ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples

Self-consistent simulation of quantum wires defined by local oxidation of Ga[Al]As heterostructures

We calculate the electronic width of quantum wires as a function of their lithographic width in analogy to experiments performed on nanostructures defined by local oxidation of Ga[Al]As heterostructures. Two--dimensional simulations of two parallel oxide lines on top of a Ga[Al]As heterostructure defining a quantum wire are carried out in the framework of Density Functional Theory in the Local Density Approximation and are found to be in agreement with measurements. Quantitative assessment of the influence of various experimental uncertainties is given. The most influential parameter turns out to be the oxide line depth, followed by its exact shape and the effect of background doping (in decreasing order).Comment: 5 pages, 6 figures; revised figures, clarified tex

A method of measuring the thermal conductivity of liquids

We described the development of an apparatus for the determination of the thermal conductivity of liquids. The apparatus is suitable for all kinds of liquids, including the strongest acids. From a given time we pass an electric current through a thin straight wire, placed in a homogeneous material of which the thermal conductivity is to be measured. The constant heat production in the wire causes a cylindrical temperature field in the material. The rise of temperature depends on the thermal properties of the material. The apparatus used is sketched in figure 1. The drawback of the old methods, viz the convection current of the liquid is evaded, because the time in which the measurement is done, is so short that the density differences can not develop a disturbing convection current within this time. The results of the measurements are given in table II. For water we found the same dependence of the thermal conductivity on temperature as F. Schmidt and W. Sellschopp (see figure 9)

The atmospheric response to a thermohaline circulation collapse: scaling relations for the Hadley circulation and the response in a coupled climate model

The response of the tropical atmosphere to a collapse of the thermohaline circulation (THC) is investigated by comparing two 5-member ensemble runs with a coupled climate model (CCM), the difference being that in one ensemble a hosing experiment was performed. An extension of the Held–Hou–Lindzen model for the Hadley circulation is developed to interpret the results. The forcing associated with a THC collapse is qualitatively similar to, but smaller in amplitude than, the solstitial shift from boreal summer to winter. This forcing results from reduced ocean heat transport creating an anomalous cross-equatorial SST gradient. The small amplitude of the forcing makes it possible to arrive at analytical expressions using standard perturbation theory. The theory predicts the latitudinal shift between the Northern Hemisphere (NH) and Southern Hemisphere (SH) Hadley cells, and the relative strength of the anomalous cross-equatorial Hadley cell compared to the solstitial cell. The poleward extent of the Hadley cells is controlled by other physics. In the NH the Hadley cell contracts, while zonal velocities increase and the subtropical jet shifts equatorward, whereas in the SH cell the opposite occurs. This behavior can be explained by assuming that the poleward extent of the Hadley cell is determined by baroclinic instability: it scales with the inverse of the isentropic slopes. Both theory and CCM results indicate that a THC collapse and changes in tropical circulation do not act in competition, as a possible explanation for abrupt climate change; they act in concert.<br/

Azimuthal ion movement in HiPIMS plasmas -- Part I: velocity distribution function

Magnetron sputtering discharges feature complex magnetic field configurations to confine the electrons close to the cathode surface. This magnetic field configuration gives rise to a strong electron drift in azimuthal direction, with typical drift velocities on the order of \SI{100}{\kilo\meter\per\second}. In high power impulse magnetron sputtering (HiPIMS) plasmas, the ions have also been observed to follow the movement of electrons with velocities of a few \si{\kilo\meter\per\second}, despite being unmagnetized. In this work, we report on measurements of the azimuthal ion velocity using spatially resolved optical emission spectroscopy, allowing for a more direct measurement compared to experiments performed using mass spectrometry. The azimuthal ion velocities increase with target distance, peaking at about \SI{1.55}{\kilo\meter\per\second} for argon ions and \SI{1.25}{\kilo\meter\per\second} for titanium ions. Titanium neutrals are also found to follow the azimuthal ion movement which is explained with resonant charge exchange collisions. The experiments are then compared to a simple test-particle simulation of the titanium ion movement, yielding good agreement to the experiments when only considering the momentum transfer from electrons to ions via Coulomb collisions as the only source of acceleration in azimuthal direction. Based on these results, we propose this momentum transfer as the primary source for ion acceleration in azimuthal direction

The lanthanum(III) molybdate(VI) La4Mo7O27

Crystals of the ortho­rhom­bic phase La4Mo7O27 (lanthanum molybdenum oxide) were obtained from a non-stoichiometric melt in the pseudo-ternary system La2O3–MoO3–B2O3. In the crystal structure, distorted square-anti­prismatic [LaO8] and monocapped square-anti­prismatic [LaO9] polyhedra are connected via common edges and faces into chains along [010]. These chains are arranged in layers that alternate with layers of [MoO4] and [MoO5] polyhedra parallel to (001). In the molybdate layers, a distorted [MoO5] trigonal bipyramid is axially connected to two [MoO4] tetra­hedra, forming a [Mo3O11] unit

Unexpected non-Wigner behavior in level-spacing distributions of next-nearest-neighbor coupled XXZ spin chains

The level-spacing distributions of XXZ spin chains with next-nearest-neighbor couplings are studied under periodic boundary conditions. We confirm that integrable XXZ spin chains mostly have the Poisson distribution as expected. On the contrary, the level-spacing distributions of next-nearest-neighbor coupled XXZ chains are given by non-Wigner distributions. It is against the expectations, since the models are nonintegrable.Comment: 4 pages, 4 figures, to be published in Physical Review

Neodymium(III) molybdenum(VI) borate, NdBO2MoO4

Single crystals of NdBO2MoO4 were obtained from a molybdenum oxide–boron oxide flux under an air atmosphere. The structure features double chains of edge- and face-sharing distorted [NdO10] bicapped square-anti­prisms, which are linked by rows of isolated [MoO4] tetra­hedra and by zigzag chains of corner-sharing [BO3] groups, all of them running along the b axis. The chains of [NdO10], chains of [BO3] and rows of [MoO4] groups are arranged in layers parallel to the bc plane

Soil microbial biodiversity promotes crop productivity and agro-ecosystem functioning in experimental microcosms

Soil biota contribute substantially to multiple ecosystem functions that are key for geochemical cycles and plant performance. However, soil biodiversity is currently threatened by land-use intensification, and a mechanistic understanding of how soil biodiversity loss interacts with the myriad of intensification elements (e.g., the application of chemical fertilizers) is still unresolved. Here we experimentally simplified soil biological communities in microcosms to test whether changes in the soil microbiome influenced soil multifunctionality including crop productivity (leek, Allium porrum). Additionally, half of microcosms were fertilized to further explore how different levels of soil biodiversity interact with nutrient additions. Our experimental manipulation achieved a significant reduction of soil alpha-diversity (45.9 % reduction in bacterial richness, 82.9 % reduction in eukaryote richness) and resulted in the complete removal of key taxa (i.e., arbuscular mycorrhizal fungi). Soil community simplification led to an overall decrease in ecosystem multifunctionality; particularly, plant productivity and soil nutrient retention capacity were reduced with reduced levels of soil biodiversity. Ecosystem multifunctionality was positively correlated with soil biodiversity (R = 0.79). Mineral fertilizer application had little effect on multifunctionality compared to soil biodiversity reduction, but it reduced leek nitrogen uptake from decomposing litter by 38.8 %. This suggests that natural processes and organic nitrogen acquisition are impaired by fertilization. Random forest analyses revealed a few members of protists (i.e., Paraflabellula), Actinobacteria (i.e., Micolunatus), and Firmicutes (i.e., Bacillus) as indicators of ecosystem multifunctionality. Our results suggest that preserving the diversity of soil bacterial and eukaryotic communities within agroecosystems is crucial to ensure the provisioning of multiple ecosystem functions, particularly those directly related to essential ecosystem services such as food provision