A Scaling for the Permeability of Loose Magma Mush Validated Using X‐Ray Computed Tomography of Packed Confectionary in 3D and Estimation Methods From 2D Crystal Shapes

Melt percolation through partially molten “mushy” regions of the crust underpins models for magma migration, accumulation, and processes that prime systems for eruption. Knowledge of the hydraulic properties of magma mush, specifically permeability, is required for accurate predictions of melt migration rates and accumulation timescales. Previous studies, validated for cuboidal crystal analogs, show that crystal shape exerts a first‐order control on the permeability, and is tested here for anisometric natural crystal shapes using X‐ray CT 3D data sets of magma mush analogs made from packed confectionary particles arranged randomly. We use a lattice‐Boltzmann fluid flow simulation tool to determine the permeability of the analogue melt phase network between the packed particles. We find excellent agreement with our data sets to within ∼0.1 log units, when the specific surface area is measured. To extend this to more typical cases where the specific surface area is unknown, we use the shape and size of the objects determined in both 3D and 2D to estimate the specific surface area assuming a cuboid approximation. These approximate solutions give good results to within ∼0.5 log units of the measured permeability and offer a method by which permeability could be estimated from a thin section of a cumulate or pluton sample. Our shape‐sensitive approach is more accurate than existing models for permeability of magma mush, most approximating natural crystal shapes to spheres. We therefore propose that these could be implemented in dynamic magma mush models for melt movement in the crust to produce more accurate flux predictions

Axial light emission and Ar metastable densities in a parallel plate dc micro discharge in steady state and transient regimes

Axial emission profiles in a parallel plate dc micro discharge (feedgas: argon; discharge gap d=1mm; pressure p=10Torr) were studied by means of time resolved imaging with a fast ICCD camera. Additionally, volt-ampere (V-A) characteristics were recorded and Ar* metastable densities were measured by tunable diode laser absorption spectroscopy (TDLAS). Axial emission profiles in the steady state regime are similar to corresponding profiles in standard size discharges (d=1cm, p=1Torr). For some discharge conditions relaxation oscillations are present when the micro discharge switches periodically between low current Townsend-like mode and normal glow. At the same time the axial emission profile shows transient behavior, starting with peak distribution at the anode, which gradually moves towards the cathode during the normal glow. The development of argon metastable densities highly correlates with the oscillating discharge current. Gas temperatures in the low current Townsend-like mode (T= 320-400K) and the high current glow mode (T=469-526K) were determined by the broadening of the recorded spectral profiles as a function of the discharge current.Comment: submitted to Plasma Sources Sci. Techno

Internal amplification controls have not been employed in fungal PCR hence potential false negative results

Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.Fundação para a Ciência e a Tecnologia (FCT

Breakthrough invasive fungal disease in patients receiving posaconazole primary prophylaxis: a 4-year study

AbstractPosaconazole (PSC) is currently recommended as primary prophylaxis in neutropenic patients with acute myeloid leukaemia (AML) and in allogenic haematopoietic stem cell transplantation (AHSCT) recipients with graft-versus-host disease (GVHD). Studies focusing on breakthrough invasive fungal disease (IFD) upon PSC prophylaxis show disparate results. In order to evaluate the incidence of IFD in patients on PSC prophylaxis and identify IFD risk factors, we carried out a retrospective study of all consecutive patients on PP from January 2007 to December 2010 in our hospital. Breakthrough IFDs were identified from the database of the central pharmacy and the French administrative database (PMSI), registering final medical diagnoses of hospitalized patients. Medical data were reviewed to study proven or probable IFD, according to EORTC/MSG definition. PSC plasma concentrations (PPC) were also retrieved. Poisson models were used for statistical analysis. Two hundred and seventy-nine patients received PSC prophylaxis for a median duration of 1.4 months (range 0.2–17.9). Proven (n = 6) or probable (n = 3) IFDs were diagnosed in nine cases (3.2%). IFD incidence rate per 100 person-month was 1.65 (95% CI, 0.79–2.97). IFDs were candidaemia (Candida glabrata, n = 2), pulmonary invasive aspergillosis (n = 3), disseminated fusariosis (n = 2) and pulmonary mucormycosis (n = 2). Seven deaths were reported, directly related to IFD in three patients (33.3%). First dosage of PPC under 0.3 mg/L was the single significant risk factor for IFD (RR, 7.77; 95% CI, 1.30–46.5; p 0.025). Breakthrough IFD in patients receiving PSC prophylaxis is rare but associated with a poor outcome. Low PSC plasma concentrations are associated with an increased risk of IFD

Collisional kinetics of non-uniform electric field, low-pressure, direct-current discharges in H2_{2}

A model of the collisional kinetics of energetic hydrogen atoms, molecules, and ions in pure H$_2$ discharges is used to predict H$_\alpha$ emission profiles and spatial distributions of emission from the cathode regions of low-pressure, weakly-ionized discharges for comparison with a wide variety of experiments. Positive and negative ion energy distributions are also predicted. The model developed for spatially uniform electric fields and current densities less than $10^{-3}$ A/m$^2$ is extended to non-uniform electric fields, current densities of $10^{3}$ A/m$^2$, and electric field to gas density ratios $E/N = 1.3$ MTd at 0.002 to 5 Torr pressure. (1 Td = $10^{-21}$ V m$^2$ and 1 Torr = 133 Pa) The observed far-wing Doppler broadening and spatial distribution of the H$_\alpha$ emission is consistent with reactions among H$^+$, H$_2^+$, H$_3^+$, and H$^-H$ ions, fast H atoms, and fast H$_2$ molecules, and with reflection, excitation, and attachment to fast H atoms at surfaces. The H$_\alpha$ excitation and H$^-$ formation occur principally by collisions of fast H, fast H$_2$, and H$^+$ with H$_2$. Simplifications include using a one-dimensional geometry, a multi-beam transport model, and the average cathode-fall electric field. The H$_\alpha$ emission is linear with current density over eight orders of magnitude. The calculated ion energy distributions agree satisfactorily with experiment for H$_2^+$ and H$_3^+$, but are only in qualitative agreement for H$^+$ and H$^-$. The experiments successfully modeled range from short-gap, parallel-plane glow discharges to beam-like, electrostatic-confinement discharges.Comment: Submitted to Plasmas Sources Science and Technology 8/18/201

Comparison of nonculture blood-based tests for diagnosing invasive Aspergillosis in an animal model

Contains fulltext : 172175.pdf (publisher's version ) (Closed access

An efficient and novel technology for the extraction of parasite genomic DNA from whole blood or culture

The aim of this study was to assess pathogen DNA extraction with a new spin column-based method (DNA-XT). DNA from either whole-blood samples spiked with Plasmodium falciparum or Leishmania donovani amastigote culture was extracted with DNA-XT and compared with that produced by a commercial extraction kit (DNeasy®). Eluates from large and small sample volumes were assessed by PCR and spectroscopy. Using a small volume (5 μl) of blood, the DNA-XT and DNeasy methods produced eluates with similar DNA concentrations (0.63 vs 1.06 ng/μl, respectively). The DNA-XT method produced DNA with lower PCR inhibition than DNeasy. The new technique was also twice as fast and required fewer plastics and manipulations but had reduced total recovered DNA compared with DNeasy

Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium.

BACKGROUND: Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS: To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS: There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk

UV continuum emission and diagnostics of hydrogen-containing non-equilibrium plasmas

For the first time the emission of the radiative dissociation continuum of the hydrogen molecule ($a^{3}\Sigma_{g}^{+} \to b^{3}\Sigma_{u}^{+}$ electronic transition) is proposed to be used as a source of information for the spectroscopic diagnostics of non-equilibrium plasmas. The detailed analysis of excitation-deactivation kinetics, rate constants of various collisional and radiative transitions and fitting procedures made it possible to develop two new methods of diagnostics of: (1) the ground $X^{1}\Sigma_{g}^{+}$ state vibrational temperature $T_{\text{vib}}$ from the relative intensity distribution, and (2) the rate of electron impact dissociation (d[\mbox{H_{2}}]/dt)_{\text{diss}} from the absolute intensity of the continuum. A known method of determination of $T_{\text{vib}}$ from relative intensities of Fulcher-$\alpha$ bands was seriously corrected and simplified due to the revision of $d \to a$ transition probabilities and cross sections of $d \gets X$ electron impact excitation. General considerations are illustrated with examples of experiments in pure hydrogen capillary-arc and H$_{2}$+Ar microwave discharges.Comment: REVTeX, 25 pages + 12 figures + 9 tables. Phys. Rev. E, eprint replaced because of resubmission to journal after referee's 2nd repor