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.

Genetic caste determination in Pogonomyrmex harvester ants imposes costs during colony founding.

Some populations of Pogonomyrmex harvester ants comprise genetically differentiated pairs of interbreeding lineages. Queens mate with males of their own and of the alternate lineage and produce pure-lineage offspring which develop into queens and inter-lineage offspring which develop into workers. Here we tested whether such genetic caste determination is associated with costs in terms of the ability to optimally allocate resources to the production of queens and workers. During the stage of colony founding, when only workers are produced, queens laid a high proportion of pure-lineage eggs but the large majority of these eggs failed to develop. As a consequence, the number of offspring produced by incipient colonies decreased linearly with the proportion of pure-lineage eggs laid by queens. Moreover, queens of the lineage most commonly represented in a given mating flight produced more pure-lineage eggs, in line with the view that they mate randomly with the two types of males and indiscriminately use their sperm. Altogether these results predict frequency-dependent selection on pairs of lineages because queens of the more common lineage will produce more pure-lineage eggs and their colonies be less successful during the stage of colony founding, which may be an important force maintaining the coexistence of pairs of lineages within populations.

Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon.

Crohn's disease (CD), a major form of human inflammatory bowel disease, is characterized by primary immunodeficiencies. The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma) is essential for intestinal homeostasis in response to both dietary- and microbiota-derived signals. Its role in host defense remains unknown, however. We show that PPARgamma functions as an antimicrobial factor by maintaining constitutive epithelial expression of a subset of beta-defensin in the colon, which includes mDefB10 in mice and DEFB1 in humans. Colonic mucosa of Ppargamma mutant animals shows defective killing of several major components of the intestinal microbiota, including Candida albicans, Bacteroides fragilis, Enterococcus faecalis, and Escherichia coli. Neutralization of the colicidal activity using an anti-mDefB10 blocking antibody was effective in a PPARgamma-dependent manner. A functional promoter variant that is required for DEFB1 expression confers strong protection against Crohn's colitis and ileocolitis (odds ratio, 0.559; P = 0.018). Consistently, colonic involvement in CD is specifically linked to reduced expression of DEFB1 independent of inflammation. These findings support the development of PPARgamma-targeting therapeutic and/or nutritional approaches to prevent colonic inflammation by restoring antimicrobial immunity in CD.

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.

NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: genotype and sex interactions.

Because the transcription factor neuronal Per-Arnt-Sim-type signal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor and an effector of intracellular energy balance, and because sleep is thought to correct an energy imbalance incurred during waking, we examined NPAS2's role in sleep homeostasis using npas2 knockout (npas2-/-) mice. We found that, under conditions of increased sleep need, i.e., at the end of the active period or after sleep deprivation (SD), NPAS2 allows for sleep to occur at times when mice are normally awake. Lack of npas2 affected electroencephalogram activity of thalamocortical origin; during non-rapid eye movement sleep (NREMS), activity in the spindle range (10-15 Hz) was reduced, and within the delta range (1-4 Hz), activity shifted toward faster frequencies. In addition, the increase in the cortical expression of the NPAS2 target gene period2 (per2) after SD was attenuated in npas2-/- mice. This implies that NPAS2 importantly contributes to the previously documented wake-dependent increase in cortical per2 expression. The data also revealed numerous sex differences in sleep; in females, sleep need accumulated at a slower rate, and REMS loss was not recovered after SD. In contrast, the rebound in NREMS time after SD was compromised only in npas2-/- males. We conclude that NPAS2 plays a role in sleep homeostasis, most likely at the level of the thalamus and cortex, where NPAS2 is abundantly expressed.

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.

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).

Role of hepatitis C virus genotype 3 in liver fibrosis progression: a systematic review and meta-analysis.

The progression of liver fibrosis in chronic hepatitis C has long been considered to be independent from viral genotypes. However, recent studies suggest an association between Hepatitis C virus (HCV) genotype 3 and accelerated liver disease progression. We completed a systematic review and meta-analysis of studies evaluating the association between HCV genotypes and fibrosis progression. PubMed, Embase and ISI Web of Knowledge databases were searched for cohort, cross-sectional and case-control studies on treatment-naïve HCV-infected adults in which liver fibrosis progression rate (FPR) was assessed by the ratio of fibrosis stage in one single biopsy to the duration of infection (single-biopsy studies) or from the change in fibrosis stage between two biopsies (paired biopsies studies). A random effect model was used to derive FPR among different HCV genotypes. Eight single-biopsy studies (3182 patients, mean/median duration of infection ranging from 9 to 21 years) and eight paired biopsies studies (mean interval between biopsies 2-12 years) met the selection criteria. The odds ratio for the association of genotype 3 with accelerated fibrosis progression was 1.52 (95% CI 1.12-2.07, P = 0.007) in single-biopsy studies and 1.37 (95% CI 0.87-2.17, P = 0.17) in paired biopsy studies. In conclusion, viral genotype 3 was associated with faster fibrosis progression in single-biopsy studies. This observation may have important consequences on the clinical management of genotype 3-infected patients. The association was not significant in paired biopsies studies, although the latter may be limited by important indication bias, short observation time and small sample size.