Numerical solution of the Boltzmann equation for the collective modes of trapped Fermi gases

We numerically solve the Boltzmann equation for trapped fermions in the normal phase using the test-particle method. After discussing a couple of tests in order to estimate the reliability of the method, we apply it to the description of collective modes in a spherical harmonic trap. The numerical results are compared with those obtained previously by taking moments of the Boltzmann equation. We find that the general shape of the response function is very similar in both methods, but the relaxation time obtained from the simulation is significantly longer than that predicted by the method of moments. It is shown that the result of the method of moments can be corrected by including fourth-order moments in addition to the usual second-order ones and that this method agrees very well with our numerical simulations.Comment: 13 pages, 8 figures, accepted for publication in Phys. Rev.

Trap anharmonicity and sloshing mode of a Fermi gas

For a gas trapped in a harmonic potential, the sloshing (or Kohn) mode is undamped and its frequency coincides with the trap frequency, independently of the statistics, interaction and temperature of the gas. However, experimental trap potentials have usually Gaussian shape and anharmonicity effects appear as the temperature and, in the case of Fermions, the filling of the trap are increased. We study the sloshing mode of a degenerate Fermi gas in an anharmonic trap within the Boltzmann equation, including in-medium effects in both the transport and collision terms. The calculated frequency shifts and damping rates of the sloshing mode due to the trap anharmonicity are in satisfactory agreement with the available experimental data. We also discuss higher-order dipole, octupole, and bending modes and show that the damping of the sloshing mode is caused by its coupling to these modes.Comment: 10 pages; v2: comparison with damping data added, minor extensions and correction

Identification of genomic indels and structural variations using split reads

<p>Abstract</p> <p>Background</p> <p>Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection.</p> <p>Results</p> <p>We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions <it>vs</it>. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs.</p> <p>Conclusions</p> <p>Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for deletions. Moreover, with the advent of the third-generation sequencing technologies that produce longer reads, we expect our method to be even more useful.</p

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

RACE sequencing of ENCODE regions shows that much of the human genome is represented in poly(A)+ RNA

Hartree-Fock-Bogoliubov theory versus local-density approximation for superfluid trapped fermionic atoms

We investigate a gas of superfluid fermionic atoms trapped in two hyperfine states by a spherical harmonic potential. We propose a new regularization method to remove the ultraviolet divergence in the Hartree-Fock-Bogoliubov equations caused by the use of a zero-range atom-atom interaction. Compared with a method used in the literature, our method is simpler and has improved convergence properties. Then we compare Hartree-Fock-Bogoliubov calculations with the semiclassical local-density approximation. We observe that for systems containing a small number of atoms shell effects, which cannot be reproduced by the semiclassical calculation, are very important. For systems with a large number of atoms at zero temperature the two calculations are in quite good agreement, which, however, is deteriorated at non-zero temperature, especially near the critical temperature. In this case the different behavior can be explained within the Ginzburg-Landau theory.Comment: 12 pages, 8 figures, revtex; v2: references and clarifying remarks adde

Efavirenz use during pregnancy and for women of child-bearing potential

BACKGROUND: Efavirenz is the preferred non-nucleoside reverse transcriptase inhibitor for first-line antiretroviral treatment in many countries. For women of childbearing potential, advantages of efavirenz are balanced by concerns that it is teratogenic. This paper reviews evidence of efavirenz teratogenicity and considers implications in common clinical scenarios. FINDINGS: Concerns of efavirenz-induced fetal effects stem from animal studies, although the predictive value of animal data for humans is unknown. Four retrospective cases of central nervous system birth defects in infants with first trimester exposure to efavirenz have been interpreted as being consistent with animal data. In a prospective pregnancy registry, which is subject to fewer potential biases, no increase was detected in overall risk of birth defects following exposure to efavirenz in the first-trimester. DISCUSSION: For women planning a pregnancy or not using contraception, efavirenz should be avoided if alternatives are available. According to WHO guidelines for resource-constrained settings, benefits of efavirenz are likely to outweigh risks for women using contraception. Women who become pregnant while receiving efavirenz often consider drug substitution or temporarily suspending treatment. Both options have substantial risks for maternal and fetal health which, we argue, appear unjustified after the critical period of organogenesis (3–8 weeks post-conception). Efavirenz-based triple regimens, initiated after the first trimester of pregnancy and discontinued after childbirth, are potentially an important alternative for reducing mother-to-child transmission in pregnant women who do not yet require antiretroviral treatment. CONCLUSION: Current recommendations for care for women who become pregnant while receiving efavirenz may need to be re-considered, particularly in settings with limited alternative drugs and laboratory monitoring. With current data limitations, additional adequately powered prospective studies are needed

Freshwater monitoring by nanopore sequencing.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices

Freshwater monitoring by nanopore sequencing.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices

Collective excitations in the neutron star inner crust

We study the spectrum of collective excitations in the inhomogeneous phases in the neutron star inner crust within a superfluid hydrodynamics approach. Our aim is to describe the whole range of wavelengths, from the long-wavelength limit which can be described by macroscopic approaches and which is crucial for the low-energy part of the spectrum, to wavelengths of the order of the dimensions of the Wigner-Seitz cells, corresponding to the modes usually described in microscopic calculations. As an application, we will discuss the contribution of these collective modes to the specific heat of the "lasagna" phase in comparison with other known contributions.Comment: 10 pages, 4 figures, v2: one reference added and typos correcte

Clusterin, a haploinsufficient tumor suppressor gene in neuroblastomas

This article is available open access through the publisher’s website. Copyright @ 2009 The Authors.Background - Clusterin expression in various types of human cancers may be higher or lower than in normal tissue, and clusterin may promote or inhibit apoptosis, cell motility, and inflammation. We investigated the role of clusterin in tumor development in mouse models of neuroblastoma. Methods - We assessed expression of microRNAs in the miR-17-92 cluster by real-time reverse transcription–polymerase chain reaction in MYCN-transfected SH-SY5Y and SH-EP cells and inhibited expression by transfection with microRNA antisense oligonucleotides. Tumor development was studied in mice (n = 66) that were heterozygous or homozygous for the MYCN transgene and/or for the clusterin gene; these mice were from a cross between MYCN-transgenic mice, which develop neuroblastoma, and clusterin-knockout mice. Tumor growth and metastasis were studied in immunodeficient mice that were injected with human neuroblastoma cells that had enhanced (by clusterin transfection, four mice per group) or reduced (by clusterin short hairpin RNA [shRNA] transfection, eight mice per group) clusterin expression. All statistical tests were two-sided. Results - Clusterin expression increased when expression of MYCN-induced miR-17-92 microRNA cluster in SH-SY5Y neuroblastoma cells was inhibited by transfection with antisense oligonucleotides compared with scrambled oligonucleotides. Statistically significantly more neuroblastoma-bearing MYCN-transgenic mice were found in groups with zero or one clusterin allele than in those with two clusterin alleles (eg, 12 tumor-bearing mice in the zero-allele group vs three in the two-allele group, n = 22 mice per group; relative risk for neuroblastoma development = 4.85, 95% confidence interval [CI] = 1.69 to 14.00; P = .005). Five weeks after injection, fewer clusterin-overexpressing LA-N-5 human neuroblastoma cells than control cells were found in mouse liver or bone marrow, but statistically significantly more clusterin shRNA-transfected HTLA230 cells (3.27%, with decreased clusterin expression) than control-transfected cells (1.53%) were found in the bone marrow (difference = 1.74%, 95% CI = 0.24% to 3.24%, P = .026). Conclusions - We report, to our knowledge, the first genetic evidence that clusterin is a tumor and metastasis suppressor gene.Sport Aiding Medical Research for Kids (SPARKS), Great Ormond Street Hospital/National Health Service, the National Cancer Institute and University of Parma