Magnetic properties of the Ag-In-rare-earth 1/1 approximants

We have performed magnetic susceptibility and neutron scattering measurements on polycrystalline Ag-In-RE (RE: rare-earth) 1/1 approximants. In the magnetic susceptibility measurements, for most of the RE elements, inverse susceptibility shows linear behaviour in a wide temperature range, confirming well localized isotropic moments for the RE$^{3+}$ ions. Exceptionally for the light RE elements, such as Ce and Pr, non-linear behaviour was observed, possibly due to significant crystalline field splitting or valence fluctuation. For RE = Tb, the susceptibility measurement clearly shows a bifurcation of the field-cooled and zero-field-cooled susceptibility at $T_{\rm f} = 3.7$~K, suggesting a spin-glass-like freezing. On the other hand, neutron scattering measurements detect significant development of short-range antiferromagnetic spin correlations in elastic channel, which accompanied by a broad peak at $\hbar\omega = 4$~meV in inelastic scattering spectrum. These features have striking similarity to those in the Zn-Mg-Tb quasicrystals, suggesting that the short-range spin freezing behaviour is due to local high symmetry clusters commonly seen in both the systems.Comment: 14 pages, 12 figure

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

<p>Abstract</p> <p>Background</p> <p>Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.</p> <p>Results</p> <p>Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from <it>Bacillus subtilis </it>and <it>Arabidopsis thaliana </it>grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.</p> <p>Conclusion</p> <p>This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.</p

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method

Complete restoration of multiple dystrophin isoforms in genetically corrected Duchenne muscular dystrophy patient–derived cardiomyocytes

Duchenne muscular dystrophy (DMD)–associated cardiac diseases are emerging as a major cause of morbidity and mortality in DMD patients, and many therapies for treatment of skeletal muscle failed to improve cardiac function. The reprogramming of patients' somatic cells into pluripotent stem cells, combined with technologies for correcting the genetic defect, possesses great potential for the development of new treatments for genetic diseases. In this study, we obtained human cardiomyocytes from DMD patient–derived, induced pluripotent stem cells genetically corrected with a human artificial chromosome carrying the whole dystrophin genomic sequence. Stimulation by cytokines was combined with cell culturing on hydrogel with physiological stiffness, allowing an adhesion-dependent maturation and a proper dystrophin expression. The obtained cardiomyocytes showed remarkable sarcomeric organization of cardiac troponin T and α-actinin, expressed cardiac-specific markers, and displayed electrically induced calcium transients lasting less than 1 second. We demonstrated that the human artificial chromosome carrying the whole dystrophin genomic sequence is stably maintained throughout the cardiac differentiation process and that multiple promoters of the dystrophin gene are properly activated, driving expression of different isoforms. These dystrophic cardiomyocytes can be a valuable source for in vitro modeling of DMD-associated cardiac disease. Furthermore, the derivation of genetically corrected, patient-specific cardiomyocytes represents a step toward the development of innovative cell and gene therapy approaches for DMD

Refined human artificial chromosome vectors for gene therapy and animal transgenesis

Human artificial chromosomes (HACs) have several advantages as gene therapy vectors, including stable episomal maintenance, and the ability to carry large gene inserts. We previously developed HAC vectors from the normal human chromosomes using a chromosome engineering technique. However, endogenous genes were remained in these HACs, limiting their therapeutic applications. In this study, we refined a HAC vector without endogenous genes from human chromosome 21 in homologous recombination-proficient chicken DT40 cells. The HAC was physically characterized using a transformation-associated recombination (TAR) cloning strategy followed by sequencing of TAR-bacterial artificial chromosome clones. No endogenous genes were remained in the HAC. We demonstrated that any desired gene can be cloned into the HAC using the Cre-loxP system in Chinese hamster ovary cells, or a homologous recombination system in DT40 cells. The HAC can be efficiently transferred to other type of cells including mouse ES cells via microcell-mediated chromosome transfer. The transferred HAC was stably maintained in vitro and in vivo. Furthermore, tumor cells containing a HAC carrying the suicide gene, herpes simplex virus thymidine kinase (HSV-TK), were selectively killed by ganciclovir in vitro and in vivo. Thus, this novel HAC vector may be useful not only for gene and cell therapy, but also for animal transgenesis

Polynomials, Riemann surfaces, and reconstructing missing-energy events

We consider the problem of reconstructing energies, momenta, and masses in collider events with missing energy, along with the complications introduced by combinatorial ambiguities and measurement errors. Typically, one reconstructs more than one value and we show how the wrong values may be correlated with the right ones. The problem has a natural formulation in terms of the theory of Riemann surfaces. We discuss examples including top quark decays in the Standard Model (relevant for top quark mass measurements and tests of spin correlation), cascade decays in models of new physics containing dark matter candidates, decays of third-generation leptoquarks in composite models of electroweak symmetry breaking, and Higgs boson decay into two tau leptons.Comment: 28 pages, 6 figures; version accepted for publication, with discussion of Higgs to tau tau deca

Leveraging public health nurses for disaster risk communication in Fukushima City: a qualitative analysis of nurses' written records of parenting counseling and peer discussions

Background: Local public health nurses (PHNs) have been recognized as the main health service providers in communities in Japan. The Fukushima nuclear disaster in 2011 has, however, created a major challenge for them in responding to mothers’ concerns. This was in part due to difficulties in assessing, understanding and communicating health risks on low-dose radiation exposure. In order to guide the development of risk communication plans, this study sought to investigate mothers’ primary concerns and possible solutions perceived by a core healthcare profession like the PHNs. Methods: A total of 150 records from parenting counseling sessions conducted between PHNs and mothers who have attended mandatory 18-month health checkups for their children at the Fukushima City Health and Welfare Center in 2010, 2011 (year of disaster) and 2012 were examined. Discussion notes of three peer discussions among PHNs organized in response to the nuclear disaster in 2012 and 2013 were also analyzed. All transcribed data were first subjected to text mining to list the words according to their frequencies and inter-relationships. The Steps Coding and Theorization method was then undertaken as a framework for qualitative analysis. Results: PHNs noted mothers to have considerable needs for information on radiation risks as they impact on decisions related to relocations, concerns for child safety, and experiences with interpersonal conflicts within the family owing to differing risk perceptions. PHNs identified themselves as the information channels in the community, recommended the building of their risk communication capacities to support residents in making well-informed decisions, and advocated for self-measurement of radiation levels to increase residents’ sense of control. PHNs also suggested a more standardized form of information dissemination and an expansion of community-based counseling services. Conclusions: Inadequate risk communication on radiation in the Fukushima nuclear incident has resulted in multiple repercussions for mothers in the community. Empowerment of local residents to assume more active roles in the understanding of their environment, increasing PHNs’ capacity in communication, and an expansion of health services such as counseling will together better address risk communication challenges in post-disaster recovery efforts

Toward Open-Closed String Theoretical Description of Rolling Tachyon

We consider how the time-dependent decay process of an unstable D-brane should be described in the full (quantum) open-closed string theory. It is argued that the system, starting from the unstable D-brane configuration, will evolve in time into the time-independent open string tachyon vacuum configuration which we assume to be finite, with the total energy conserved. As a concrete realization of this idea, we construct a toy model describing the open and closed string tachyons which admits such a time-dependent solution. The structure of our model has some resemblance to that of open-closed string field theory.Comment: 1+10 pages, 6 figures. v2: a reference adde