pinecone/core-2020-05-10-deduplication huggingface dataset:
Functional profiling of single-nucleotide polymorphisms associated with bipolar disorder

List of papers. The papers are removed from the thesis due to publisher restrictions.

Paper I Linkage-disequilibrium-based binning affects the interpretation of GWASs. Christoforou A, Dondrup M, Mattingsdal M, Mattheisen M, Giddaluru S, Nöthen MM, Rietschel M, Cichon S, Djurovic S, Andreassen OA, Jonassen I, Steen VM, Puntervoll P, Le Hellard S. Am J Hum Genet. 2012 Apr 6;90(4):727-33 <a href="http://dx.doi.org/10.1016/j.ajhg.2012.02.025">doi:10.1016/j.ajhg.2012.02.025</a>

Paper II Pathway analysis of genetic markers associated with a functional MRI faces paradigm implicates polymorphisms in calcium responsive pathways. Mattingsdal M, Brown AA, Djurovic S, Sønderby IE, Server A, Melle I, Agartz I, Hovig E, Jensen J, Andreassen OA. Neuroimage. 2013 Apr 15;70:143-9. <a href="http://dx.doi.org/10.1016/j.neuroimage.2012.12.035">doi:10.1016/j.neuroimage.2012.12.035</a>

Paper III Network-based gene set enrichment of genomic regions associated with bipolar disorder reveals susceptibility genes responsive to oestrogen stimulus. Mattingsdal M, Wang Y, Thompson WK, Hovig E, Djurovic S, Dale AM, Andreassen OA Manuscript
Pain and pain tolerance in whiplash-associated disorders: A population-based study

Background Pain is a cardinal symptom in individuals with whiplash-associated disorders (WAD). We aimed to compare pain characteristics between individuals with WAD and individuals reporting chronic pain from other causes, and to determine whether potential differences were accounted for by experimental pain tolerance.
Methods Data from the 6th Tromsø Study (2007–2008, n = 12,981) were analysed. The number of painful locations was compared between individuals with WAD and individuals reporting chronic pain from other causes using negative binomial regression, pain frequency using multinomial logistic regression and pain intensity using multiple linear regression. Differences in experimental pain tolerance (cold pressor test) were tested using Cox regression; one model compared individuals with WAD to those with chronic pain from other causes, one compared the two groups with chronic pain to individuals without chronic pain. Subsequently, regression models investigating clinical pain characteristics were adjusted for pain tolerance.
Results Of individuals with WAD, 96% also reported other causes for pain. Individuals with WAD reported a higher number of painful locations [median (inter-quartile range): 5 (3.5–7) vs. 3 (2–5), p < 0.001] and higher pain intensity (crude mean difference = 0.78, p < 0.001) than individuals with chronic pain from other causes. Pain tolerance did not differ between these two groups. Compared to individuals without chronic pain, individuals with WAD and individuals with chronic pain from other causes had reduced pain tolerance.
Conclusions Individuals with WAD report more additional causes of pain, more painful locations and higher pain intensity than individuals with chronic pain from other causes. The increased pain reporting was not accounted for by pain tolerance
The bottomonium spectrum at finite temperature from N f = 2 + 1 lattice QCD

We present results on the bottomonium spectrum at temperatures above and below the deconfinement crossover temperature, T c , from dynamical lattice QCD simulations. The heavy quark is treated with a non-relativistic effective field theory on the lattice and serves as a probe of the hot medium. Ensembles with a finer spatial lattice spacing and a greater range of temperatures below T c than those previously employed by this collaboration are used. In addition, there are N f = 2 + 1 flavours of Wilson clover quark in the sea with M π ≈ 400 MeV and we perform a more careful tuning of the bottom quark mass in this work. We calculate the spectral functions of S and P wave bottomonium states using the maximum entropy method and confirm earlier findings on the survival of the ground state S wave states up to at least 2 T c and the immediate dissociation of the P wave states above T c
Leptogenesis in crossing and runaway regimes

We study the impact of effective thermal masses and widths on resonant lepto-genesis. We identify two distinct possibilities which we refer to as ‘crossing’ and ‘runaway’ regimes. In the runaway regime the mass difference grows monotonously with temperature, whereas it initially decreases in the crossing regime, such that the effective masses become equal at some temperature. Following the conventional logic the source of the asymmetry would vanish in the latter case. Using non-equilibrium quantum field theory, we analytically demonstrate that the vanishing of the difference of the effective masses does however neither imply a suppression nor a strong enhancement of the source for the lepton asymmetry. In the vicinity of the crossing point the asymmetry calculated in an (improved) Boltzmann limit develops a spurious peak, which signals the breakdown of the quasiparticle approximation. In the exact result this spurious enhancement is compensated by coherent transitions between the two mass shells. Despite the breakdown of the quasiparticle approximation off-shell contributions remain negligibly small even at the crossing point
Dynamics of monopole walls

The moduli space of centred Bogomolny–Prasad–Sommerfield 2-monopole fields is a 4-dimensional manifold <math altimg="si1.gif" xmlns="http://www.w3.org/1998/Math/MathML"><mi mathvariant="script">M</mi></math> with a natural metric, and the geodesics on <math altimg="si1.gif" xmlns="http://www.w3.org/1998/Math/MathML"><mi mathvariant="script">M</mi></math> correspond to slow-motion monopole dynamics. The best-known case is that of monopoles on <math altimg="si2.gif" xmlns="http://www.w3.org/1998/Math/MathML"><msup><mrow><mi mathvariant="double-struck">R</mi></mrow><mrow><mn>3</mn></mrow></msup></math> , where <math altimg="si1.gif" xmlns="http://www.w3.org/1998/Math/MathML"><mi mathvariant="script">M</mi></math> is the Atiyah–Hitchin space. More recently, the case of monopoles periodic in one direction (monopole chains) was studied a few years ago. Our aim in this note is to investigate <math altimg="si1.gif" xmlns="http://www.w3.org/1998/Math/MathML"><mi mathvariant="script">M</mi></math> for doubly-periodic fields, which may be visualized as monopole walls. We identify some of the geodesics on <math altimg="si1.gif" xmlns="http://www.w3.org/1998/Math/MathML"><mi mathvariant="script">M</mi></math> as fixed-point sets of discrete symmetries, and interpret these in terms of monopole scattering and bound orbits, concentrating on novel features that arise as a consequence of the periodicity
Generalized μ – τ symmetry and discrete subgroups of O(3)

The generalized μ – τ interchange symmetry in the leptonic mixing matrix U corresponds to the relations: |Uμi|=|Uτi| with i=1,2,3 . It predicts maximal atmospheric mixing and maximal Dirac CP violation given θ13≠0 . We show that the generalized μ – τ symmetry can arise if the charged lepton and neutrino mass matrices are invariant under specific residual symmetries contained in the finite discrete subgroups of O(3) . The groups A4 , S4 and A5 are the only such groups which can entirely fix U at the leading order. The neutrinos can be (a) non-degenerate or (b) partially degenerate depending on the choice of their residual symmetries. One obtains either vanishing or very large θ13 in case of (a) while only A5 can provide θ13 close to its experimental value in the case (b). We provide an explicit model based on A5 and discuss a class of perturbations which can generate fully realistic neutrino masses and mixing maintaining the generalized μ – τ symmetry in U . Our approach provides generalization of some of the ideas proposed earlier in order to obtain the predictions, θ23=π/4 and δCP=±π/2
Detecting X-ray filaments in the low redshift Universe with XEUS and
  Constellation-X

We propose a possible way to detect baryons at low redshifts from the
analysis of X-ray absorption spectra of bright AGN pairs. A simple
semi-analytical model to simulate the spectra is presented. We model the
diffuse warm-hot intergalactic medium (WHIM) component, responsible for the
X-ray absorption, using inputs from high-resolution hydro-dynamical simulations
and analytical prescriptions. We show that the number of OVII absorbers per
unit redshift with column density larger than $10^{13.5}$ cm$^{-2}$ -
corresponding to an equivalent width of $\sim$ 1 km/s - which will be possibly
detectable by {\it XEUS}, is $\magcir 30$ per unit redshift. {\it
Constellation-X} will detect $\sim 6$ OVII absorptions per unit redshift with
an equivalent width of 10 km/s. Our results show that, in a $\Lambda$CDM
Universe, the characteristic size of these absorbers at $z\sim 0.1$ is $\sim 1$
$h^{-1}$ Mpc. The filamentary structure of WHIM can be probed by finding
coincident absorption lines in the spectra of background AGN pairs. We estimate
that at least 20 AGN pairs at separation $\mincir 20$ arcmin are needed to
detect this filamentary structure at a 3$\sigma$ level. Assuming observations
of distant sources using {\it XEUS} for exposure times of 500 ksec, we find
that the minimum source flux to probe the filamentary structure is $\sim
2\times 10^{-12}$ erg cm$^{-2}$ s$^{-1}$, in the 0.1-2.4 keV energy band. Thus,
most pairs of these extragalactic X-ray bright sources have already been
identified in the {\it ROSAT} All-Sky Survey. Re-observation of these objects
by future missions could be a powerful way to search for baryons in the low
redshift Universe
Production of cellulase by Clostridium papyrosolvens CFR-703.

Clostridium papyrosolvens producing filter paperase, carboxymethyl cellulase and cellobiase under anaerobic cultivation conditions at 35 Â°C is described.  Higher activities of filter paperase and carboxymethylcellulases were assayed in 48 h culture filtrate, while max. cellobiase accumulated in the culture broth at 72 h.  Filter paperase, carboxymethylcellulase and cellobiase activities were optimum at 35 Â°C and pH values of 7.0, 6.5 and 7.5 resp.  Cultivation of the strain in 1000 mL Hungate bottles with 1% cellulose at pH 6.5 and 35 Â°C produced carboxymethyl cellulase, filter paperase and cellobiase activities of 45, 35 and 20 IU/mL resp. [on SciFinder(R)
Mechanical versus manual chest compression for out-of-hospital cardiac arrest (PARAMEDIC): a pragmatic, cluster randomised controlled trial.

BACKGROUND\ud
\ud
Mechanical chest compression devices have the potential to help maintain high-quality cardiopulmonary resuscitation (CPR), but despite their increasing use, little evidence exists for their effectiveness. We aimed to study whether the introduction of LUCAS-2 mechanical CPR into front-line emergency response vehicles would improve survival from out-of-hospital cardiac arrest.\ud
\ud
METHODS\ud
\ud
The pre-hospital randomised assessment of a mechanical compression device in cardiac arrest (PARAMEDIC) trial was a pragmatic, cluster-randomised open-label trial including adults with non-traumatic, out-of-hospital cardiac arrest from four UK Ambulance Services (West Midlands, North East England, Wales, South Central). 91 urban and semi-urban ambulance stations were selected for participation. Clusters were ambulance service vehicles, which were randomly assigned (1:2) to LUCAS-2 or manual CPR. Patients received LUCAS-2 mechanical chest compression or manual chest compressions according to the first trial vehicle to arrive on scene. The primary outcome was survival at 30 days following cardiac arrest and was analysed by intention to treat. Ambulance dispatch staff and those collecting the primary outcome were masked to treatment allocation. Masking of the ambulance staff who delivered the interventions and reported initial response to treatment was not possible. The study is registered with Current Controlled Trials, number ISRCTN08233942.\ud
\ud
FINDINGS\ud
\ud
We enrolled 4471 eligible patients (1652 assigned to the LUCAS-2 group, 2819 assigned to the control group) between April 15, 2010 and June 10, 2013. 985 (60%) patients in the LUCAS-2 group received mechanical chest compression, and 11 (<1%) patients in the control group received LUCAS-2. In the intention-to-treat analysis, 30 day survival was similar in the LUCAS-2 group (104 [6%] of 1652 patients) and in the manual CPR group (193 [7%] of 2819 patients; adjusted odds ratio [OR] 0·86, 95% CI 0·64-1·15). No serious adverse events were noted. Seven clinical adverse events were reported in the LUCAS-2 group (three patients with chest bruising, two with chest lacerations, and two with blood in mouth). 15 device incidents occurred during operational use. No adverse or serious adverse events were reported in the manual group.\ud
\ud
INTERPRETATION\ud
\ud
We noted no evidence of improvement in 30 day survival with LUCAS-2 compared with manual compressions. On the basis of ours and other recent randomised trials, widespread adoption of mechanical CPR devices for routine use does not improve survival.\ud
\ud
FUNDING\ud
\ud
National Institute for Health Research HTA - 07/37/69
Circulating CD133 +VEGFR2 + and CD34 +VEGFR2 + cells and arterial function in patients with beta-thalassaemia major

Arterial dysfunction has been documented in patients with beta-thalassaemia major. This study aimed to determine the quantity and proliferative capacity of circulating CD133+VEGFR2+ and CD34+VEGFR2+ cells in patients with beta-thalassaemia major and those after haematopoietic stem cell transplantation (HSCT), and their relationships with arterial function. Brachial arterial flow-mediated dilation (FMD), carotid arterial stiffness, the quantity of these circulating cells and their number of colony-forming units (CFUs) were determined in 17 transfusion-dependent thalassaemia patients, 14 patients after HSCT and 11 controls. Compared with controls, both patient groups had significantly lower FMD and greater arterial stiffness. Despite having increased CD133+VEGFR2+ and CD34+VEGFR2+ cells, transfusion-dependent patients had significantly reduced CFUs compared with controls (p = 0.002). There was a trend of increasing CFUs across the three groups with decreasing iron load (p = 0.011). The CFUs correlated with brachial FMD (p = 0.029) and arterial stiffness (p = 0.02), but not with serum ferritin level. Multiple linear regression showed that CFU was a significant determinant of FMD (p = 0.043) and arterial stiffness (p = 0.02) after adjustment of age, sex, body mass index, blood pressure and serum ferritin level. In conclusion, arterial dysfunction found in patients with beta-thalassaemia major before and after HSCT may be related to impaired proliferation of CD133+VEGFR2+ and CD34+VEGFR2+ cells. © 2011 The Author(s).published_or_final_versionSpringer Open Choice, 21 Feb 201
The South African human language technology audit

Human language technology (HLT) has been identified as a priority area by the South African government. However, despite efforts by government and the research and development (R&D) community, South Africa has not yet been able to maximise the opportunities of HLT and create a thriving HLT industry. One of the key challenges is the fact that there is insufficient codified knowledge about the current South African HLT components, their attributes and existing relationships. Hence a technology audit was conducted for the South African HLT landscape, to create a systematic and detailed inventory of the status of the HLT components across the eleven official languages. Based on the Basic Language Resource Kit (BLaRK) framework Krauwer (ELRA Newslett 3(2), 1998), we used various data collection methods (such as focus groups, questionnaires and personal consultations with HLT experts) to gather detailed information. The South African HLT landscape is analysed using a number of complementary approaches and based on the interpretations of the results, recommendations are made on how to accelerate HLT development in South Africa, as well as on how to conduct similar audits in other countries and contexts.http://dx.doi.org/10.1007/s10579-011-9151-
Study of resonances in 1 x 25 kV AC traction systems

AC traction systems are 1 x 25 or 2 x 25 kV 50-Hz single-phase, non-linear, time-varying loads that can cause power quality problems. One of the main concerns about these systems is voltage distortion, because adjustable-speed drives for trains may inject harmonic currents of frequencies below 2kHz. Since the presence of parallel resonances in the contact feeder section of the traction circuit worsens the scenario, traction system resonance phenomena should be analyzed to prevent problems. Several works addressed these phenomena, but they only drew weak numerical conclusions based on the frequency scan method. This article studies 1 x 25 kV traction system resonances at pantograph terminals and provides more effective analytical expressions to locate them and determine the impact of traction system parameters on them. These expressions are validated from several traction systems in the literature.Postprint (author's final draft
Ventilated Post-mortem computed tomography

The Accepted manuscript version can be found at  http://hdl.handle.net/2381/36218In an attempt to improve the diagnostic quality of post-mortem computed tomography (PMCT) lung \ud
image interpretation, a series of authors have developed an approach that mimics clinical thoracic \ud
CT imaging in the dead. Known as ventilated post-mortem computed tomography or VPMCT this  \ud
technique has now been developed and applied to adult and paediatric PMCT imaging. This review, \ud
authored by the principal pioneers of this system, outlines the developmental stages of VPMCT, \ud
bringing the reader up to date with current knowledge and practice.Pre-prin
Colour constancy for an unseen surface.

The illumination of a scene strongly affects our perception of objects in that scene, e.g., the pages of a book illuminated by candlelight will appear quite yellow relative to other types of artificial illuminants. Yet at the same time, the reader still judges the pages as white, their surface color unaffected by the interplay of paper and illuminant. It has been shown empirically [ 1 ] that we can indeed report two quite different interpretations of “color”: one is dependent on the constant surface spectral reflectance of an object (surface color) and the other on the power of light of different wavelengths reflected from that object (reflected color). How then are these two representations related? The common view, dating from Aristotle, is that our experience of surface color is derived from reflected color or, in more familiar terms, that color perception follows from color sensation [ 2–4 ]. By definition, color constancy requires that vision “discounts the illuminant”; thus, it seems reasonable that vision begins with the color of objects as they naively appear and that we infer from their appearances their surface color. Here, we question this classic view. We use metacontrast-masked priming and, by presenting the unseen prime and the visible mask under different illuminants, dissociate two ways in which the prime matched the mask: in surface color or in reflected color. We find that priming of the mask occurs when it matches the prime in surface color, not reflected color. It follows that color perception can arise without prior color sensation
Tracking millennial-scale Holocene glacial advance and retreat using osmium isotopes : insights from the Greenland ice sheet.

High-resolution Os isotope stratigraphy can aid in reconstructing Pleistocene ice sheet fluctuation and elucidating the role of local and regional weathering fluxes on the marine Os residence time. This paper presents new Os isotope data from ocean cores adjacent to the West Greenland ice sheet that have excellent chronological controls. Cores MSM-520 and DA00-06 represent distal to proximal sites adjacent to two West Greenland ice streams. Core MSM-520 has a steadily decreasing Os signal over the last 10 kyr (187Os/188Os = 1.35–0.81). In contrast, Os isotopes from core DA00-06 (proximal to the calving front of Jakobshavn Isbræ) highlight four stages of ice stream retreat and advance over the past 10 kyr (187Os/188Os = 2.31; 1.68; 2.09; 1.47). Our high-resolution chemostratigraphic records provide vital benchmarks for ice-sheet modelers as we attempt to better constrain the future response of major ice sheets to climate change. Variations in Os isotope composition from sediment and macro-algae (seaweed) sourced from regional and global settings serve to emphasize the overwhelming effect weathering sources have on seawater Os isotope composition. Further, these findings demonstrate that the residence time of Os is shorter than previous estimates of ∼104 yr
Z/γ∗ plus multiple hard jets in high energy collisions.

We present a description of the production of di-lepton pair production (through Z boson and virtual photon) in association with at least two jets. This calculation adds to the fixed-order accuracy the dominant logarithms in the limit of large partonic centre-of-mass energy to all orders in the strong coupling αs. This is achieved within the framework of High Energy Jets. This calculation is made possible by extending the high energy treatment to take into account the multiple t-channel exchanges arising from Z and γ∗-emissions off several quark lines. The correct description of the interference effects from the various t-channel exchanges requires an extension of the subtraction terms in the all-order calculation. We describe this construction and compare the resulting predictions to a number of recent analyses of LHC data. The description of a wide range of observables is good, and, as expected, stands out from other approaches in particular in the regions of large dijet invariant mass and large dijet rapidity spans
The panchromatic spectroscopic evolution of the classical CO nova V339
  Del (Nova Del 2013) until X-ray turnoff

Classical novae are the product of thermonuclear runaway-initiated explosions
occurring on accreting white dwarfs. V339 Del (Nova Delphinus 2013) was one of
the brightest classical novae of the last hundred years. Spectroscopy and
photometry are available from $\gamma$-rays through infrared at stages that
have frequently not been well observed. The complete data set is intended to
provide a benchmark for comparison with modeling and for understanding more
sparsely monitored historical classical and recurrent novae. This paper is the
first in the series of reports on the development of the nova. We report here
on the early stages of the outburst, through the X-ray active stage. A time
sequence of optical, flux calibrated high resolution spectra was obtained with
the Nordic Optical Telescope (NOT) using FIES simultaneously, or
contemporaneously, with the Space Telescope Imaging Spectrograph (STIS) aboard
the Hubble Space Telescope during the early stages of the outburst. These were
supplemented with MERCATOR/HERMES optical spectra. High resolution IUE
ultraviolet spectra of OS And 1986, taken during the Fe curtain phase, served
as a template for the distance determination. We used standard plasma
diagnostics (e.g., [O III] and [N II] line ratios, and the H$\beta$ line flux)
to constrain electron densities and temperatures of the ejecta. Using Monte
Carlo modeling of the ejecta, we derived the structure, filling factor, and
mass from comparisons of the optical and ultraviolet line profiles.Comment: 14 pages, 18 figure