Natural classification of knots

The principal objective of the knot theory is to provide a simple way of classifying and ordering all the knot types. Here, we propose a natural classification of knots based on their intrinsic position in the knot space that is defined by the set of knots to which a given knot can be converted by individual intersegmental passages. In addition, we characterize various knots using a set of simple quantum numbers that can be determined upon inspection of minimal crossing diagram of a knot. These numbers include: crossing number; average three-dimensional writhe; number of topological domains; and the average relaxation value

An architecture for adaptive replication-based multimedia streaming in P2P networks

This PhD thesis addresses the issue of scalable media streaming in large-scale networking environments. Multimedia streaming is one of the largest sink of network resources and this trend is still growing as testified by the success of services like Skype, Netflix, Spotify and Popcorn Time (BitTorrent-based). In traditional client-server solutions, when the number of consumers increases, the server becomes the bottleneck. To overcome this problem, the Content-Delivery Network (CDN) model was invented. In CDN model, the server copies the media content to some CDN servers, which are located in different strategic locations on the network. However, they require heavy infrastructure investment around the world, which is too expensive. Peer-to-peer (P2P) solutions are another way to achieve the same result. These solutions are naturally scalable, since each peer can act as both a receiver and a forwarder. Most of the proposed streaming solutions in P2P networks focus on routing scenarios to achieve scalability. However, these solutions cannot work properly in video-on-demand (VoD) streaming, when resources of the media server are not sufficient. Replication is a solution that can be used in these situations. This thesis specifically provides a family of replication-based media streaming protocols, which are scalable, efficient and reliable in P2P networks. First, it provides SCALESTREAM, a replication-based streaming protocol that adaptively replicates media content in different peers to increase the number of consumers that can be served in parallel. The adaptiveness aspect of this solution relies on the fact that it takes into account different constraints like bandwidth capacity of peers to decide when to add or remove replicas. SCALESTREAM routes media blocks to consumers over a tree topology, assuming a reliable network composed of homogenous peers in terms of bandwidth. Second, this thesis proposes RESTREAM, an extended version of SCALESTREAM that addresses the issues raised by unreliable networks composed of heterogeneous peers. Third, this thesis proposes EAGLEMACAW, a multiple-tree replication streaming protocol in which two distinct trees, named EAGLETREE and MACAWTREE, are built in a decentralized manner on top of an underlying mesh network. These two trees collaborate to serve consumers in an efficient and reliable manner. The EAGLETREE is in charge of improving efficiency, while the MACAWTREE guarantees reliability. Finally, this thesis provides TURBOSTREAM, a hybrid replication-based streaming protocol in which a tree overlay is built on top of a mesh overlay network. Both these overlays cover all peers of the system and collaborate to improve efficiency and low-latency in streaming media to consumers. This protocol is implemented and tested in a real networking environment using PlanetLab Europe testbed composed of peers distributed in different places in Europe.

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence from stochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect dramatically impacts the geometry and topology of DNA inside phages. Accounting for this local potential allows us to reproduce the main experimental data on DNA organization in phages, including the cryo-EM observations and detailed features of the spectrum of DNA knots formed inside viral capsids. The DNA knots we observe are strongly delocalized and, intriguingly, this is shown not to interfere with genome ejection out of the phage.

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

BACKGROUND: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.

Construction and electrophoretic migration of single-stranded DNA knots and catenanes.

In recent years there has been growing interest in the question of how the particular topology of polymeric chains affects their overall dimensions and physical behavior. The majority of relevant studies are based on numerical simulation methods or analytical treatment; however, both these approaches depend on various assumptions and simplifications. Experimental verification is clearly needed but was hampered by practical difficulties in obtaining preparative amounts of knotted or catenated polymers with predefined topology and precisely set chain length. We introduce here an efficient method of production of various single-stranded DNA knots and catenanes that have the same global chain length. We also characterize electrophoretic migration of the produced single-stranded DNA knots and catenanes with increasing complexity.

The evolutionary host switches of Polychromophilus: a multi-gene phylogeny of the bat malaria genus suggests a second invasion of mammals by a haemosporidian parasite.

BACKGROUND: The majority of Haemosporida species infect birds or reptiles, but many important genera, including Plasmodium, infect mammals. Dipteran vectors shared by avian, reptilian and mammalian Haemosporida, suggest multiple invasions of Mammalia during haemosporidian evolution; yet, phylogenetic analyses have detected only a single invasion event. Until now, several important mammal-infecting genera have been absent in these analyses. This study focuses on the evolutionary origin of Polychromophilus, a unique malaria genus that only infects bats (Microchiroptera) and is transmitted by bat flies (Nycteribiidae). METHODS: Two species of Polychromophilus were obtained from wild bats caught in Switzerland. These were molecularly characterized using four genes (asl, clpc, coI, cytb) from the three different genomes (nucleus, apicoplast, mitochondrion). These data were then combined with data of 60 taxa of Haemosporida available in GenBank. Bayesian inference, maximum likelihood and a range of rooting methods were used to test specific hypotheses concerning the phylogenetic relationships between Polychromophilus and the other haemosporidian genera. RESULTS: The Polychromophilus melanipherus and Polychromophilus murinus samples show genetically distinct patterns and group according to species. The Bayesian tree topology suggests that the monophyletic clade of Polychromophilus falls within the avian/saurian clade of Plasmodium and directed hypothesis testing confirms the Plasmodium origin. CONCLUSION: Polychromophilus' ancestor was most likely a bird- or reptile-infecting Plasmodium before it switched to bats. The invasion of mammals as hosts has, therefore, not been a unique event in the evolutionary history of Haemosporida, despite the suspected costs of adapting to a new host. This was, moreover, accompanied by a switch in dipteran host.

Nicotine vaccines for smoking cessation.

BACKGROUND: By reducing the amount of nicotine that reaches the brain when a person smokes a cigarette, nicotine vaccines may help people to stop smoking or to prevent recent quitters from relapsing. OBJECTIVES: The aims of this review are to assess the efficacy of nicotine vaccines for smoking cessation and for relapse prevention, and to assess the frequency and type of adverse events associated with the use of nicotine vaccines. SEARCH METHODS: We searched the Cochrane Tobacco Addiction Review Group specialised register for trials, using the term 'vaccine' in the title or abstract, or in a keyword (date of most recent search April 2012). To identify any other material including reviews and papers potentially relevant to the background or discussion sections, we also searched MEDLINE, EMBASE, and PsycINFO, combining terms for nicotine vaccines with terms for smoking and tobacco use, without design limits or limits for human subjects. We searched the Annual Meeting abstracts of the Society for Research on Nicotine and Tobacco up to 2012, using the search string 'vaccin'. We searched Google Scholar for 'nicotine vaccine'. We also searched company websites and Google for information related to specific vaccines. We searched clinicaltrials.gov in March 2012 for 'nicotine vaccine' and for the trade names of known vaccine candidates. SELECTION CRITERIA: We included randomized controlled trials of nicotine vaccines, at Phase II and Phase III trial stage and beyond, in adult smokers or recent ex-smokers. We included studies of nicotine vaccines used as part of smoking cessation or relapse prevention interventions. DATA COLLECTION AND ANALYSIS: We extracted data on the type of participants, the dose and duration of treatment, the outcome measures, the randomization procedure, concealment of allocation, blinding of participants and personnel, reporting of outcomes, and completeness of follow-up.Our primary outcome measure was a minimum of six months abstinence from smoking. We used the most rigorous definition of abstinence, and preferred cessation rates at 12 months and biochemically validated rates where available. We have used the risk ratio (RR) to summarize individual trial outcomes. We have not pooled the current group of included studies as they cover different vaccines and variable regimens. MAIN RESULTS: There are no nicotine vaccines currently licensed for public use, but there are a number in development. We found four trials which met our inclusion criteria, three comparing NicVAX to placebo and one comparing NIC002 (formerly NicQbeta) to placebo. All were smoking cessation trials conducted by pharmaceutical companies as part of the drug development process, and all trials were judged to be at high or unclear risk of bias in at least one domain. Overall, 2642 smokers participated in the included studies in this review. None of the four included studies detected a statistically significant difference in long-term cessation between participants receiving vaccine and those receiving placebo. The RR for 12 month cessation in active and placebo groups was 1.35 (95% Confidence Interval (CI) 0.82 to 2.22) in the trial of NIC002 and 1.74 (95% CI 0.73 to 4.18) in one NicVAX trial. Two Phase III NicVAX trials, for which full results were not available, reported similar quit rates of approximately 11% in both groups. In the two studies with full results available, post hoc analyses detected higher cessation rates in participants with higher levels of nicotine antibodies, but these findings are not readily generalisable. The two studies with full results showed nicotine vaccines to be well tolerated, with the majority of adverse events classified as mild or moderate. In the study of NIC002, participants receiving the vaccine were more likely to report mild to moderate adverse events, most commonly flu-like symptoms, whereas in the study of NicVAX there was no significant difference between the two arms. Information on adverse events was not available for the large Phase III trials of NicVAX.Vaccine candidates are likely to undergo significant changes before becoming available to the general public, and those included in this review may not be the first to reach market; this limits the external validity of the results reported in this review in terms of both effectiveness and tolerability. AUTHORS' CONCLUSIONS: There is currently no evidence that nicotine vaccines enhance long-term smoking cessation. Rates of serious adverse events recorded in the two trials with full data available were low, and the majority of adverse events reported were at mild to moderate levels. The evidence available suggests nicotine vaccines do not induce compensatory smoking or affect withdrawal symptoms. No nicotine vaccines are currently licensed for use in any country but a number are under development.Further trials of nicotine vaccines are needed, comparing vaccines with placebo for smoking cessation. Further trials are also needed to explore the potential of nicotine vaccines to prevent relapse. Results from past, current and future research should be reported in full. Adverse events and serious adverse events should continue to be carefully monitored and thoroughly reported.

Trans-SNARE pairing can precede a hemifusion intermediate in intracellular membrane fusion.

The question concerning whether all membranes fuse according to the same mechanism has yet to be answered satisfactorily. During fusion of model membranes or viruses, membranes dock, the outer membrane leaflets mix (termed hemifusion), and finally the fusion pore opens and the contents mix. Viral fusion proteins consist of a membrane-disturbing 'fusion peptide' and a helical bundle that pin the membranes together. Although SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complexes form helical bundles with similar topology, it is unknown whether SNARE-dependent fusion events on intracellular membranes proceed through a hemifusion state. Here we identify the first hemifusion state for SNARE-dependent fusion of native membranes, and place it into a sequence of molecular events: formation of helical bundles by SNAREs precedes hemifusion; further progression to pore opening requires additional peptides. Thus, SNARE-dependent fusion may proceed along the same pathway as viral fusion: both use a docking mechanism via helical bundles and additional peptides to destabilize the membrane and efficiently induce lipid mixing. Our results suggest that a common lipidic intermediate may underlie all fusion reactions of lipid bilayers.

Spatial analysis of erythrocyte membrane fluctuations by digital holographic microscopy.

Red blood cell (RBC) membrane fluctuations provide important insights into cell states. We present a spatial analysis of red blood cell membrane fluctuations by using digital holographic microscopy (DHM). This interferometric and dye-free technique, possessing nanometric axial and microsecond temporal sensitivities enables to measure cell membrane fluctuations (CMF) on the whole cell surface. DHM acquisition is combined with a model which allows extracting the membrane fluctuation amplitude, while taking into account cell membrane topology. Uneven distribution of CMF amplitudes over the RBC surface is observed, showing maximal values in a ring corresponding to the highest points on the RBC torus as well as in some scattered areas in the inner region of the RBC. CMF amplitudes of 35.9+/-8.9 nm and 4.7+/-0.5 nm (averaged over the cell surface) were determined for normal and ethanol-fixed RBCs, respectively.

Structural organization of alpha-subunit from purified and microsomal toad kidney (Na+ + K+)-ATPase as assessed by controlled trypsinolysis

The membrane organization of the alpha-subunit of purified (Na+ + K+)-ATPase ((Na+ + K+)-dependent adenosine triphosphate phosphorylase, EC 3.6.1.3) and of the microsomal enzyme of the kidney of the toad Bufo marinus was compared by using controlled trypsinolysis. With both enzyme preparations, digestions performed in the presence of Na+ yielded a 73 kDa fragment and in the presence of K+ a 56 kDa, a 40 kDa and small amounts of a 83 kDa fragment from the 96 kDa alpha-subunit. In contrast to mammalian preparations (Jørgensen, P.L. (1975) Biochim. Biophys. Acta 401, 399-415), trypsinolysis of the purified amphibian enzyme led to a biphasic loss of (Na+ + K+)-ATPase activity in the presence of both Na+ and K+. These data could be correlated with an early rapid cleavage of 3 kDa from the alpha-subunit in both ionic conditions and a slower degradation of the remaining 93 kDa polypeptide. On the other hand, in the microsomal enzyme, a 3 kDa shift of the alpha-subunit could only be produced in the presence of Na+. Our data indicate that (1) purification of the amphibian enzyme with detergent does not influence the overall topology of the alpha-subunit but produces a distinct structural alteration of its N-terminus and (2) the amphibian kidney enzyme responds to cations with similar conformational transitions as the mammalian kidney enzyme. In addition, anti alpha-serum used on digested enzyme samples revealed on immunoblots that the 40 kDa fragment was better recognized than the 56 kDa fragment. It is concluded that the NH2-terminal of the alpha-subunit contains more antigenic sites than the COOH-terminal domain in agreement with the results of Farley et al. (Farley, R.A., Ochoa, G.T. and Kudrow, A. (1986) Am. J. Physiol. 250, C896-C906).

Effect of orthographic processes on letter identity and letter-position encoding in dyslexic children.

The ability to identify letters and encode their position is a crucial step of the word recognition process. However and despite their word identification problem, the ability of dyslexic children to encode letter identity and letter-position within strings was not systematically investigated. This study aimed at filling this gap and further explored how letter identity and letter-position encoding is modulated by letter context in developmental dyslexia. For this purpose, a letter-string comparison task was administered to French dyslexic children and two chronological age (CA) and reading age (RA)-matched control groups. Children had to judge whether two successively and briefly presented four-letter strings were identical or different. Letter-position and letter identity were manipulated through the transposition (e.g., RTGM vs. RMGT) or substitution of two letters (e.g., TSHF vs. TGHD). Non-words, pseudo-words, and words were used as stimuli to investigate sub-lexical and lexical effects on letter encoding. Dyslexic children showed both substitution and transposition detection problems relative to CA-controls. A substitution advantage over transpositions was only found for words in dyslexic children whereas it extended to pseudo-words in RA-controls and to all type of items in CA-controls. Letters were better identified in the dyslexic group when belonging to orthographically familiar strings. Letter-position encoding was very impaired in dyslexic children who did not show any word context effect in contrast to CA-controls. Overall, the current findings point to a strong letter identity and letter-position encoding disorder in developmental dyslexia.

Merkel cells and the individuality of friction ridge skin

There is no definite theory yet for the mechanism by which the pattern of epidermal ridges on fingers, palms and soles forming friction ridge skin (FRS) patterns is created. For a long time growth forces in the embryonal epidermis have been believed to be involved in FRS formation. More recent evidence suggests that Merkel cells play an important part in this process as well. Here we suggest a model for the formation of FRS patterns that links Merkel cells to the epidermal stress distribution. The Merkel cells are modeled as agents in an agent based model that move anisotropically where the anisotropy is created by the epidermal stress tensor. As a result ridge patterns are created with pattern defects as they occur in real FRS patterns. As a consequence we suggest why the topology of FRS patterns is indeed unique as the arrangement of pattern defects is sensitive to the initial configuration of Merkel cells.

DNA knots and DNA supercoiling.

Comment on: Witz G, et al. Proc Natl Acad Sci USA 2011; 108:3608-11.

Information sharing and social network dynamics : a coevolutionary approach

The capacity to interact socially and share information underlies the success of many animal species, humans included. Researchers of many fields have emphasized the evo¬lutionary significance of how patterns of connections between individuals, or the social networks, and learning abilities affect the information obtained by animal societies. To date, studies have focused on the dynamics either of social networks, or of the spread of information. The present work aims to study them together. We make use of mathematical and computational models to study the dynamics of networks, where social learning and information sharing affect the structure of the population the individuals belong to. The number and strength of the relationships between individuals, in turn, impact the accessibility and the diffusion of the shared information. Moreover, we inves¬tigate how different strategies in the evaluation and choice of interacting partners impact the processes of knowledge acquisition and social structure rearrangement. First, we look at how different evaluations of social interactions affect the availability of the information and the network topology. We compare a first case, where individuals evaluate social exchanges by the amount of information that can be shared by the partner, with a second case, where they evaluate interactions by considering their partners' social status. We show that, even if both strategies take into account the knowledge endowments of the partners, they have very different effects on the system. In particular, we find that the first case generally enables individuals to accumulate higher amounts of information, thanks to the more efficient patterns of social connections they are able to build. Then, we study the effects that homophily, or the tendency to interact with similar partners, has on knowledge accumulation and social structure. We compare the case where individuals who know the same information are more likely to learn socially from each other, to the opposite case, where individuals who know different information are instead more likely to learn socially from each other. We find that it is not trivial to claim which strategy is better than the other. Depending on the possibility of forgetting information, the way new social partners can be chosen, and the population size, we delineate the conditions for which each strategy allows accumulating more information, or in a faster way For these conditions, we also discuss the topological characteristics of the resulting social structure, relating them to the information dynamics outcome. In conclusion, this work paves the road for modeling the joint dynamics of the spread of information among individuals and their social interactions. It also provides a formal framework to study jointly the effects of different strategies in the choice of partners on social structure, and how they favor the accumulation of knowledge in the population. - La capacité d'interagir socialement et de partager des informations est à la base de la réussite de nombreuses espèces animales, y compris les humains. Les chercheurs de nombreux domaines ont souligné l'importance évolutive de la façon dont les modes de connexions entre individus, ou réseaux sociaux et les capacités d'apprentissage affectent les informations obtenues par les sociétés animales. À ce jour, les études se sont concentrées sur la dynamique soit des réseaux sociaux, soit de la diffusion de l'information. Le présent travail a pour but de les étudier ensemble. Nous utilisons des modèles mathématiques et informatiques pour étudier la dynamique des réseaux, où l'apprentissage social et le partage d'information affectent la structure de la population à laquelle les individus appartiennent. Le nombre et la solidité des relations entre les individus ont à leurs tours un impact sur l'accessibilité et la diffusion de l'informa¬tion partagée. Par ailleurs, nous étudions comment les différentes stratégies d'évaluation et de choix des partenaires d'interaction ont une incidence sur les processus d'acquisition des connaissances ainsi que le réarrangement de la structure sociale. Tout d'abord, nous examinons comment des évaluations différentes des interactions sociales influent sur la disponibilité de l'information ainsi que sur la topologie du réseau. Nous comparons un premier cas, où les individus évaluent les échanges sociaux par la quantité d'information qui peut être partagée par le partenaire, avec un second cas, où ils évaluent les interactions en tenant compte du statut social de leurs partenaires. Nous montrons que, même si les deux stratégies prennent en compte le montant de connaissances des partenaires, elles ont des effets très différents sur le système. En particulier, nous constatons que le premier cas permet généralement aux individus d'accumuler de plus grandes quantités d'information, grâce à des modèles de connexions sociales plus efficaces qu'ils sont capables de construire. Ensuite, nous étudions les effets que l'homophilie, ou la tendance à interagir avec des partenaires similaires, a sur l'accumulation des connaissances et la structure sociale. Nous comparons le cas où des personnes qui connaissent les mêmes informations sont plus sus¬ceptibles d'apprendre socialement l'une de l'autre, au cas où les individus qui connaissent des informations différentes sont au contraire plus susceptibles d'apprendre socialement l'un de l'autre. Nous constatons qu'il n'est pas trivial de déterminer quelle stratégie est meilleure que l'autre. En fonction de la possibilité d'oublier l'information, la façon dont les nouveaux partenaires sociaux peuvent être choisis, et la taille de la population, nous déterminons les conditions pour lesquelles chaque stratégie permet d'accumuler plus d'in¬formations, ou d'une manière plus rapide. Pour ces conditions, nous discutons également les caractéristiques topologiques de la structure sociale qui en résulte, les reliant au résultat de la dynamique de l'information. En conclusion, ce travail ouvre la route pour la modélisation de la dynamique conjointe de la diffusion de l'information entre les individus et leurs interactions sociales. Il fournit également un cadre formel pour étudier conjointement les effets de différentes stratégies de choix des partenaires sur la structure sociale et comment elles favorisent l'accumulation de connaissances dans la population.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.

The main goal of CleanEx is to provide access to public gene expression data via unique gene names. A second objective is to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-data set comparisons. A consistent and up-to-date gene nomenclature is achieved by associating each single experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of human genes and genes from model organisms. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing cross-references to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resource, such as cDNA clones or Affymetrix probe sets. The web-based query interfaces offer access to individual entries via text string searches or quantitative expression criteria. CleanEx is accessible at: http://www.cleanex.isb-sib.ch/.