Malaria haplotype frequency estimation.

We present a Bayesian approach for estimating the relative frequencies of multi-single nucleotide polymorphism (SNP) haplotypes in populations of the malaria parasite Plasmodium falciparum by using microarray SNP data from human blood samples. Each sample comes from a malaria patient and contains one or several parasite clones that may genetically differ. Samples containing multiple parasite clones with different genetic markers pose a special challenge. The situation is comparable with a polyploid organism. The data from each blood sample indicates whether the parasites in the blood carry a mutant or a wildtype allele at various selected genomic positions. If both mutant and wildtype alleles are detected at a given position in a multiply infected sample, the data indicates the presence of both alleles, but the ratio is unknown. Thus, the data only partially reveals which specific combinations of genetic markers (i.e. haplotypes across the examined SNPs) occur in distinct parasite clones. In addition, SNP data may contain errors at non-negligible rates. We use a multinomial mixture model with partially missing observations to represent this data and a Markov chain Monte Carlo method to estimate the haplotype frequencies in a population. Our approach addresses both challenges, multiple infections and data errors.

Critical frequency for vortex nucleation in Bose-Fermi mixtures in optical lattices

We investigate within mean-field theory the influence of a one-dimensional optical lattice and of trapped degenerate fermions on the critical rotational frequency for vortex line creation in a Bose-Einstein condensate. We consider laser intensities of the lattice such that quantum coherence across the condensate is ensured. We find a sizable decrease of the thermodynamic critical frequency for vortex nucleation with increasing applied laser strength and suggest suitable parameters for experimental observation. Since 87Rb-40K mixtures may undergo collapse, we analyze the related question of how the optical lattice affects the mechanical stability of the system.

Microstructure of highly oriented, hexagonal, boron nitride thin films grown on crystalline silicon by radio frequency plasma-assisted chemical vapor deposition

We present a high‐resolution electron microscopy study of the microstructure of boron nitride thin films grown on silicon (100) by radio‐frequency plasma‐assisted chemical vapor deposition using B2H6 (1% in H2) and NH3 gases. Well‐adhered boron nitride films grown on the grounded electrode show a highly oriented hexagonal structure with the c‐axis parallel to the substrate surface throughout the film, without any interfacial amorphous layer. We ascribed this textured growth to an etching effect of atomic hydrogen present in the gas discharge. In contrast, films grown on the powered electrode, with compressive stress induced by ion bombardment, show a multilayered structure as observed by other authors, composed of an amorphous layer, a hexagonal layer with the c‐axis parallel to the substrate surface and another layer oriented at random

Frequency-dependent attenuation as a potential indicator of oil saturation

At seismic frequencies, wave-induced fluid flow is a major cause of P-wave attenuation in partially saturated porous rocks. Attenuation is of great importance for the oil industry in the interpretation of seismic field data. Here, the effects on P-wave attenuation resulting from changes in oil saturation are studied for media with coexisting water, oil, and gas. For that, creep experiments are numerically simulated by solving Biot's equations for consolidation of poroelastic media with the finite-element method. The experiments yield time-dependent stress?strain relations that are used to calculate the complex P-wave modulus from which frequency-dependent P-wave attenuation is determined. The models are layered media with periodically alternating triplets of layers. Models consisting of triplets of layers having randomly varying layer thicknesses are also considered. The layers in each triplet are fully saturated with water, oil, and gas. The layer saturated with water has lower porosity and permeability than the layers saturated with oil and gas. These models represent hydrocarbon reservoirs in which water is the wetting fluid preferentially saturating regions of lower porosity. The results from the numerical experiments showed that increasing oil saturation, connected to a decrease in gas saturation, resulted in a significant increase of attenuation at low frequencies (lower than 2 Hz). Furthermore, replacing the oil with water resulted in a distinguishable behavior of the frequency-dependent attenuation. These results imply that, according to the physical mechanism of wave-induced fluid flow, frequency-dependent attenuation in media saturated with water, oil, and gas is a potential indicator of oil saturation.

Polymorphous Si thin films from radio frequency plasmas of SiH4 diluted in Ar: A study by transmission electron microscopy and Raman spectroscopy

In this study, we present a detailed structural characterization by means of transmission electron microscopy and Raman spectroscopy of polymorphous silicon (pm-Si:H) thin films deposited using radio-frequency dust-forming plasmas of SiH4 diluted in Ar. Square-wave modulation of the plasma and gas temperature was varied to obtain films with different nanostructures. Transmission electron microscopy and electron diffraction have shown the presence of Si crystallites of around 2 nm in the pm-Si:H films, which are related to the nanoparticles formed in the plasma gas phase coming from their different growth stages, named particle nucleation and coagulation. Raman scattering has proved the role of the film nanostructure in the crystallization process induced ¿in situ¿ by laser heating.

Ion assisted deposition of thin films by substrate tuned radio frequency magnetron sputtering

The substrate tuning technique was applied to a radio frequency magnetron sputtering system to obtain a variable substrate bias without an additional source. The dependence of the substrate bias on the value of the external impedance was studied for different values of chamber pressure, gas composition and rf input power. A qualitative explanation of the results is given, based on a simple model, and the role of the stray capacitance is clearly disclosed. Langmuir probe measurements show that this system allows independent control of the ion flux and the ion energy bombarding the growing film. For an argon flow rate of 2.8 sccm and a radio frequency power of 300 W (intermediate values of the range studied) the ion flux incident on the substrate was 1.3 X 1020-m-2-s-1. The maximum ion energy available in these conditions can be varied in the range 30-150 eV. As a practical application of the technique, BN thin films were deposited under different ion bombardment conditions. An ion energy threshold of about 80 eV was found, below which only the hexagonal phase was present in the films, while for higher energies both hexagonal and cubic phase were present. A cubic content of about 60% was found for an ion energy of 120 V.

Influence of pressure and radio frequency power on deposition rate and structural properties of hydrogenated amorphous silicon thin films prepared by plasma deposition

The influence of radio frequency (rf) power and pressure on deposition rate and structural properties of hydrogenated amorphous silicon (a-Si:H) thin films, prepared by rf glow discharge decomposition of silane, have been studied by phase modulated ellipsometry and Fourier transform infrared spectroscopy. It has been found two pressure regions separated by a threshold value around 20 Pa where the deposition rate increases suddenly. This behavior is more marked as rf power rises and reflects the transition between two rf discharges regimes. The best quality films have been obtained at low pressure and at low rf power but with deposition rates below 0.2 nm/s. In the high pressure region, the enhancement of deposition rate as rf power increases first gives rise to a reduction of film density and an increase of content of hydrogen bonded in polyhydride form because of plasma polymerization reactions. Further rise of rf power leads to a decrease of polyhydride bonding and the material density remains unchanged, thus allowing the growth of a-Si:H films at deposition rates above 1 nm/s without any important detriment of material quality. This overcoming of deposition rate limitation has been ascribed to the beneficial effects of ion bombardment on the a-Si:H growing surface by enhancing the surface mobility of adsorbed reactive species and by eliminating hydrogen bonded in polyhydride configurations.

Ventilation-induced pulmonary vasodilatation in lambs with congenital diaphragmatic hernia is modulated by nitric oxide.

Endogenous nitric oxide (NO) mediates pulmonary vasodilatation at birth, but inhaled NO fails to reduce pulmonary vascular resistance (PVR) in newborns with congenital diaphragmatic hernia (CDH). This study was designed to investigate the effects of ventilation, and the nature of its endogenous mediator, in fetal lambs with experimental CDH. Investigations at 138 days of gestation showed that ventilation markedly decreased PVR. Inhibition of NO synthesis reduced ventilation-induced pulmonary vasodilatation in vivo and increased in vitro isometric tension of vascular rings. Ventilation therefore reduces PVR at birth in lambs with CDH, and endogenous NO seems to contribute to this reduction.

Adaptive tracking of EEG oscillations.

Neuronal oscillations are an important aspect of EEG recordings. These oscillations are supposed to be involved in several cognitive mechanisms. For instance, oscillatory activity is considered a key component for the top-down control of perception. However, measuring this activity and its influence requires precise extraction of frequency components. This processing is not straightforward. Particularly, difficulties with extracting oscillations arise due to their time-varying characteristics. Moreover, when phase information is needed, it is of the utmost importance to extract narrow-band signals. This paper presents a novel method using adaptive filters for tracking and extracting these time-varying oscillations. This scheme is designed to maximize the oscillatory behavior at the output of the adaptive filter. It is then capable of tracking an oscillation and describing its temporal evolution even during low amplitude time segments. Moreover, this method can be extended in order to track several oscillations simultaneously and to use multiple signals. These two extensions are particularly relevant in the framework of EEG data processing, where oscillations are active at the same time in different frequency bands and signals are recorded with multiple sensors. The presented tracking scheme is first tested with synthetic signals in order to highlight its capabilities. Then it is applied to data recorded during a visual shape discrimination experiment for assessing its usefulness during EEG processing and in detecting functionally relevant changes. This method is an interesting additional processing step for providing alternative information compared to classical time-frequency analyses and for improving the detection and analysis of cross-frequency couplings.

Home Tightening, Insulation and Ventilation, 2011

The average Iowa family spends more than half of its annual household energy bill on heating and cooling. That’s a significant number, but you can dramatically reduce these costs—up to 20 percent, according to ENERGY STAR®—by making some simple energy-saving weatherization and insulation improvements to your home. In addition—with a little attention to proper ventilation—you can protect your home from moisture damage year-round, reduce problems caused by ice dams on the roof during the winter and significantly cut summer cooling costs. As a bonus, these projects can extend the life of your home and may increase the resale value of your property. If you like to fix things around the house, you can handle many of the projects suggested in this book and make the most of your energy-improvement budget. However, don’t hesitate to call a professional for help if you’d rather not do the work yourself; the dollars gained through energy savings in upcoming years will be worth the expense.

Pratique du scanner en Suisse: fréquence et évolution temporelle [CT utilisation in Switzerland: frequency and secular trends]

PURPOSE: This study analyzes CT examinations in Switzerland. MATERIALS AND METHODS: Using different sources (administrative data on the equipment, a 1998 nationwide inquiry into practices, and data provided by the Swiss University Hospitals of Basel, Zurich, and Lausanne), we determined the frequency of CT examinations (hospitals and private radiologists) in 1998 according to different descriptive variables and studied the progression in CT use over time. RESULTS: CT scanners increased by 7% between 1998 and 2004. The average annual number of CT examinations in 1998 was 46.3/1000 population, 3.4% of all radiological examinations in Switzerland in 1997-1998. The most frequent examination was CT of the skull (24%), while private radiology institutes perform more CTs of the spine. More CT examinations were performed for men than for women (sex ratio M/F=1.17). The average annual increase in CT in Swiss hospitals varied from 8% for Basel to 18% for Lausanne. Finally, the proportion of pediatric examinations was 5%; their numbers appear to be stabilizing. CONCLUSION: There is a significant increase in CT examinations. It is hoped that our study will heighten awareness among doctors of CT examinations in order to optimize their use.

Use of combined suspension laryngoscopy and jet ventilation for Y-shaped airway stents delivery.

Airway stenting is a common endoscopic procedure that is used to treat a variety of central airway lesions. Obstructions or fistulas involving the carina or nearby tracheobronchial structures require the use of specially designed stents, commonly referred to as Y-stents. Conventional methods of endobronchial Y-stent delivery are all characterized by a blind and apneic period during the procedure that carries the risk of stent misplacement or ventilation/oxygenation problems or both. Using combined suspension laryngoscopy, flexible bronchoscopy, and jet ventilation, we describe a technique that makes challenging bronchoscopic interventions--such as self-expandable Y-shaped airway stent delivery--easy, precise, and safe.

BK virus infection in hematopoietic stem cell transplant recipients: frequency, risk factors, and association with postengraftment hemorrhagic cystitis.

Blood samples from 132 consecutive hematopoietic stem cell transplant recipients were obtained and tested weekly for BK virus DNA by use of quantitative real-time PCR. Forty-four patients (33%) developed BK viremia at a median of 41 days (range, 9-91 days) after transplantation. Patients with hemorrhagic cystitis that occurred after platelet engraftment had higher levels of viremia than did patients without hemorrhagic cystitis (median, 9.7x10(3) vs. 0 copies/mL; P=.008) and patients with hemorrhagic cystitis that occurred before platelet engraftment (median, 9.7x10(3) vs. 0 copies/mL; P=.0006). BK viremia also was strongly associated with postengraftment hemorrhagic cystitis in a time-dependent analysis (P=.004).