Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

Formal comparison of SUSY in the nuclear U(6/2) model and in quantum field theory

A nuclear physics example of the U(6/2) supersymmetry group is considered. It is shown that this group contains a supersymmetric subgroup with a structure similar to the SUSY model of the quantum field theory (QFT). A comparison of two models help to clarify the relation between the supersymmetry schemes of QFT and of nuclear physics. Using this similarity a relation between the numbers of the bosonic and fermionic states similar to the fundamental relation in QFT is obtained. For those supermultiplets with at least two fermions the number of the bosonic and fermionic states are equal as in QFT.Comment: 11 pages and one eps-figure. Phys.Rev.C (1999) in pres

Longitudinal transformation of nitrogen and carbon in the hyporheic zone of an N-rich stream: A combined modelling and field study

A combined modelling and field study approach was used to examine biogeochemical functioning of the hyporheic zone in two gravel bars in an N-rich fourth-order stream (River Hers, south-west France). Surfacewater and interstitial water were sampledmonthly (August 1994–January 1995), the latter in a network of 29 piezometers in the first gravel bar and 17 in the second. In both gravel bars, the hyporheic zone was created only by advected channelwater without any connectionwith groundwater. Longitudinal chemical profiles of Dissolved Organic Carbon (DOC), nitrate (NO3–N), ammonium (NH4–N) and Dissolved Oxygen (DO) were established for both gravel bars. Ambient and potential denitrification weremeasured in the laboratory during the same period using the acetylene inhibition technique. Factors limiting denitrification were also examined by testing the separate effects of nitrate or nitrate + carbon additions. A 1D reactive-transport model was used to simulate longitudinal transformation of nitrogen in the hyporheic zone, and to estimate the role of organic matter (DOC and POC) in the biogeochemical functioning of the hyporheic zone. Denitrification measurements with nitrate and nitrate + carbon additions both showed increased denitrification, suggesting that denitrification might not be C-limited at this site. Observations and model results showed the hyporheic zone to be a sink of DOC and nitrate, but DOC consumption appeared insufficient to explain nitrate depletion measured in the two gravel bars. Field data were better modelled when an additional DOC source from the POC fraction degraded by anaerobic respiration was included in the model

A standardised method for measuring in situ denitrification in shallow aquifers: numerical validation and measurements in riparian wetlands

A tracer test to examine in situ denitrification in shallow groundwater by a piezometer with a packer system used bromide as a tracer of dilution and acetylene (10%) to block the denitrification process at the nitrous oxide stage. During the test, dissolved oxygen, nitrate (NO3-), bromide (Br-), nitrous oxide (N2O) and dissolved organic carbon (DOC) were measured. To calibrate the experimental method, comparison with numerical simulations of the groundwater transfer were carried out, taking into account the environmental characteristics. The method was tested by measurements undertaken in different environmental conditions (geology, land use and hydrology) in two riparian wetlands. Denitrification rates measured by this method ranged from 5.7 10-6 g N-NO3-L-1 h-1 to 1.97 10-3 g N-NO3-L-1 h-1 The method is applicable in shallow aquifers with a permeability from 10-2 to 10-4m s-1

Tests on a mock-up of the feedback controlled matching options for the ITER ICRH system

For the ICRH of ITER 20MW must be coupled to the plasma in the 40-55MHz frequency band via an array of 24 radiating shorted straps fed by four generators. The matching system must provide automatic matching control on the mean load provided by the plasma and be resilient (|Γ| < 0.2) to a wide range of fast antenna load excursions occurring in ELMy plasmas. Furthermore, good control of the current distribution in the strap array must be possible for the various heating and current drive scenarios. Two load resilient matching options have been considered for ITER: the 4 “Conjugate-T” (CT) and the 4 hybrids ones, the first being presently considered as a back-up option. Automatic control of these 2 options is presently developed, and tested for optimization on a low-powered scaled mock-up. Successful implementation of the simultaneous feedback control of 11 actuators for the matching of the 4CT and for the control of the toroidal phasing has already been achieved. The matching and the array current control of the 3dB hybrid option is provided by simultaneous feedback control of the decouplers and double stub tuners (in total 23 actuators) and is being progressively implemented. The simultaneous control of matching and antenna current has already been successfully tested on part of the array

Nitrogen dynamics in the shallow groundwater of a riparian wetland zone of the Garonne, SW France: nitrate inputs, bacterial densities, organic matter supply and denitrification measurements

This study highlights the role of interactions between surface and sub-surface water of the riparian zone of a large river (the Garonne, SW France). Information is given about the role of surface water in supplying Dissolved Organic Carbon (DOC ) to the riparian zone for nitrate removal processes. The densities of bacteria (up to 3.3106 cell m L-1) in groundwater are strongly conditioned by the water moving during flood events. Total bacterial densities in groundwater were related to surface water bacterial densities. In sediment, total bacteria are attached mainly to fine particles (90 % in the fraction < 1 mm). Spatial variations in organic carbon and nitrate content in groundwater at the site studied are correlated with exchanges between the groundwater and the river, from the upstream to the downstream part of the meander. Total bacterial densities, nitrate and decressing organic carbon concentrations follow the same pattern. These results suggest that, in this kind of riparian wetland, nitrate from alluvial groundwater influenced by agricultural practices may be denitrified by bacteria in the presence of organic carbon from river surface water

Long range absorption in the scattering of 6He on 208Pb and 197Au at 27 MeV

Quasi-elastic scattering of 6He at E_lab=27 MeV from 197Au has been measured in the angular range of 6-72 degrees in the laboratory system employing LEDA and LAMP detection systems. These data, along with previously analysed data of 6He + 208Pb at the same energy, are analyzed using Optical Model calculations. The role of Coulomb dipole polarizability has been investigated. Large imaginary diffuseness parameters are required to fit the data. This result is an evidence for long range absorption mechanisms in 6He induced reactions.Comment: 10 pages, 10 figures, minor corrections. To appear in Nucl. Phys.