Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data

To make digital resources on the web verifiable, immutable, and permanent, we propose a technique to include cryptographic hash values in URIs. We call them trusty URIs and we show how they can be used for approaches like nanopublications to make not only specific resources but their entire reference trees verifiable. Digital artifacts can be identified not only on the byte level but on more abstract levels such as RDF graphs, which means that resources keep their hash values even when presented in a different format. Our approach sticks to the core principles of the web, namely openness and decentralized architecture, is fully compatible with existing standards and protocols, and can therefore be used right away. Evaluation of our reference implementations shows that these desired properties are indeed accomplished by our approach, and that it remains practical even for very large files.Comment: Small error corrected in the text (table data was correct) on page 13: "All average values are below 0.8s (0.03s for batch mode). Using Java in batch mode even requires only 1ms per file.

How Many Topics? Stability Analysis for Topic Models

Topic modeling refers to the task of discovering the underlying thematic structure in a text corpus, where the output is commonly presented as a report of the top terms appearing in each topic. Despite the diversity of topic modeling algorithms that have been proposed, a common challenge in successfully applying these techniques is the selection of an appropriate number of topics for a given corpus. Choosing too few topics will produce results that are overly broad, while choosing too many will result in the "over-clustering" of a corpus into many small, highly-similar topics. In this paper, we propose a term-centric stability analysis strategy to address this issue, the idea being that a model with an appropriate number of topics will be more robust to perturbations in the data. Using a topic modeling approach based on matrix factorization, evaluations performed on a range of corpora show that this strategy can successfully guide the model selection process.Comment: Improve readability of plots. Add minor clarification

Expression of chicken hepatic type I and type III iodothyronine deiodinases during embryonic development

In embryonic chicken liver (ECL) two types of iodothyronine deiodinases are expressed: D1 and D3. D1 catalyzes the activation as well as the inactivation of thyroid hormone by outer and inner ring deiodination, respectively. D3 only catalyzes inner ring deiodination. D1 and D3 have been cloned from mammals and amphibians and shown to contain a selenocysteine (Sec) residue. We characterized chicken D1 and D3 complementary DNAs (cDNAs) and studied the expression of hepatic D1 and D3 messenger RNAs (mRNAs) during embryonic development. Oligonucleotides based on two amino acid sequences strongly conserved in the different deiodinases (NFGSCTSecP and YIEEAH) were used for reverse transcription-PCR of poly(A+) RNA isolated from embryonic day 17 (E17) chicken liver, resulting in the amplification of two 117-bp DNA fragments. Screening of an E17 chicken liver cDNA library with these probes led to the isolation of two cDNA clones, ECL1711 and ECL1715. The ECL1711 clone was 1360 bp long and lacked a translation start site. Sequence alignment showed that it shared highest sequence identity with D1s from other vertebrates and that the coding sequence probably lacked the first five nucleotides. An ATG start codon was engineered by site-directed mutagenesis, generating a mutant (ECL1711M) with four additional codons (coding for MGTR). The open reading frame of ECL1711M coded for a 249-amino acid protein showing 58-62% identity with mammalian D1s. An in-frame TGA codon was located at position 127, which is translated as Sec in the presence ofa Sec insertion sequence (SECIS) identified in the 3'-untranslated region. Enzyme activity expressed in COS-1 cells by transfection with ECL1711M showed the same catalytic, substrate, and inhibitor specificities as native chicken D1. The ECL1715 clone was 1366 bp long and also lacked a translation start site. Sequence alignment showed that it was most homologous with D3 from other species and that the coding sequence lacked approximately the first 46 nucleotides. The deduced amino acid sequence showed 62-72% identity with the D3 sequences from other species, including a putative Sec residue at a corresponding position. The 3'-untranslated region of ECL1715 also contained a SECIS element. These results indicate that ECL1711 and ECL1715 are near-full-length cDNA clones for chicken D1 and D3 selenoproteins, respectively. The ontogeny of D1 and D3 expression in chicken liver was studied between E14 and 1 day after hatching (C1). D1 activity showed a gradual increase from E14 until C1, whereas D1 mRNA level remained relatively constant. D3 activity and mRNA level were highly significantly correlated, showing an increase from E14 to E17 and a strong decrease thereafter. These results suggest that the regulation of chicken hepatic D3 expression during embryonic development occurs predominantly at the pretranslational level

Characterization of a propylthiouracil-insensitive type I iodothyronine deiodinase

Mammalian type I iodothyronine deiodinase (D1) activates and inactivates thyroid hormone by outer ring deiodination (ORD) and inner ring deiodination (IRD), respectively, and is potently inhibited by propylthiouracil (PTU). Here we describe the cloning and characterization of a complementary DNA encoding a PTU-insensitive D1 from teleost fish (Oreochromis niloticus, tilapia). This complementary DNA codes for a protein of 248 amino acids, including a putative selenocysteine (Sec) residue, encoded by a TGA triplet, at position 126. The 3' untranslated region contains two putative Sec insertion sequence (SECIS) elements. Recombinant enzyme expressed in COS-1 cells catalyzes both ORD of T4 and rT3 and IRD of T3 and T3 sulfate with the same substrate specificity as native tilapia D1 (tD1), i.e. rT3 >> T4 > T3 sulfate > T3. Native and recombinant tD1 show equally low sensitivities to inhibition by PTU, iodoacetate, and gold thioglucose compared with the potent inhibitions observed with mammalian D1s. Because the residue 2 positions downstream from Sec is Pro in tD1 and in all (PTU-insensitive) type II and type III iodothyronine deiodinases but Ser in all PTU-sensitive D1s, we prepared the Pro128Ser mutant of tD1. The mutant enzyme showed strongly decreased ORD and somewhat increased IRD activity, but was still insensitive to PTU. These results provide new information about the structure-activity relationship of D1 concerning two characteristic properties, i.e. catalysis of both ORD and IRD, and inhibition by PTU

Determinisitic Optical Fock State Generation

We present a scheme for the deterministic generation of N-photon Fock states from N three-level atoms in a high-finesse optical cavity. The method applies an external laser pulsethat generates an $N$-photon output state while adiabatically keeping the atom-cavity system within a subspace of optically dark states. We present analytical estimates of the error due to amplitude leakage from these dark states for general N, and compare it with explicit results of numerical simulations for N \leq 5. The method is shown to provide a robust source of N-photon states under a variety of experimental conditions and is suitable for experimental implementation using a cloud of cold atoms magnetically trapped in a cavity. The resulting N-photon states have potential applications in fundamental studies of non-classical states and in quantum information processing.Comment: 25 pages, 9 figure

Continuum limit of amorphous elastic bodies: A finite-size study of low frequency harmonic vibrations

The approach of the elastic continuum limit in small amorphous bodies formed by weakly polydisperse Lennard-Jones beads is investigated in a systematic finite-size study. We show that classical continuum elasticity breaks down when the wavelength of the sollicitation is smaller than a characteristic length of approximately 30 molecular sizes. Due to this surprisingly large effect ensembles containing up to N=40,000 particles have been required in two dimensions to yield a convincing match with the classical continuum predictions for the eigenfrequency spectrum of disk-shaped aggregates and periodic bulk systems. The existence of an effective length scale \xi is confirmed by the analysis of the (non-gaussian) noisy part of the low frequency vibrational eigenmodes. Moreover, we relate it to the {\em non-affine} part of the displacement fields under imposed elongation and shear. Similar correlations (vortices) are indeed observed on distances up to \xi~30 particle sizes.Comment: 28 pages, 13 figures, 3 table

Confirmation of a pi_1^0 Exotic Meson in the \eta \pi^0 System

The exclusive reaction $\pi^- p \to \eta \pi^0 n$, $\eta \to \pi^+ \pi^- \pi^0$ at 18 GeV$/c$ has been studied with a partial wave analysis on a sample of 23~492 $\eta \pi^0 n$ events from BNL experiment E852. A mass-dependent fit is consistent with a resonant hypothesis for the $P_+$ wave, thus providing evidence for a neutral exotic meson with $J^{PC} = 1^{-+}$, a mass of $1257 \pm 20 \pm 25$ MeV$/c^2$, and a width of $354 \pm 64 \pm 60$ MeV$/c^2$. New interpretations of the meson exotics in neutral $\eta \pi^0$ system observed in E852 and Crystal Barrel experiments are discussed.Comment: p3, rewording the paragraph (at the bottom) about the phase variations. p4, rewording paragrath "The second method ..." . p4, at the bottom of paragrath "The third method ..." added consistent with the results of methods 1 and 2

The STAR Silicon Strip Detector (SSD)

The STAR Silicon Strip Detector (SSD) completes the three layers of the Silicon Vertex Tracker (SVT) to make an inner tracking system located inside the Time Projection Chamber (TPC). This additional fourth layer provides two dimensional hit position and energy loss measurements for charged particles, improving the extrapolation of TPC tracks through SVT hits. To match the high multiplicity of central Au+Au collisions at RHIC the double sided silicon strip technology was chosen which makes the SSD a half million channels detector. Dedicated electronics have been designed for both readout and control. Also a novel technique of bonding, the Tape Automated Bonding (TAB), was used to fullfill the large number of bounds to be done. All aspects of the SSD are shortly described here and test performances of produced detection modules as well as simulated results on hit reconstruction are given.Comment: 11 pages, 8 figures, 1 tabl

Exotic Meson Production in the f1(1285)π−f_{1}(1285)\pi^{-} System observed in the Reaction π−p→ηπ+π−π−p\pi^{-} p \to \eta\pi^{+}\pi^{-}\pi^{-} p at 18 GeV/c

This letter reports results from the partial wave analysis of the $\pi^{-}\pi^{-}\pi^{+}\eta$ final state in $\pi^{-}p$ collisions at 18GeV/c. Strong evidence is observed for production of two mesons with exotic quantum numbers of spin, parity and charge conjugation, $J^{PC} = 1^{-+}$ in the decay channel $f_{1}(1285)\pi^{-}$. The mass $M = 1709 \pm 24 \pm 41$ MeV/c^2 and width $\Gamma = 403 \pm 80 \pm 115$ MeV/c^2 of the first state are consistent with the parameters of the previously observed $\pi_{1}(1600)$. The second resonance with mass $M = 2001 \pm 30 \pm 92$ MeV/c^2 and width $\Gamma = 333 \pm 52 \pm 49$ MeV/c^2 agrees very well with predictions from theoretical models. In addition, the presence of $\pi_{2}(1900)$ is confirmed with mass $M = 2003 \pm 88 \pm 148$ MeV/c^2 and width $\Gamma = 306 \pm 132 \pm 121$ MeV/c^2 and a new state, $a_{1}(2096)$, is observed with mass $M = 2096 \pm 17 \pm 121$ MeV/c^2 and width $\Gamma = 451 \pm 41 \pm 81$ MeV/c^2. The decay properties of these last two states are consistent with flux tube model predictions for hybrid mesons with non-exotic quantum numbers

Spatial competition in a global disturbance minimum; the seabed under an Antarctic ice shelf

The marine habitat beneath Antarctica's ice shelves spans ∼1.6 million km2, and life in this vast and extreme environment is among Earth's least accessible, least disturbed and least known, yet likely to be impacted by climate-forced warming and environmental change. Although competition among biota is a fundamental structuring force of ecological communities, hence ecosystem functions and services, nothing was known of competition for resources under ice shelves, until this study. Boreholes drilled through a ∼ 200 m thick ice shelf enabled collections of novel sub-ice-shelf seabed sediment which contained fragments of biogenic substrata rich in encrusting (lithophilic) macrobenthos, principally bryozoans – a globally-ubiquitous phylum sensitive to environmental change. Analysis of sub-glacial biogenic substrata, by stereo microscopy, provided first evidence of spatial contest competition, enabling generation of a new range of competition measures for the sub-ice-shelf benthic space. Measures were compared with those of global open-water datasets traversing polar, temperate and tropical latitudes (and encompassing both hemispheres). Spatial competition in sub-ice-shelf samples was found to be higher in intensity and severity than all other global means. The likelihood of sub-ice-shelf competition being intraspecific was three times lower than for open-sea polar continental shelf areas, and competition complexity, in terms of the number of different types of competitor pairings, was two-fold higher. As posited for an enduring disturbance minimum, a specific bryozoan clade was especially competitively dominant in sub-ice-shelf samples compared with both contemporary and fossil assemblage records. Overall, spatial competition under an Antarctic ice shelf, as characterised by bryozoan interactions, was strikingly different from that of open-sea polar continental shelf sites, and more closely resembled tropical and temperate latitudes. This study represents the first analysis of sub-ice-shelf macrobenthic spatial competition and provides a new ecological baseline for exploring, monitoring and comparing ecosystem response to environmental change in a warming world