Finite-temperature time-dependent variation with multiple Davydov states

The Dirac-Frenkel time-dependent variational approach with Davydov Ans\"atze is a sophisticated, yet efficient technique to obtain an acuurate solution to many-body Schr\"odinger equations for energy and charge transfer dy- namics in molecular aggregates and light-harvesting complexes. We extend this variational approach to finite temperatures dynamics of the spin-boson model by adopting a Monte Carlo importance sampling method. In or- der to demonstrate the applicability of this approach, we compare real-time quantum dynamics of the spin-boson model calculated with that from numerically exact iterative quasiadiabatic propagator path integral (QUAPI) technique. The comparison shows that our variational approach with the single Davydov Ans\"atze is in excellent agreement with the QUAPI method at high temperatures, while the two differ at low temperatures. Accuracy in dynamics calculations employing a multitude of Davydov trial states is found to improve substantially over the single Davydov Ansatz, especially at low temperatures. At a moderate computational cost, our variational approach with the multiple Davydov Ansatz is shown to provide accurate spin-boson dynamics over a wide range of temperatures and bath spectral densities.Comment: 8 pages, 3 figure

ALIX binds a YPX(3)L motif of the GPCR PAR1 and mediates ubiquitin-independent ESCRT-III/MVB sorting.

The sorting of signaling receptors to lysosomes is an essential regulatory process in mammalian cells. During degradation, receptors are modified with ubiquitin and sorted by endosomal sorting complex required for transport (ESCRT)-0, -I, -II, and -III complexes into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs). However, it remains unclear whether a single universal mechanism mediates MVB sorting of all receptors. We previously showed that protease-activated receptor 1 (PAR1), a G protein-coupled receptor (GPCR) for thrombin, is internalized after activation and sorted to lysosomes independent of ubiquitination and the ubiquitin-binding ESCRT components hepatocyte growth factor-regulated tyrosine kinase substrate and Tsg101. In this paper, we report that PAR1 sorted to ILVs of MVBs through an ESCRT-III-dependent pathway independent of ubiquitination. We further demonstrate that ALIX, a charged MVB protein 4-ESCRT-III interacting protein, bound to a YPX(3)L motif of PAR1 via its central V domain to mediate lysosomal degradation. This study reveals a novel MVB/lysosomal sorting pathway for signaling receptors that bypasses the requirement for ubiquitination and ubiquitin-binding ESCRTs and may be applicable to a subset of GPCRs containing YPX(n)L motifs

Can the Federal Baldrige Survey Measure Workforce Well-being in an Academic Health Center?

Introduction. Experts suggest health care institutions switch focusfrom measuring burnout to measuring positive organizational psychology.Concerns include burnout being a late sign of organizationaldecline. The Baldrige survey is promoted by the U.S. Departmentof Commerce to measure positive worksite conditions (e.g., workforcewellbeing of industries, including health care and education).For years, the survey has been completed by managers within organizations,but now the same survey is promoted for completion byan organization’s workforce. We tested the structure of the Baldrigesurvey when completed by an academic health care workforce. Inaddition, we tested whether the results in an academic worksite correlatewith an example metric of an organizational mission.Methods.xIn 2015, our academic health center surveyed facultyand staff with the Baldrige survey. The validity of the Baldrige wastested with confirmatory factor analyses. Within the School of Medicine,responses for the Baldrige’s concepts were correlated againsta measure of organizational outcome: graduates’ assessments ofDepartmental educational quality.Results. The structure of the Baldrige survey did not validate whenassessed by a workforce (RMSEA = 0.086; CFI = 0.829; TLI = 0.815).None of its concepts correlated with learner reported educationalquality.Conclusions. The Baldrige survey, when administered to a workforcerather than managers, did not appear to measure workforcewell-being within an academic health care center. We discourage useof the current survey for this purpose. Kans J Med 2019;12(1):4-6

Theoretical predictions for vehicular headways and their clusters

This article presents a derivation of analytical predictions for steady-state distributions of netto time gaps among clusters of vehicles moving inside a traffic stream. Using the thermodynamic socio-physical traffic model with short-ranged repulsion between particles (originally introduced in [Physica A \textbf{333} (2004) 370]) we firstly derive the time-clearance distribution in the model. Consecutively, the statistical distributions for the so-called time multi-clearances are calculated by means of theory of functional convolutions. Moreover, all the theoretical surmises used during the above-mentioned calculations are proven by the statistical analysis of traffic data. The mathematical predictions acquired in this paper are thoroughly compared with relevant empirical quantities and discussed in the context of three-phase traffic theory.Comment: 23 pages, 10 figure

Superficial papular neuroma: Case series of a new entity

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138273/1/cup12981.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138273/2/cup12981_am.pd

Small world yields the most effective information spreading

Spreading dynamics of information and diseases are usually analyzed by using a unified framework and analogous models. In this paper, we propose a model to emphasize the essential difference between information spreading and epidemic spreading, where the memory effects, the social reinforcement and the non-redundancy of contacts are taken into account. Under certain conditions, the information spreads faster and broader in regular networks than in random networks, which to some extent supports the recent experimental observation of spreading in online society [D. Centola, Science {\bf 329}, 1194 (2010)]. At the same time, simulation result indicates that the random networks tend to be favorable for effective spreading when the network size increases. This challenges the validity of the above-mentioned experiment for large-scale systems. More significantly, we show that the spreading effectiveness can be sharply enhanced by introducing a little randomness into the regular structure, namely the small-world networks yield the most effective information spreading. Our work provides insights to the understanding of the role of local clustering in information spreading.Comment: 6 pages, 7 figures, accepted by New J. Phy

Proteins associated with pancreatic cancer survival in patients with resectable pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease with a dismal prognosis. However, while most patients die within the first year of diagnosis, very rarely, a few patients can survive for >10 years. Better understanding the molecular characteristics of the pancreatic adenocarcinomas from these very-long-term survivors (VLTS) may provide clues for personalized medicine and improve current pancreatic cancer treatment. To extend our previous investigation, we examined the proteomes of individual pancreas tumor tissues from a group of VLTS patients (survival ≥10 years) and short-term survival patients (STS, survival <14 months). With a given analytical sensitivity, the protein profile of each pancreatic tumor tissue was compared to reveal the proteome alterations that may be associated with pancreatic cancer survival. Pathway analysis of the differential proteins identified suggested that MYC, IGF1R and p53 were the top three upstream regulators for the STS-associated proteins, and VEGFA, APOE and TGFβ-1 were the top three upstream regulators for the VLTS-associated proteins. Immunohistochemistry analysis using an independent cohort of 145 PDAC confirmed that the higher abundance of ribosomal protein S8 (RPS8) and prolargin (PRELP) were correlated with STS and VLTS, respectively. Multivariate Cox analysis indicated that 'High-RPS8 and Low-PRELP' was significantly associated with shorter survival time (HR=2.69, 95% CI 1.46-4.92, P=0.001). In addition, galectin-1, a previously identified protein with its abundance aversely associated with pancreatic cancer survival, was further evaluated for its significance in cancer-associated fibroblasts. Knockdown of galectin-1 in pancreatic cancer-associated fibroblasts dramatically reduced cell migration and invasion. The results from our study suggested that PRELP, LGALS1 and RPS8 might be significant prognostic factors, and RPS8 and LGALS1 could be potential therapeutic targets to improve pancreatic cancer survival if further validated

Haplotype Network Branch Diversity, a New Metric Combining Genetic and Topological Diversity to Compare the Complexity of Haplotype Networks

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values’ implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics

The avian β-adrenergic receptor: primary structure and membrane topology

Partial amino acid sequence information allowed the isolation of cDNA clones encoding the turkey erythrocyte β-adrenergic receptor. Antisera raised against synthetic peptides encoded by the cDNA crossreacted with the purified receptor and appropriate tryptic fragments, confirming the identity of the cDNA. The receptor is composed of 483 amino acids and has a molecular mass of 54 kDa. Its sequence suggests that it is arranged predominantly in seven membrane-spanning sequences and a long cytoplasmic carboxyl-terminal domain. The extracellular amino-terminal domain contains a consensus sequence for N-glycosylation. The β-adrenergic receptor displays overall structural similarity and weak sequence homology with rhodopsin. Because both proteins act by regulating GTP-binding proteins, a compact structure based on seven membrane-spanning regions may be a general model for receptors that act on G proteins