Surface-hopping dynamics and decoherence with quantum equilibrium structure

In open quantum systems decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments evolving exclusively on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.Comment: 11, pages, 8 figure

Einfluss von separater und kombinierter Einarbeitung von Gülle und Biokohle auf die Bildung von Makroaggregaten bei konstanter und variierender Bodenfeuchte

Organische Bodenzusatzstoffe können einen positiven Einfluss auf die Bildung von Makroaggregaten (>250 µm) im Boden haben was sich wiederum positiv auf die Kohlenstoffspeicherung auswirkt. Die diesbezüglichen Effekte von Gülle und Biokohle sowie der Bodenfeuchte sind aber weitestgehend unbekannt. Ziel dieser Studie war daher zu klären, welchen Einfluss die separate und kombinierte Einarbeitung von Gülle und Biokohle auf die Bildung von Makroaggregaten unter konstanter und variierender Bodenfeuchte haben. Hierfür wurden vier schluffig-lehmige Böden beprobt und anschließend die Makroaggregate zerstört. Die Proben wurden dann bei 15 °C für 60 Tage bei konstanter Bodenfeuchte und drei Trocknungs-Wiederbefeuchtungszyklen und nach Einarbeitung der folgenden Gülle- (in kg N ha-1) und Biokohlegaben (in % der Bodentrockenmasse) inkubiert: Kontrolle, Biokohle (12), Gülle (150), Biokohle (6) + Gülle (75), Biokohle (12) + Gülle (75), Biokohle (6) + Gülle (150) und Biokohle (12) + Gülle (150). Im Verlauf der Inkubation wurden die CO2 Emission gemessen und nach Abschluss des Experimentes die mikrobielle Biomasse bestimmt. Anschließend wurden die Makroaggregate abgetrennt und hinsichtlich ihres Kohlenstoffgehaltes analysiert. Die Makroaggregate der Biokohlevarianten mit und ohne zusätzlicher Gülleeinbringung wiesen gleiche oder höhere Kohlenstoffgehalte im Vergleich zur Kontrolle und der Variante mit separater Gülleeinbringung auf was auf einen Einschluss von Biokohle in diese Aggregate hindeutet. Die Trocknung und Wiederbefeuchtung der Proben resultierte in geringeren Mengen an Makroaggregaten was besonders für die Böden zutraf in denen Biokohle und Gülle eingebracht wurde. Die Trocknung der Gülle scheint einen irreversiblen negativen Effekt auf deren Aggregierungswirkung zu haben, was zu einer Abnahme in den Makroaggregaten im Vergleich zu den Proben führt, die bei konstanter Bodenfeuchte inkubiert wurden. Darüber hinaus deuten die geringere mikrobielle Biomasse und CO2 Emissionen für die Proben unter variierender Bodenfeuchte auf eine geringere mikrobielle Aktivität und Eintrag mikrobieller Aggregatbildner hin. Neben Menge und Typ der organischen Bodenzusatzstoffe scheinen auch klimatisch bedingte Unterschiede in der Bodenfeuchte einen Einfluss auf die Bildung und Stabilität von Makroaggregaten im Boden zu haben

Thermoelectric Response of an Interacting Two-Dimensional Electron Gas in Quantizing Magnetic Field

We present a discussion of the linear thermoelectric response of an interacting electron gas in a quantizing magnetic field. Boundary currents can carry a significant fraction of the net current passing through the system. We derive general expressions for the bulk and boundary components of the number and energy currents. We show that the local current density may be described in terms of ``transport'' and ``internal magnetization'' contributions. The latter carry no net current and are not observable in standard transport experiments. We show that although Onsager relations cannot be applied to the local current, they are valid for the transport currents and hence for the currents observed in standard transport experiments. We relate three of the four thermoelectric response coefficients of a disorder-free interacting two-dimensional electron gas to equilibrium thermodynamic quantities. In particular, we show that the diffusion thermopower is proportional to the entropy per particle, and we compare this result with recent experimental observations.Comment: 18 pages, 2 postscript figures included. Revtex with epsf.tex and multicol.sty. In the revised version, the comparison with experimental observations at $\nu=1/2, 3/2$ is extended to include the possibility of corrections due to weak impurity scattering. The conclusions that we reach regarding the applicability of the composite fermion model at these filling fractions are not affecte

First-line treatment of metastatic clear cell renal cell carcinoma: a decision-making analysis among experts

Background: The treatment landscape of metastatic clear cell renal cell carcinoma (mccRCC) has been transformed by targeted therapies with tyrosine kinase inhibitors (TKI) and more recently by the incorporation of immune checkpoint inhibitors (ICI). Today, a spectrum of single agent TKI to TKI/ICI and ICI/ICI combinations can be considered and the choice of the best regimen is complex. Materials and methods: We performed an updated decision-making analysis among 11 international kidney cancer experts. Each expert provided their treatment strategy and relevant decision criteria in the first line treatment of mccRCC. After the collection of all input a list of unified decision criteria was determined and compatible decision trees were created. We used a methodology based on diagnostic nodes, which allows for an automated cross-comparison of decision trees, to determine the most common treatment recommendations as well as deviations. Results: Diverse parameters were considered relevant for treatment selection, various drugs and drug combinations were recommended by the experts. The parameters, chosen by the experts, were performance status, International Metastatic renal cell carcinoma Database Consortium (IMDC) risk group, PD-L1 status, zugzwang and contraindication to immunotherapy. The systemic therapies selected for first line treatment were sunitinib, pazopanib, tivozanib, cabozantinib, ipilimumab/nivolumab or pembrolizumab/axitinib. Conclusion: A wide spectrum of treatment recommendations based on multiple decision criteria was demonstrated. Significant inter-expert variations were observed. This demonstrates how data from randomized trials are implemented differently when transferred into daily practice

Impaired value-based decision-making in Parkinson’s Disease Apathy

Apathy is a common and disabling complication of Parkinson’s disease characterized by reduced goal-directed behaviour. Several studies have reported dysfunction within prefrontal cortical regions and projections from brainstem nuclei whose neuromodulators include dopamine, serotonin and noradrenaline. Work in animal and human neuroscience have confirmed contributions of these neuromodulators on aspects of motivated decision-making. Specifically, these neuromodulators have overlapping contributions to encoding the value of decisions, and influence whether to explore alternative courses of action or persist in an existing strategy to achieve a rewarding goal. Building upon this work, we hypothesized that apathy in Parkinson’s disease should be associated with an impairment in value-based learning. Using a four-armed restless bandit reinforcement learning task, we studied decision-making in 75 volunteers; 53 patients with Parkinson’s disease, with and without clinical apathy, and 22 age-matched healthy control subjects. Patients with apathy exhibited impaired ability to choose the highest value bandit. Task performance predicted an individual patient’s apathy severity measured using the Lille Apathy Rating Scale (R = −0.46, P &lt; 0.001). Computational modelling of the patient’s choices confirmed the apathy group made decisions that were indifferent to the learnt value of the options, consistent with previous reports of reward insensitivity. Further analysis demonstrated a shift away from exploiting the highest value option and a reduction in perseveration, which also correlated with apathy scores (R = −0.5, P &lt; 0.001). We went on to acquire functional MRI in 59 volunteers; a group of 19 patients with and 20 without apathy and 20 age-matched controls performing the Restless Bandit Task. Analysis of the functional MRI signal at the point of reward feedback confirmed diminished signal within ventromedial prefrontal cortex in Parkinson’s disease, which was more marked in apathy, but not predictive of their individual apathy severity. Using a model-based categorization of choice type, decisions to explore lower value bandits in the apathy group activated prefrontal cortex to a similar degree to the age-matched controls. In contrast, Parkinson’s patients without apathy demonstrated significantly increased activation across a distributed thalamo-cortical network. Enhanced activity in the thalamus predicted individual apathy severity across both patient groups and exhibited functional connectivity with dorsal anterior cingulate cortex and anterior insula. Given that task performance in patients without apathy was no different to the age-matched control subjects, we interpret the recruitment of this network as a possible compensatory mechanism, which compensates against symptomatic manifestation of apathy in Parkinson’s disease.</p

Virtual reality, ultrasound-guided liver biopsy simulator: Development and performance discrimination

Objectives: The aim of this article was to identify and prospectively investigate simulated ultrasound-guided targeted liver biopsy performance metrics as differentiators between levels of expertise in interventional radiology. Methods: Task analysis produced detailed procedural step documentation allowing identification of critical procedure steps and performance metrics for use in a virtual reality ultrasound-guided targeted liver biopsy procedure. Consultant (n=14; male=11, female=3) and trainee (n=26; male=19, female=7) scores on the performance metrics were compared. Ethical approval was granted by the Liverpool Research Ethics Committee (UK). Independent t-tests and analysis of variance (ANOVA) investigated differences between groups. Results: Independent t-tests revealed significant differences between trainees and consultants on three performance metrics: targeting, p=0.018, t=22.487 (22.040 to 20.207); probe usage time, p=0.040, t=2.132 (11.064 to 427.983); mean needle length in beam, p=0.029, t=22.272 (20.028 to 20.002). ANOVA reported significant differences across years of experience (0–1, 1–2, 3+ years) on seven performance metrics: no-go area touched, p=0.012; targeting, p=0.025; length of session, p=0.024; probe usage time, p=0.025; total needle distance moved, p=0.038; number of skin contacts, p<0.001; total time in no-go area, p=0.008. More experienced participants consistently received better performance scores on all 19 performance metrics. Conclusion: It is possible to measure and monitor performance using simulation, with performance metrics providing feedback on skill level and differentiating levels of expertise. However, a transfer of training study is required

Impaired value-based decision-making in Parkinson’s Disease Apathy

Apathy is a common and disabling complication of Parkinson’s disease characterized by reduced goal-directed behaviour. Several studies have reported dysfunction within prefrontal cortical regions and projections from brainstem nuclei whose neuromodulators include dopamine, serotonin and noradrenaline. Work in animal and human neuroscience have confirmed contributions of these neuromodulators on aspects of motivated decision-making. Specifically, these neuromodulators have overlapping contributions to encoding the value of decisions, and influence whether to explore alternative courses of action or persist in an existing strategy to achieve a rewarding goal. Building upon this work, we hypothesized that apathy in Parkinson’s disease should be associated with an impairment in value-based learning. Using a four-armed restless bandit reinforcement learning task, we studied decision-making in 75 volunteers; 53 patients with Parkinson’s disease, with and without clinical apathy, and 22 age-matched healthy control subjects. Patients with apathy exhibited impaired ability to choose the highest value bandit. Task performance predicted an individual patient’s apathy severity measured using the Lille Apathy Rating Scale (R = −0.46, P &lt; 0.001). Computational modelling of the patient’s choices confirmed the apathy group made decisions that were indifferent to the learnt value of the options, consistent with previous reports of reward insensitivity. Further analysis demonstrated a shift away from exploiting the highest value option and a reduction in perseveration, which also correlated with apathy scores (R = −0.5, P &lt; 0.001). We went on to acquire functional MRI in 59 volunteers; a group of 19 patients with and 20 without apathy and 20 age-matched controls performing the Restless Bandit Task. Analysis of the functional MRI signal at the point of reward feedback confirmed diminished signal within ventromedial prefrontal cortex in Parkinson’s disease, which was more marked in apathy, but not predictive of their individual apathy severity. Using a model-based categorization of choice type, decisions to explore lower value bandits in the apathy group activated prefrontal cortex to a similar degree to the age-matched controls. In contrast, Parkinson’s patients without apathy demonstrated significantly increased activation across a distributed thalamo-cortical network. Enhanced activity in the thalamus predicted individual apathy severity across both patient groups and exhibited functional connectivity with dorsal anterior cingulate cortex and anterior insula. Given that task performance in patients without apathy was no different to the age-matched control subjects, we interpret the recruitment of this network as a possible compensatory mechanism, which compensates against symptomatic manifestation of apathy in Parkinson’s disease.</p

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources