Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)

CV and BY were supported by the the Austrian Science Fund (FWF; DK W1225-B20); MK and HK were supported by the the Austrian Science Fund (FWF; SFB F6101 and F6106). This work was also partially funded by the Vienna Science and Technology Fund (WWTF) (10.47379/MA16061 to CK). LCM’s research was funded by the School of Biology at the University of StAndrews.Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim to quantify this variation, account for it during inference procedures, and ultimately determine the causal processes behind it. Since sequential observations along chromosomes are not independent, it is unsurprising that autocorrelation patterns have been observed e.g., in human base composition. In this article, we develop a class of Hidden Markov Models (HMMs) called oHMMed (ordered HMM with emission densities, the corresponding R package of the same name is available on CRAN): They identify the number of comparably homogeneous regions within autocorrelated observed sequences. These are modelled as discrete hidden states; the observed data points are realisations of continuous probability distributions with state-specific means that enable ordering of these distributions. The observed sequence is labelled according to the hidden states, permitting only neighbouring states that are also neighbours within the ordering of their associated distributions. The parameters that characterise these state-specific distributions are inferred.Peer reviewe

Azimuthal anisotropy of charged jet production in root s(NN)=2.76 TeV Pb-Pb collisions

We present measurements of the azimuthal dependence of charged jet production in central and semi-central root s(NN) = 2.76 TeV Pb-Pb collisions with respect to the second harmonic event plane, quantified as nu(ch)(2) (jet). Jet finding is performed employing the anti-k(T) algorithm with a resolution parameter R = 0.2 using charged tracks from the ALICE tracking system. The contribution of the azimuthal anisotropy of the underlying event is taken into account event-by-event. The remaining (statistical) region-to-region fluctuations are removed on an ensemble basis by unfolding the jet spectra for different event plane orientations independently. Significant non-zero nu(ch)(2) (jet) is observed in semi-central collisions (30-50% centrality) for 20 <p(T)(ch) (jet) <90 GeV/c. The azimuthal dependence of the charged jet production is similar to the dependence observed for jets comprising both charged and neutral fragments, and compatible with measurements of the nu(2) of single charged particles at high p(T). Good agreement between the data and predictions from JEWEL, an event generator simulating parton shower evolution in the presence of a dense QCD medium, is found in semi-central collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Forward-central two-particle correlations in p-Pb collisions at root s(NN)=5.02 TeV

Two-particle angular correlations between trigger particles in the forward pseudorapidity range (2.5 2GeV/c. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B. V.Peer reviewe

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Pseudorapidity and transverse-momentum distributions of charged particles in proton-proton collisions at root s=13 TeV

The pseudorapidity (eta) and transverse-momentum (p(T)) distributions of charged particles produced in proton-proton collisions are measured at the centre-of-mass energy root s = 13 TeV. The pseudorapidity distribution in vertical bar eta vertical bar <1.8 is reported for inelastic events and for events with at least one charged particle in vertical bar eta vertical bar <1. The pseudorapidity density of charged particles produced in the pseudorapidity region vertical bar eta vertical bar <0.5 is 5.31 +/- 0.18 and 6.46 +/- 0.19 for the two event classes, respectively. The transverse-momentum distribution of charged particles is measured in the range 0.15 <p(T) <20 GeV/c and vertical bar eta vertical bar <0.8 for events with at least one charged particle in vertical bar eta vertical bar <1. The evolution of the transverse momentum spectra of charged particles is also investigated as a function of event multiplicity. The results are compared with calculations from PYTHIA and EPOS Monte Carlo generators. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Centrality evolution of the charged-particle pseudorapidity density over a broad pseudorapidity range in Pb-Pb collisions at root s(NN)=2.76TeV

Peer reviewe

Elliptic flow of muons from heavy-flavour hadron decays at forward rapidity in Pb-Pb collisions at root s(NN)=2.76TeV

The elliptic flow, v(2), of muons from heavy-flavour hadron decays at forward rapidity (2.5 <y <4) is measured in Pb-Pb collisions at root s(NN)= 2.76TeVwith the ALICE detector at the LHC. The scalar product, two- and four-particle Q cumulants and Lee-Yang zeros methods are used. The dependence of the v(2) of muons from heavy-flavour hadron decays on the collision centrality, in the range 0-40%, and on transverse momentum, p(T), is studied in the interval 3 <p(T)<10 GeV/c. A positive v(2) is observed with the scalar product and two-particle Q cumulants in semi-central collisions (10-20% and 20-40% centrality classes) for the p(T) interval from 3 to about 5GeV/c with a significance larger than 3 sigma, based on the combination of statistical and systematic uncertainties. The v(2) magnitude tends to decrease towards more central collisions and with increasing pT. It becomes compatible with zero in the interval 6 <p(T)<10 GeV/c. The results are compared to models describing the interaction of heavy quarks and open heavy-flavour hadrons with the high-density medium formed in high-energy heavy-ion collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V.Peer reviewe

Measurement of charged jet production cross sections and nuclear modification in p-Pb collisions at root s(NN)=5.02 TeV

Charged jet production cross sections in p-Pb collisions at root s(NN) = 5.02 TeV measured with the ALICE detector at the LHC are presented. Using the anti-k(T) algorithm, jets have been reconstructed in the central rapidity region from charged particles with resolution parameters R = 0.2 and R = 0.4. The reconstructed jets have been corrected for detector effects and the underlying event background. To calculate the nuclear modification factor, R-pPb, of charged jets in p-Pb collisions, a pp reference was constructed by scaling previously measured charged jet spectra at root s = 7 TeV. In the transverse momentum range 20Peer reviewe

Modelling of low probability high impact events

In vielen Problemstellungen ist es erforderlich Verluste zu modellieren, verursacht durch den zugrundeliegenden Prozess, der eine große Anzahl von Ereignissen mit geringer Verlusthöhe und wenige Ereignisse mit sehr hohen Verlusten erzeugt. Prominente Beispiele sind Naturkatastrophen (wie beispielsweise Erdbeben, Wirbelstürme, Tornados), Betriebsverluste in stark regulierten Institutionen oder Versicherungsfälle. In jedem Fall kann die Gesamtverlustverteilung mit einer sogenannten zusammengesetzten Verteilung modelliert werden, bei der zwei getrennte Verteilungen zusammengeführt werden, die die Anzahl der Ereignisse und ihre Verlusthöhe beschreiben. Letzteres kann weiter in das empirische Verteilungszentrum und den Verteilungsrand aufgeteilt werden. Diese Unterscheidung erlaubt die Modellierung der Aspekte hoher Wahrscheinlichkeit mit geringer Auswirkung und niedriger Wahrscheinlichkeit mit hoher Auswirkung der zugrunde liegenden Daten mittels einer empirischen Verteilungsfunktion bzw. einer kontinuierlichen Verteilung, die jeweils durch das Glivenko-Cantelli-Theorem und der Extremwerttheorie gerechtfertigt sind. Das entwickelte Model wird dann auf eine Untersuchung der jährlichen Gesamtverluste durch Tornados in den Vereinigten Staaten von 1988 bis 2017 angewendet. Basierend auf theoretischen Überlegungen und statistischen Nachweisen wird die generalisierte Pareto-Verteilung gewählt. Dies wird dann mit der "minimum distance estimation" Methode mittels der Anderson-Darling-Distanz kalibriert. Die Häufigkeitsanalyse zeigt, dass die negative Binomialverteilung eine gute Beschreibung der jährlichen Tornado-Zählungen liefert. Die daraus resultierende zusammengesetzte negativ Binomial Verteilung bietet eine realistische Beschreibung der jährlichen Verlustereignisse und kann um saisonale und räumliche Effekte erweitert werden.In many real world phenomena the need for modelling of losses caused by an underlying process that generates both large number of occurrences with minor losses and occurrences with severe impact exists. Prominent examples are natural disasters (earthquakes, hurricanes, tornadoes etc.), operational losses in highly regulated institutions or claims generated by an insurance policy. In each case, the aggregated loss distribution can be modelled with a so called compound model that is a combination of two separate distributions describing the number of events and their severities. The latter can be further split into the empirical body and tail. This distinction allows the modelling of the high-probability-low impact and low-probability-high-impact aspects of the underlying data with an empirical distribution function and a continuous distribution as justified by the Glivenko–Cantelli theorem and the extreme value theory, respectively. The developed model is then applied to a study of yearly total losses caused by tornadoes in the United States from 1988 till 2017. Based on theoretical considerations and empirical evidence the Generalized Pareto Distribution is chosen to model tail events separated from the empirical body by a threshold of $50M. It is then calibrated applying the minimum distance estimation with the Anderson-Darling distance. The frequency analysis reveals that the negative binomial distribution provides a good fit of yearly tornado counts. The resulting compound negative binomial model provides a realistic description of yearly loss events and can be further extended to include seasonal and spatial effects

U-Pb Zircon Dating of Migmatitic Paragneisses and Garnet Amphibolite from the High Pressure Seve Nappe Complex in Kittelfjäll, Swedish Caledonides

The Seve Nappe Complex exposed in the Kittelfjäll area of the northern Scandinavian Caledonides comprises a volcano-sedimentary succession representing the Baltica passive margin, which was metamorphosed during the Iapetus Ocean closure. Garnet amphibolites, together with their host migmatitic paragneisses, record a potential (U)HP event followed by decompression-driven migmatization. The garnet amphibolites were originally thought to represent retrogressively altered granulites. The petrological and geochemical features of a studied garnet amphibolite allow for speculation about a peridotitic origin. Zirconium (Zr) content in rutile inclusions hosted in garnet in paragneisses points to near-peak temperatures between 738 ◦C and 780 ◦C, which is in agreement with the c. 774 ◦C obtained from the matrix rutile in the garnet amphibolite. The matrix rutile in multiple paragneiss samples records temperatures below 655 ◦C and 726 ◦C. Whereas the LA-ICP-MS U-Pb dating of zircon cores revealed the age spectrum from Paleoproterozoic to early Paleozoic, suggesting a detrital origin of zircon cores in paragneisses, the metamorphic zircon rims show an Early Ordovician cluster c. 475–469 Ma. Additionally, zircon cores and rims from the garnet amphibolite yielded an age of c. 473 Ma. The REE patterns of the Caledonian zircon rims from the paragneisses show overall low LREE concentrations, different from declining to rising trends in HREE (LuN/GdN = 0.49–38.76). Despite the textural differences, the cores and rims in zircon from the garnet amphibolite show similar REE patterns of low LREE and flat to rising HREE (LuN/GdN = 3.96–65.13). All zircon rims in both lithologies display a negative Eu anomaly. Hence, we interpret the reported ages as the growth of metamorphic zircon during migmatization, under granulite facies conditions related to exhumation from (U)HP conditions.National Science Centre "CALSUB" grant 2014/14/E/ST10/00321Polish National Agency for the Academic Exchange scholarship PPN/IWA/2018/1/00046/U/000