FormCalc 8: Better Algebra and Vectorization

We present Version 8 of the Feynman-diagram calculator FormCalc. New features include in particular significantly improved algebraic simplification as well as vectorization of the generated code. The Cuba Library, used in FormCalc, features checkpointing to disk for all integration algorithms.Comment: 7 pages, LaTeX, proceedings contribution to ACAT 2013, Beijing, China, 16-21 May 201

Efficient calculation of local dose distribution for response modelling in proton and ion beams

We present an algorithm for fast and accurate computation of the local dose distribution in MeV beams of protons, carbon ions or other heavy-charged particles. It uses compound Poisson-process modelling of track interaction and succesive convolutions for fast computation. It can handle mixed particle fields over a wide range of fluences. Since the local dose distribution is the essential part of several approaches to model detector efficiency or cellular response it has potential use in ion-beam dosimetry and radiotherapy.Comment: 9 pages, 3 figure

The Ah receptor: adaptive metabolism, ligand diversity, and the xenokine model

Author Posting. © American Chemical Society, 2020. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Chemical Research in Toxicology, 33(4), (2020): 860-879, doi:10.1021/acs.chemrestox.9b00476.The Ah receptor (AHR) has been studied for almost five decades. Yet, we still have many important questions about its role in normal physiology and development. Moreover, we still do not fully understand how this protein mediates the adverse effects of a variety of environmental pollutants, such as the polycyclic aromatic hydrocarbons (PAHs), the chlorinated dibenzo-p-dioxins (“dioxins”), and many polyhalogenated biphenyls. To provide a platform for future research, we provide the historical underpinnings of our current state of knowledge about AHR signal transduction, identify a few areas of needed research, and then develop concepts such as adaptive metabolism, ligand structural diversity, and the importance of proligands in receptor activation. We finish with a discussion of the cognate physiological role of the AHR, our perspective on why this receptor is so highly conserved, and how we might think about its cognate ligands in the future.This review is dedicated in memory of the career of Alan Poland, one of the truly great minds in pharmacology and toxicology. This work was supported by the National Institutes of Health Grants R35-ES028377, T32-ES007015, P30-CA014520, P42-ES007381, and U01-ES1026127, The UW SciMed GRS Program, and The Morgridge Foundation. The authors would like to thank Catherine Stanley of UW Media Solutions for her artwork

Methylation Status of Imprinted Genes and Repetitive Elements in Sperm DNA from Infertile Males

Stochastic, environmentally and/or genetically induced disturbances in the genome-wide epigenetic reprogramming processes during male germ-cell development may contribute to male infertility. To test this hypothesis, we have studied the methylation levels of 2 paternally (H19 and GTL2) and 5 maternally methylated (LIT1, MEST, NESPAS, PEG3, and SNRPN) imprinted genes, as well as of ALU and LINE1 repetitive elements in 141 sperm samples, which were used for assisted reproductive technologies (ART), including 106 couples with strictly male-factor or combined male and female infertility and 28 couples with strictly female-factor infertility. Aberrant methylation imprints showed a significant association with abnormal semen parameters, but did not seem to influence ART outcome. Repeat methylation also differed significantly between sperm samples from infertile and presumably fertile males. However, in contrast to imprinted genes, ALU methylation had a significant impact on pregnancy and live-birth rate in couples with male-factor or combined infertility. ALU methylation was significantly high-er in sperm samples leading to pregnancy and live-birth than in those that did not. Sperm samples leading to abortions showed significantly lower ALU methylation levels than those leading to the birth of a baby. Copyright (C) 2011 S. Karger AG, Base

Bone mineral content after renal transplantation

Forearm bone mineral content (BMC), as evaluated by photonabsorption densitometry, was measured in 28 cadaver kidney donor recipients who entered the study 8 weeks postoperatively and were followed up for 18 months. BMC decreased signifiantly (p<0.05) but marginally in placebo-treated patients (n=14) (initial BMC 1.09±0.25 g/cm; final BMC 1.05±0.24). Fourteen patients were prophylactically given 1,25(OH)2vitamin D3 in a dose which avoided hypercalcemia and hypercalciuria (sim0.25 µg/day); under 1,25(OH)2 vitamin D3 prophylaxis a significant decrease of forearm BMC was observed no longer (initial BMC 0.94±0.21 g/cm; final BMC 0.95±0.21), but the difference between placebo and 1,25(OH)2 vitamin D3 narrowly missed statistical significance (p=0.066). It is concluded that the decrease of forearm BMC is negligible in transplant recipients with low steroid regimens. The data suggest a trend for prophylaxis with 1,25(OH)2 vitamin D3 to slightly ameliorate forearm (cortical) BMC loss

Correlation of the Havemeyer endoscopic laryngeal grading system with histopathological changes in equine Cricoarytenoideus dorsalis muscles

The establishment of a single validated endoscopic laryngeal grading system for assessing recurrent laryngeal neuropathy (RLN) is desirable to facilitate direct comparisons between the findings of different clinical and research groups worldwide. The objective of this study was to assess the relationship between the Havemeyer endoscopic laryngeal grading system and histopathological changes consistent with RLN in the left cricoarytenoideus dorsalis (CAD) muscle of horses of different breeds with a full range of clinical severities of RLN, i.e., from normal endoscopic laryngeal function to complete laryngeal hemiplegia. Endoscopic grading of laryngeal function of 22 horses was performed using the Havemeyer endoscopic laryngeal grading system. A biopsy sample of the left CAD muscle was obtained from each horse, either at post mortem examination (n = 16), or during routine laryngoplasty surgery (n = 6). A semi-quantitative histopathological scoring system was used to grade the severity of histopathological lesions consistent with RLN in the left CAD muscle of each horse. A significant positive correlation (rs = 0.705, p < 0.001) was found between the Havemeyer grades and sub-grades of laryngeal function and the semi-quantitative assessment of histopathological lesions consistent with RLN in the left CAD muscle. However, a wide spread of muscle histopathological scores was obtained, particularly from horses with Havemeyer sub-grades II.1, III.1 and III.2. In conclusion, the Havemeyer endoscopic laryngeal grading system was found to broadly correlate with histopathological changes consistent with RLN in equine cricoarytenoideus dorsalis muscle

Inverse problems with inexact forward operator : iterative regularization and application in dynamic imaging

The classic regularization theory for solving inverse problems is built on the assumption that the forward operator perfectly represents the underlying physical model of the data acquisition. However, in many applications, for instance in microscopy or magnetic particle imaging, this is not the case. Another important example represent dynamic inverse problems, where changes of the searchedfor quantity during data collection can be interpreted as model uncertainties. In this article, we propose a regularization strategy for linear inverse problems with inexact forward operator based on sequential subspace optimization methods (SESOP). In order to account for local modelling errors, we suggest to combine SESOP with the Kaczmarz’ method. We study convergence and regularization properties of the proposed method and discuss several practical realizations. Relevance and performance of our approach are evaluated at simulated data from dynamic computerized tomography with various dynamic scenarios

Unusual temperature dependence of band dispersion in Ba(Fe(1-x)Ru(x))2As2 and its consequences for antiferromagnetic ordering

We have performed detailed studies of the temperature evolution of the electronic structure in Ba(Fe(1-x)Ru(x))2As2 using Angle Resolved Photoemission Spectroscopy (ARPES). Surprisingly, we find that the binding energy of both hole and electron bands changes significantly with temperature in pure and Ru substituted samples. The hole and electron pockets are well nested at low temperature in unsubstituted (BaFe2As2) samples, which likely drives the spin density wave (SDW) and resulting antiferromagnetic order. Upon warming, this nesting is degraded as the hole pocket shrinks and the electron pocket expands. Our results demonstrate that the temperature dependent nesting may play an important role in driving the antiferromagnetic/paramagnetic phase transition.Comment: 5 pages, 6 figure

Path integral formulation of Hodge duality on the brane

In the warped compactification with a single Randall-Sundrum brane, a puzzling claim has been made that scalar fields can be bound to the brane but their Hodge dual higher-rank anti-symmetric tensors cannot. By explicitly requiring the Hodge duality, a prescription to resolve this puzzle was recently proposed by Duff and Liu. In this note, we implement the Hodge duality via path integral formulation in the presence of the background gravity fields of warped compactifications. It is shown that the prescription of Duff and Liu can be naturally understood within this framework.Comment: 7 pages, LaTe