Quark Condensate in the Deuteron

We study the changes produced by the deuteron on the QCD quark condensate by means the Feynman-Hellmann theorem and find that the pion mass dependence of the pion-nucleon coupling could play an important role. We also discuss the relation between the many body effect of the condensate and the meson exchange currents, as seen by photons and pions. For pion probes, the many-body term in the physical amplitude differs significantly from that of soft pions, the one linked to the condensate. Thus no information about the many-body term of the condensate can be extracted from the pion-deuteron scattering length. On the other hand, in the Compton amplitude, the relationship with the condensate is a more direct one.Comment: to appear in Physics Review C (19 pages, 3 figures

Spontaneous Magnetization of the O(3) Ferromagnet at Low Temperatures

We investigate the low-temperature behavior of ferromagnets with a spontaneously broken symmetry O(3) $\to$ O(2). The analysis is performed within the perspective of nonrelativistic effective Lagrangians, where the dynamics of the system is formulated in terms of Goldstone bosons. Unlike in a Lorentz-invariant framework (chiral perturbation theory), where loop graphs are suppressed by two powers of momentum, loops involving ferromagnetic spin waves are suppressed by three momentum powers. The leading coefficients of the low-temperature expansion for the partition function are calculated up to order $p^{10}$. In agreement with Dyson's pioneering microscopic analysis of the cubic ferromagnet, we find that, in the spontaneous magnetization, the magnon-magnon interaction starts manifesting itself only at order $T^4$. The striking difference with respect to the low-temperature properties of the O(3) antiferromagnet is discussed from a unified point of view, relying on the effective Lagrangian technique.Comment: 23 pages, 4 figure

Meeting Report: Application of Genotyping Methods to Assess Risks from Cryptosporidium in Watersheds

A workshop titled "Application of Genotyping Methods to Assess Pathogen Risks from Cryptosporidium in Drinking Water Catchments" was held at the International Water Association biennial conference, Marrakech, Morocco, 23 September 2004. The workshop presented and discussed the findings of an interlaboratory trial that compared methods for genotyping Cryptosporidium oocysts isolated from feces. The primary goal of the trial and workshop was to assess the utility of current Cryptosporidium genotyping methods for determining the public health significance of oocysts isolated from feces in potable-water-supply watersheds. An expert panel of 16 watershed managers, public health practitioners, and molecular parasitologists was assembled for the workshop. A subordinate goal of the workshop was to educate watershed management and public health practitioners. An open invitation was extended to all conference delegates to attend the workshop, which drew approximately 50 interested delegates. In this report we summarize the peer consensus emerging from the workshop. Recommendations on the use of current methods by watershed managers and public health practitioners were proposed. Importantly, all the methods that were reported in the trial were mutually supporting and found to be valuable and worthy of further utility and development. Where there were choices as to which method to apply, the small-subunit ribosomal RNA gene was considered to be the optimum genetic locus to target. The single-strand conformational polymorphism method was considered potentially the most valuable for discriminating to the subtype level and where a large number of samples were to be analyzed. A research agenda for protozoan geneticists was proposed to improve the utility of methods into the future. Standardization of methods and nomenclature was promoted

Detection of cyclospora in captive chimpanzees and macaques by a quantitative PCR-based mutation scanning approach

BACKGROUND: Cyclospora is a protistan parasite that causes enteritis in several species of animals including humans. The aim of this study was to investigate the presence of Cyclospora in captive non-human primates. METHODS: A total of 119 faecal samples from Pan troglodytes, Macaca sylvanus, Cercopithecus cephus, Erythrocebus patas, Chlorocebus aethiops and Macaca fascicularis from a wildlife animal rescue center as well as from Macaca fascicularis from an experimental primate research center were tested for the presence of Cyclospora by quantitative real-time PCR (qPCR) and single-strand conformation polymorphism (SSCP) analysis. RESULTS: Cyclospora was detected in three Pan troglodytes (13.6%) and nine (9.3%) Macaca fascicularis. CONCLUSIONS: The present study represents the first record of Cyclospora in captive primates in Europe, suggesting the presence of Cyclospora cayetanensis, which is transmissible to humans

Towards a high precision calculation for the pion-nucleus scattering lengths

We calculate the leading isospin conserving few-nucleon contributions to pion scattering on $^2$H, $^3$He, and $^4$He. We demonstrate that the strong contributions to the pion-nucleus scattering lengths can be controlled theoretically to an accuracy of a few percent for isoscalar nuclei and of 10% for isovector nuclei. In particular, we find the $\pi$-$^3$He scattering length to be $(62 \pm 4\pm 7)\times 10^{-3} m_{\pi}^{-1}$ where the uncertainties are due to ambiguities in the $\pi$-N scattering lengths and few-nucleon effects, respectively. To establish this accuracy we need to identify a suitable power counting for pion-nucleus scattering. For this purpose we study the dependence of the two-nucleon contributions to the scattering length on the binding energy of $^2$H. Furthermore, we investigate the relative size of the leading two-, three-, and four-nucleon contributions. For the numerical evaluation of the pertinent integrals, aMonte Carlo method suitable for momentum space is devised. Our results show that in general the power counting suggested by Weinberg is capable to properly predict the relative importance of $N$-nucleon operators, however, it fails to capture the relative strength of $N$- and $(N+1)$-nucleon operators, where we find a suppression by a factor of 5 compared to the predicted factor of 50. The relevance for the extraction of the isoscalar $\pi$-N scattering length from pionic $^2$H and $^4$He is discussed. As a side result, we show that beyond the calculation of the $\pi$-$^2$H scattering length is already beyond the range of applicability of heavy pion effective field theory.Comment: 24 pages, 14 figures, 10 table

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines

OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info

Resonance saturation for four-nucleon operators

In the modern description of nuclear forces based on chiral effective field theory, four-nucleon operators with unknown coupling constants appear. These couplings can be fixed by a fit to the low partial waves of neutron-proton scattering. We show that the so determined numerical values can be understood on the basis of phenomenological one-boson-exchange models. We also extract these values from various modern high accuracy nucleon-nucleon potentials and demonstrate their consistency and remarkable agreement with the values in the chiral effective field theory approach. This paves the way for estimating the low-energy constants of operators with more nucleon fields and/or external probes.Comment: 16 pp, REVTeX, 3 figure

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets

The rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and accurate manner. Notwithstanding several computational tools that characterize protein or nucleic acids data, there are no one-stop computational toolkits that comprehensively characterize a wide range of biomolecules. We address this vital need by developing a holistic platform that generates features from sequence and structural data for a diverse collection of molecule types. Our freely available and easy-to-use iFeatureOmega platform generates, analyzes and visualizes 189 representations for biological sequences, structures and ligands. To the best of our knowledge, iFeatureOmega provides the largest scope when directly compared to the current solutions, in terms of the number of feature extraction and analysis approaches and coverage of different molecules. We release three versions of iFeatureOmega including a webserver, command line interface and graphical interface to satisfy needs of experienced bioinformaticians and less computer-savvy biologists and biochemists. With the assistance of iFeatureOmega, users can encode their molecular data into representations that facilitate construction of predictive models and analytical studies. We highlight benefits of iFeatureOmega based on three research applications, demonstrating how it can be used to accelerate and streamline research in bioinformatics, computational biology, and cheminformatics areas. The iFeatureOmega webserver is freely available at http://ifeatureomega.erc.monash.edu and the standalone versions can be downloaded from https://github.com/Superzchen/iFeatureOmega-GUI/ and https://github.com/Superzchen/iFeatureOmega-CLI/.Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz Kurgan, and Jiangning Son

Three-Nucleon Forces from Chiral Effective Field Theory

We perform the first complete analysis of nd scattering at next-to-next-to-leading order in chiral effective field theory including the corresponding three-nucleon force and extending our previous work, where only the two-nucleon interaction has been taken into account. The three-nucleon force appears first at this order in the chiral expansion and depends on two unknown parameters. These two parameters are determined from the triton binding energy and the nd doublet scattering length. We find an improved description of various scattering observables in relation to the next-to-leading order results especially at moderate energies (E_lab = 65 MeV). It is demonstrated that the long-standing A_y-problem in nd elastic scattering is still not solved by the leading 3NF, although some visible improvement is observed. We discuss possibilities of solving this puzzle. The predicted binding energy for the alpha-particle agrees with the empirical value.Comment: 36 pp, 20 figure

Astrophysical Axion Bounds

Axion emission by hot and dense plasmas is a new energy-loss channel for stars. Observational consequences include a modification of the solar sound-speed profile, an increase of the solar neutrino flux, a reduction of the helium-burning lifetime of globular-cluster stars, accelerated white-dwarf cooling, and a reduction of the supernova SN 1987A neutrino burst duration. We review and update these arguments and summarize the resulting axion constraints.Comment: Contribution to Axion volume of Lecture Notes in Physics, 20 pages, 3 figure