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

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

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

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

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

Unexpected Accumulation of ncm\u3csup\u3e5\u3c/sup\u3eU and ncm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU in a \u3cem\u3etrm9\u3c/em\u3e Mutant Suggests an Additional Step in the Synthesis of mcm\u3csup\u3e5\u3c/sup\u3eU and mcm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU

Background Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm5U), 5-carbamoylmethyl-2′-O-methyluridine (ncm5Um), 5-methoxycarbonylmethyl-uridine (mcm5U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The formation of mcm5 and ncm5 side chains involves a complex pathway, where the last step in formation of mcm5 is a methyl esterification of cm5 dependent on the Trm9 and Trm112 proteins. Methodology and Principal Findings Both Trm9 and Trm112 are required for the last step in formation of mcm5 side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm5U or mcm5s2U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm5U and mcm5s2U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm5U and ncm5s2U, not the expected cm5U and cm5s2U. Conclusions Trm9p and Trm112p function together at the final step in formation of mcm5U in tRNA by using the intermediate cm5U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm5U and ncm5s2U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm5 side chain. We propose two alternative explanations for this observation. One is that the intermediate cm5U is generated from ncm5U by a yet unknown mechanism and the other is that cm5U is formed before ncm5U and mcm5U

Dynamical Generation of Spin Current and Phase Slip in Exciton-Polariton Condensates

We show that how to generate propagation of spin degree in spin-symmetric exciton-polariton condensates in a semiconductor microcavity. Due to the stimulated spin-dependent scattering between hot excitons and condensates, exciton polaritons form a circular polarized condensate with spontaneous breaking of the spin rotation symmetry. The spin antiferromagnetic state is developed evidently from the density and spin flow pumped by localized laser source. The low energy spin current is identified where the steady state is characterized by the oscillating spin pattern. Finally, we predict via simulation how to dynamical generation of phase slip where ring-shape phase jump shows the behavior of splitting and joining together.Comment: 6 figure