Exciting, Cooling And Vortex Trapping In A Bose-Condensed Gas

A straight forward numerical technique, based on the Gross-Pitaevskii equation, is used to generate a self-consistent description of thermally-excited states of a dilute boson gas. The process of evaporative cooling is then modelled by following the time evolution of the system using the same equation. It is shown that the subsequent rethermalisation of the thermally-excited state produces a cooler coherent condensate. Other results presented show that trapping vortex states with the ground state may be possible in a two-dimensional experimental environment.Comment: 9 pages, 7 figures. It's worth the wait! To be published in Physical Review A, 1st February 199

DNA damage is overcome by TRIP13 overexpression during cisplatin nephrotoxicity

Cisplatin is a commonly used chemotherapeutic agent to treat a wide array of cancers that is frequently associated with toxic injury to the kidney due to oxidative DNA damage and perturbations in cell cycle progression leading to cell death. In this study, we investigated whether thyroid receptor interacting protein 13 (TRIP13) plays a central role in the protection of the tubular epithelia following cisplatin treatment by circumventing DNA damage. Following cisplatin treatment, double-stranded DNA repair pathways were inhibited using selective blockers to proteins involved in either homologous recombination or non-homologous end joining. This led to increased blood markers of acute kidney injury (AKI) (creatinine and neutrophil gelatinase–associated lipocalin), tubular damage, activation of DNA damage marker (γ-H2AX), elevated appearance of G2/M blockade (phosphorylated histone H3 Ser10 and cyclin B1), and apoptosis (cleaved caspase-3). Conditional proximal tubule–expressing Trip13 mice were observed to be virtually protected from the cisplatin nephrotoxicity by restoring most of the pathological phenotypes back toward normal conditions. Our findings suggest that TRIP13 could circumvent DNA damage in the proximal tubules during cisplatin injury and that TRIP13 may constitute a new therapeutic target in protecting the kidney from nephrotoxicants and reduce outcomes leading to AKI

Higher-order mutual coherence of optical and matter waves

We use an operational approach to discuss ways to measure the higher-order cross-correlations between optical and matter-wave fields. We pay particular attention to the fact that atomic fields actually consist of composite particles that can easily be separated into their basic constituents by a detection process such as photoionization. In the case of bosonic fields, that we specifically consider here, this leads to the appearance in the detection signal of exchange contributions due to both the composite bosonic field and its individual fermionic constituents. We also show how time-gated counting schemes allow to isolate specific contributions to the signal, in particular involving different orderings of the Schr\"odinger and Maxwell fields.Comment: 11 pages, 2 figure

Alkali Metal Trihalides: MX ̄ Ion Pair or MX-X Complex?

The alkali metal trihalides MX3 (M = Li, Na, K, Rb, and Cs; X = Cl, Br, and I) are systematically studied using coupled-cluster methods. Benchmarks using CCSD(T) against diatomic experimental results suggest satisfactory performance for the weighted core-valence basis sets (new basis sets for K, Rb, and Cs) selected for predicting reliable structures and harmonic vibrational frequencies. An isomer search using the B3LYP functional yields a planar, yet asymmetric T-shaped Cs structure as the global minimum for all MX3 species. Much higher level CCSD(T) computations show a moderate to strong distortion of the X3ˉ anion by the M+ cation in the respective equilibrium geometries. Most obviously, for LiCl3 the two Cl-Cl distances are separated by 0.786 Å. Even for CsI3, the structure least distorted from the M+X3ˉ model, the two I-I distances differ by 0.243 Å. It does not take much energy to distort the parent anions along an asymmetric stretch, so this is no surprise. The normal modes of vibration of the MX3 molecules are in better agreement with matrix isolation experiments than previous calculations. And these normal modes are revealing -- instead of the well-established antisymmetric and symmetric stretches of the “free” X3ˉ anions, relatively localized and mutually-perturbed X-X and M-X stretches are calculated. The suggestion emerges that the MX3 system may be alternatively described as an MX-X2 complex, rather than the M+X3ˉ ion pair. This perspective is supported by bonding analyses showing low electron densities at the bond critical points and natural bond orders between the MX and X2 moieties. The thermochemistry of fragmentations of MX3 to MX + X2 vs. M+ + X3ˉ also supports the alternative viewpoint of the bonding in this class of molecules

Evaluating G2G for use in Rapid Response Catchments: Final Report

Flood impacts can be severe for rapid response catchments (RRCs). Providing targeted flood warnings is challenging using existing methodologies and on account of the typical absence of river flow gauging. The Pitt Review of the Summer 2007 floods recognised the need for new alert procedures for RRCs able to exploit the new distributed flood forecasting capability being progressed from research into operations. Work on the G2G (Grid-to-Grid) distributed hydrological model was accelerated into operational practice to support 5-day countrywide flood outlooks, a major recommendation of the Pitt Review. The present study aims to explore the potential of G2G to support more frequent and detailed alerts relevant to flood warning in RRCs. Integral to this study is the use of emerging rainfall forecast products, in deterministic and ensemble form, which allow the lead-time of G2G flow forecasts to be extended and given an uncertainty context. This Report sets down the overall scope of the project, provides an introduction to G2G by way of background and then reports on the outcomes of the R&D study. This includes extensive preparatory work on collating historical datasets to support G2G model assessment, both relating to hydrometry and new rainfall forecast products. A framework is developed for assessing G2G in both simulation-mode and forecast-mode (as a function of lead-time) targeted at the RRC requirement. Relevant to the requirement is the RRC Register of points and areas of interest compiled by the Environment Agency, and the characteristics of RRCs (occurring in isolation or in combination): small catchment area, urban/sub-urban land-cover and steep slopes. The assessment framework is first applied assuming perfect knowledge of rainfall observations for past and future times, so as not to confound the analysis with errors from rainfall forecasts. Variability of performance measures across groups of sites is summarised through box and whisker plots, groups being differentiated on size of catchment area and nature of G2G run (simulation, and with the addition of state updating and flow insertion in turn). Skill scores judge how well the model performs in detecting a flood event exceeding a flow threshold, taken as the median annual flood (as an indicator of bankfull flow exceedance for natural channels) and fractional multipliers of it. The skill scores include POD (Probability of Detection) and FAR (False Alarm Ratio). Performance maps of R2 Efficiency, indicating the variability in the observations accounted for by the model, are used to portray the spatial variability of G2G accuracy across the country. G2G performance in small catchments, relevant to the RRC requirement, is best over South West, North East and North West regions; also median performance appears robust from one year to the next. Larger catchments benefit most in forecast-mode from flow insertion, whilst smaller headwater catchments gain particularly from ARMA (AutoRegressive Moving Average) error-prediction. An assessment is made of using deterministic rainfall forecasts from NWP UKV - the Numerical Weather Prediction UK Variable Resolution form of the Met Office Unified Model - in a full emulation of G2G in real-time, and using foreknowledge of rainfall observations as a reference baseline. Forecast quality can deteriorate strongly beyond 12 hours, especially for smaller catchments, whilst for some locations good performance is maintained even for long lead-times. Diagnostic analysis reveals that the UKV rainfall forecasts have patterns of overestimation in some lowland areas (e.g. over London) and leeward of high elevation areas (e.g. north and south Pennines). Overall performance is better in Scotland although there is evidence of UKV overestimating rainfall near the coast at Edinburgh and Elgin in the north. The assessment framework is extended to include rainfall forecast ensembles and probabilistic flood forecasting, using a combination of case-study and longer-term analyses. Blended Ensemble rainfall forecasts are assessed in two forms: forecasts out to 24 hours updated 4 times a day, and nowcasts out to 7 hours updated every 15 minutes. The 24 hour forecasts generally perform well as input to G2G in the case studies, the G2G flow forecasts typically signalling a flood peak 12 to 18 hours in advance and ahead of any observed response for small catchments. New regional summary map displays of the probability of flow threshold exceedances over a forecast horizon, and for increasing levels of severity, are developed to highlight evolving hotspots of flood risk over time. The first ever continuous assessment of G2G probability flow forecasts is reported using national maps of probabilistic skill scores - Relative Operating Characteristic (ROC) Skill Score and Brier Skill Score (BSS) - to spatially assess their performance. It is noted that the short periods available for assessment - a 7½ month period over England & Wales and 4 ½ months over Scotland - limit the analyses to low return period flow thresholds. Half the median (2-year) flood is used although a regional pooled analysis allows some assessment up to 5-year. The G2G probability forecast assessed is the probability of the chosen flow threshold being exceeded at any time over the forecast horizon (taken to be 24 hours). Comparison of these scores when applied to deterministic and probabilistic forecasts from G2G provides strong evidence of the value of G2G ensemble forecasts as an indicator of flood risk over Britain. Noticeably poorer performance indicated by the BSS across Scotland is in part attributed to the short, summer-dominated assessment period. Operational tools available to FFC and the SFFS for using G2G flow ensembles are reviewed and options for improvement identified drawing on the experience and findings of the study. This leads to identifying some work of an operational nature for consideration in Phase 3 of the project. The report closes with a summary of project achievements grouped thematically, a set of recommendations both of a general nature and specific to FFC and SFFS needs, and finally some proposals for consideration under Phase 3 of the G2G for Rapid Response Catchments project. Some key benefits arising from the project are summarised below. • Evidence has been produced that shows G2G has good skill in providing strategic forecasts for RRCs. The evidence is stratified by catchment type (area, urbanisation, headwater), form of forecast (simulation or forecast mode) and nature of rainfall input (raingauge, deterministic forecast, ensemble forecast). • Strong evidence has been presented on the advantage of using an ensemble rainfall forecast as input to G2G to obtain a probabilistic flood forecast for an RRC, relative to an approach where only a single deterministic rainfall and flood forecast is obtained. This indicates better guidance can be given on forecast flood risk for RRCs, improving the level of service provision for such catchments which are currently not well served. • An improved G2G model configuration, exploiting gauged flows from 912 sites and including new locally calibrated parameters, has been delivered and made operational for the FFC with England & Wales coverage. The benefit is improved operational flood forecast accuracy. For Scotland, an enhanced configuration will be delivered to SFFS in Spring 2014. • Detailed recommendations on how the visual presentation of G2G ensemble results could be improved are set down in this report. When further developed and implemented, these will prove of benefit to the preparation of Flood Guidance Statements issued by FFC and the SFFS across Britain

Input-output theory for fermions in an atom cavity

We generalize the quantum optical input-output theory developed for optical cavities to ultracold fermionic atoms confined in a trapping potential, which forms an "atom cavity". In order to account for the Pauli exclusion principle, quantum Langevin equations for all cavity modes are derived. The dissipative part of these multi-mode Langevin equations includes a coupling between cavity modes. We also derive a set of boundary conditions for the Fermi field that relate the output fields to the input fields and the field radiated by the cavity. Starting from a constant uniform current of fermions incident on one side of the cavity, we use the boundary conditions to calculate the occupation numbers and current density for the fermions that are reflected and transmitted by the cavity

Coherent dynamics of Bose-Einstein condensates in high-finesse optical cavities

We study the mutual interaction of a Bose-Einstein condensed gas with a single mode of a high-finesse optical cavity. We show how the cavity transmission reflects condensate properties and calculate the self-consistent intra-cavity light field and condensate evolution. Solving the coupled condensate-cavity equations we find that while falling through the cavity, the condensate is adiabatically transfered into the ground state of the periodic optical potential. This allows time dependent non-destructive measurements on Bose-Einstein condensates with intriguing prospects for subsequent controlled manipulation.Comment: 5 pages, 5 figures; revised version: added reference

Competition between quantum-liquid and electron-solid phases in intermediate Landau levels

On the basis of energy calculations we investigate the competition between quantum-liquid and electron-solid phases in the Landau levels n=1,2, and 3 as a function of their partial filling factor. Whereas the quantum-liquid phases are stable only in the vicinity of quantized values 1/(2s+1) of the partial filling factor, an electron solid in the form of a triangular lattice of clusters with a few number of electrons (bubble phase) is energetically favorable between these fillings. This alternation of electron-solid phases, which are insulating because they are pinned by the residual impurities in the sample, and quantum liquids displaying the fractional quantum Hall effect explains a recently observed reentrance of the integral quantum Hall effect in the Landau levels n=1 and 2. Around half-filling of the last Landau level, a uni-directional charge density wave (stripe phase) has a lower energy than the bubble phase.Comment: 12 pages, 9 figures; calculation of exact exchange potential for n=1,2,3 included, energies of electron-solid phases now calculated with the help of the exact potential, and discussion of approximation include

National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue

Variable and suboptimal biospecimen handling practices have been identified as impediments to biomarker discovery, including predictive biomarkers for oncology indicating a clear and present need for evidence-based, standardized practices. The United States and international efforts have been launched to better understand andmitigate variability during the preanalytical phase and decrease associated effects by promoting harmonization of procedures both within and across institutions. The Biorepositories and Biospecimen Research Branch (BBRB) of the United States National Cancer Institute (NCI) publishes best practice documents aimed at improving the quality of data generated from human biospecimens (https://biospecimens.cancer.gov/bestpractices/overview.asp) and sponsors research initiatives (https://biospecimens.cancer.gov/programs/default.asp) and the Biospecimen Research Database (BRD; http://biospecimens.cancer.gov/brd) to better understand thresholds and effects of individual preanalytical factors in biospecimen handling. The BRD allows users to query both a curated literature repository and standard operating procedure (SOP) library for a specific preservative, diagnosis, analyte, or preanalytical factor. The BRD incorporates information from international efforts, including those by the International Society for Biological and Environmental Repositories (ISBER) and the European Union-sponsored SPIDIA program (standardization and improvement of generic preanalytical tools and procedures for in vitro diagnostics; www.spidia.eu), among others

High biomass, low export regimes in the Southern Ocean

Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 54 (2007): 601-638, doi:10.1016/j.dsr2.2007.01.013.This paper investigates ballasting and remineralization controls of carbon sedimentation in the twilight zone (100-1000 m) of the Southern Ocean. Size-fractionated (<1 μm, 1-51 μm, >51 μm) suspended particulate matter was collected by large volume in-situ filtration from the upper 1000 m in the Subantarctic (55°S, 172°W) and Antarctic (66°S, 172°W) zones of the Southern Ocean during the Southern Ocean Iron Experiment (SOFeX) in January-February 2002. Particles were analyzed for major chemical constituents (POC, P, biogenic Si, CaCO3), and digital and SEM image analyses of particles were used to aid in the interpretation of the chemical profiles. Twilight zone waters at 66°S in the Antarctic had a steeper decrease in POC with depth than at 55°S in the Subantarctic, with lower POC concentrations in all size fractions at 66°S than at 55°S, despite up to an order of magnitude higher POC in surface waters at 66°S. The decay length scale of >51 μm POC was significantly shorter in the upper twilight zone at 66°S (δe=26 m) compared to 55°S (δe=81 m). Particles in the carbonate-producing 55°S did not have higher excess densities than particles from the diatom-dominated 66°S, indicating that there was no direct ballast effect that accounted for deeper POC penetration at 55°S. An indirect ballast effect due to differences in particle packaging and porosities cannot be ruled out, however, as aggregate porosities were high (~97%) and variable. Image analyses point to the importance of particle loss rates from zooplankton grazing and remineralization as determining factors for the difference in twilight zone POC concentrations at 55°S and 66°S, with stronger and more focused shallow remineralization at 66°S. At 66°S, an abundance of large (several mm long) fecal pellets from the surface to 150 m, and almost total removal of large aggregates by 200 m, reflected the actions of a single or few zooplankton species capable of grazing diatoms in the euphotic zone, coupled with a more diverse particle feeding zooplankton community immediately below. Surface waters with high biomass levels and high proportion of biomass in the large size fraction were associated with low particle loading at depth, with all indications implying conditions of low export. The 66°S region exhibits this “High Biomass, Low Export” (HBLE) condition, with very high >51 μm POC concentrations at the surface (~2.1 μM POC), but low concentrations below 200 m (<0.07 μM POC). The 66°S region remained HBLE after iron fertilization. Iron addition at 55°S caused a ten fold increase in >51 μm biomass concentrations in the euphotic zone, bringing surface POC concentrations to levels found at 66°S (~3.8 μM), and a concurrent decrease in POC concentrations below 200 m. The 55°S region, which began with moderate levels of biomass and stronger particle export, transitioned to being HBLE after iron fertilization. We propose that iron addition to already HBLE waters will not cause mass sedimentation events. The stability of an iron-induced HBLE condition is unknown. Better understanding of biological pump processes in non-HBLE Subantarctic waters is needed.This work was supported by the DOE Office of Science, Biological and Environmental Research Program. Shiptime for SOFeX was funded by NSF