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Microbiome dysbiosis across the respiratory tract has been implicated in the development and exacerbations of asthma. Little is known regarding the short-term temporal variability of the respiratory microbiome in health and asthma. In this study, we evaluate six scenarios of dysbiosis by investigating the inter- and intra-individual variability of the nasopharyngeal microbiome, measured with metagenomic sequencing. We characterized 239 microbiome samples from thirteen healthy individuals and from seventeen patients with well-controlled mild to moderate persistent asthma collected during a one-month period in which patients experienced no asthma exacerbations or infections. We controlled for sex, age (range 5 to 38 years), population (Greece and Poland), and microbiome type, for multiple levels of species incidence (expanded to core). Microbiomes collected from the same individual at different time points were more similar than those collected from the same group (health or asthma), but some individuals’ microbiomes were more variable than others. Microbiomes drawn from asthma patients were less likely to resemble each other than the microbiomes of healthy individuals, suggesting increased inter-sample variability and susceptibility to stochastic changes in asthma. In addition, the microbiomes of asthma patients became increasingly dissimilar over time, suggesting increased intra-individual temporal dynamics. Finally, microbiomes of individuals with asthma were more diverse than those of healthy individuals, while species diversity was negatively associated with temporal change in both the asthma and health groups. We propose that the increased diversity, inter-sample variability and intra-individual temporal dynamics during stable disease state(s) are intrinsic properties of the microbial system in asthma and characterise dysbiosis. Our work has significant implications for the relevance of the respiratory microbiome in asthma.

Ice cream is essentially a foam consisting of air bubbles dispersed in a mixture of fat, water and ice crystals. The air fraction is typically around 50% by volume, and this is crucial for the product to have the consistency and texture desired by customers. A common manufacturing method involves mixing the air and other ingredients under high pressure before discharging the product to atmospheric pressure for further processing. As the pressure is released, air may escape from the foam into the atmosphere. The Study Group was asked to quantify this air loss and to predict how it might depend on, for example, the rheological properties of the foam mixture, the bubble size distribution and the rate at which the pressure is released.

The Romer Labs RapidChek®Listeria monocytogenes test system (Performance Tested Method 011805) was validated against the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook (USDA-FSIS/MLG), U.S. Food and Drug Association Bacteriological Analytical Manual (FDA/BAM), and AOAC Official Methods of Analysis (AOAC/OMA) cultural reference methods for the detection of L. monocytogenes on selected foods including hot dogs, frozen cooked breaded chicken, frozen cooked shrimp, cured ham, and ice cream, and environmental surfaces including stainless steel and plastic in an unpaired study design. The RapidChek method uses a proprietary enrichment media system, a 44–48 h enrichment at 30 ± 1°C, and detects L. monocytogenes on an immunochromatographic lateral flow device within 10 min. Different L. monocytogenes strains were used to spike each of the matrixes. Samples were confirmed based on the reference method confirmations and an alternate confirmation method. A total of 140 low-level spiked samples were tested by the RapidChek method after enrichment for 44–48 h in parallel with the cultural reference method. There were 88 RapidChek presumptive positives. One of the presumptive positives was not confirmed culturally. Additionally, one of the culturally confirmed samples did not exhibit a presumptive positive. No difference between the alternate confirmation method and reference confirmation method was observed. The respective cultural reference methods (USDA-FSIS/MLG, FDA/BAM, and AOAC/OMA) produced a total of 63 confirmed positive results. Nonspiked samples from all foods were reported as negative for L. monocytogenes by all methods. Probability of detection analysis demonstrated no significant differences in the number of positive samples detected by the RapidChek method and the respective cultural reference method.

Summary Single-cell gene expression is inherently variable, but how this variability is controlled in response to stimulation remains unclear. Here, we use single-cell RNA-seq and single-molecule mRNA counting (smFISH) to study inducible gene expression in the immune toll-like receptor system. We show that mRNA counts of tumor necrosis factor α conform to a standard stochastic switch model, while transcription of interleukin-1β involves an additional regulatory step resulting in increased heterogeneity. Despite different modes of regulation, systematic analysis of single-cell data for a range of genes demonstrates that the variability in transcript count is linearly constrained by the mean response over a range of conditions. Mathematical modeling of smFISH counts and experimental perturbation of chromatin state demonstrates that linear constraints emerge through modulation of transcriptional bursting along with gene-specific relationships. Overall, our analyses demonstrate that the variability of the inducible single-cell mRNA response is constrained by transcriptional bursting.

Toll-like receptor (TLR) signaling regulates macrophage activation and effector cytokine propagation in the constrained environment of a tissue. In macrophage populations, TLR4 stimulates the dose-dependent transcription of nuclear factor B (NF-B) target genes. However, using single-RNA counting, we found that individual cells exhibited a wide range (three orders of magnitude) of expression of the gene encoding the proinflammatory cytokine tumor necrosis factor  (TNF-). The TLR4-induced TNFA transcriptional response correlated with the extent of NF-B signaling in the cells and their size. We compared the rates of TNF- production and uptake in macrophages and mouse embryonic fibroblasts and generated a mathematical model to explore the heterogeneity in the response of macrophages to TLR4 stimulation and the propagation of the TNF- signal in the tissue. The model predicts that the local propagation of the TLR4-dependent TNF- response and cellular NF-B signaling are limited to small distances of a few cell diameters between neighboring tissue-resident macrophages. In our predictive model, TNF- propagation was constrained by competitive uptake of TNF- from the environment, rather than by heterogeneous production of the cytokine. We propose that the highly constrained architecture of tissues enables effective localized propagation of inflammatory cues, while avoiding out-of-context responses at longer distances.

An effective HIV-1 vaccine should elicit sufficient breadth of immune recognition to protect against the genetically diverse forms of the circulating virus. Evaluation of the breadth and magnitude of cellular immune responses to epitope variants is important for HIV-1 vaccine assessment. We compared HIV-1 Gag-specific T-lymphocyte responses in 20 HIV-1-infected individuals representing two different HIV-1 subtypes, B and C. By assessing T lymphocyte responses with peptides based on natural HIV-1 variants, we found evidence for limited cross-reactivity and significantly enhanced within-clade responses among clade B-infected subjects, and not among clade C-infected subjects.

Human immunodeficiency virus type 1 (HIV-1) vaccine development requires selection of appropriate envelope (Env) immunogens. Twenty HIV-1 Env glycoproteins were examined for their ability to bind human anti-HIV-1 monoclonal antibodies (MAbs) and then used as immunogens in guinea pigs to identify promising immunogens. These included five Envs derived from chronically infected individuals, each representing one of five common clades and eight consensus Envs based on these five clades, as well as the consensus of the entire HIV-1 M group, and seven transmitted/founder (T/F) Envs from clades B and C. Sera from immunized guinea pigs were tested for neutralizing activity using 36 HIV-1 Env-pseudotyped viruses. All Envs bound to CD4 binding site, membrane-proximal, and V1/V2 MAbs with similar apparent affinities, although the T/F Envs bound with higher affinity to the MAb 17b, a CCR5 coreceptor binding site antibody. However, the various Envs differed in their ability to induce neutralizing antibodies. Consensus Envs elicited the most potent responses, but neutralized only a subset of viruses, including mostly easy-to-neutralize tier 1 and some more-difficult-to-neutralize tier 2 viruses. T/F Envs elicited fewer potent neutralizing antibodies but exhibited greater breadth than chronic or consensus Envs. Finally, chronic Envs elicited the lowest level and most limited breadth of neutralizing antibodies overall. Thus, each group of Env immunogens elicited a different antibody response profile. The complementary benefits of consensus and T/F Env immunogens raise the possibility that vaccines utilizing a combination of consensus and T/F Envs may be able to induce neutralizing responses with greater breadth and potency than single Env immunogens.

Defining the virus–host interactions responsible for HIV-1 transmission, including the phenotypic requirements of viruses capable of establishing de novo infections, could be important for AIDS vaccine development. Previous analyses have failed to identify phenotypic properties other than chemokine receptor 5 (CCR5) and CD4+ T-cell tropism that are preferentially associated with viral transmission. However, most of these studies were limited to examining envelope (Env) function in the context of pseudoviruses. Here, we generated infectious molecular clones of transmitted founder (TF; n = 27) and chronic control (CC; n = 14) viruses of subtypes B ( n = 18) and C ( n = 23) and compared their phenotypic properties in assays specifically designed to probe the earliest stages of HIV-1 infection. We found that TF virions were 1.7-fold more infectious ( P = 0.049) and contained 1.9-fold more Env per particle ( P = 0.048) compared with CC viruses. TF viruses were also captured by monocyte-derived dendritic cells 1.7-fold more efficiently ( P = 0.035) and more readily transferred to CD4+ T cells ( P = 0.025). In primary CD4+ T cells, TF and CC viruses replicated with comparable kinetics; however, when propagated in the presence of IFN-α, TF viruses replicated to higher titers than CC viruses. This difference was significant for subtype B ( P = 0.000013) but not subtype C ( P = 0.53) viruses, possibly reflecting demographic differences of the respective patient cohorts. Together, these data indicate that TF viruses are enriched for higher Env content, enhanced cell-free infectivity, improved dendritic cell interaction, and relative IFN-α resistance. These viral properties, which likely act in concert, should be considered in the development and testing of AIDS vaccines.

Serotyping of Shiga toxin-producing Escherichia coli (STEC) has been contingent upon the availability of antisera. Here we describe a 7-plex microbead-based immunoassay to simultaneously serotype seven STECs (i.e., belonging to serogroups O26, O45, O103, O111, O121, O145, and O157) by the Luminex xMAP® technology. This technology presents many advantages: Its multiplexed format (up to 100 analytes) saves time, reagents, and test sample, and many regulatory agencies currently utilize this platform for other assays. In this study, a total of seventy-nine STEC strains belonging to the 7 different serogroups of interest were tested. These strains had been previously serotyped and their serogroup was confirmed by PCR. Except for one strain belonging to the O111 serogroup, nearly all strains (i.e., 98.7%; 78/79) were correctly identified on the Bio-Plex 100 instrument in less than 4 h. This newly developed microbead-based immunoassay could be extended to include other STEC serogroups, virulence factors, and/or bacterial species.

The SDIX RapidChekTMListeria F.A.S.T. test system was validated against the U. S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) cultural reference method for the detection of Listeria species on stainless steel, plastic, rubber, and painted concrete. The SDIX method uses a proprietary RapidChek Listeria enrichment media for a one-step, 24–40 h enrichment at 30°C, and detects Listeria on an immunochromatographic lateral flow device in 10 min. Different Listeria species were used to spike each of the environmental surfaces. Environmental surfaces were spiked at levels ranging from 50 to 400 CFU/surface (1 in.2 swabs for painted concrete, 4 in.2 for sponge). A total of 120 spiked samples were tested by the SDIX method at 24 and 40 h and the cultural reference method. Total confirmed positives were 49, 54, and 48 for the SDIX 24 h method, the SDIX 40 h method, and the USDA-FSIS cultural reference method, respectively. Nonspiked samples from all environmental surfaces were reported as negative for Listeria spp. by all methods. The overall Chi square was 0.017 (P = 0.104) and 0.611 (P = 0.566) after a 24 and 40 h enrichment, respectively, indicating that the test method was equivalent in performance to the reference method at both enrichment times. The SDIX method was evaluated for the detection of 50 Listeria and 35 non-Listeria bacterial strains. All 50 Listeria strains were detected by the method (100% sensitivity). Five out of 35 non-Listeria species gave light test signals when grown in nonselective broth culture and tested undiluted. However, when grown in the RapidChek Listeria F.A.S.T. proprietary media, only one bacterial strain (Staphylococcus aureus) was detected, giving a very low test signal (97% specificity). The method was shown to be robust toward several alterations in testing and storage conditions.

White's lab established that strong, continuous stimulation with tumour necrosis factor-α (TNFα) can induce sustained oscillations in the subcellular localisation of the transcription factor nuclear factor κB (NF-κB). But the intensity of the TNFα signal varies substantially, from picomolar in the blood plasma of healthy organisms to nanomolar in diseased states. We report on a systematic survey using computational bifurcation theory to explore the relationship between the intensity of TNFα stimulation and the existence of sustained NF-κB oscillations. Using a deterministic model developed by Ashall et al. in 2009, we find that the system's responses to TNFα are characterised by a supercritical Hopf bifurcation point: above a critical intensity of TNFα the system exhibits sustained oscillations in NF-kB localisation. For TNFα below this critical value, damped oscillations are observed. This picture depends, however, on the values of the model's other parameters. When the values of certain reaction rates are altered the response of the signalling pathway to TNFα stimulation changes: in addition to the sustained oscillations induced by high-dose stimulation, a second oscillatory regime appears at much lower doses. Finally, we define scores to quantify the sensitivity of the dynamics of the system to variation in its parameters and use these scores to establish that the qualitative dynamics are most sensitive to the details of NF-κB mediated gene transcription.

In earlier work [D.S. Broomhead, J.P. Huke, M.R. Muldoon, and J. Stark, Iterated function system models of digital channels, Proc. R. Soc. Lond. A 460 (2004), pp. 3123-3142], aimed at developing an approach to signal processing that can be applied as well to nonlinear systems as linear ones, we produced mathematical models of digital communications channels that took the form of iterated function systems (IFS). For finite-dimensional systems these models have observability properties indicating they could be used for signal processing applications. Here we see how far the same approach can be taken towards the modelling of an infinite-dimensional system. The cable equation is a well-known partial differential equation (PDE) model of an imperfectly insulated uniform conductor, coupled to its surroundings by capacitive effects. (It is also much used as a basic model in theoretical neurobiology.) In this article we study the dynamics of this system when it is subjected to randomly selected discrete input pulses. The resulting IFS has a unique finite-dimensional attractor; we use results of Falconer and Solomyak to investigate the dimension of this attractor, relating it to the physical parameters of the system. Using work of Robinson, we show how some of the observability properties of the IFS model are retained. © 2012 Copyright Taylor and Francis Group, LLC.

Neutralizing antibodies (Nabs) are thought to play an important role in prevention and control of HIV-1 infection and should be targeted by an AIDS vaccine. It is critical to understand how HIV-1 induces Nabs by analyzing viral sequences in both tested viruses and sera. Neutralization susceptibility to antibodies in autologous and heterologous plasma was determined for multiple Envs (3-6) from each of 15 subtype-C-infected individuals. Heterologous neutralization was divided into two distinct groups: plasma with strong, cross-reactive neutralization (n = 9) and plasma with weak neutralization (n = 6). Plasma with cross-reactive heterologous Nabs also more potently neutralized contemporaneous autologous viruses. Analysis of Env sequences in plasma from both groups revealed a three-amino-acid substitution pattern in the V4 region that was associated with greater neutralization potency and breadth. Identification of such potential neutralization signatures may have important implications for the development of HIV-1 vaccines capable of inducing Nabs to subtype C HIV-1. © 2010 Elsevier Inc.

Vaccine design is challenging when the infectious agent is genetically diverse. Polyvalent 'mosaic' antigens might be used to address this challenge, and these two studies show promising results in monkeys infected with HIV-1.

Background/aims: To devise and evaluate a novel Ocular Anaesthetic Scoring System (OASS) for nontopical local anaesthesia. Methods: In OASS, a score of between 0 (poor) and 14 (excellent) was devised measuring motor (ocular motility, levator and orbicularis function) and sensory functions (digital spear pressure at limbus and topical anaesthetic sting). 40 patients were studied prospectively to analyse interobserver consistency in OASS. A further 100 patients were collected into four groups receiving either sub-Tenon or peribulbar block with 150 or 300 units of hyaluronidase. Patient satisfaction was determined using the Visual Analogue Pain Scale and Iowa Satisfaction with Anaesthesia Scale. Results: There was no significant difference in OASS scores between two independent observers (p = 0.8910). The sub-Tenon approach achieved significantly better OASS scores than the peribulbar approach (p,0.0004). 300 units of hyaluronidase gave significantly higher OASS scores in both sub-Tenon (p,0.0001) and peribulbar groups (p,0.0001). Spearman rank correlation showed that OASS correlates significantly with VAPS (20.82, p,0.0001) and ISAS (0.70, p,0.0001). The median satisfaction score was significant in order of magnitude: sub-Tenon with 300 units of hyaluronidase. sub-Tenon with 150 units of hyaluronidase.peribulbar with 300 units of hyaluronidase.peribulbar with 150 units of hyaluronidase. Conclusion: OASS is a simple and robust system for assessing and comparing non-topical local anaesthetic techniques. Of the techniques evaluated, a sub-Tenon block with 300 units of hyaluronidase gives the best anaesthesia, analgesia and patient satisfaction results. Non-topical local anaesthesia is used for many ocular procedures and has a major role in cataract surgery. In the last decade the use of local anaesthesia has increased from 20% in 1991 1 to

One of the major challenges that must be met in developing an HIV-1 vaccine is devising a strategy to generate cellular immunity with sufficient breadth to deal with the extraordinary genetic diversity of the virus. Amino acids in the envelopes of viruses from the same clade can differ by >15%, and those from different clades can differ by >30%. It has been proposed that creating immunogens using centralized HIV-1 gene sequences might provide a practical solution to this problem. Such centralized genes can be generated by employing a number of different strategies: consensus, ancestral, or center of tree sequences. These computer-generated sequences are a shorter genetic distance from any two contemporary virus sequences than those contemporary sequences are from each other. The present study was initiated to evaluate the breadth of cellular immunity generated through immunization of rhesus monkeys with vaccine constructs expressing either an HIV-1 global consensus envelope sequence (CON-S) or a single patient isolate clade B envelope sequence (clade B). We show that vaccine immunogens expressing the single centralized gene CON-S generated cellular immune responses with significantly increased breadth compared with immunogens expressing a wild-type virus gene. In fact, CON-S immunogens elicited cellular immune responses to 3- to 4-fold more discrete epitopes of the envelope proteins from clades A, C, and G than did clade B immunogens. These findings suggest that immunization with centralized genes is a promising vaccine strategy for developing a global vaccine for HIV-1 as well as vaccines for other genetically diverse viruses.

The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss responses to regions where test set and infecting virus differ. In this study, we report the design of a peptide test set with significantly increased coverage of HIV sequence diversity by including alternative amino acids at variable positions during the peptide synthesis step. In an IFN-γ ELISpot assay, these “toggled” peptides detected HIV-specific CD4+ and CD8+ T cell responses of significantly higher breadth and magnitude than matched consensus peptides. The observed increases were explained by a closer match of the toggled peptides to the autologous viral sequence. Toggled peptides therefore afford a cost-effective and significantly more complete view of the host immune response to HIV and are directly applicable to other variable pathogens.

The genetic diversity among globally circulating human immunodeficiency virus type 1 (HIV-1) strains is a serious challenge for HIV-1 vaccine design. We have generated a synthetic group M consensus env gene (CON6) for induction of cross-subtype immune responses and report here a comparative study of T-cell responses to this and natural strain env immunogens in a murine model. Three different strains of mice were immunized with CON6 as well as subtype A, B, or C env immunogens, using a DNA prime-recombinant vaccinia virus boost strategy. T-cell epitopes were mapped by gamma interferon enzyme-linked immunospot analysis using five overlapping Env peptide sets from heterologous subtype A, B, and C viruses. The CON6-derived vaccine was immunogenic and induced a greater number of T-cell epitope responses than any single wild-type subtype A, B, and C env immunogen and similar T-cell responses to a polyvalent vaccine. The responses were comparable to within-clade responses but significantly more than between-clade responses. The magnitude of the T-cell responses induced by CON6 (measured by individual epitope peptides) was also greater than the magnitude of responses induced by individual wild-type env immunogens. Though the limited major histocompatibility complex repertoire in inbred mice does not necessarily predict responses in nonhuman primates and humans, these results suggest that synthetic centralized env immunogens represent a promising approach for HIV-1 vaccine design that merits further characterization.

This paper introduces a new class of models of digital communications channels. Physically, these models take account of the digital nature of the input. Mathematically, they are iterated function systems. As a consequence of making explicit assumptions about the role of discreteness in the models, it is possible to make general statements about the behaviour of these channels without needing to assume that they are linear. We provide the mathematical background necessary to understand the behaviour of these models and prove a number of results about their observability. We also provide a number of examples intended to demonstrate their connection with linear state-space models, and to suggest how the nonlinear theory might be developed towards applications.

Heterosexual transmission accounts for the majority of human immunodeficiency virus–1 (HIV-1) infections worldwide, yet the viral properties that determine transmission fitness or outgrowth have not been elucidated. Here we show, for eight heterosexual transmission pairs, that recipient viruses were monophyletic, encoding compact, glycan-restricted envelope glycoproteins. These viruses were also uniquely sensitive to neutralization by antibody from the transmitting partner. Thus, the exposure of neutralizing epitopes, which are lost in chronic infection because of immune escape, appears to be favored in the newly infected host. This reveals characteristics of the envelope glycoprotein that influence HIV-1 transmission and may have implications for vaccine design.

The eukaryotic 40S ribosomal subunit locates the translation initiation codon on an mRNA via the so-called scanning process that follows 40S binding to the capped 5' end. This key step in translation is required for the expression of almost all eukaryotic genes, yet the mechanism and dynamics of scanning are unknown. We have performed quantitative studies in vivo and in vitro of the movement of yeast 40S ribosomes along 5' untranslated regions (UTRs) of different lengths. 40S subunits perform cap-dependent scanning with high processivity for more than 1700 nucleotides in cells of Saccharomyces cerevisiae. Moreover, the observed rates of expression indicate that scanning is performed by an untethered 40S subunit that has been released from the 5' cap complex. Unexpectedly, the capability to maintain scanning competence on a long 5' UTR is more dependent on the Ded1/Dbp1 type of helicase than on eIF4A or eIF4B. In a yeast cell-free extract, scanning shows reduced processivity, with an estimated net 5'-->3' rate of approximately 10 nucleotides per second at 26 degrees C. We have developed a biased bidirectional walking model of ribosomal scanning that provides a framework for understanding the above observations as well as other known quantitative and qualitative features of this process.

In earlier work, human immunodeficiency virus type 1 (HIV–1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV–1, the virus that is responsible for the acquired immune deficiency syndrome pandemic, yielding a best estimate of 1931 (95% confidence interval of 1915–1941). That work will be briefly reviewed, outlining how phylogenetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of latency, and how the approach was validated by correctly estimating the timing of two historically documented dates. The advantages, limitations, and assumptions of the approach will be summarized, with particular consideration of the implications of branch length uncertainty and recombination. We have recently undertaken new phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo (the DRC, formerly Zaire). This analysis both corroborates and extends the conclusions of our original study. Coalescent methods were used to infer the demographic history of the HIV–1 epidemic in the DRC, and the results suggest an increase in the exponential growth rate of the infected population through time.

Models of the mechanisms of normal eye movements are typically described in terms of the block diagrams which are used in control theory. An alternative approach to understanding the mechanisms of normal eye movements involves describing the eye movement behaviour in terms of smooth changes in state variables. The latter approach captures the burst cell firing against motor error (difference between target gaze angle and current gaze angle) phase plane behaviour which is found experimentally and facilitates the modelling of variations in burst cell behaviour. A novel explanation of several types of congenital nystagmus waveforms is given in terms of a saccadic termination abnormality.

We present a new embedding theorem for time series, in the spirit of Takens's theorem, but requiring multivariate signals. Our result is part of a growing body of work that extends the domain of geometric time series analysis to some genuinely stochastic systems---including such natural examples as x_{j+1} = \phi(x_j) + \eta_j where \phi is some fixed map and the \eta_j are i.i.d. random displacements.

Analysis of protein data sets often requires prior removal of redundancy, so that data is not biased by containing similar proteins. This is usually achieved by pairwise comparison of sequences, followed by purging so that no two pairs have similarities above a chosen threshold. From a starting set, such as the PDB or a genome, one should remove as few sequences as possible, to give the largest possible non-redundant set for subsequent analysis. Protein redundancy can be represented as a graph, with proteins as nodes connected by undirected edges, if they have a pairwise similarity above the chosen threshold. The problem is then equivalent to finding the maximum independent set (MIS), where as few nodes are removed as possible to remove all edges. We tested seven MIS algorithms, three of which are new. We applied the methods to the PDB, subsets of the PDB, various genomes and the BHOLSIB benchmark datasets. For PDB subsets of up to 1000 proteins, we could compare to the exact MIS, found by the Cliquer algorithm. The best algorithm was the new method, Leaf. This works by adding clique members that have no edges to nodes outside the clique to the MIS, starting with the smallest cliques. For PDB subsets of up to 1000 members, it usually finds the MIS and is fast enough to apply to data sets of tens of thousands of proteins. Leaf gives sets that are around 10% larger than the commonly used PISCES algorithm, that are of identical quality. We therefore suggest that Leaf should be the method of choice for generating non-redundant protein data sets, though it is ineffective on dense graphs, such as the BHOLSIB benchmarks. The Leaf algorithm is available at: https://github.com/SimonCB765/Leaf, and sets from genomes and the PDB are available at: http://www.bioinf.manchester.ac.uk/leaf/. © 2013 Bull et al.

Background Sustained stimulation with tumour necrosis factor alpha (TNF-alpha) induces substantial oscillations—observed at both the single cell and population levels—in the nuclear factor kappa B (NF-kappa B) system. Although the mechanism has not yet been elucidated fully, a core system has been identified consisting of a negative feedback loop involving NF-kappa B (RelA:p50 hetero-dimer) and its inhibitor I-kappa B-alpha. Many authors have suggested that this core oscillator should couple to other oscillatory pathways. Results First we analyse single-cell data from experiments in which the NF-kappa B system is forced by short trains of strong pulses of TNF-alpha. Power spectra of the ratio of nuclear-to-cytoplasmic concentration of NF-kappa B suggest that the cells' responses are entrained by the pulsing frequency. Using a recent model of the NF-kappa B system due to Caroline Horton, we carried out extensive numerical simulations to analyze the response frequencies induced by trains of pulses of TNF-alpha stimulation having a wide range of frequencies and amplitudes. These studies suggest that for sufficiently weak stimulation, various nonlinear resonances should be observable. To explore further the possibility of probing alternative feedback mechanisms, we also coupled the model to sinusoidal signals with a wide range of strengths and frequencies. Our results show that, at least in simulation, frequencies other than those of the forcing and the main NF-kappa B oscillator can be excited via sub- and superharmonic resonance, producing quasiperiodic and even chaotic dynamics. Conclusions Our numerical results suggest that the entrainment phenomena observed in pulse-stimulated experiments is a consequence of the high intensity of the stimulation. Computational studies based on current models suggest that resonant interactions between periodic pulsatile forcing and the system's natural frequencies may become evident for sufficiently weak stimulation. Further simulations suggest that the nonlinearities of the NF-kappa B feedback oscillator mean that even sinusoidally modulated forcing can induce a rich variety of nonlinear interactions.

The relative involvement of different temporal frequency-selective filters underlying detection of chromatic stimuli was studied. Diverse spectral stimuli were used, namely flashed blue and yellow light spots, wide bars, and narrow bars. The stimuli were temporally modulated in luminance having constant wavelength. Although the bar-like stimuli apparently reduced the sensitivity at short and long wavelengths, the cone-opponent mechanism still remained responsible for the actual stimulus detection at different temporal frequencies. The bar-like stimuli increased sensitivity for temporal frequencies around 3-6 Hz, revealing involvement of an intermediate temporal frequency-selective filter in detection, the so-called transient-1 filter. A probability summation model for the method of adjustment was developed that assumes that detection depends on the properties of the temporal filters underlying the temporal frequency-sensitivity curve. The model supports the notion that at least two temporal frequency-selective filters are necessary to account for the shape of the sensitivity curves obtained for blue bar-like stimuli. © 2010 Optical Society of America.

It has been asserted in the literature that the low pass filtering of time series data may lead to erroneous results when calculating attractor dimensions. Here we prove that finite order, non-recursive filters do not have this effect. In fact, a generic, finite order, non-recursive filter leaves invariant all the quantities that can be estimated by using embedding techniques such as the method of delays.

In this chapter we investigate the ownership and control of UK firms using contemporary methods from computational graph theory. Specifically, we analyze a ‘small-world’ model of ownership and control. A small-world is a network whose actors are linked by a short chain of acquaintances (short path lengths), but at the same time have a strongly overlapping circle of friends (high clustering). We simulate a set of corporate worlds using an ensemble of random graphs introduced by Chung and Lu (2002a, 2002b). We find that the corporate governance network structures analyzed here are more clustered (‘clubby’) than would be predicted by the random-graph model. Path lengths, though, are generally not shorter than expected. In addition, we investigate the role of financial institutions: potentially important conduits creating connectivity in corporate networks. We find such institutions give rise to systematically different network topologies.

The eukaryotic 40S ribosomal subunit locates the translation initiation codon on an mRNA via the so-called scanning process that follows 40S binding to the capped 5' end. This key step in translation is required for the expression of almost all eukaryotic genes, yet the mechanism and dynamics of scanning are unknown. We have performed quantitative studies in vivo and in vitro of the movement of yeast 40S ribosomes along 5' untranslated regions (UTRs) of different lengths. 40S subunits perform cap-dependent scanning with high processivity for more than 1700 nucleotides in cells of Saccharomyces cerevisiae. Moreover, the observed rates of expression indicate that scanning is performed by an untethered 40S subunit that has been released from the 5' cap complex. Unexpectedly, the capability to maintain scanning competence on a long 5' UTR is more dependent on the Ded1/Dbp1 type of helicase than on eIF4A or eIF4B. In a yeast cell-free extract, scanning shows reduced processivity, with an estimated net 5'--3' rate of approximately 10 nucleotides per second at 26 degrees C. We have developed a biased bidirectional walking model of ribosomal scanning that provides a framework for understanding the above observations as well as other known quantitative and qualitative features of this process.

In this paper we present a random graph model to explain the network structure of boards of directors. We investigate the conditions under which corporate boards can be said to be a "small-world". Our empirical results show that the random graph model is remarkably good at explaining board structure and connectedness in the United States, the United Kingdom and Germany. Although there are small-world traits such as "clustering" and "short-paths" in the corporate world, they are no more pronounced than would be expected by chance in a statistically similar, but randomly assembled corporate universe. Finally, our results show the existence of positive degree correlation: directors who sit on many boards do so in the company of other directors who sit on many boards. This result helps explain the distribution of board interlocks.

HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915–41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

Most HIV-1 infections of children result from mother-to-infant transmission, which may occur perinatally or postnatally, as a consequence of breast feeding1−8. In this study, the influence of maternal viral load on transmission of infection to infants from non-breast-feeding mothers was examined using samples of plasma and peripheral blood mononuclear cells (PBMCs) collected at several time points during pregnancy and the 6-month period after delivery. These samples were analyzed by several quantitative methods, including virus cultures of PBMCs and polymerase chain reaction (PCR) assays for HIV-1 RNA in plasma and DMA in PBMCs. The risk of transmission increased slightly with a higher viral load, but transmission and nontransmission occurred over the entire range of values for each assay. No threshold value of virus load was identified which discriminated between transmitters and nontransmitters. We also noted a significant rise in viral load and a decline in CD4+ lymphocytes in the six months after delivery. These findings suggest that a high maternal viral load is insufficient to fully explain vertical transmission of HIV-1. Additional studies are needed to examine the post-partum increase in viremia.

Although the Research Article from B. Korber et al. [“Timing the ancestor of the HIV-1 pandemic strains,” (9 June, p. [1789][1])] and the excellent commentary thereon by D. M. Hillis (p. [1757][2]) both acknowledge the possibility that AIDS began through an iatrogenic event involving an oral

Because the oscillatory eye movements of congenital nystagmus vary from cycle to cycle, there is no clear relationship between the waveform produced and the underlying abnormality of the ocular motor system. We consider the durations of successive cycles of nystagmus which could be (1) completely determined by the lengths of the previous cycles, (2) completely independent of the lengths of the previous cycles or (3) a mixture of the two. The behaviour of a deterministic system can be characterised in terms of a collection of (unstable) oscillations, referred to as periodic orbits, which make up the system. By using a recently developed technique for identifying periodic orbits in noisy data, we find evidence for periodic orbits in nystagmus waveforms, eliminating the possibility that each cycle is independent of the previous cycles. The technique also enables us to identify the waveforms which correspond to the deterministic behaviour of the ocular motor system. These waveforms pose a challenge to our understanding of the ocular motor system because none of the current extensions to models of the normal behaviour of the ocular motor system can explain the range of identified waveforms.

“Centralized” (ancestral and consensus) HIV-1 envelope immunogens induce broadly cross-reactive T cell responses in laboratory animals; however, their potential to elicit cross-reactive neutralizing antibodies has not been fully explored. Here, we report the construction of a panel of consensus subtype B (ConB) envelopes and compare their biologic, antigenic, and immunogenic properties to those of two wild-type Env controls from individuals with early and acute HIV-1 infection. Glycoprotein expressed from full-length (gp160), uncleaved (gp160-UNC), truncated (gp145), and N-linked glycosylation site deleted (gp160-201N/S) versions of the ConB env gene were packaged into virions and, except for the fusion defective gp160-UNC, mediated infection via the CCR5 co-receptor. Pseudovirions containing ConB Envs were sensitive to neutralization by patient plasma and monoclonal antibodies, indicating the preservation of neutralizing epitopes found in contemporary subtype B viruses. When used as DNA vaccines in guinea pigs, ConB and wild-type env immunogens induced appreciable binding, but overall only low level neutralizing antibodies. However, all four ConB immunogens were significantly more potent than one wild-type vaccine at eliciting neutralizing antibodies against a panel of tier 1 and tier 2 viruses, and ConB gp145 and gp160 were significantly more potent than both wild-type vaccines at inducing neutralizing antibodies against tier 1 viruses. Thus, consensus subtype B env immunogens appear to be at least as good as, and in some instances better than, wild-type B env immunogens at inducing a neutralizing antibody response, and are amenable to further improvement by specific gene modifications.

To create an HIV-1 vaccine that generates sufficient breadth of immune recognition to protect against the genetically diverse forms of the circulating virus, we have been exploring vaccines based on consensus and mosaic protein designs. Increasing the valency of a mosaic immunogen cocktail increases epitope coverage but with diminishing returns, as increasingly rare epitopes are incorporated into the mosaic proteins. In this study we compared the immunogenicity of 2-valent and 3-valent HIV-1 envelope mosaic immunogens in rhesus monkeys. Immunizations with the 3-valent mosaic immunogens resulted in a modest increase in the breadth of vaccine-elicited T lymphocyte responses compared to the 2-valent mosaic immunogens. However, the 3-valent mosaic immunogens elicited significantly higher neutralizing responses to Tier 1 viruses than the 2-valent mosaic immunogens. These findings underscore the potential utility of polyvalent mosaic immunogens for eliciting both cellular and humoral immune responses to HIV-1.

An approach to finding codes for use in direct sequence spread spectrum communications systems is described. It is based upon an analogy between codes having auto-and cross-correlation properties desirable for spread spectrum systems, and certain dynamical systems encountered in ergodic theory called systems with 'Lebesgue spectrum'. Such systems are associated with collections of orthogonal functions and these functions can be used to generate collections of time series with zero cross-correlation functions. To generate codewords we must use truncated versions of these time series, for which the cross-correlations are no longer precisely zero: these truncated sequences correspond to periodic orbits of the dynamical system. The method for finding a code from a suitable periodic orbit is described, and an example, using a simple dynamical system known as the doubling map, is worked through in some detail.