Scaling Digital Humanities on (and utilising) the Web

The work of a humanities e-researcher is scoped by the possibilities offered in digital artefacts: in their ever increasing number and their distribution and access over the Internet. This is recognised through a shift to an increasingly data-intensive method characterised as the "fourth paradigm" of e-Research and enabled by the new computational tools and techniques that characterise e-Science and e-Research. To realise these systems we propose an approach built upon the defining properties of the Web: adopting the REST style and Linked Data principles to enable the radical publication, sharing, and linking of data for, and by, researchers. Within this Resource Oriented architecture we utilise distinct but interwoven models to represent services, data collections, workflows, and -- so to simplify the rapid development of integrated applications to explore specific findings -- the domain of the application. We illustrate this conceptual framework in a prototype system for enhancing the application of Music Information Retrieval workflows, driven by several related aims: to enable MIR researchers to utilise these datasets through incorporation in their research systems and workflows; to publish MIR research output on the Semantic Web linked to existing datasets; and to present MIR research output, with cross-referencing to other linked data sources, for manipulation and evaluation by MIR and musicology researchers and re-use within the wider Semantic Web and Digital Humanities communities. As an illustration of a specific domain-driven application with which to explore findings, we gather and publish metadata describing audio collections derived from the country of an artist. Genre analysis over these collections, and integration of this analysis with collection metadata enables us to ask: "how country is my country?"

Volume reduction of municipal solid wastes contaminated with radioactive cesium by ferrocyanide coprecipitation technique

Municipal solid wastes (MSW) with elevated concentrations of radioactive cesium (rad-Cs hereafter) have been generated in some areas of Japan in the aftermath of the Fukushima Daiichi Nuclear Power Plant (F1 hereafter) accident. Both recycling and final disposal of the contaminated MSW have become a difficult problem in the affected areas, resulting in accumulation of treated residues in the treatment facilities. The rad-Cs in MSW, especially fly ash, often showed a high leaching rate. Extraction of contaminated MSW with water or hot oxalic acid followed by selective removal of rad-Cs from the extract using ferrocyanide (Fer hereafter) coprecipitation technique could be an ultimate solution for waste volume reduction. The MSW extracts contain various metal components as well as chelating reagents like oxalic acid, and are often very saline. The composition of the extract varies widely depending on waste sources, applied treatment techniques, and rad-Cs extraction method etc. The applicability of the Fer coprecipitation technique had to be tested and validated before it could be applied for actual treatment. In this work, we applied the Fer technique and observed removal of cesium (Cs) from water and oxalic acid extracts (all spiked with rad-Cs tracer or stable Cs) of various MSW samples collected from uncontaminated areas. Finally, the Fer technique was applied on site for removal of rad-Cs in the extracts of contaminated MSW. By modifying coprecipitation conditions according to solution matrix, Cs removal rates of higher than 95 % could be obtained

Auxiliary-level-assisted operations with charge qubits in semiconductors

We present a new scheme for rotations of a charge qubit associated with a singly ionized pair of donor atoms in a semiconductor host. The logical states of such a qubit proposed recently by Hollenberg et al. are defined by the lowest two energy states of the remaining valence electron localized around one or another donor. We show that an electron located initially at one donor site can be transferred to another donor site via an auxiliary molecular level formed upon the hybridization of the excited states of two donors. The electron transfer is driven by a single resonant microwave pulse in the case that the energies of the lowest donor states coincide or two resonant pulses in the case that they differ from each other. Depending on the pulse parameters, various one-qubit operations, including the phase gate, the NOT gate, and the Hadamard gate, can be realized in short times. Decoherence of an electron due to the interaction with acoustic phonons is analyzed and shown to be weak enough for coherent qubit manipulation being possible, at least in the proof-of-principle experiments on one-qubit devices.Comment: Extended version of cond-mat/0411605 with detailed discussion of phonon-induced decoherence including dephasing and relaxation; to be published in JET

Gas phase characterization of the noncovalent quaternary structure of Cholera toxin and the Cholera toxin B subunit pentamer

Cholera toxin (CTx) is an AB5 cytotonic protein that has medical relevance in cholera and as a novel mucosal adjuvant. Here, we report an analysis of the noncovalent homopentameric complex of CTx B chain (CTx B5) using electrospray ionization triple quadrupole mass spectrometry and tandem mass spectrometry and the analysis of the noncovalent hexameric holotoxin usingelectrospray ionization time-of-flight mass spectrometry over a range of pH values that correlate with those encountered by this toxin after cellular uptake. We show that noncovalent interactions within the toxin assemblies were maintained under both acidic and neutral conditions in the gas phase. However, unlike the related Escherichia coli Shiga-like toxin B5 pentamer (SLTx B), the CTx B5 pentamer was stable at low pH, indicating that additional interactions must be present within the latter. Structural comparison of the CTx B monomer interface reveals an additional α-helix that is absent in the SLTx B monomer. In silico energy calculations support interactions between this helix and the adjacent monomer. These data provide insight into the apparent stabilization of CTx B relative to SLTx B

The Composition of Cosmic Rays at the Knee

The observation of a small change in spectral slope, or 'knee' in the fluxes of cosmic rays near energies 10^15 eV has caused much speculation since its discovery over 40 years ago. The origin of this feature remains unknown. A small workshop to review some modern experimental measurements of this region was held at the Adler Planetarium in Chicago, USA in June 2000. This paper summarizes the results presented at this workshop and the discussion of their interpretation in the context of hadronic models of atmospheric airshowers.Comment: 36 pages, 10 figure

Anaerobic Carbon Monoxide Dehydrogenase Diversity in the Homoacetogenic Hindgut Microbial Communities of Lower Termites and the Wood Roach

Anaerobic carbon monoxide dehydrogenase (CODH) is a key enzyme in the Wood-Ljungdahl (acetyl-CoA) pathway for acetogenesis performed by homoacetogenic bacteria. Acetate generated by gut bacteria via the acetyl-CoA pathway provides considerable nutrition to wood-feeding dictyopteran insects making CODH important to the obligate mutualism occurring between termites and their hindgut microbiota. To investigate CODH diversity in insect gut communities, we developed the first degenerate primers designed to amplify cooS genes, which encode the catalytic (β) subunit of anaerobic CODH enzyme complexes. These primers target over 68 million combinations of potential forward and reverse cooS primer-binding sequences. We used the primers to identify cooS genes in bacterial isolates from the hindgut of a phylogenetically lower termite and to sample cooS diversity present in a variety of insect hindgut microbial communities including those of three phylogenetically-lower termites, Zootermopsis nevadensis, Reticulitermes hesperus, and Incisitermes minor, a wood-feeding cockroach, Cryptocercus punctulatus, and an omnivorous cockroach, Periplaneta americana. In total, we sequenced and analyzed 151 different cooS genes. These genes encode proteins that group within one of three highly divergent CODH phylogenetic clades. Each insect gut community contained CODH variants from all three of these clades. The patterns of CODH diversity in these communities likely reflect differences in enzyme or physiological function, and suggest that a diversity of microbial species participate in homoacetogenesis in these communities

RNA polymerase II stalling promotes nucleosome occlusion and pTEFb recruitment to drive immortalization by Epstein-Barr virus

Epstein-Barr virus (EBV) immortalizes resting B-cells and is a key etiologic agent in the development of numerous cancers. The essential EBV-encoded protein EBNA 2 activates the viral C promoter (Cp) producing a message of ~120 kb that is differentially spliced to encode all EBNAs required for immortalization. We have previously shown that EBNA 2-activated transcription is dependent on the activity of the RNA polymerase II (pol II) C-terminal domain (CTD) kinase pTEFb (CDK9/cyclin T1). We now demonstrate that Cp, in contrast to two shorter EBNA 2-activated viral genes (LMP 1 and 2A), displays high levels of promoter-proximally stalled pol II despite being constitutively active. Consistent with pol II stalling, we detect considerable pausing complex (NELF/DSIF) association with Cp. Significantly, we observe substantial Cp-specific pTEFb recruitment that stimulates high-level pol II CTD serine 2 phosphorylation at distal regions (up to +75 kb), promoting elongation. We reveal that Cp-specific pol II accumulation is directed by DNA sequences unfavourable for nucleosome assembly that increase TBP access and pol II recruitment. Stalled pol II then maintains Cp nucleosome depletion. Our data indicate that pTEFb is recruited to Cp by the bromodomain protein Brd4, with polymerase stalling facilitating stable association of pTEFb. The Brd4 inhibitor JQ1 and the pTEFb inhibitors DRB and Flavopiridol significantly reduce Cp, but not LMP1 transcript production indicating that Brd4 and pTEFb are required for Cp transcription. Taken together our data indicate that pol II stalling at Cp promotes transcription of essential immortalizing genes during EBV infection by (i) preventing promoter-proximal nucleosome assembly and ii) necessitating the recruitment of pTEFb thereby maintaining serine 2 CTD phosphorylation at distal regions

Radial volumetric imaging breath-hold examination (VIBE) with k-space weighted image contrast (KWIC) for dynamic gadoxetic acid (Gd-EOB-DTPA)-enhanced MRI of the liver: advantages over Cartesian VIBE in the arterial phase

To compare radial volumetric imaging breath-hold examination with k-space weighted image contrast reconstruction (r-VIBE-KWIC) to Cartesian VIBE (c-VIBE) in arterial phase dynamic gadoxetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (DCE-MRI) of the liver. We reviewed 53 consecutive DCE-MRI studies performed on a 3-T unit using c-VIBE and 53 consecutive cases performed using r-VIBE-KWIC with full-frame image subset (r-VIBEfull) and sub-frame image subsets (r-VIBEsub; temporal resolution, 2.5-3 s). All arterial phase images were scored by two readers on: (1) contrast-enhancement ratio (CER) in the abdominal aorta; (2) scan timing; (3) artefacts; (4) visualisation of the common, right, and left hepatic arteries. Mean abdominal aortic CERs for c-VIBE, r-VIBEfull, and r-VIBEsub were 3.2, 4.3 and 6.5, respectively. There were significant differences between each group (P < 0.0001). The mean score for c-VIBE was significantly lower than that for r-VIBEfull and r-VIBEsub in all factors except for visualisation of the common hepatic artery (P < 0.05). The mean score of all factors except for scan timing for r-VIBEsub was not significantly different from that for r-VIBEfull. Radial VIBE-KWIC provides higher image quality than c-VIBE, and r-VIBEsub features high temporal resolution without image degradation in arterial phase DCE-MRI. aEuro cent Radial VIBE-KWIC minimised artefact and produced high-quality and high-temporal-resolution images. aEuro cent Maximum abdominal aortic enhancement was observed on sub-frame images of r-VIBE-KWIC. aEuro cent Using r-VIBE-KWIC, optimal arterial phase images were obtained in over 90 %. aEuro cent Using r-VIBE-KWIC, visualisation of the hepatic arteries was improved. aEuro cent A two-reader study revealed r-VIBE-KWIC's advantages over Cartesian VIBE.ArticleEUROPEAN RADIOLOGY. 24(6):1290-1299 (2014)journal articl

Preferential Entry of Botulinum Neurotoxin A Hc Domain through Intestinal Crypt Cells and Targeting to Cholinergic Neurons of the Mouse Intestine

Botulism, characterized by flaccid paralysis, commonly results from botulinum neurotoxin (BoNT) absorption across the epithelial barrier from the digestive tract and then dissemination through the blood circulation to target autonomic and motor nerve terminals. The trafficking pathway of BoNT/A passage through the intestinal barrier is not yet fully understood. We report that intralumenal administration of purified BoNT/A into mouse ileum segment impaired spontaneous muscle contractions and abolished the smooth muscle contractions evoked by electric field stimulation. Entry of BoNT/A into the mouse upper small intestine was monitored with fluorescent HcA (half C-terminal domain of heavy chain) which interacts with cell surface receptor(s). We show that HcA preferentially recognizes a subset of neuroendocrine intestinal crypt cells, which probably represent the entry site of the toxin through the intestinal barrier, then targets specific neurons in the submucosa and later (90–120 min) in the musculosa. HcA mainly binds to certain cholinergic neurons of both submucosal and myenteric plexuses, but also recognizes, although to a lower extent, other neuronal cells including glutamatergic and serotoninergic neurons in the submucosa. Intestinal cholinergic neuron targeting by HcA could account for the inhibition of intestinal peristaltism and secretion observed in botulism, but the consequences of the targeting to non-cholinergic neurons remains to be determined