Molecular Epidemiology of Anthrax Cases Associated with Recreational Use of Animal Hides and Yarn in the United States

To determine potential links between the clinical isolate to animal products and their geographic origin, we genotyped (MLVA-8, MVLA-15, and canSNP analysis) 80 environmental and 12 clinical isolates and 2 clinical specimens from five cases of anthrax (California in 1976 [n = 1], New York in 2006 [n = 1], Connecticut in 2007 [n = 2], and New Hampshire in 2009[n = 1]) resulting from recreational handling of animal products. For the California case, four clinical isolates were identified as MLVA-8 genotype (GT) 76 and in the canSNP A.Br.Vollum lineage, which is consistent with the Pakistani origin of the yarn. Twenty eight of the California isolates were in the A.Br.Vollum canSNP lineage and one isolate was in the A.Br. 003/004 canSNP sub-group. All 52 isolates and both clinical specimens related to the New York and Connecticut cases were MLVA-8 GT 1. The animal products associated with the NY and CT cases were believed to originate from West Africa, but no isolates from this region are available to be genotyped for comparison. All isolates associated with the New Hampshire case were identical and had a new genotype (GT 149). Isolates from the NY, CT and NH cases diverge from the established canSNP phylogeny near the base of the A.Br.011/009. This report illustrates the power of the current genotyping methods and the dramatically different epidemiological conditions that can lead to infections (i.e., contamination by a single genotype versus widespread contamination of numerous genotypes). These cases illustrate the need to acquire and genotype global isolates so that accurate assignments can be made about isolate origins

Particle-in-cell simulations of rf breakdown

Breakdown voltages of a capacitively coupled radio frequency argon discharge at 27 MHz are studied. We use a one-dimensional electrostatic PIC code to investigate the effect of changing the secondary emission properties of the electrodes on the breakdown voltage, particularly at low pd values. Simulation results are compared with the available experimental results and a satisfactory agreement is found.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Disease variants in genomes of 44 centenarians

To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30x coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as pathogenic or likely pathogenic based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE epsilon4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer\u27s disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions

Expression of Foxp3 in colorectal cancer but not in Treg cells correlates with disease progression in patients with colorectal cancer

Background: Regulatory T cells (Treg) expressing the transcription factor forkhead-box protein P3 (Foxp3) have been identified to counteract anti-tumor immune responses during tumor progression. Besides, Foxp3 presentation by cancer cells itself may also allow them to evade from effector T-cell responses, resulting in a survival benefit of the tumor. For colorectal cancer (CRC) the clinical relevance of Foxp3 has not been evaluated in detail. Therefore the aim of this study was to study its impact in colorectal cancer (CRC). Methods and Findings: Gene and protein analysis of tumor tissues from patients with CRC was performed to quantify the expression of Foxp3 in tumor infiltrating Treg and colon cancer cells. The results were correlated with clinicopathological parameters and patients overall survival. Serial morphological analysis demonstrated Foxp3 to be expressed in cancer cells. High Foxp3 expression of the cancer cells was associated with poor prognosis compared to patients with low Foxp3 expression. In contrast, low and high Foxp3 level in tumor infiltrating Treg cells demonstrated no significant differences in overall patient survival. Conclusions: Our findings strongly suggest that Foxp3 expression mediated by cancer cells rather than by Treg cells contribute to disease progression

Photon Radiation with MadDipole

We present the automation of a subtraction method for photon radiation using the dipole formalism within the MadGraph framework. The subtraction terms are implemented both in dimensional regularization and mass regularization for massless and massive cases and non-collinear-safe observables are accounted for.Comment: 23 pages, 2 figures, minor additions, references added, version published in JHE

NLL soft and Coulomb resummation for squark and gluino production at the LHC

We present predictions of the total cross sections for pair production of squarks and gluinos at the LHC, including the stop-antistop production process. Our calculation supplements full fixed-order NLO predictions with resummation of threshold logarithms and Coulomb singularities at next-to-leading logarithmic (NLL) accuracy, including bound-state effects. The numerical effect of higher-order Coulomb terms can be as big or larger than that of soft-gluon corrections. For a selection of benchmark points accessible with data from the 2010-2012 LHC runs, resummation leads to an enhancement of the total inclusive squark and gluino production cross section in the 15-30 % range. For individual production processes of gluinos, the corrections can be much larger. The theoretical uncertainty in the prediction of the hard-scattering cross sections is typically reduced to the 10 % level.Comment: 45 pages, 16 Figures, LaTex. v2: published version. Grids with numerical results for the NLL cross sections for squark and gluino production at the 7/8 TeV LHC are included in the submission and are also available at http://omnibus.uni-freiburg.de/~cs1010/susy.htm

Hadronic production of squark-squark pairs: The electroweak contributions

We compute the electroweak (EW) contributions to squark--squark pair production processes at the LHC within the framework of the Minimal Supersymmetric Standard Model (MSSM). Both tree-level EW contributions, of O(alpha_s alpha + alpha^2), and next-to-leading order (NLO) EW corrections, of O(alpha_s^2 alpha), are calculated. Depending on the flavor and chirality of the produced quarks, many interferences between EW-mediated and QCD-mediated diagrams give non-zero contributions at tree-level and NLO. We discuss the computational techniques and present an extensive numerical analysis for inclusive squark--squark production as well as for subsets and single processes. While the tree-level EW contributions to the integrated cross sections can reach the 20% level, the NLO EW corrections typically lower the LO prediction by a few percent.Comment: 36 pages, 18 figure

Soil moisture and matric potential-an open field comparison of sensor systems

Soil water content and matric potential are central hydrological state variables. A large variety of automated probes and sensor systems for state monitoring exist and are frequently applied. Most applications solely rely on the calibration by the manufacturers. Until now, there has been no commonly agreed-upon calibration procedure. Moreover, several opinions about the capabilities and reliabilities of specific sensing methods or sensor systems exist and compete. A consortium of several institutions conducted a comparison study of currently available sensor systems for soil water content and matric potential under field conditions. All probes were installed at 0.2mb.s. (metres below surface), following best-practice procedures. We present the set-up and the recorded data of 58 probes of 15 different systems measuring soil moisture and 50 further probes of 14 different systems for matric potential. We briefly discuss the limited coherence of the measurements in a cross-correlation analysis. The measuring campaign was conducted during the growing period of 2016. The monitoring data, results from pedophysical analyses of the soil and laboratory reference measurements for calibration are published in Jackisch et al. (2018, https://doi.org/10.1594/PANGAEA.892319)

A Novel Hepatitis C Virus Genotyping Method Based on Liquid Microarray

The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5′UTR — the most highly conserved region of HCV — and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany) were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%). The concordance between the two methods was 100% for genotype determination (74/74). At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively). Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype “1” subtypes (1a and 1b) were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping