Distribution of label spacings for genome mapping in nanochannels

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.Comment: 18 pages, 4 figures, 1 tabl

Phase transitions and the internal noise structure of nonlinear Schr\"odi nger equation solitons

We predict phase-transitions in the quantum noise characteristics of systems described by the quantum nonlinear Schr\"odinger equation, showing them to be related to the solitonic field transition at half the fundamental soliton amplitude. These phase-transitions are robust with respect to Raman noise and scattering losses. We also describe the rich internal quantum noise structure of the solitonic fields in the vicinity of the phase-transition. For optical coherent quantum solitons, this leads to the prediction that eliminating the peak side-band noise due to the electronic nonlinearity of silica fiber by spectral filtering leads to the optimal photon-number noise reduction of a fundamental soliton.Comment: 10 pages, 5 figure

Entangled Mixed States and Local Purification

Linden, Massar and Popescu have recently given an optimization argument to show that a single two-qubit Werner state, or any other mixture of the maximally entangled Bell states, cannot be purified by local operations and classical communications. We generalise their result and give a simple explanation. In particular, we show that no purification scheme using local operations and classical communications can produce a pure singlet from any mixed state of two spin-1/2 particles. More generally, no such scheme can produce a maximally entangled state of any pair of finite-dimensional systems from a generic mixed state. We also show that the Werner states belong to a large class of states whose fidelity cannot be increased by such a scheme.Comment: 3 pages, Latex with Revtex. Small clarifications and reference adde

A Method to Determine the In-Air Spatial Spread of Clinical Electron Beams

We propose and analyze in detail a method to measure the in-air spatial spread parameter of clinical electron beams. Measurements are performed at the center of the beam and below the adjustable collimators sited in asymmetrical configuration in order to avoid the distortions due to the presence of the applicator. The main advantage of our procedure lies in the fact that the dose profiles are fitted by means of a function which includes, additionally to the Gaussian step usually considered, a background which takes care of the dose produced by different mechanisms that the Gaussian model does not account for. As a result, the spatial spread is obtained directly from the fitting procedure and the accuracy permits a good determination of the angular spread. The way the analysis is done is alternative to that followed by the usual methods based on the evaluation of the penumbra width. Besides, the spatial spread found shows the quadratic-cubic dependence with the distance to the source predicted by the Fermi-Eyges theory. However, the corresponding values obtained for the scattering power are differing from those quoted by ICRU nr. 35 by a factor ~2 or larger, what requires of a more detailed investigation.Comment: 11 pages, 5 Postscript figures, to be published in Medical Physic

Capacity of different cell types to stimulate cytotoxic T lymphocyte precursor cells in the presence of interleukin 2

Plastic-adherent cells enriched for dendritic cells (AC) were found to be among the most potent stimulator cells for the activation of cytotoxic T lymphocytes (CTL) in vitro in the presence of interleukin 2 (IL 2) and a constant second set of allogeneic stimulator cells. Concanavalin A-activated nylon wool-nonadherent spleen cells ( CNWT ), concanavalin A-activated unfractionated spleen cells ( Cspl ), and some variants of the ESb T lymphoma line were equally effective as stimulator cells, however, and provoked a substantial cytotoxic response at concentrations of 10(4) cells per culture or less. In contrast, nonactivated nylon wool-nonadherent spleen cells ( NWT ) or unfractionated spleen cells (Spl) and cells of the P815 mastocytoma, the Meth A fibrosarcoma, and the T cell lymphomas Ly 5178 Eb and ESb did not stimulate cytotoxic responses at these cell concentrations. The strong stimulatory potential of the Cspl preparation was reduced by treatment with anti-Thy-1 antibody plus complement, whereas the stimulatory activity of the AC preparation was resistant to this treatment. All cell types tested expressed class I major histocompatibility antigens. Nonactivated NWT cells, in contrast to the CNWT preparation, showed no detectable staining with anti-I-E or anti-I-A antibodies and also a slightly weaker staining with class I antisera. Experiments with the tumor cell lines revealed, however, that there was no strict correlation between stimulatory potential and density of class I alloantigens or the expression of I-E determinants. Experiments on primary cytotoxic responses in vivo gave similar results. Experiments in cultures with a single set of stimulator cells and I region-compatible responder cells indicated that AC and Cspl or CNWT also have a markedly stronger capacity than NWT to induce IL 2-dependent DNA synthesis

Morphology and hardness ratio exploitation under limited statistics

Gamma-ray astronomy has produced for several years now sky maps for low photon statistics, non-negligible background and comparatively poor angular resolution. Quantifying the significance of spatial features remains difficult. Besides, spectrum extraction requires regions with large statistics while maps in energy bands allow only qualitative interpretation. The two main competing mechanisms in the VHE domain are the Inverse-Compton emission from accelerated electrons radiating through synchrotron in the X-ray domain and the interactions between accelerated hadrons and the surrounding medium, leading to the production and subsequent decay of Pi0 mesons. The spectrum of the VHE emission from leptons is predicted to steepen with increasing distance from the acceleration zone, owing to synchrotron losses (i.e. cooled population). It would remain approximately constant for hadrons. Ideally, spectro-imaging analysis would have the same spatial scale in the TeV and X-ray domains, to distinguish the local emission mechanisms. More realistically, we investigate here the possibility of improving upon the currently published HESS results by using more sophisticated tools.Comment: 4 pages, 6 figures, Proceeding for a poster at the GAMMA08 Heidelberg Symposiu

Adsorption structure of glycine on TiO2(1 1 0): a photoelectron diffraction determination

High-resolution core-level photoemission and scanned-energy mode photoelectron diffraction (PhD) of the O 1s and N 1s states have been used to investigate the interaction of glycine with the rutile TiO2(1 1 0) surface. Whilst there is clear evidence for the presence of the zwitterion View the MathML sourceCH2COO− with multilayer deposition, at low coverage only the deprotonated glycinate species, NH2CH2COO is present. Multiple-scattering simulations of the O 1s PhD data show the glycinate is bonded to the surface through the two carboxylate O atoms which occupy near-atop sites above the five-fold-coordinated surface Ti atoms, with a Ti–O bondlength of 2.12 ± 0.06 Å. Atomic hydrogen arising from the deprotonation is coadsorbed to form hydroxyl species at the bridging oxygen sites with an associated Ti–O bondlength of 2.01 ± 0.03 Å. Absence of any significant PhD modulations of the N 1s emission is consistent with the amino N atom not being involved in the surface bonding, unlike the case of glycinate on Cu(1 1 0) and Cu(1 0 0)

Accelerated return to sport after osteochondral autograft plug transfer

Background:Previous studies have reported varying return-to-sport protocols after knee cartilage restoration procedures.Purpose:To (1) evaluate the time for return to sport in athletes with an isolated chondral injury who underwent an accelerated return-to-sport protocol after osteochondral autograft plug transfer (OAT) and (2) evaluate clinical outcomes to assess for any consequences from the accelerated return to sport.Study Design:Case series; Level of evidence, 4.Methods:An institutional cohort of 152 OAT procedures was reviewed, of which 20 competitive athletes met inclusion and exclusion criteria. All patients underwent a physician-directed accelerated rehabilitation program after their procedure. Return to sport was determined for all athletes. Clinical outcomes were assessed using International Knee Documentation Committee (IKDC) and Tegner scores as well as assessment of level of participation on return to sport.Results:Return-to-sport data were available for all 20 athletes; 13 of 20 athletes (65%) were available for clinical evaluation at a mean 4.4-year follow-up. The mean time for return to sport for all 20 athletes was 82.9 ± 25 days (range, 38-134 days). All athletes were able to return to sport at their previous level and reported that they were satisfied or very satisfied with their surgical outcome and ability to return to sport. The mean postoperative IKDC score was 84.5 ± 9.5. The mean Tegner score prior to injury was 8.9 ± 1.7; it was 7.7 ± 1.9 at final follow-up.Conclusion:Competitive athletes with traumatic chondral defects treated with OAT managed using this protocol had reduced time to preinjury activity levels compared with what is currently reported, with excellent clinical outcomes and no serious long-term sequelae.</jats:sec

Homozygous disruption of P450 side-chain cleavage (CYP11A1) is associated with prematurity, complete 46,XY sex reversal, and severe adrenal failure

Disruption of the P450 side-chain cleavage cytochrome (P450scc) enzyme due to deleterious mutations of the CYP11A1 gene is thought to be incompatible with fetal survival because of impaired progesterone production by the fetoplacental unit. We present a 46, XY patient with a homozygous disruption of CYP11A1.The child was born prematurely with complete sex reversal and severe adrenal insufficiency. Laboratory data showed diminished or absent steroidogenesis in all pathways. Molecular genetic analysis of the CYP11A1 gene revealed a homozygous single nucleotide deletion leading to a premature termination at codon position 288. This mutation will delete highly conserved regions of the P450scc enzyme and thus is predicted to lead to a nonfunctional protein. Both healthy parents were heterozygous for this mutation.Our report demonstrates that severe disruption of P450scc can be compatible with survival in rare instances. Furthermore, defects in this enzyme are inherited in an autosomal-recessive fashion, and heterozygote carriers can be healthy and fertile. The possibility of P450scc-independent pathways of steroid synthesis in addition to the current concept of luteoplacental shift of progesterone synthesis in humans has to be questioned