Evolutionary Inference via the Poisson Indel Process

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classical evolutionary process, the TKF91 model, is a continuous-time Markov chain model comprised of insertion, deletion and substitution events. Unfortunately this model gives rise to an intractable computational problem---the computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a new stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The new model is closely related to the TKF91 model, differing only in its treatment of insertions, but the new model has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared to separate inference of phylogenies and alignments.Comment: 33 pages, 6 figure

Political Ecology of REDD+ in Indonesia

Indonesia’s commitment to reducing land-based greenhouse gas emissions significantly includes the expansion of conservation areas, but these developments are not free of conflicts. This book provides a comprehensive analysis of agrarian conflicts in the context of the implementation of REDD+ (Reducing Emissions from Deforestation and Forest Degradation) and forest carbon offsetting in Indonesia, a country where deforestation is a major issue. The author analyzes new kinds of transnational agrarian conflicts which have strong implications for global environmental justice in the REDD+ pilot province of Jambi on the island of Sumatra. The chapters cover: the rescaling of the governance of forests; privatization of conservation; and the transnational dimensions of agrarian conflicts and peasants’ resistance in the context of REDD+. The book builds on an innovative conceptual approach linking political ecology, politics of scale and theories of power. It fills an important knowledge and research gap by focusing on the socially differentiated impacts of REDD+ and new forest carbon offsetting initiatives in Southeast Asia, providing a multi-scalar perspective. It is aimed at scholars in the areas of political ecology, human geography, climate change mitigation, forest and natural resource management, as well as environmental justice and agrarian studies

DC-assisted microwave quenching of YBa2Cu3O7-{\delta} coplanar waveguide to a highly dissipative state

The paper reports on finding the effect of a strong change in the microwave losses in an HTS-based coplanar waveguide (CPW) at certain values of the input power Pin and direct current Idc. CPW on the basis of 150 nm thick YBa2Cu3O7-{\delta} epitaxial film on a single crystal MgO substrate was studied experimentally. A sharp and reversible transition of the CPW into a strongly dissipative state at the certain meanings of Pin and Idc depending on temperature was observed. Apparently the effect can be explained by self-heating of HTS structure caused by magnetic flux flow under the joint influence of MW and DC.Comment: 9 pages, 5 figures, 17 reference

Simulating the Electroweak Phase Transition in the SU(2) Higgs Model

Numerical simulations are performed to study the finite temperature phase transition in the SU(2) Higgs model on the lattice. In the presently investigated range of the Higgs boson mass, below 50 GeV, the phase transition turns out to be of first order and its strength is rapidly decreasing with increasing Higgs boson mass. In order to control the systematic errors, we also perform studies of scaling violations and of finite volume effects.Comment: 46 pages with 16 figures, DESY-94-15

Sensitivity of depth of maximum and absorption depth of EAS to hadron production mechanism

Comparison of experimental data on depth of extensive air showers (EAS) development maximum in the atmosphere, T sub M and path of absorption, lambda, in the lower atmosphere of EAS with fixed particle number in the energy region eV with the results of calculation show that these parameters are sensitive mainly to the inelastic interaction cross section and scaling violation in the fragmentation and pionization region. The data are explained in a unified manner within the framework of a model in which scaling is violated slightly in the fragmentation region and strongly in the pionization region at primary cosmic rays composition close to the normal one and a permanent increase of inelastic interaction cross section. It is shown that, while interpreting the experimental data, disregard of two methodical points causes a systematic shift in T sub M: (1) shower selection system; and (2) EAS electron lateral distribution when performing the calculations on basis of which the transfer is made from the Cerenkov pulse FWHM to the depth of shower maximum, T sub M

O(αsa)O(\alpha_{s}a) matching coefficients for axial vector current and ΔB\Delta B==2 operator

We present a calculation of the perturbative matching coefficients including mixing with higher dimensional operators for the temporal component of the heavy-light axial current, $A_{4}$, and the $\Delta B=2$ operator, $O_S$. For $A_{4}^{\scriptsize static, NRQCD}$, calculations with various RG-improved gauge actions are peformed. Matching coefficients with NRQCD and heavy-clover actions are also compared.Comment: LATTICE99 (Heavy Quarks), 3 pages, 2 figures, espcrc2.st

First report of molecular detection of Carnivore bocaparvovirus 1 (former CnMV: Canine Minute Virus) in Chilean domestic dogs

Carnivore bocaparvovirus 1 (CnMV) infects dogs worldwide and can be responsible for different clinical signs in neonates and bitches during gestation. There is a limited number of CnMV sequences available in the NCBI database, so far. The present preliminary study aimed to obtain evidence of CnMV infection status among domestic dogs in Chile and evaluate the genetic relatedness of the sequences obtained with any type of bocaparvovirus already reported. Two partial nucleotide sequences of the VP2 coding gene were obtained from forty blood samples and compared with 23 available sequences of Carnivore bocaparvovirus from 1 to 6. Chilean sequences grouped within Carnivore bocaparvovirus 1 group, being sequence 5434 (Accession number, MH544475) more similar to the Japanese strain HM-6 and sequence 5423 (Accession number, MH544476) to the Chinese strain SH1

The pandemic that shocked managers across the world:The impact of the COVID-19 crisis on leadership behavior

In March 2020, the COVID-19 virus turned into a pandemic that hit organizations globally. This pandemic qualifies as an exogenous shock. Based on the threat-rigidity hypothesis, we hypothesize that this shock led to an increase in directive leadership behavior. We also argue that this relationship depends on the magnitude of the crisis and on well-learned responses of managers. In our empirical analysis we employ a differences-in-differences design with treatment intensity and focus on the period of the first lockdown, March until June 2020. Using a dataset covering monthly data for almost 27,000 managers across 48 countries and 32 sectors for January 2019 to December 2020, we find support for the threat-rigidity hypothesis. During the first lockdown, directive leadership increased significantly. We also find that this relationship is moderated by COVID-19 deaths per country, the sectoral working from home potential, and the organizational level of management. Our findings provide new evidence how large exogenous shocks like COVID-19 can impact leadership behavior

Electroweak phase transition by four dimensional simulations

The finite temperature phase transition in the SU(2)-Higgs model at a Higgs boson mass $M_H \simeq 35$ GeV is studied in numerical simulations on four dimensional lattices with time-like extensions up to $L_t=5$. $T_c/M_H$ is extrapolated to the continuum limit and a comparison with the perturbative prediction is made. A one-loop calculation to the coupling anisotropies of the SU(2)-Higgs model on lattices with asymmetric lattice spacings is presented. Our numerical simulations show that the above perturbative result is applicable in the phenomenologically interesting parameter region.Comment: 3 pages, Latex, 3 figures, Talk presented at LATTICE96(electroweak) by Z. Fodo