A quantum-classical decomposition of Gaussian quantum environments: a stochastic pseudomode model

We show that the effect of a Gaussian Bosonic environment linearly coupled to a quantum system can be simulated by a stochastic Lindblad master equation characterized by a set of ancillary Bosonic modes initially at zero temperature and classical stochastic fields. We test the method for Ohmic environments with exponential and polynomial cut-offs against, respectively, the Hierarchical Equations of Motion and the deterministic pseudomode model with respect to which the number of ancillary quantum degrees of freedom is reduced. For a subset of rational spectral densities, all parameters are explicitly specified without the need of any fitting procedure, thereby simplifying the modeling strategy. Interestingly, the classical fields in this decomposition must sometimes be imaginary-valued, which can have counter-intuitive effects on the system properties which we demonstrate by showing that they can decrease the entropy of the system, in contrast to real-valued fields.Comment: 41 pages, 11 figure

Modeling the unphysical pseudomode model with physical ensembles: simulation, mitigation, and restructuring of non-Markovian quantum noise

The influence of a Gaussian environment on a quantum system can be described by effectively replacing the continuum with a discrete set of ancillary quantum and classical degrees of freedom. This defines a pseudomode model which can be used to classically simulate the reduced system dynamics. Here, we consider an alternative point of view and analyze the potential benefits of an analog or digital quantum simulation of the pseudomode model itself. Superficially, such a direct experimental implementation is, in general, impossible due to the unphysical properties of the effective degrees of freedom involved. However, we show that the effects of the unphysical pseudomode model can still be reproduced using measurement results over an ensemble of physical systems involving ancillary harmonic modes and an optional stochastic driving field. This is done by introducing an extrapolation technique whose efficiency is limited by stability against imprecision in the measurement data. We examine how such a simulation would allow us to (i) perform accurate quantum simulation of the effects of complex non-perturbative and non-Markovian environments in regimes that are challenging for classical simulation, (ii) conversely, mitigate potential unwanted non-Markovian noise present in quantum devices, and (iii) restructure some of some of the properties of a given physical bath, such as its temperature.Comment: 30 pages, 10 figure

Ecological correlates of mammal β-diversity in Amazonian land-bridge islands: from small- to large-bodied species

Aim: Mega hydroelectric dams have become one of the main drivers of biodiversity loss in the lowland tropics. In these reservoirs, vertebrate studies have focused on local (α) diversity measures, whereas between‐site (β) diversity remains poorly assessed despite its pivotal importance in understanding how species diversity is structured and maintained. Here, we unravel the patterns and ecological correlates of mammal β‐diversity, including both small (SM) and midsized to large mammal species (LM) across 23 islands and two continuous forest sites within a mega hydroelectric reservoir. Location: Balbina Hydroelectric Dam, Central Brazilian Amazonia. Methods: Small mammals were sampled using live and pitfall traps (48,350 trap‐nights), and larger mammals using camera traps (8,160 trap‐nights). β‐diversity was examined for each group using multiplicative diversity decomposition of Hill numbers, which considers the importance of rare, common and dominant species, and tested to what extent those were related to a set of environmental characteristics measured at different spatial scales. Results: β‐diversity for both mammal groups was higher when considering species presence–absence. When considering species abundance, β‐diversity was significantly higher for SM than for LM assemblages. Habitat variables, such as differences in tree species richness and percentage of old‐growth trees, were strong correlates of β‐diversity for both SMs and LMs. Conversely, β‐diversity was weakly related to patch and landscape characteristics, except for LMs, for which β‐diversity was correlated with differences in island sizes. Main conclusions: The lower β‐diversity of LMs between smaller islands suggests subtractive homogenization of this group. Although island size plays a major role in structuring mammal α‐diversity in several land‐bridge islands, local vegetation characteristics were additional key factors determining β‐diversity for both mammal groups. Maintaining the integrity of vegetation characteristics and preventing the formation of a large set of small islands within reservoirs should be considered in long‐term management plans in both existing and planned hydropower development in lowland tropical forests

Neuroendocrine carcinoma of the seminal vesicles presenting with Lambert Eaton syndrome: a case report

Lambert Eaton syndrome may be the initial symptom of a seminal vesicle mass. Diagnosis needs to be obtained by transrectal biopsy and chemotherapy may delay progression of the tumor

Minimum sample size calculations for external validation of a clinical prediction model with a time-to-event outcome.

Previous articles in Statistics in Medicine describe how to calculate the sample size required for external validation of prediction models with continuous and binary outcomes. The minimum sample size criteria aim to ensure precise estimation of key measures of a model's predictive performance, including measures of calibration, discrimination, and net benefit. Here, we extend the sample size guidance to prediction models with a time-to-event (survival) outcome, to cover external validation in datasets containing censoring. A simulation-based framework is proposed, which calculates the sample size required to target a particular confidence interval width for the calibration slope measuring the agreement between predicted risks (from the model) and observed risks (derived using pseudo-observations to account for censoring) on the log cumulative hazard scale. Precise estimation of calibration curves, discrimination, and net-benefit can also be checked in this framework. The process requires assumptions about the validation population in terms of the (i) distribution of the model's linear predictor and (ii) event and censoring distributions. Existing information can inform this; in particular, the linear predictor distribution can be approximated using the C-index or Royston's D statistic from the model development article, together with the overall event risk. We demonstrate how the approach can be used to calculate the sample size required to validate a prediction model for recurrent venous thromboembolism. Ideally the sample size should ensure precise calibration across the entire range of predicted risks, but must at least ensure adequate precision in regions important for clinical decision-making. Stata and R code are provided

Inner ear hair cells produced in vitro by a mesenchymal-to-epithelial transition

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of National academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 104 (2007): 16675-16680, doi:10.1073/pnas.0704576104.Sensory hair cell loss is a major contributor to disabling hearing and balance deficits that affect >250 million people worldwide. Sound exposures, infections, drug toxicity, genetic disorders, and aging all can cause hair cell loss and lead to permanent sensory deficits. Progress toward treatments for these deficits has been limited, in part because hair cells have only been obtainable via microdissection of the anatomically complex internal ear. Attempts to produce hair cells in vitro have resulted in reports of some success, but have required transplantation into embryonic ears or co-culturing with other tissues. Here we show that avian inner ear cells can be cultured and passaged for months, frozen, and expanded to large numbers without other tissues. At any point from passage 6 up to at least passage 23, these cultures can be fully dissociated and then aggregated in suspension to induce a mesenchymal-to-epithelial transition that reliably yields new polarized sensory epithelia. Those epithelia develop numerous hair cells that are crowned by hair bundles, comprised of a single kinocilium and an asymmetric array of stereocilia. These hair cells exhibit rapid permeance to FM1-43, a dye that passes through open mechanotransducing channels. Since a vial of frozen cells can now provide the capacity to produce bona fide hair cells completely in vitro, these discoveries should open new avenues of research that may ultimately contribute to better treatments for hearing loss and other inner ear disorders.Supported by NIH grants DC00200 and DC006182to J.T.C

The changing environment of conservation conflict: geese and farming in Scotland

Conflict between conservation objectives and human livelihoods is ubiquitous and can be highly damaging, but the processes generating it are poorly understood. Ecological elements are central to conservation conflict, and changes in their dynamics — for instance due to anthropogenic environmental change — are likely to influence the emergence of serious human–wildlife impacts and, consequently, social conflict.  We used mixed-effects models to examine the drivers of historic spatio-temporal dynamics in numbers of Greenland barnacle geese (Branta leucopsis) on the Scottish island of Islay to identify the ecological processes that have shaped the environment in which conflict between goose conservation and agriculture has been triggered.  Barnacle goose numbers on Islay increased from 20,000 to 43,000 between 1987 and 2016. Over the same period, the area of improved grassland increased, the number of sheep decreased and the climate warmed.  Goose population growth was strongly linked to the increasing area of improved grassland, which provided geese with more high quality forage. Changing climatic conditions, particularly warming temperatures on Islay and breeding grounds in Greenland, have also boosted goose numbers.  As the goose population has grown, farms have supported geese more frequently and in larger numbers, with subsequent damaging effects on grassland. The creation of high-quality grassland appears to have largely driven the problem of serious economic damage by geese. Our analysis also reveals the drivers of spatial variation in goose impacts: geese were more likely to occur on farms closer to roosts and those with more improved grassland. However, as geese numbers have increased they have spread to previously less favoured farms.  Synthesis and applications. Our study demonstrates the primary role of habitat modification in the emergence of conflict between goose conservation and agriculture, alongside a secondary role of climate change. Our research illustrates the value of exploring socio-ecological history to understand the processes leading to conservation conflict. In doing so, we identify those elements that are more controllable, such as local habitat management, and less controllable, such as climate change, but which both need to be taken into account when managing conservation conflict

Flavonoids: Antioxidants Against Atherosclerosis

Oxidative stress results from an imbalance between excessive formation of reactive oxygen species (ROS) and/or reactive nitrogen species and limited antioxidant defences. Endothelium and nitric oxide (NO) are key regulators of vascular health. NO bioavailability is modulated by ROS that degrade NO, uncouple NO synthase, and inhibit synthesis. Cardiovascular risk conditions contribute to oxidative stress, causing an imbalance between NO and ROS, with a relative decrease in NO bioavailability. Dietary flavonoids represent a range of polyphenolic compounds naturally occurring in plant foods. Flavonoids are potentially involved in cardiovascular prevention mainly by decreasing oxidative stress and increasing NO bioavailability

All-optical switching in granular ferromagnets caused by magnetic circular dichroism

Magnetic recording using circularly polarised femto-second laser pulses is an emerging technology that would allow write speeds much faster than existing field driven methods. However, the mechanism that drives the magnetisation switching in ferromagnets is unclear. Recent theories suggest that the interaction of the light with the magnetised media induces an opto-magnetic field within the media, known as the inverse Faraday effect. Here we show that an alternative mechanism, driven by thermal excitation over the anisotropy energy barrier and a difference in the energy absorption depending on polarisation, can create a net magnetisation over a series of laser pulses in an ensemble of single domain grains. Only a small difference in the absorption is required to reach magnetisation levels observed experimentally and the model does not preclude the role of the inverse Faraday effect but removes the necessity that the opto-magnetic field is 10 s of Tesla in strength

K-Ras Mediated Murine Epidermal Tumorigenesis Is Dependent upon and Associated with Elevated Rac1 Activity

A common goal for potential cancer therapies is the identification of differences in protein expression or activity that would allow for the selective targeting of tumor vs. normal cells. The Ras proto-oncogene family (K-Ras, H-Ras and N-Ras) are amongst the most frequently mutated genes in human cancers. As a result, there has been substantial effort dedicated to determining which pathways are activated by Ras signaling and, more importantly, which of these contribute to cancer. Although the most widely studied Ras-regulated signaling pathway is the Raf/mitogen-activated protein kinase cascade, previous research in model systems has revealed that the Rac1 GTP-binding protein is also required for Ras-induced biological responses. However, what have been lacking are rigorous in vivo Rac1 target validation data and a clear demonstration that in Ras-driven hyperplastic lesions, Rac1 activity is increased. Using a combination of genetically-modified mouse models that allow for the tissue-selective activation or deletion of signaling molecules and an activation-state sensitive Rac1 antibody that detects GTP-bound Rac1, we found that Rac1 contributes to K-Ras induced epidermal papilloma initiation and growth and that Rac1 activity is elevated by oncogenic K-Ras in vivo. Previously, it was not practical to assess Rac1 activation status in the most commonly used format for clinical tumor specimens, formalin-fixed paraffin embedded (FFPE) tissues samples. However, this study clearly demonstrates that Rac1 is essential for K-Ras driven epithelial cell hyperproliferation and that Rac1 activity is elevated in tissues expressing mutant oncogenic K-Ras, while also characterizing the activation-state specific Rac1-GTP antibody as a probe to examine Rac1 activation status in FFPE samples. Our findings will facilitate further research on the status of Rac1 activity in human tumors and will help to define the tumor types of the patient population that could potentially benefit from therapies targeting Rac activation or downstream effector signaling pathways