Sequestration of noble gases in giant planet interiors

The Galileo probe showed that Jupiter's atmosphere is severely depleted in neon compared to protosolar values. We show, via ab initio simulations of the partitioning of neon between hydrogen and helium phases, that the observed depletion can be explained by the sequestration of neon into helium-rich droplets within the postulated hydrogen-helium immiscibility layer of the planet's interior. We also demonstrate that this mechanism will not affect argon, explaining the observed lack of depletion of this gas. This provides strong indirect evidence for hydrogen-helium immiscibility in Jupiter

Effects of Helium Phase Separation on the Evolution of Extrasolar Giant Planets

We build on recent new evolutionary models of Jupiter and Saturn and here extend our calculations to investigate the evolution of extrasolar giant planets of mass 0.15 to 3.0 M_J. Our inhomogeneous thermal history models show that the possible phase separation of helium from liquid metallic hydrogen in the deep interiors of these planets can lead to luminosities ~2 times greater than have been predicted by homogeneous models. For our chosen phase diagram this phase separation will begin to affect the planets' evolution at ~700 Myr for a 0.15 M_J object and ~10 Gyr for a 3.0 M_J object. We show how phase separation affects the luminosity, effective temperature, radii, and atmospheric helium mass fraction as a function of age for planets of various masses, with and without heavy element cores, and with and without the effect of modest stellar irradiation. This phase separation process will likely not affect giant planets within a few AU of their parent star, as these planets will cool to their equilibrium temperatures, determined by stellar heating, before the onset of phase separation. We discuss the detectability of these objects and the likelihood that the energy provided by helium phase separation can change the timescales for formation and settling of ammonia clouds by several Gyr. We discuss how correctly incorporating stellar irradiation into giant planet atmosphere and albedo modeling may lead to a consistent evolutionary history for Jupiter and Saturn.Comment: 22 pages, including 14 figures. Accepted to the Astrophysical Journa

The Interiors of Giant Planets: Models and Outstanding Questions

We know that giant planets played a crucial role in the making of our Solar System. The discovery of giant planets orbiting other stars is a formidable opportunity to learn more about these objects, what is their composition, how various processes influence their structure and evolution, and most importantly how they form. Jupiter, Saturn, Uranus and Neptune can be studied in detail, mostly from close spacecraft flybys. We can infer that they are all enriched in heavy elements compared to the Sun, with the relative global enrichments increasing with distance to the Sun. We can also infer that they possess dense cores of varied masses. The intercomparison of presently caracterised extrasolar giant planets show that they are also mainly made of hydrogen and helium, but that they either have significantly different amounts of heavy elements, or have had different orbital evolutions, or both. Hence, many questions remain and are to be answered for significant progresses on the origins of planets.Comment: 43 pages, 11 figures, 3 tables. To appear in Annual Review of Earth and Planetary Sciences, vol 33, (2005

PCR and microarray analysis of AmpC and ESBLs producing Pseudomonas aeruginosa isolates from intensive care units

Detection of AmpC and ESBL producing P. aeruginosa by phenotypic methods is challenging, especially in low-income countries such as Pakistan. Therefore, a molecular method was developed for rapid detection of these resistance markers. A total of 303 clinical samples were collected from intensive care units (ICUs) of the Jinnah postgraduate medical centre (JPMC) Karachi, Pakistan. The isolates were identified by traditional and matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF-MS). Isolates were phenotypically analyzed for AmpCs and ESBL by D-test and by double disc synergy, respectively. The Check MDR CT103 XL and PCR techniques were used for the detection AmpCs and ESBLs. Out of 303 isolates, 148 (48.8%) were P. aeruginosa. The resistance pattern of P. aeruginosa against piperacillin, cefatizidime and cefepime was 59.4%, 64.8% and 59.4% respectively. More than 60% isolates were resistant to aminoglycosides and ciprofloxacin. All (148) strains were found sensitive to colistin. Phenotypic ESBL prevalence was 8.8% whereas genotypic resistance was 29.1%. bla was the most prevalent ESBL. Although 25.67% of P. aeruginosa isolates were positive phenotypically for AmpC, microarray (Check-MDR) analysis did not detect chromosomally located AmpC in any of the isolates. VE

A novel chromosomal inversion at 11q23 in infant acute myeloid leukemia fuses MLL to CALM, a gene that encodes a clathrin assembly protein

Rearrangements involving the MLL gene at chromosome band 11q23 are common in infant acute myeloid leukemias (AMLs). We recently encountered an infant patient with rapidly progressive AML whose leukemic cells harbored a previously undescribed MLL rearrangement involving an inversion of 11q [inv(11)(q14q23)]. We used panhandle PCR to determine that this rearrangement juxtaposed the MLL ( M ixed- L ineage L eukemia) gene to the CALM ( C lathrin A ssembly L ymphoid M yeloid leukemia) gene at 11q14–q21. The CALM protein participates in recruitment of clathrin to internal membrane surfaces, thereby regulating vesicle formation in both endocytosis and intracellular protein transport. Intriguingly, CALM has been identified in other cases of AML as a translocation partner for the AF10 gene, which has independently been found to be an MLL partner in AML. We identified the MLL - CALM fusion transcript (but not the reciprocal CALM - MLL transcript) in leukemia cell RNA by RT-PCR. The predicted 1803 amino acid MLL-CALM fusion protein includes amino-terminal MLL domains involved in transcriptional repression, and carboxy-terminal CALM-derived clathrin-binding domains. The genomic breakpoint in MLL is in the 7th intron (within the breakpoint cluster region); the corresponding CALM breakpoint is in the 7th CALM intron. In contrast, breakpoints in CALM - AF10 translocations lie in the 17th–19th CALM introns (30 kb downstream); also, in these translocations, CALM provides the 5′ end of the fusion transcript. Together with its previously recognized association with AF10 in AML, the identification of CALM as an MLL fusion partner suggests that interference with clathrin-mediated trafficking pathways may be an underappreciated mechanism in leukemogenesis. © 2002 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/35133/1/10136_ftp.pd

The Encoding of Temporally Irregular and Regular Visual Patterns in the Human Brain

In the work reported here, we set out to study the neural systems that detect predictable temporal patterns and departures from them. We used functional magnetic resonance imaging (fMRI) to locate activity in the brains of subjects when they viewed temporally regular and irregular patterns produced by letters, numbers, colors and luminance. Activity induced by irregular sequences was located within dorsolateral prefrontal cortex, including an area that was responsive to irregular patterns regardless of the type of visual stimuli producing them. Conversely, temporally regular arrangements resulted in activity in the right frontal lobe (medial frontal gyrus), in the left orbito-frontal cortex and in the left pallidum. The results show that there is an abstractive system in the brain for detecting temporal irregularity, regardless of the source producing it

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

A Novel Estimator for the Rate of Information Transfer by Continuous Signals

The information transfer rate provides an objective and rigorous way to quantify how much information is being transmitted through a communications channel whose input and output consist of time-varying signals. However, current estimators of information content in continuous signals are typically based on assumptions about the system's linearity and signal statistics, or they require prohibitive amounts of data. Here we present a novel information rate estimator without these limitations that is also optimized for computational efficiency. We validate the method with a simulated Gaussian information channel and demonstrate its performance with two example applications. Information transfer between the input and output signals of a nonlinear system is analyzed using a sensory receptor neuron as the model system. Then, a climate data set is analyzed to demonstrate that the method can be applied to a system based on two outputs generated by interrelated random processes. These analyses also demonstrate that the new method offers consistent performance in situations where classical methods fail. In addition to these examples, the method is applicable to a wide range of continuous time series commonly observed in the natural sciences, economics and engineering

Human papillomavirus in amniotic fluid

BACKGROUND: There is evidence to suggest that human papillomavirus (HPV) can cross the placenta resulting in in-utero transmission. The goal of this study was to determine if HPV can be detected in amniotic fluid from women with intact amniotic membranes. METHODS: Residual amniotic fluid and cultured cell pellets from amniocentesis performed for prenatal diagnosis were used. PGMY09/11 L1 consensus primers and GP5+/GP6+ primers were used in a nested polymerase chain reaction assay for HPV. RESULTS: There were 146 paired samples from 142 women representing 139 singleton pregnancies, 2 twin pregnancies, and 1 triplet pregnancy. The women were 78% Caucasian, 5% African American, 14% Asian, and 2% Hispanic. The average age was 35.2 years with a range of 23–55 years. All samples were β-globin positive. HPV was not detected in any of the paired samples. CONCLUSION: Given the age range, race, and ethnicity of the study population, one would anticipate some evidence of HPV if it could easily cross the placenta, but there was none