Functionals in stochastic thermodynamics: how to interpret stochastic integrals

In stochastic thermodynamics standard concepts from macroscopic thermodynamics, such as heat, work, and entropy production, are generalized to small fluctuating systems by defining them on a trajectory-wise level. In Langevin systems with continuous state-space such definitions involve stochastic integrals along system trajectories, whose specific values depend on the discretization rule used to evaluate them (i.e. the 'interpretation' of the noise terms in the integral). Via a systematic mathematical investigation of this apparent dilemma, we corroborate the widely used standard interpretation of heat-and work-like functionals as Stratonovich integrals. We furthermore recapitulate the anomalies that are known to occur for entropy production in the presence of temperature gradients

Simple Theoretical Models for Resonant Cold Atom Interactions

Magnetically tunable scattering resonances have been used with great success for precise control of s-wave scattering lengths in ultracold atomic collisions. We describe relatively simple yet quite powerful analytic treatments of such resonances based on the analytic properties of the van der Waals long range potential. This theory can be used to characterize a number of properties of specific resonances that have been used successfully in various experiments with $^{87}$Rb, $^{85}$Rb, $^{40}$K, and $^{6}$Li. Optical Feshbach resonances are also possible and may be practical with narrow intercombination line photoassociative transitions in species like Sr and Yb.Comment: To be published in the Proceedings of the 20th International Conference on Atomic Physics, held in Innsbruck, Austria, July 200

DARCOF II. Danish research in Organic Food and Farming systems 2000-2005

The aim of this book is to present a comprehensive overview of the 41 research projects undertaken in the period 2000-2005 in the research programme DARCOF II.For each project there is a description of its background and objective in terms of which issues gave rise to the project and what the project aims to achieve. This is followed by a short description of the experiments or investigations that have been undertaken in the project. The general and applicable results derived from the project are finally described. For each project there is a reference to a project home page on www.darcof.dk. Via this page there is direct access to "Organic Eprints", which is the site containing all the project publications – both technical and scientific

Bayesian nonparametric tests via sliced inverse modeling

We study the problem of independence and conditional independence tests between categorical covariates and a continuous response variable, which has an immediate application in genetics. Instead of estimating the conditional distribution of the response given values of covariates, we model the conditional distribution of covariates given the discretized response (aka "slices"). By assigning a prior probability to each possible discretization scheme, we can compute efficiently a Bayes factor (BF)-statistic for the independence (or conditional independence) test using a dynamic programming algorithm. Asymptotic and finite-sample properties such as power and null distribution of the BF statistic are studied, and a stepwise variable selection method based on the BF statistic is further developed. We compare the BF statistic with some existing classical methods and demonstrate its statistical power through extensive simulation studies. We apply the proposed method to a mouse genetics data set aiming to detect quantitative trait loci (QTLs) and obtain promising results.Comment: 32 pages, 7 figure

Proton spin in a light-cone chiral quark model

We discuss the spin structure of the proton in a light-cone treatment of the chiral quark model. Based on the fact that the quark helicity ($\Delta q$) measured in polarized deep inelastic scattering experiments is actually the quark spin defined in the light-cone formalism, rather than the quark spin ($\Delta q_{QM}$) defined in the conventionally quark model (or in the rest frame of the nucleon), we calculate the $x$-dependence of the polarized quark distribution functions $\Delta q(x)$, and the polarized structure functions $g_1 (x)$. Special attention is focused on the Melosh-Wigner rotation due to the transversal motions of quarks inside the nucleon and its effects on the bare quark input. It is shown that our results match the experimental data well.Comment: 11 latex pages, 8 figures, final version published in PR

Beyond Concurrent Chemoradiation: The Emerging Role of PD-1/PD-L1 Inhibitors in Stage III Lung Cancer.

Concurrent chemoradiation (cCRT) with platinum-based chemotherapy is standard-of-care therapy for patients with stage III unresectable non-small cell lung cancer (NSCLC). Although cCRT is potentially curative, 5-year overall survival has hovered around 20%, despite extensive efforts to improve outcomes with increasing doses of conformal radiation and intensification of systemic therapy with either induction or consolidation chemotherapy. PD-1/PD-L1 immune checkpoint inhibitors have demonstrated unprecedented efficacy in patients with stage IV NSCLC. In addition, preclinical and early clinical evidence suggests that chemotherapy and radiation may work synergistically with anti-PD-1/PD-L1 therapy to promote antitumor immunity, which has led to the initiation of clinical trials testing these drugs in patients with stage III NSCLC. A preliminary report of a randomized phase III trial, the PACIFIC trial, demonstrated an impressive increase in median progression-free survival with consolidative durvalumab, a PD-L1 inhibitor, compared with observation after cCRT. Here, we discuss the clinical and translational implications of integrating PD-1/PD-L1 inhibitors in the management of patients with unresectable stage III NSCLC

Cool transition region loops observed by the Interface Region Imaging Spectrograph

We report on the first Interface Region Imaging Spectrograph (IRIS) study of cool transition region loops. This class of loops has received little attention in the literature. A cluster of such loops was observed on the solar disk in active region NOAA11934, in the Si IV 1402.8 \AA\ spectral raster and 1400 \AA\ slit-jaw (SJ) images. We divide the loops into three groups and study their dynamics and interaction. The first group comprises relatively stable loops, with 382--626\,km cross-sections. Observed Doppler velocities are suggestive of siphon flows, gradually changing from -10 km/s at one end to 20 km/s at the other end of the loops. Nonthermal velocities from 15 to 25 km/s were determined. These physical properties suggest that these loops are impulsively heated by magnetic reconnection occurring at the blue-shifted footpoints where magnetic cancellation with a rate of $10^{15}$ Mx/s is found. The released magnetic energy is redistributed by the siphon flows. The second group corresponds to two footpoints rooted in mixed-magnetic-polarity regions, where magnetic cancellation occurred at a rate of $10^{15}$ Mx/s and line profiles with enhanced wings of up to 200 km/s were observed. These are suggestive of explosive-like events. The Doppler velocities combined with the SJ images suggest possible anti-parallel flows in finer loop strands. In the third group, interaction between two cool loop systems is observed. Evidence for magnetic reconnection between the two loop systems is reflected in the line profiles of explosive events, and a magnetic cancellation rate of $3\times10^{15}$ Mx/s observed in the corresponding area. The IRIS observations have thus opened a new window of opportunity for in-depth investigations of cool transition region loops. Further numerical experiments are crucial for understanding their physics and their role in the coronal heating processes.Comment: Accepted for publication in Ap

Communication and re-use of chemical information in bioscience.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.An article submitted to BiomedCentral Bioinformatics, created on request with their Publicon system. The transformed manuscript is archived as PDF. Although it has been through the publishers system this is purely automatic and the contents are those of a pre-refereed preprint. The formatting is provided by the system and tables and figures appear at the end. An accommpanying submission, http://www.dspace.cam.ac.uk/handle/1810/34580, describes the rationale and cultural aspects of publishing , abstracting and aggregating chemical information. BMC is an Open Access publisher and we emphasize that all content is re-usable under Creative Commons Licens