modes in the eigenvalue spectrum of the atom-cavity system. A new Raman scheme for cooling atomic motion along the cavity axis enables a complete spectrum to be recorded for an individual atom trapped within the cavity mode, in contrast to all previous measurements in cavity QED that have required averaging over many atoms.Comment: 5 pages with 4 figure

Muscle architectural and force-velocity curve adaptations following 10 weeks of training with weightlifting catching and pulling derivatives

The aims of this study were to examine the muscle architectural, rapid force production, and force-velocity curve adaptations following 10 weeks of resistance training with either submaximal weightlifting catching (CATCH) or pulling (PULL) derivatives or pulling derivatives with phase-specific loading (OL). 27 re-sistance-trained men were randomly assigned to the CATCH, PULL, or OL groups and completed pre-and post-intervention ultrasound, countermovement jump (CMJ), and isometric mid-thigh pull (IMTP). Vastus lateralis and biceps femoris muscle thickness, pennation angle, and fascicle length, CMJ force at peak power, velocity at peak power, and peak power, and IMTP peak force and force at 100-, 150-, 200-, and 250 ms were assessed. There were no significant or meaningful differences in muscle architecture measures for any group (p \u3e 0.05). The PULL group displayed small-moderate (g = 0.25 - 0.81) improvements in all CMJ variables while the CATCH group displayed trivial effects (g = 0.00 - 0.21). In addition, the OL group displayed trivial and small effects for CMJ force (g = -0.12 - 0.04) and velocity variables (g = 0.32 - 0.46), respectively. The OL group displayed moderate (g = 0.48 - 0.73) improvements in all IMTP variables while to PULL group displayed small-moderate (g = 0.47 - 0.55) im-provements. The CATCH group displayed trivial-small (g = -0.39 - 0.15) decreases in IMTP performance. The PULL and OL groups displayed visible shifts in their force-velocity curves; however, these changes were not significant (p \u3e 0.05). Perform-ing weightlifting pulling derivatives with either submaximal or phase-specific loading may enhance rapid and peak force production characteristics. Strength and conditioning practitioners should load pulling derivatives based on the goals of each specific phase, but also allow their athletes ample exposure to achieve each goal

An examination of prospective memory in multiple sclerosis: a theoretical approach using objective and subjective measures

Objective: Prospective Memory (PM) is the ability to complete a task at some specific point in the future without constant rehearsal. PM is noteworthy for the impact it may have on everyday functioning in patient populations, but it is difficult to assess using objective neuropsychological tests, and thus self-report has commonly been used as a measure of PM function. One problem with this method of assessment is the lack of a theoretical basis for current measures, especially in light of the many recent advances toward a theory of PM. Individuals with Multiple Sclerosis (MS) are often high-functioning, but 50-72% suffer from some form of cognitive impairment, especially in cognitive domains thought to be essential to PM. The goals of the current study were to a) use a theoretically-based approach to examining PM in the MS population, using objective and subjective measures of PM; and b) assess the usefulness of a novel measure of subjective PM problems (the Prospective Memory Complaints Questionnaire (PMCQ)) in the MS population. Participants: Twenty-seven individuals with MS and twenty healthy controls, matched on distributions of gender, age, and education level. Methods: Participants underwent a series of 3 measures, which included 1) a novel self-report questionnaire (the PMCQ) assessing PM difficulties administered in an interview format; 2) a standardized, objective measure of PM (the MIST); and 3) a theoretically-based experimental PM task (the Complex Prospective Memory (CPM) task). Demographic variables, depression level, fatigue, quality of life, and level of MS symptom severity were also collected.Results: No significant between-group differences were found in performance on any of the objective and subjective measures of PM in the MS vs. HC groups. Within-groups analyses indicated that distinct factors in each group predicted objective PM (MIST) performance, and factors related to the utility of both the CPM task and the PMCQ (and the underlying theoretical model of each) were identified. Discussion: Overall, the current study demonstrated discrepant predictors of PM performance in MS and HCs, despite nonsignificant overall differences in performance when controlling for significant psychosocial and symptom severity factors. While much further research is needed to isolate the factors impacting PM performance in the MS population, the usefulness of a theoretical model of PM was demonstrated, as was the utility of examining PM using both performance-based and self-report measures.Ph.D., Clinical Psychology -- Drexel University, 201

Experimental realization of a one-atom laser in the regime of strong coupling

Conventional lasers (from table-top systems to microscopic devices) typically operate in the so-called weak-coupling regime, involving large numbers of atoms and photons; individual quanta have a negligible impact on the system dynamics. However, this is no longer the case when the system approaches the regime of strong coupling for which the number of atoms and photons can become quite small. Indeed, the lasing properties of a single atom in a resonant cavity have been extensively investigated theoretically. Here we report the experimental realization of a one-atom laser operated in the regime of strong coupling. We exploit recent advances in cavity quantum electrodynamics that allow one atom to be isolated in an optical cavity in a regime for which one photon is sufficient to saturate the atomic transition. The observed characteristics of the atom–cavity system are qualitatively different from those of the familiar many-atom case. Specifically, our measurements of the intracavity photon number versus pump intensity indicate that there is no threshold for lasing, and we infer that the output flux from the cavity mode exceeds that from atomic fluorescence by more than tenfold. Observations of the second-order intensity correlation function demonstrate that our one-atom laser generates manifestly quantum (nonclassical) light, typified by photon anti-bunching and sub-poissonian photon statistics