Contact time periods in immunological synapse

This paper resolves the long standing debate as to the proper time scale τ of the onset of the immunological synapse bond, the noncovalent chemical bond defining the immune pathways involving T cells and antigen presenting cells. Results from our model calculations show τ to be of the order of seconds instead of minutes. Close to the linearly stable regime, we show that in between the two critical spatial thresholds defined by the integrin:ligand pair (Δ2∼ 40-45 nm) and the T-cell receptor TCR:peptide-major-histocompatibility-complex pMHC bond (Δ1∼ 14-15 nm), τ grows monotonically with increasing coreceptor bond length separation δ (= Δ2-Δ1∼ 26-30 nm) while τ decays with Δ1 for fixed Δ2. The nonuniversal δ-dependent power-law structure of the probability density function further explains why only the TCR:pMHC bond is a likely candidate to form a stable synapse.

Validação de espécies de Centropomus (Centropomidae, Perciformes) do litoral do Rio Grande do Norte através de caracterização citogenética e molecular

The Centropomidae family consists of three genera, Centropomus, Lates and Psammoperca. Centropomus is the most diverse group, with six Centropomus species occur in the Western Atlantic Ocean C. poeyi Chávez, 1961, C. parallelus Poey, 1860, C. mexicanus Bocourt, 1868, C. pectinatus Poey, 1860 and C. ensiferus Poey, 1860. Some of these species are considered cryptic, because of its morphological traits showed low resolution for identification purposes. Despite showing great interest as a natural resource and fish culture, aspects of their diversity and karyotypic patterns are poorly understood. In this work morphological identification and comparison of mitochondrial 16S gene sequence were used to identify the species of the genus Centropomus occurring in Rio Grande do Norte, northeastern Brazil. Two sepecies were identified, C. undecimalis and C. mexicanus, which had the chromosomal aspects analyzed, through Classical cytogenetic method analyzes (conventional staining, C-banding, Ag-NORs), fluorochrome staining AT- and GC-specific, replication bands by incorporating of the base analog 5-Bromo-2’-deoxyuridine (5-BrdU), in situ chromosomal mapping of (TTAGGG)n sequences and in situ chromosome mapping 18S and 5S rRNA genes. Both species show 2n=48 acrocentric chromosomes, with ribosomal sites (Ag-NOR/18S rDNA/ Mitramycin+) in second chromosomal pair, in telomeric position on the long arm in C. mexicanus and interstitial in C. undecimalis. The nuclear organization pair (pair 2) shown a resolutive cytotaxonomic marker for these two species. The generated data reveal a lower species diversity than previously believed, suggesting that greater attention should be paid in taxonomic identification of the species, in view of optimize commercial actions exploitation, biological conservation and cultivation.

Experimental study study of antiproton-proton annihilation into a pair of charged Pi-Mesons or K-Mesons for incident antiproton mementa in the range from 0.72 GeV/c to 2.62 GeV/c

The cross sections for the two antiproton-proton annihilation-in-flight modes,

ˉp + p → π⁺ + π^-

ˉp + p → k⁺ + k^-

were measured for fifteen laboratory antiproton beam momenta ranging from 0.72 to 2.62 GeV/c. No magnets were used to determine the charges in the final state. As a result, the angular distributions were obtained in the form [dσ/dΩ (Θ_C.M.) + dσ/dΩ (π – Θ_C.M.)] for 45 ≲ Θ_C.M. ≲ 135°.

A hodoscope-counter system was used to discriminate against events with final states having more than two particles and antiproton-proton elastic scattering events. One spark chamber was used to record the track of each of the two charged final particles. A total of about 40,000 pictures were taken. The events were analyzed by measuring the laboratory angle of the track in each chamber. The value of the square of the mass of the final particles was calculated for each event assuming the reaction

ˉp + p → a pair of particles with equal masses.

About 20,000 events were found to be either annihilation into π ^±-pair or k ^±-pair events. The two different charged meson pair modes were also distinctly separated.

The average differential cross section of ˉp + p → π⁺ + π^- varied from ~ 25 µb/sr at antiproton beam momentum 0.72 GeV/c (total energy in center-of-mass system, √s = 2.0 GeV) to ~ 2 µb/sr at beam momentum 2.62 GeV/c (√s = 2.64 GeV). The most striking feature in the angular distribution was a peak at Θ_C.M. = 90° (cos Θ_C.M. = 0) which increased with √s and reached a maximum at √s ~ 2.1 GeV (beam momentum ~ 1.1 GeV/c). Then it diminished and seemed to disappear completely at √s ~ 2.5 GeV (beam momentum ~ 2.13 GeV/c). A valley in the angular distribution occurred at cos Θ_C.M. ≈ 0.4. The differential cross section then increased as cos Θ_C.M. approached 1.

The average differential cross section for ˉp + p → k⁺ + k^- was about one third of that of the π^±-pair mode throughout the energy range of this experiment. At the lower energies, the angular distribution, unlike that of the π^±-pair mode, was quite isotropic. However, a peak at Θ_C.M. = 90° seemed to develop at √s ~ 2.37 GeV (antiproton beam momentum ~ 1.82 GeV/c). No observable change was seen at that energy in the π^±-pair cross section.

The possible connection of these features with the observed meson resonances at 2.2 GeV and 2.38 GeV, and its implications, were discussed.

Construction of 2-D directional filter bank by cascading checkerboard-shaped filter pair and CMFB

In this paper, we propose a new approach to construct a 2-dimensional (2-D) directional filter bank (DFB) by cascading a 2-D nonseparable checkerboard-shaped filter pair and 2-D separable cosine modulated filter bank (CMFB). Similar to diagonal subbands in 2-D separable wavelets, most of the subbands in 2-D separable CMFBs, tensor products of two 1-D CMFBs, are poor in directional selectivity due to the fact that the frequency supports of most of the subband filters are concentrated along two different directions. To improve the directional selectivity, we propose a new DFB to realize the subband decomposition. First, a checkerboard-shaped filter pair is used to decompose an input image into two images containing different directional information of the original image. Next, a 2-D separable CMFB is applied to each of the two images for directional decomposition. The new DFB is easy in design and has merits: low redundancy ratio and fine directional-frequency tiling. As its application, the BLS-GSM algorithm for image denoising is extended to use the new DFBs. Experimental results show that the proposed DFB achieves better denoising performance than the methods using other DFBs for images of abundant textures. (C) 2008 Elsevier B.V. All rights reserved.

Proton Formation in 2+1 Resonance Enhanced Multiphoton Excitation of HCl and HBr via „=0… Rydberg and Ion-Pair States

Molecular beam cooled HCl was state selected by two-photon excitation of the V (1) summation operator(0(+)) [v=9,11-13,15], E (1) summation operator(0(+)) [v=0], and g (3) summation operator(-)(0(+)) [v=0] states through either the Q(0) or Q(1) lines of the respective (1,3) summation operator(0(+))<--<--X (1) summation operator(0(+)) transition. Similarly, HBr was excited to the V (1) summation operator(0(+)) [v=m+3, m+5-m+8], E (1) summation operator(0(+)) [v=0], and H (1) summation operator(0(+)) [v=0] states through the Q(0) or Q(1) lines. Following absorption of a third photon, protons were formed by three different mechanisms and detected using velocity map imaging. (1) H(*)(n=2) was formed in coincidence with (2)P(i) halogen atoms and subsequently ionized. For HCl, photodissociation into H(*)(n=2)+Cl((2)P(12)) was dominant over the formation of Cl((2)P(32)) and was attributed to parallel excitation of the repulsive [(2) (2)Pi4llambda] superexcited (Omega=0) states. For HBr, the Br((2)P(32))Br((2)P(12)) ratio decreases with increasing excitation energy. This indicates that both the [(3) (2)Pi(12)5llambda] and the [B (2) summation operator5llambda] superexcited (Omega=0) states contribute to the formation of H(*)(n=2). (2) For selected intermediate states HCl was found to dissociate into the H(+)+Cl(-) ion pair with over 20% relative yield. A mechanism is proposed by which a bound [A (2) summation operatornlsigma] (1) summation operator(0(+)) superexcited state acts as a gateway state to dissociation into the ion pair. (3) For all intermediate states, protons were formed by dissociation of HX(+)[v(+)] following a parallel, DeltaOmega=0, excitation. The quantum yield for the dissociation process was obtained using previously reported photoionization efficiency data and was found to peak at v(+)=6-7 for HCl and v(+)=12 for HBr. This is consistent with excitation of the repulsive A(2) summation operator(12) and (2) (2)Pi states of HCl(+), and the (3) (2)Pi state of HBr(+). Rotational alignment of the Omega=0(+) intermediate states is evident from the angular distribution of the excited H(*)(n=2) photofragments. This effect has been observed previously and was used here to verify the reliability of the measured spatial anisotropy parameters.

Anion-pi, Lone-Pair-pi, pi-pi and Hydrogen-Bonding Interactions in a Cu-II Complex of 2-Picolinate and Protonated 4,4 '-Bipyridine: Crystal Structure and Theoretical Studies

A Cu-II complex of protonated 4,4'-bipyridine (Hbyp) and 2-picolinate (pic), [Cu-2(pic)(3)(Hbyp)(H2O)(ClO4)(2)], has been synthesised and characterised by single-crystal X-ray analysis. The structure consists of two copper atoms that have different environments, bridged by a carboxylate group. The equatorial plane is formed by the two bidentate picolinate groups in one Cu-II, and one picolinate, one monodentate 4,4'-bipyridyl ligand and a water molecule in the other. Each copper atom is also weakly bonded to a perchlorate anion in an axial position. One of the coordinated perchlorate groups displays anion-pi interaction with the coordinated pyridine ring. The noncoordinated carboxylate oxygen is involved in lone-pair (l.p.)-pi interaction with the protonated pyridine ring. In addition there are pi-pi and H-bonding interactions in the structure. Bader's theory of "atoms in molecules" (AIM) is used to characterise the anion-pi and l.p.-pi interactions observed in the solid state. A high-level ab initio study (RI-MP2/aug-cc-pVTZ level of theory) has been performed to analyse the anion-pi binding affinity of the pyridine ring when it is coordinated to a transition metal and also when the other pyridine ring of the 4,4'-bipyridine moiety is protonated. Theoretical investigations support the experimental findings of an intricate network of intermolecular interactions, which is characterised in the studied complex, and also indicate that protonation as well as coordination to the transition metal have important roles in influencing the pi-binding properties of the aromatic ring. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Search for a narrow, spin-2 resonance decaying to a pair of Z bosons in the qq̄ℓ+ℓ- final state

Results are presented from a search for a narrow, spin-2 resonance decaying into a pair of Z bosons, with one Z-boson decaying into leptons (e+e- or μ+μ-) and the other into jets. An example of such a resonance is the Kaluza-Klein graviton, GKK, predicted in Randall-Sundrum models. The analysis is based on a 4.9 fb-1 sample of proton-proton collisions at a center-of-mass energy of 7 TeV, collected with the CMS detector at the LHC. Kinematic and topological properties including decay angular distributions are used to discriminate between signal and background. No evidence for a resonance is observed, and upper limits on the production cross sections times branching fractions are set. In two models that predict Z-boson spin correlations in graviton decays, graviton masses are excluded lower than a value which varies between 610 and 945 GeV, depending on the model and the strength of the graviton couplings. © 2012 CERN.

Course of psychological variables in whiplash injury--a 2-year follow-up with age, gender and education pair-matched patients

This study evaluated the course of psychological variables during a 2-year follow-up in patients after common whiplash of the cervical spine. From a sample of 117 non-selected patients with common whiplash (investigated on average 7.2 +/- 4.2 days after trauma) a total of 21 suffered trauma-related symptoms over 2 years following initial injury. These patients (symptomatic group) were compared with 21 age, gender and education pair-matched patients, who showed complete recovery from trauma-related symptoms during the 2-year follow-up (asymptomatic group). Both groups underwent standardised testing procedures (i.e., Freiburg Personality Inventory and Well-Being Scale) at referral, and at 3, 6 and 24 months. In the symptomatic group during follow-up no significant changes in rating of neck pain or headache were found. Significant differences between the groups and significant deviation of scores over time were found on the Well-Being and Nervousness Scales. There was a lack of significant difference between the groups on the Depression Scale, indicating a possible somatic basis for changes in psychological functioning in the investigated sample. With regard to scales of Extraversion or Neuroticism, there were neither significant differences between the groups nor significant deviation over time. These results highlight that patients' psychological problems are rather a consequence than a cause of somatic symptoms in whiplash.

Evidence for DNA phosphate backbone alkylation and cleavage by pyrrolo[1,2-a]benzimidazoles: small molecules capable of causing base-pair-specific phosphodiester bond hydrolysis.

This report presents evidence that a reduced pyrrolo[1,2-a]benzimidazole (PBI) cleaves DNA as a result of phosphate alkylation followed by hydrolysis of the resulting phosphate triester. The base-pair specificity of the phosphate alkylation results from Hoogsteen-type hydrogen bonding of the reduced PBI in the major groove at only A.T and G.C base pairs. Alkylated phosphates were detected by 31P NMR and the cleavage products were detected by 1H NMR and HPLC. Evidence is also presented that a reduced PBI interacts with DNA in the major groove rather than in the minor groove or by intercalation.

Perturbative 2-body parent Hamiltonians for projected entangled pair states

We construct parent Hamiltonians involving only local 2-body interactions for a broad class of projected entangled pair states (PEPS). Making use of perturbation gadget techniques, we define a perturbative Hamiltonian acting on the virtual PEPS space with a finite order low energy effective Hamiltonian that is a gapped, frustration-free parent Hamiltonian for an encoded version of a desired PEPS. For topologically ordered PEPS, the ground space of the low energy effective Hamiltonian is shown to be in the same phase as the desired state to all orders of perturbation theory. An encoded parent Hamiltonian for the double semion string net ground state is explicitly constructed as a concrete example.

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Expression of mammalian glutathione S-transferase 5-5 in Salmonella typhimurium TA1535 leads to base-pair mutations upon exposure to dihalomethanes

Dihalomethanes can produce liver tumors in mice but not in rats, and concern exists about the risk of these compounds to humans. Glutathione (GSH) conjugation of dihalomethanes has been considered to be a critical event in the bioactivation process, and risk assessment is based upon this premise; however, there is little experimental support for this view or information about the basis of genotoxicity. A plasmid vector containing rat GSH S-transferase 5-5 was transfected into the Salmonella typhimurium tester strain TA1535, which then produced active enzyme. The transfected bacteria produced base-pair revertants in the presence of ethylene dihalides or dihalomethanes, in the order CH2Br2 > CH2BrCl > CH2Cl2. However, revertants were not seen when cells were exposed to GSH, CH2Br2, and an amount of purified GSH S-transferase 5-5 (20-fold excess in amount of that expressed within the cells). HCHO, which is an end product of the reaction of GSH with dihalomethanes, also did not produce mutations. S-(1-Acetoxymethyl)GSH was prepared as an analog of the putative S-(1-halomethyl)GSH reactive intermediates. This analog did not produce revertants, consistent with the view that activation of dihalomethanes must occur within the bacteria to cause genetic damage, presenting a model to be considered in studies with mammalian cells. S-(1-Acetoxymethyl)GSH reacted with 2′-deoxyguanosine to yield a major adduct, identified as S-[1-(N2-deoxyguanosinyl)methyl]GSH. Demonstration of the activation of dihalomethanes by this mammalian GSH S-transferase theta class enzyme should be of use in evaluating the risk of these chemicals, particularly in light of reports of the polymorphic expression of a similar activity in humans.

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F-2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.

Spectral analysis of pair-correlation bandwidth: Application to cell biology images

Images from cell biology experiments often indicate the presence of cell clustering, which can provide insight into the mechanisms driving the collective cell behaviour. Pair-correlation functions provide quantitative information about the presence, or absence, of clustering in a spatial distribution of cells. This is because the pair-correlation function describes the ratio of the abundance of pairs of cells, separated by a particular distance, relative to a randomly distributed reference population. Pair-correlation functions are often presented as a kernel density estimate where the frequency of pairs of objects are grouped using a particular bandwidth (or bin width), Δ>0. The choice of bandwidth has a dramatic impact: choosing Δ too large produces a pair-correlation function that contains insufficient information, whereas choosing Δ too small produces a pair-correlation signal dominated by fluctuations. Presently, there is little guidance available regarding how to make an objective choice of Δ. We present a new technique to choose Δ by analysing the power spectrum of the discrete Fourier transform of the pair-correlation function. Using synthetic simulation data, we confirm that our approach allows us to objectively choose Δ such that the appropriately binned pair-correlation function captures known features in uniform and clustered synthetic images. We also apply our technique to images from two different cell biology assays. The first assay corresponds to an approximately uniform distribution of cells, while the second assay involves a time series of images of a cell population which forms aggregates over time. The appropriately binned pair-correlation function allows us to make quantitative inferences about the average aggregate size, as well as quantifying how the average aggregate size changes with time.