Efficient computation of matched solutions of the Kapchinskij-Vladimirskij envelope equations for periodic focusing lattices

A new iterative method is developed to numerically calculate the periodic, matched beam envelope solution of the coupled Kapchinskij-Vladimirskij (KV) equations describing the transverse evolution of a beam in a periodic, linear focusing lattice of arbitrary complexity. Implementation of the method is straightforward. It is highly convergent and can be applied to all usual parameterizations of the matched envelope solutions. The method is applicable to all classes of linear focusing lattices without skew couplings, and also applies to all physically achievable system parameters -- including where the matched beam envelope is strongly unstable. Example applications are presented for periodic solenoidal and quadrupole focusing lattices. Convergence properties are summarized over a wide range of system parameters.Comment: 20 pages, 5 figures, Mathematica source code provide

Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency.</p> <p>Results</p> <p>We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties.</p> <p>Conclusions</p> <p>For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.</p

230 Th normalization: new insights on an essential tool for quantifying sedimentary fluxes in the modern and quaternary ocean

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Costa, K. M., Hayes, C. T., Anderson, R. F., Pavia, F. J., Bausch, A., Deng, F., Dutay, J., Geibert, W., Heinze, C., Henderson, G., Hillaire-Marcel, C., Hoffmann, S., Jaccard, S. L., Jacobel, A. W., Kienast, S. S., Kipp, L., Lerner, P., Lippold, J., Lund, D., Marcantonio, F., McGee, D., McManus, J. F., Mekik, F., Middleton, J. L., Missiaen, L., Not, C., Pichat, S., Robinson, L. F., Rowland, G. H., Roy-Barman, M., Alessandro, Torfstein, A., Winckler, G., & Zhou, Y. 230 Th normalization: new insights on an essential tool for quantifying sedimentary fluxes in the modern and quaternary ocean. Paleoceanography and Paleoclimatology, 35(2), (2020): e2019PA003820, doi:10.1029/2019PA003820.230Th normalization is a valuable paleoceanographic tool for reconstructing high‐resolution sediment fluxes during the late Pleistocene (last ~500,000 years). As its application has expanded to ever more diverse marine environments, the nuances of 230Th systematics, with regard to particle type, particle size, lateral advective/diffusive redistribution, and other processes, have emerged. We synthesized over 1000 sedimentary records of 230Th from across the global ocean at two time slices, the late Holocene (0–5,000 years ago, or 0–5 ka) and the Last Glacial Maximum (18.5–23.5 ka), and investigated the spatial structure of 230Th‐normalized mass fluxes. On a global scale, sedimentary mass fluxes were significantly higher during the Last Glacial Maximum (1.79–2.17 g/cm2kyr, 95% confidence) relative to the Holocene (1.48–1.68 g/cm2kyr, 95% confidence). We then examined the potential confounding influences of boundary scavenging, nepheloid layers, hydrothermal scavenging, size‐dependent sediment fractionation, and carbonate dissolution on the efficacy of 230Th as a constant flux proxy. Anomalous 230Th behavior is sometimes observed proximal to hydrothermal ridges and in continental margins where high particle fluxes and steep continental slopes can lead to the combined effects of boundary scavenging and nepheloid interference. Notwithstanding these limitations, we found that 230Th normalization is a robust tool for determining sediment mass accumulation rates in the majority of pelagic marine settings (>1,000 m water depth).We thank Zanna Chase and one anonymous reviewer for valuable feedback. K. M. C. was supported by a Postdoctoral Scholarship at WHOI. L. M. acknowledges funding from the Australian Research Council grant DP180100048. The contribution of C. T. H., J. F. M., and R. F. A. were supported in part by the U.S. National Science Foundation (US‐NSF). G. H. R. was supported by the Natural Environment Research Council (grant NE/L002434/1). S. L. J. acknowledges support from the Swiss National Science Foundation (grants PP002P2_144811 and PP00P2_172915). This study was supported by the Past Global Changes (PAGES) project, which in turn received support from the Swiss Academy of Sciences and the US‐NSF. This work grew out of a 2018 workshop in Aix‐Marseille, France, funded by PAGES, GEOTRACES, SCOR, US‐NSF, Aix‐Marseille Université, and John Cantle Scientific. All data are publicly available as supporting information to this document and on the National Center for Environmental Information (NCEI) at https://www.ncdc.noaa.gov/paleo/study/28791

Dynamics of a Vortex in a Trapped Bose-Einstein Condensate

We consider a large condensate in a rotating anisotropic harmonic trap. Using the method of matched asymptotic expansions, we derive the velocity of an element of vortex line as a function of the local gradient of the trap potential, the line curvature and the angular velocity of the trap rotation. This velocity yields small-amplitude normal modes of the vortex for 2D and 3D condensates. For an axisymmetric trap, the motion of the vortex line is a superposition of plane-polarized standing-wave modes. In a 2D condensate, the planar normal modes are degenerate, and their superposition can result in helical traveling waves, which differs from a 3D condensate. Including the effects of trap rotation allows us to find the angular velocity that makes the vortex locally stable. For a cigar-shape condensate, the vortex curvature makes a significant contribution to the frequency of the lowest unstable normal mode; furthermore, additional modes with negative frequencies appear. As a result, it is considerably more difficult to stabilize a central vortex in a cigar-shape condensate than in a disc-shape one. Normal modes with imaginary frequencies can occur for a nonaxisymmetric condensate (in both 2D and 3D). In connection with recent JILA experiments, we consider the motion of a straight vortex line in a slightly nonspherical condensate. The vortex line changes its orientation in space at the rate proportional to the degree of trap anisotropy and can exhibit periodic recurrences.Comment: 19 pages, 6 eps figures, REVTE

Stability of vortices in rotating taps: a 3d analysis

We study the stability of vortex-lines in trapped dilute gases subject to rotation. We solve numerically both the Gross-Pitaevskii and the Bogoliubov equations for a 3d condensate in spherically and cilyndrically symmetric stationary traps, from small to very large nonlinearities. In the stationary case it is found that the vortex states with unit and $m=2$ charge are energetically unstable. In the rotating trap it is found that this energetic instability may only be suppressed for the $m=1$ vortex-line, and that the multicharged vortices are never a local minimum of the energy functional, which implies that the absolute minimum of the energy is not an eigenstate of the $L_z$ operator, when the angular speed is above a certain value, $\Omega > \Omega_2$.Comment: 10 pages, 7 figures in EPS forma

Assessment of correlation between knee notch width index and the three-dimensional notch volume

This study was done to determine whether there is a correlation between the notch volume and the notch width index (NWI) as measured on the three most frequently used radiographic views: the Holmblad 45°, Holmblad 70°, and Rosenberg view. The notch volume of 20 cadaveric knees was measured using Computed Tomography (CT). The Holmblad 45°, Holmblad 70°, and Rosenberg notch view radiographs were digitally re-created from the CT scans for each specimen, and the NWI was measured by two observers. The Pearson correlation coefficient between the NWI and notch volume was calculated, as well as between the three views. An independent t test was performed to determine the difference in NWI and notch volume between male and female specimens. The reliability for each view was also determined. There was no correlation between the NWI as measured on the Holmblad 45°, Holmblad 70°, or Rosenberg view and the notch volume. All three radiographic views proved reliable, but showed only a moderate correlation with each other. Men had larger notch volumes than women, but there was no difference in NWI. A knee with a small intercondylar notch is often considered an increased risk for ACL rupture. The NWI is a frequently used two-dimensional method to determine notch size. However, in the present study, this index was not positively correlated with the overall volume of the notch. Based on the results of the current study, the authors would advice to use caution when using notch view radiographs in a clinical setting to predict risk of ACL rupture

Intercultural ethics: questions of methods in language and intercultural communication

This paper explores how questions of ethics and questions of method are intertwined and unavoidable in any serious study of language and intercultural communication. It argues that the focus on difference and solution orientations to intercultural conflict has been a fundamental driver for theory, data collection and methods in the field. These approaches, the paper argues, have created a considerable consciousness raising industry, with methods, trainings and ‘critical incidents’, which ultimately focus intellectual energy in areas which may be productive in terms of courses and publications but which have a problematic basis in their ethical terrain. Dieser Artikel untersucht wie ethische und methodische Fragen nicht nur ineinander greifen, sondern in keiner ernstzunehmenden Studie ueber Sprache und interkulturelle Kommunikation ausgelassen werden duerfen. Es wird hier argumentiert, dass der Schwerpunkt auf Verschiedenheit und Problemorientierung im interkulturellen Konflikt einen wesentlichen Einfluss auf theoretische Entwicklungen, Datenerhebung und Methoden in diesem Bereich hatte. Dieser Artikel legt auch dar, wie diese Ansaetze eine betraechtliche ‘Bewusstseinsbildungs – Branche' erzeugt haben, mit Methoden, Trainings, und ‘kritischen Interaktionssituationen’, welche letztendlich allen intellektuellen Arbeitseifer auf Bereiche konzentriert hat, die zwar ertragreich sind in Bezug auf Kurse und Publikationen, jedoch eine problematische Grundlage im ethischen Bereich aufweisen

Association between surgeon special interest and mortality after emergency laparotomy

© 2019 BJS Society Ltd Published by John Wiley & Sons Ltd Background: Approximately 30 000 emergency laparotomies are performed each year in England and Wales. Patients with pathology of the gastrointestinal tract requiring emergency laparotomy are managed by general surgeons with an elective special interest focused on either the upper or lower gastrointestinal tract. This study investigated the impact of special interest on mortality after emergency laparotomy. Methods: Adult patients having emergency laparotomy with either colorectal or gastroduodenal pathology were identified from the National Emergency Laparotomy Audit database and grouped according to operative procedure. Outcomes included all-cause 30-day mortality, length of hospital stay and return to theatre. Logistic and Poisson regression were used to analyse the association between consultant special interest and the three outcomes. Results: A total of 33 819 patients (28 546 colorectal, 5273 upper gastrointestinal (UGI)) were included. Patients who had colorectal procedures performed by a consultant without a special interest in colorectal surgery had an increased adjusted 30-day mortality risk (odds ratio (OR) 1·23, 95 per cent c.i. 1·13 to 1·33). Return to theatre also increased in this group (OR 1·13, 1·05 to 1·20). UGI procedures performed by non-UGI special interest surgeons carried an increased adjusted risk of 30-day mortality (OR 1·24, 1·02 to 1·53). The risk of return to theatre was not increased (OR 0·89, 0·70 to 1·12). Conclusion: Emergency laparotomy performed by a surgeon whose special interest is not in the area of the pathology carries an increased risk of death at 30 days. This finding potentially has significant implications for emergency service configuration, training and workforce provision, and should stimulate discussion among all stakeholders

Quantum Particles as Conceptual Entities: A Possible Explanatory Framework for Quantum Theory

We put forward a possible new interpretation and explanatory framework for quantum theory. The basic hypothesis underlying this new framework is that quantum particles are conceptual entities. More concretely, we propose that quantum particles interact with ordinary matter, nuclei, atoms, molecules, macroscopic material entities, measuring apparatuses, ..., in a similar way to how human concepts interact with memory structures, human minds or artificial memories. We analyze the most characteristic aspects of quantum theory, i.e. entanglement and non-locality, interference and superposition, identity and individuality in the light of this new interpretation, and we put forward a specific explanation and understanding of these aspects. The basic hypothesis of our framework gives rise in a natural way to a Heisenberg uncertainty principle which introduces an understanding of the general situation of 'the one and the many' in quantum physics. A specific view on macro and micro different from the common one follows from the basic hypothesis and leads to an analysis of Schrodinger's Cat paradox and the measurement problem different from the existing ones. We reflect about the influence of this new quantum interpretation and explanatory framework on the global nature and evolutionary aspects of the world and human worldviews, and point out potential explanations for specific situations, such as the generation problem in particle physics, the confinement of quarks and the existence of dark matter.Comment: 45 pages, 10 figure

Single-agent gemcitabine in pretreated patients with non-small-cell lung cancer: results of an Argentinean multicentre phase II trial

The activity and mild toxicity profile of single-agent gemcitabine therapy in untreated (chemonaive) patients with non-small-cell lung cancer (NSCLC) is well documented. This phase II trial was conducted to determine the objective tumour response rate and toxicity profile of single-agent gemcitabine in pretreated patients with NSCLC. Patients with histological evidence of advanced NCSLC stage IIIB or IV; at least one prior chemotherapy regimen including a platinum or taxane analogue; an Eastern Cooperative Oncology Group (ECOG) performance status of 0–2; clinically measurable disease; adequate bone marrow reserve; and adequate renal function; received 1000 mg m–2 gemcitabine administered over 30 min on days 1, 8 and 15 of a 28-day cycle defined as 3 weekly treatments followed by 1 week of rest. Twenty-nine patients were evaluated for efficacy and 32 for toxicity. One patient achieved a complete response and five patients had a partial response resulting in a total response rate of 20.6% (95% confidence interval (CI) 6–34). Median response duration was 7 months (range 4–11 months). Twelve (41%) patients reached stable disease after two cycles of therapy and 11 (38%) patients had disease progression. Median progression-free survival time was 3 months and median overall survival time was 5.5 months. Toxicity was generally mild (grades 0–2). Severe (grade 3 or 4) haematological toxicities included grade 3 anaemia in one patient and grade 3 thrombocytopenia in two patients. Severe non-haematological toxicities included one patient each with grade 3 liver transaminase elevations, nausea/vomiting and diarrhoea. This study confirms the activity and safety of single-agent gemcitabine in pretreated patients with advanced NSCLC who are refractory or sensitive to first-line therapy. © 1999 Cancer Research Campaig