Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its ...features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/
We implement the proof of principle for the quantum walk of one ion in a linear ion trap. With a single-step fidelity exceeding 0.99, we perform three steps of an asymmetric walk on the line. We ...clearly reveal the differences to its classical counterpart if we allow the walker or ion to take all classical paths simultaneously. Quantum interferences enforce asymmetric, nonclassical distributions in the highly entangled degrees of freedom (of coin and position states). We theoretically study and experimentally observe the limitation in the number of steps of our approach that is imposed by motional squeezing. We propose an altered protocol based on methods of impulsive steps to overcome these restrictions, allowing to scale the quantum walk to many, in principal to several hundreds of steps.
Past climates inform our future Tierney, Jessica E; Poulsen, Christopher J; Montañez, Isabel P ...
Science (American Association for the Advancement of Science),
11/2020, Letnik:
370, Številka:
6517
Journal Article
Recenzirano
Odprti dostop
As the world warms, there is a profound need to improve projections of climate change. Although the latest Earth system models offer an unprecedented number of features, fundamental uncertainties ...continue to cloud our view of the future. Past climates provide the only opportunity to observe how the Earth system responds to high carbon dioxide, underlining a fundamental role for paleoclimatology in constraining future climate change. Here, we review the relevancy of paleoclimate information for climate prediction and discuss the prospects for emerging methodologies to further insights gained from past climates. Advances in proxy methods and interpretations pave the way for the use of past climates for model evaluation-a practice that we argue should be widely adopted.
Periprocedural thrombus fragmentation is a relevant risk in endovascular stroke treatment. Because factors influencing its occurrence are largely unknown, this study addresses a potential ...relationship between thrombus histology and clot stability.
Eighty-five patients with anterior circulation stroke treated with thrombectomy were included in this retrospective study. The number and location of emboli after retrieving the primary thrombus, the number of maneuvers, and TICI scores were evaluated. H&E and neutrophil elastase staining of retrieved clots was performed, and semiquantitative measurements of thrombus components were correlated with procedural parameters.
An inverse correlation between maneuvers required for thrombus retrieval and the number of distal and intermediate emboli was observed (Spearman
, -0.23;
= .032). Younger patients were at higher risk for periprocedural thrombus fragmentation (Spearman
, -0.23;
= .032). Bridging thrombolysis tended to be associated with fewer maneuvers (2 vs 3,
= .054) but more emboli (1 vs 0,
= .067). While no consistent correlation between procedural parameters and red/white blood cells and fibrin-/platelet fractions could be found, higher amounts of neutrophil elastase-positive cells within the thrombus were independently associated with the occurrence of multiple emboli (adjusted OR, 4.6; 95% CI, 1.1-19.7;
= .041) and lower rates of complete recanalization (adjusted OR, 0.3; 95% CI, 0.1-0.9;
= .050).
Younger age, easy-to-retrieve thrombi, and bridging thrombolysis may be risk factors for periprocedural thrombus fragmentation. Findings from standard histologic stains did not provide insight into thrombectomy-relevant thrombus stability. However, higher neutrophil levels in the thrombus tissue were related to an increased risk of periprocedural thrombus fragmentation. This observation aligns with the proposed thrombolytic capacity of neutrophil elastase and points to its potential clinical relevance in the context of stroke thrombectomy.
We describe the calculation of the three-loop QCD corrections to quark and gluon form factors. The relevant three-loop Feynman diagrams are evaluated and the resulting three-loop Feynman integrals ...are reduced to a small set of known master integrals by using integration-by-parts relations. Our calculation confirms the recent results by Baikov et al. for the three-loop form factors. In addition, we derive the subleading
terms for the fermion-loop type contributions to the three-loop form factors which are required for the extraction of the fermionic contributions to the four-loop quark and gluon collinear anomalous dimensions. The finite parts of the form factors are used to determine the hard matching coefficients for the Drell-Yan process and inclusive Higgs-production in soft-collinear effective theory.
We present the
Mathematica package
HypExp which allows to expand hypergeometric functions
F
J
−
1
J
around integer parameters to arbitrary order. At this, we apply two methods, the first one being ...based on an integral representation, the second one on the nested sums approach. The expansion works for both symbolic argument
z and unit argument. We also implemented new classes of integrals that appear in the first method and that are, in part, yet unknown to
Mathematica.
Title of program:HypExp
Catalogue identifier:ADXF_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/ADXF_v1_0
Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland
Licence:none
Computers:Computers running
Mathematica under
Linux or
Windows
Operating system:
Linux, Windows
Program language:
Mathematica
No. of bytes in distributed program, including test data, etc.:739 410
No. of lines in distributed program, including test data, etc.:89 747
Distribution format:tar.gz
Other package needed:the package
HPL, included in the distribution
External file required:none
Nature of the physical problem:Expansion of hypergeometric functions around integer-valued parameters. These are needed in the context of dimensional regularization for loop and phase space integrals.
Method of solution:Algebraic manipulation of nested sums and integral representation.
Restrictions on complexity of the problem:Limited by the memory available
Typical running time:Strongly depending on the problem and the availability of libraries.
Using femtosecond time-resolved x-ray diffraction, we directly monitor the coherent lattice dynamics through an ultrafast charge-density-wave-to-metal transition in the prototypical Peierls system ...K(0.3)MoO(3) over a wide range of relevant excitation fluences. While in the low fluence regime we directly follow the structural dynamics associated with the collective amplitude mode; for fluences above the melting threshold of the electronic density modulation we observe a transient recovery of the periodic lattice distortion. We can describe these structural dynamics as a motion along the coordinate of the Peierls distortion triggered by the prompt collapse of electronic order after photoexcitation. The results indicate that the dynamics of a structural symmetry-breaking transition are determined by a high-symmetry excited state potential energy surface distinct from that of the initial low-temperature state.
The glomerulus represents a highly structured filtration unit, composed of glomerular endothelial cells, mesangial cells, podocytes and parietal epithelial cells. During glomerulogenesis an intricate ...network of signaling pathways involving transcription factors, secreted factors and cell–cell communication is required to guarantee accurate evolvement of a functional, complex 3-dimensional glomerular architecture. Here, we want to provide an overview on the critical steps and relevant signaling cascades of glomerular development.
Mass extinction at the Cretaceous–Paleogene (K-Pg) boundary coincides with the Chicxulub bolide impact and also falls within the broader time frame of Deccan trap emplacement. Critically, though, ...empirical evidence as to how either of these factors could have driven observed extinction patterns and carbon cycle perturbations is still lacking. Here, using boron isotopes in foraminifera, we document a geologically rapid surface-ocean pH drop following the Chicxulub impact, supporting impact-induced ocean acidification as amechanism for ecological collapse in the marine realm. Subsequently, surface water pH rebounded sharply with the extinction of marine calcifiers and the associated imbalance in the global carbon cycle. Our reconstructed water-column pH gradients, combined with Earth system modeling, indicate that a partial ∼50% reduction in global marine primary productivity is sufficient to explain observed marine carbon isotope patterns at the K-Pg, due to the underlying action of the solubility pump. While primary productivity recovered within a few tens of thousands of years, inefficiency in carbon export to the deep sea lasted much longer. This phased recovery scenario reconciles competing hypotheses previously put forward to explain the K-Pg carbon isotope records, and explains both spatially variable patterns of change in marine productivity across the event and a lack of extinction at the deep sea floor. In sum, we provide insights into the drivers of the last mass extinction, the recovery of marine carbon cycling in a postextinction world, and the way in which marine life imprints its isotopic signal onto the geological record.
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