Computation of local exchange coefficients in strongly interacting one-dimensional few-body systems: local density approximation and exact results

One-dimensional multi-component Fermi or Bose systems with strong zero-range interactions can be described in terms of local exchange coefficients and mapping the problem into a spin model is thus possible. For arbitrary external confining potentials the local exchanges are given by highly non-trivial geometric factors that depend solely on the geometry of the confinement through the single-particle eigenstates of the external potential. To obtain accurate effective Hamiltonians to describe such systems one needs to be able to compute these geometric factors with high precision which is difficult due to the computational complexity of the high-dimensional integrals involved. An approach using the local density approximation would therefore be a most welcome approximation due to its simplicity. Here we assess the accuracy of the local density approximation by going beyond the simple harmonic oscillator that has been the focus of previous studies and consider some double-wells of current experimental interest. We find that the local density approximation works quite well as long as the potentials resemble harmonic wells but break down for larger barriers. In order to explore the consequences of applying the local density approximation in a concrete setup we consider quantum state transfer in the effective spin models that one obtains. Here we find that even minute deviations in the local exchange coefficients between the exact and the local density approximation can induce large deviations in the fidelity of state transfer for four, five, and six particles.Comment: 12 pages, 7 figures, 1 table, final versio

Variability-aware Datalog

Variability-aware computing is the efficient application of programs to different sets of inputs that exhibit some variability. One example is program analyses applied to Software Product Lines (SPLs). In this paper we present the design and development of a variability-aware version of the Souffl\'{e} Datalog engine. The engine can take facts annotated with Presence Conditions (PCs) as input, and compute the PCs of its inferred facts, eliminating facts that do not exist in any valid configuration. We evaluate our variability-aware Souffl\'{e} implementation on several fact sets annotated with PCs to measure the associated overhead in terms of processing time and database size.Comment: PADL'20 pape

An Experimental Evaluation of Deliberate Unsoundness in a Static Program Analyzer

Abstract. Many practical static analyzers are not completely sound by design. Their designers trade soundness in order to increase automa-tion, improve performance, and reduce the number of false positives or the annotation overhead. However, the impact of such design decisions on the effectiveness of an analyzer is not well understood. In this pa-per, we report on the first systematic effort to document and evaluate the sources of unsoundness in a static analyzer. We present a code in-strumentation that reflects the sources of deliberate unsoundness in the.NET static analyzer Clousot. We have instrumented code from several open source projects to evaluate how often concrete executions violate Clousot’s unsound assumptions. In our experiments, this was the case in 8–29 % of all analyzed methods. Our approach and findings can guide users of static analyzers in using them fruitfully, and designers in finding good trade-offs.

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide–oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design

Imaging Modalities for the Glenoid Track in Recurrent Shoulder Instability: A Systematic Review

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Background: The glenoid track (GT) concept illustrates how the degree of glenoid bone loss and humeral bone loss in the glenohumeral joint can guide further treatment in a patient with anterior instability. The importance of determining which lesions are at risk for recurrent instability involves imaging of the glenohumeral joint, but no studies have determined which type of imaging is the most appropriate. Purpose/Hypothesis: The purpose of this study was to determine the validity and accuracy of different imaging modalities for measuring the GT in shoulders with recurrent anterior instability. We hypothesized that 3-dimensional computed tomography (3D-CT) would be the most accurate imaging technique. Study Design: Systematic review; Level of evidence, 4. Methods: A systematic review was performed according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines using PubMed, Scopus, Medline, and Cochrane libraries between database inception and July 2019. We included all clinical trials or cadaveric studies that evaluated imaging modalities for assessing the GT. Results: A total of 13 studies were included in this review: 1 study using 2-dimensional CT, 6 studies using 3D-CT, 4 studies using magnetic resonance imaging (MRI), 1 study using magnetic resonance arthrography (MRA)/MRI, and 1 study combining CT and MRI. The mean sensitivity, specificity, and accuracy for 2D-CT was 92%, 100%, and 96%, respectively. For MRI, the means were 72.2%, 87.9%, and 84.2%, respectively. No papers included 3D-CT metrics. The mean intraclass correlation coefficients (ICCs) for intraobserver reliability were 0.9046 for 3D-CT and 0.867 for MRI. ICCs for interobserver reliability were 0.8164, 0.8845, and 0.43 for 3D-CT, MRI, and MRA/MRI, respectively. Conclusion: There is evidence to support the use of both CT and MRI imaging modalities in assessing the GT. In addition, few studies have compared radiographic measurements with a gold standard, and even fewer have looked at the GT concept as a predictor of outcomes. Thus, future studies are needed to further evaluate which imaging modality is the most accurate to assess the GT

Crystal structure of the TLDc domain of oxidation resistance protein 2 from zebrafish

The oxidation resistance proteins (OXR) help to protect eukaryotes from reactive oxygen species. The sole C-terminal domain of the OXR, named TLDc is sufficient to perform this function. However, the mechanism by which oxidation resistance occurs is poorly understood. We present here the crystal structure of the TLDc domain of the oxidation resistance protein 2 from zebrafish. The structure was determined by X-ray crystallography to atomic resolution (0.97Å) and adopts an overall globular shape. Two antiparallel β-sheets form a central β-sandwich, surrounded by two helices and two one-turn helices. The fold shares low structural similarity to known structures.Animal science

Developing a digital intervention for cancer survivors: an evidence-, theory- and person-based approach

This paper illustrates a rigorous approach to developing digital interventions using an evidence-, theory- and person-based approach. Intervention planning included a rapid scoping review which identified cancer survivors’ needs, including barriers and facilitators to intervention success. Review evidence (N=49 papers) informed the intervention’s Guiding Principles, theory-based behavioural analysis and logic model. The intervention was optimised based on feedback on a prototype intervention through interviews (N=96) with cancer survivors and focus groups with NHS staff and cancer charity workers (N=31). Interviews with cancer survivors highlighted barriers to engagement, such as concerns about physical activity worsening fatigue. Focus groups highlighted concerns about support appointment length and how to support distressed participants. Feedback informed intervention modifications, to maximise acceptability, feasibility and likelihood of behaviour change. Our systematic method for understanding user views enabled us to anticipate and address important barriers to engagement. This methodology may be useful to others developing digital interventions