Restoring human nature : constructive theological anthropologies engaging the psychological sciences

Over the past decade, a growing number of theologians and philosophers from a variety of sub disciplines have expressed an interest in the possibilities of a “science-engaged theology.” The specific projects that fall under this somewhat broad conceptual umbrella are rather diverse, but at its most basic, science-engaged theology is a form of inquiry that is deeply engaged with one or more of the sciences in the service of articulating, defending, or critiquing existing theological and philosophical frameworks. Some operating in this fertile domain even seek to construct entirely new theological (and occasionally, scientific) categories in light of the generative insights born from a robust interaction between the sciences and theology.Publisher PDFPeer reviewe

Validation of a fully autonomous phosphate analyser based on a microfluidic lab-on-a-chip

This work describes the design of a phosphate analyser that utilises a microfluidic lab-on-a-chip. The analyser contains all the required chemical storage, pumping and electronic components to carry out a complete phosphate assay. The system is self-calibrating and self-cleaning, thus capable of long-term operation. This was proven by a bench top calibration of the analyser using standard solutions and also by comparing the analyser's performance to a commercially available phosphate monitor installed at a waste water treatment plant. The output of the microfluidic lab-on-a-chip analyser was shown to have sensitivity and linear range equivalent to the commercially available monitor and also the ability to operate over an extended period of time

Latent regulatory potential of human-specific repetitive elements

At least half of the human genome is derived from repetitive elements, which are often lineage specific and silenced by a variety of genetic and epigenetic mechanisms. Using a transchromosomic mouse strain that transmits an almost complete single copy of human chromosome 21 via the female germline, we show that a heterologous regulatory environment can transcriptionally activate transposon-derived human regulatory regions. In the mouse nucleus, hundreds of locations on human chromosome 21 newly associate with activating histone modifications in both somatic and germline tissues, and influence the gene expression of nearby transcripts. These regions are enriched with primate and human lineage-specific transposable elements, and their activation corresponds to changes in DNA methylation at CpG dinucleotides. This study reveals the latent regulatory potential of the repetitive human genome and illustrates the species specificity of mechanisms that control it

Rapid turnover of long noncoding RNAs and the evolution of gene expression.

A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs. However, the roles in mammalian biology of long noncoding RNA (lncRNA) are not well understood. Few lncRNAs have experimentally determined roles, with some of these being lineage-specific. Determining the extent by which transcription of lncRNA loci is retained or lost across multiple evolutionary lineages is essential if we are to understand their contribution to mammalian biology and to lineage-specific traits. Here, we experimentally investigated the conservation of lncRNA expression among closely related rodent species, allowing the evolution of DNA sequence to be uncoupled from evolution of transcript expression. We generated total RNA (RNAseq) and H3K4me3-bound (ChIPseq) DNA data, and combined both to construct catalogues of transcripts expressed in the adult liver of Mus musculus domesticus (C57BL/6J), Mus musculus castaneus, and Rattus norvegicus. We estimated the rate of transcriptional turnover of lncRNAs and investigated the effects of their lineage-specific birth or death. LncRNA transcription showed considerably greater gain and loss during rodent evolution, compared with protein-coding genes. Nucleotide substitution rates were found to mirror the in vivo transcriptional conservation of intergenic lncRNAs between rodents: only the sequences of noncoding loci with conserved transcription were constrained. Finally, we found that lineage-specific intergenic lncRNAs appear to be associated with modestly elevated expression of genomically neighbouring protein-coding genes. Our findings show that nearly half of intergenic lncRNA loci have been gained or lost since the last common ancestor of mouse and rat, and they predict that such rapid transcriptional turnover contributes to the evolution of tissue- and lineage-specific gene expression

Mechanical response of plectonemic DNA: an analytical solution

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact pressure, twisting moment and geometrical parameters of the supercoiled region. We apply our model to magnetic tweezer experiments of a DNA molecule subjected to a tensile force and a torque, and extract mechanical and geometrical quantities from the linear part of the experimental response curve. These reconstructed values are derived in a self-contained manner, and are found to be consistent with those available in the literature.Comment: 14 pages, 4 figure

Scintillator counters with WLS fiber/MPPC readout for the side muon range detector (SMRD)of the T2K experiment

The T2K neutrino experiment at J-PARC uses a set of near detectors to measure the properties of an unoscillated neutrino beam and neutrino interaction cross-sections. One of the sub-detectors of the near-detector complex, the side muon range detector (SMRD), is described in the paper. The detector is designed to help measure the neutrino energy spectrum, to identify background and to calibrate the other detectors. The active elements of the SMRD consist of 0.7 cm thick extruded scintillator slabs inserted into air gaps of the UA1 magnet yokes. The readout of each scintillator slab is provided through a single WLS fiber embedded into a serpentine shaped groove. Two Hamamatsu multi-pixel avalanche photodiodes (MPPC's) are coupled to both ends of the WLS fiber. This design allows us to achieve a high MIP detection efficiency of greater than 99%. A light yield of 25-50 p.e./MIP, a time resolution of about 1 ns and a spatial resolution along the slab better than 10 cm were obtained for the SMRD counters.Comment: 7 pages, 4 figures; talk at TIPP09, March 12-17, Tsukuba, Japan; to be published in the conference proceeding

The T2K Side Muon Range Detector

The T2K experiment is a long baseline neutrino oscillation experiment aiming to observe the appearance of {\nu} e in a {\nu}{\mu} beam. The {\nu}{\mu} beam is produced at the Japan Proton Accelerator Research Complex (J-PARC), observed with the 295 km distant Super- Kamiokande Detector and monitored by a suite of near detectors at 280m from the proton target. The near detectors include a magnetized off-axis detector (ND280) which measures the un-oscillated neutrino flux and neutrino cross sections. The present paper describes the outermost component of ND280 which is a side muon range detector (SMRD) composed of scintillation counters with embedded wavelength shifting fibers and Multi-Pixel Photon Counter read-out. The components, performance and response of the SMRD are presented.Comment: 13 pages, 19 figures v2: fixed several typos; fixed reference

Seismic Performance Assessment in Dense Urban Environments: Evaluation of Nonlinear Building-Foundation Systems Using Centrifuge Tests

In dense urban areas, buildings are generally constructed in clusters, forming city blocks. New buildings are designed assuming their response is independent of adjacent buildings, which ignores potentially important structure-soil-structure-interaction (SSSI) effects. Although a few studies have revealed the significance of SSSI effects, validated simulation and design tools do not exist. In this paper, we present the results from the first in a series of centrifuge tests intended to investigate SSSI effects. Results herein are focused on the design and measured response of two model building-foundation systems placed on dense dry Nevada sand and tested at 55-g. The two models represent prototypical nine-story and three-story special moment resisting frame buildings, with the former structure supported by a three-level basement-mat and the later on isolated spread footings. Nonlinear response-history simulations are performed to aid in the design of the models, with particular attention to reproducing prototype building periods and nonlinear characteristics. Yielding of the model buildings is achieved using custom-designed fuses placed strategically throughout the superstructures. At present, the two models are placed as far apart as possible to characterize soil-structure interaction on individual buildings; subsequent experiments will move the structures in near proximity, allowing direct experimental assessment of structuresoil- structure-interaction

Earthquake Input Motions and Seismic Site Response in a Centrifuge Test Examining SFSI Effects

This paper describes the ground motion selection process and reports observed seismic site response and SFSI effects during a dynamic centrifuge test (Test-1). The centrifuge test is the first in a series of tests examining the effects of SFSI in dense urban environments. The objective of Test-1 is to examine SFSI effects for two structures that are located a significant distance apart and essentially isolated. The model structures represent a three-story building founded on spread footings and a nine-story structure founded on a threestory basement. The structures are sited on a dry, dense bed of Nevada Sand. The centrifuge model is subjected to a series of shaking events that represent near-fault and “ordinary” ground motions at a site in Los Angeles. Results show that site periods degrade as ground motion intensity increases with more pronounced degradation observed for near-fault ground motions as compared with ordinary ground motions. Additionally, the results indicate the importance of kinematic effects of embedded structures when considering SFSI effects