Quantum tunneling dynamics of an interacting Bose-Einstein condensate through a Gaussian barrier

The transmission of an interacting Bose-Einstein condensate incident on a repulsive Gaussian barrier is investigated through numerical simulation. The dynamics associated with interatomic interactions are studied across a broad parameter range not previously explored. Effective 1D Gross-Pitaevskii equation (GPE) simulations are compared to classical Boltzmann-Vlasov equation (BVE) simulations in order to isolate purely coherent matterwave effects. Quantum tunneling is then defined as the portion of the GPE transmission not described by the classical BVE. An exponential dependence of transmission on barrier height is observed in the purely classical simulation, suggesting that observing such exponential dependence is not a sufficient condition for quantum tunneling. Furthermore, the transmission is found to be predominately described by classical effects, although interatomic interactions are shown to modify the magnitude of the quantum tunneling. Interactions are also seen to affect the amount of classical transmission, producing transmission in regions where the non-interacting equivalent has none. This theoretical investigation clarifies the contribution quantum tunneling makes to overall transmission in many-particle interacting systems, potentially informing future tunneling experiments with ultracold atoms.Comment: Close to the published versio

NamesforLife Semantic Resolution Services for the Life Sciences

A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. 

To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others who use biological data in their routine work), we developed a generalizable semantic model that represents names, concepts, and exemplars (representations of biological entities) as distinct objects. By identifying each object with a Digital Object Identifier (DOI) it becomes possible to place forward-pointing links in the published literature, in databases, and vector graphics that can be used as part of a mechanism for resolving ambiguities, thereby “future proofing” a nomenclature or terminology. A full implementation of the N4L model for the _Bacteria_ and _Archaea_ was released in April, 2010. The system is professionally curated and represents a Tier III resource in Parkhill’s view of bioinformatic services. A variety of tools and web services have been developed for readers, publishers, and others (N4L Guide, N4L Autotagger, N4L Semantic Search, N4L Taxonomic Abstracts) and we are incorporating other taxonomies into the N4L data model, as well as adding additional phenotypic, genotypic, and genomic information to the existing exemplars to add greater value to end users

Ocean variability and its influence on the detectability of greenhouse warming signals

Recent investigations have considered whether it is possible to achieve early detection of greenhouse-gas-induced climate change by observing changes in ocean variables. In this study we use model data to assess some of the uncertainties involved in estimating when we could expect to detect ocean greenhouse warming signals. We distinguish between detection periods and detection times. As defined here, detection period is the length of a climate time series required in order to detect, at some prescribed significance level, a given linear trend in the presence of the natural climate variability. Detection period is defined in model years and is independent of reference time and the real time evolution of the signal. Detection time is computed for an actual time-evolving signal from a greenhouse warming experiment and depends on the experiment's start date. Two sources of uncertainty are considered: those associated with the level of natural variability or noise, and those associated with the time-evolving signals. We analyze the ocean signal and noise for spatially averaged ocean circulation indices such as heat and fresh water fluxes, rate of deep water formation, salinity, temperature, transport of mass, and ice volume. The signals for these quantities are taken from recent time-dependent greenhouse warming experiments performed by the Max Planck Institute for Meteorology in Hamburg with a coupled ocean-atmosphere general circulation model. The time-dependent greenhouse gas increase in these experiments was specified in accordance with scenario A of the Intergovernmental Panel on Climate Change. The natural variability noise is derived from a 300-year control run performed with the same coupled atmosphere-ocean model and from two long (>3000 years) stochastic forcing experiments in which an uncoupled ocean model was forced by white noise surface flux variations. In the first experiment the stochastic forcing was restricted to the fresh water fluxes, while in the second experiment the ocean model was additionally forced by variations in wind stress and heat fluxes. The mean states and ocean variability are very different in the three natural variability integrations. A suite of greenhouse warming simulations with identical forcing but different initial conditions reveals that the signal estimated from these experiments may evolve in noticeably different ways for some ocean variables. The combined signal and noise uncertainties translate into large uncertainties in estimates of detection time. Nevertheless, we find that ocean variables that are highly sensitive indicators of surface conditions, such as convective overturning in the North Atlantic, have shorter signal detection times (35?65 years) than deep-ocean indicators (≥100 years). We investigate also whether the use of a multivariate detection vector increases the probability of early detection. We find that this can yield detection times of 35?60 years (relative to a 1985 reference date) if signal and noise are projected onto a common ?fingerprint? which describes the expected signal direction. Optimization of the signal-to-noise ratio by (spatial) rotation of the fingerprint in the direction of low-noise components of the stochastic forcing experiments noticeably reduces the detection time (to 10?45 years). However, rotation in space alone does not guarantee an improvement of the signal-to-noise ratio for a time-dependent signal. This requires an ?optimal fingerprint? strategy in which the detection pattern (fingerprint) is rotated in both space and time

Observation of a Modulational Instability in Bose-Einstein condensates

We observe the breakup dynamics of an elongated cloud of condensed $^{85}$Rb atoms placed in an optical waveguide. The number of localized spatial components observed in the breakup is compared with the number of solitons predicted by a plane-wave stability analysis of the nonpolynomial nonlinear Schr\"odinger equation, an effective one-dimensional approximation of the Gross-Pitaevskii equation for cigar-shaped condensates. It is shown that the numbers predicted from the fastest growing sidebands are consistent with the experimental data, suggesting that modulational instability is the key underlying physical mechanism driving the breakup.Comment: 6 pages, 5 figure

Maximizing Science Return from Future Rodent Experiments on the International Space Station (ISS): Tissue Preservation

To better understand how mammals adapt to long duration habitation in space, a system for performing rodent experiments on the ISS is under development; Rodent Research-1 is the first flight and will include validation of both on-orbit animal support and tissue preservation. To evaluate plans for on-orbit sample dissection and preservation, we simulated conditions for euthanasia, tissue dissection, and prolonged sample storage on the ISS, and we also developed methods for post-flight dissection and recovery of high quality RNA from multiple tissues following prolonged storage in situ for future science. Mouse livers and spleens were harvested under conditions that simulated nominal, on-orbit euthanasia and dissection operations including storage at -80 C for 4 months. The RNA recovered was of high quality (RNA Integrity Number, RIN(is) greater than 8) and quantity, and the liver enzyme contents and activities (catalase, glutathione reductase, GAPDH) were similar to positive controls, which were collected under standard laboratory conditions. We also assessed the impact of possible delayed on-orbit dissection scenarios (off-nominal) by dissecting and preserving the spleen (RNAlater) and liver (fast-freezing) at various time points post-euthanasia (from 5 min up to 105 min). The RNA recovered was of high quality (spleen, RIN (is) greater than 8; liver, RIN (is) greater than 6) and liver enzyme activities were similar to positive controls at all time points, although an apparent decline in select enzyme activities was evident at the latest time (105 min). Additionally, various tissues were harvested from either intact or partially dissected, frozen carcasses after storage for approximately 2 months; most of the tissues (brain, heart, kidney, eye, adrenal glands and muscle) were of acceptable RNA quality for science return, whereas some tissues (small intestine, bone marrow and bones) were not. These data demonstrate: 1) The protocols developed for future flight experiments will support science return despite delayed preservation post-euthanasia or prolonged storage, and 2) Many additional tissues for gene expression analysis can be obtained by dissection following prolonged storage of the tissue in situ at -80 C. These findings have relevance both to high value, ground-based experiments when sample collection capability is severely constrained, and to all future spaceflight experiments that entail on-orbit sample recovery by the ISS crew

Locally recurrent chondrosarcoma of the pelvis and limbs can only be controlled by wide local excision

Aims The purpose of this study was to investigate the potential for achieving local and systemic control after local recurrence of a chondrosarcoma of bone. Patients and Methods A total of 126 patients with local recurrence (LR) of chondrosarcoma (CS) of the pelvis or a limb bone were identified from a prospectively maintained database, between 1990 and 2015 at the Royal Orthopaedic Hospital, Birmingham, United Kingdom. There were 44 female patients (35%) and 82 male patients (65%) with a mean age at the time of LR of 56 years (13 to 96). The 126 patients represented 24.3% of the total number of patients with a primary CS (519) who had been treated during this period. Clinical data collected at the time of primary tumour and LR included the site (appendicular, extremity, or pelvis); primary and LR tumour size (in centimetres); type of operation at the time of primary or LR (limb-salvage or amputation); surgical margin achieved at resection of the primary tumour and the LR; grade of the primary tumour and the LR; gender; age; and oncological outcomes, including local recurrence-free survival and disease-specific survival. A minimum two years' follow-up and complete histopathology records were available for all patients included in the study. Results For patients without metastases prior to or at the time of local recurrence, the disease-specific survival after local recurrence was 62.5% and 45.5% at one and five years, respectively, After univariable analysis, significant factors predicting disease-specific survival were grade (p <0.001) and surgical margin (p = 0.044). After multivariable analysis, grade, increasing age at the time of diagnosis of local recurrence, and a greater time interval from primary surgery to local recurrence were significant factors for disease-specific survival. A secondary local recurrence was seen in 26% of patients. Wide margins were a good predictor of local recurrence-free survival for subsequent recurrences after univariable analysis when compared with intralesional margins (p = 0.002) but marginal margins did not reach statistical significance when compared with intralesional margins (p = 0.084). Conclusion In cases of local recurrence of a chondrosarcoma of bone, we have shown that if the tumour is non-metastatic at re-staging, an increase in disease-specific survival and in local recurrence-free survival is achievable, but only by resection of the local recurrence with a wide margin.Peer reviewe

Telangiectases in Scleroderma: A Potential Clinical Marker of Pulmonary Arterial Hypertension

ABSTRACT. Objective. Clinical markers are needed to identify scleroderma patients at risk for pulmonary arterial hypertension (PAH) since early therapy may improve survival. We investigated whether increased numbers of telangiectases in scleroderma associate with measures of pulmonary vascular disease. Methods. One hundred forty-seven consecutive adult patients with scleroderma were enrolled in this cross-sectional study and scored for the presence of matted telangiectases on 11 body areas. Per body area, telangiectases were scored as 0 if none were present, 1 if there were fewer than 10 telangiectases, and 2 if 10 or more telangiectases were counted. Linear regression analysis was performed to assess the association between right ventricular systolic pressure (RVSP) and telangiectasia score, adjusted for age, race, smoking status, scleroderma subtype, disease duration, and autoantibody status. Logistic regression analysis was performed with PAH by right-heart catheterization (RHC) as the dependent variable. Results. The mean telangiectasia score was 6.0 (SD 4.5, range 0-20). RVSP and telangiectasia score were positively correlated (r = 0.271, p = 0.001). The mean RVSP increased by 10.9 mm Hg for every 10-point increase in telangiectasia score (95% CI 3.6-18.3 mm Hg, p = 0.004), adjusted for potential confounders. The adjusted relative odds of PAH by RHC were 12.4 for patients with a 10-point increase in telangiectasia score (95% CI 1.78-85.9, p = 0.01). Conclusion. Increased numbers of telangiectases strongly associate with the presence of pulmonary vascular disease. Telangiectases may be a clinical marker of more widespread aberrant microvascular disease i

Rodent Research Development for Long Duration Studies on the International Space Station

Rodent research in space is needed to advance our understanding of the health risks,consequences and possible countermeasures to protect crew during future, long duration missions. TheAnimal Enclosure Module (AEM) was designed originally to support habitation of rats and mice onrelatively short duration, Shuttle missions (<19 days). The AEM was flown previously on 27 SpaceShuttle missions, and recently was modified extensively to support future long duration space biology andbiomedical research on the International Space Station (ISS). In consultation with a Science WorkingGroup comprised of veterinarians and investigators experienced in rodent spaceflight experimentation inspace, the Rodent Habitat project team at Ames Research Center modified existing hardware, developednew hardware, operations, and science activities, and performed a series of ground-based operational andscience habitat verification tests in preparation for the first validation flight