Sputum microscopy with fluorescein diacetate predicts tuberculosis infectiousness

Background. Sputum from patients with tuberculosis contains subpopulations of metabolically active and inactive Mycobacterium tuberculosis with unknown implications for infectiousness. Methods. We assessed sputum microscopy with fluorescein diacetate (FDA, evaluating M. tuberculosis metabolic activity) for predicting infectiousness. Mycobacterium tuberculosis was quantified in pretreatment sputum of patients with pulmonary tuberculosis using FDA microscopy, culture, and acid-fast microscopy. These 35 patients’ 209 household contacts were followed with prevalence surveys for tuberculosis disease for 6 years. Results. FDA microscopy was positive for a median of 119 (interquartile range [IQR], 47–386) bacteria/µL sputum, which was 5.1% (IQR, 2.4%–11%) the concentration of acid-fast microscopy–positive bacteria (2069 [IQR, 1358–3734] bacteria/μL). Tuberculosis was diagnosed during follow-up in 6.4% (13/209) of contacts. For patients with lower than median concentration of FDA microscopy–positive M. tuberculosis, 10% of their contacts developed tuberculosis. This was significantly more than 2.7% of the contacts of patients with higher than median FDA microscopy results (crude hazard ratio [HR], 3.8; P = .03). This association maintained statistical significance after adjusting for disease severity, chemoprophylaxis, drug resistance, and social determinants (adjusted HR, 3.9; P = .02). Conclusions. Mycobacterium tuberculosis that was FDA microscopy negative was paradoxically associated with greater infectiousness. FDA microscopy–negative bacteria in these pretreatment samples may be a nonstaining, slowly metabolizing phenotype better adapted to airborne transmission

Robustness Through Regime Flips in Collapsing Ecological Networks

© 2019, Crown. There has been considerable progress in our perception of organized complexity in recent years. Recurrent debates on the dynamics and stability of complex systems have provided several insights, but it is very difficult to find identifiable patterns in the relationship between complex network structure and dynamics. Traditionally an arena for theoreticians, much of this research has been invigorated by demonstration of alternate stable states in real world ecosystems such as lakes, coral reefs, forests and grasslands. In this work, we use topological connectivity attributes of eighty six ecological networks and link these with random and targeted perturbations, to obtain general patterns of behaviour of complex real world systems. We have analyzed the response of each ecological network to individual, grouped and cascading extinctions, and the results suggest that most networks are robust to loss of specialists until specific thresholds are reached in terms of network geodesics. If the extinctions persist beyond these thresholds, a state change or ‘flip’ occurs and the structural properties are altered drastically, although the network does not collapse. As opposed to simpler or smaller networks, we find larger networks to contain multiple states that may in turn, ensure long-term persistence, suggesting that complexity can endow resilience to ecosystems. The concept of critical transitions in ecological networks and the implications of these findings for complex systems characterized by networks are likely to be profound with immediate significance for ecosystem conservation, invasion biology and restoration ecology.Non

On the Complex Network Structure of Musical Pieces: Analysis of Some Use Cases from Different Music Genres

This paper focuses on the modeling of musical melodies as networks. Notes of a melody can be treated as nodes of a network. Connections are created whenever notes are played in sequence. We analyze some main tracks coming from different music genres, with melodies played using different musical instruments. We find out that the considered networks are, in general, scale free networks and exhibit the small world property. We measure the main metrics and assess whether these networks can be considered as formed by sub-communities. Outcomes confirm that peculiar features of the tracks can be extracted from this analysis methodology. This approach can have an impact in several multimedia applications such as music didactics, multimedia entertainment, and digital music generation.Comment: accepted to Multimedia Tools and Applications, Springe

Emergence of structural and dynamical properties of ecological mutualistic networks

Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the organization of ecological communities. Such networks in ecology have generically evolved a nested architecture independent of species composition and latitude - specialists interact with proper subsets of the nodes with whom generalists interact. Despite sustained efforts to explain observed network structure on the basis of community-level stability or persistence, such correlative studies have reached minimal consensus. Here we demonstrate that nested interaction networks could emerge as a consequence of an optimization principle aimed at maximizing the species abundance in mutualistic communities. Using analytical and numerical approaches, we show that because of the mutualistic interactions, an increase in abundance of a given species results in a corresponding increase in the total number of individuals in the community, as also the nestedness of the interaction matrix. Indeed, the species abundances and the nestedness of the interaction matrix are correlated by an amount that depends on the strength of the mutualistic interactions. Nestedness and the observed spontaneous emergence of generalist and specialist species occur for several dynamical implementations of the variational principle under stationary conditions. Optimized networks, while remaining stable, tend to be less resilient than their counterparts with randomly assigned interactions. In particular, we analytically show that the abundance of the rarest species is directly linked to the resilience of the community. Our work provides a unifying framework for studying the emergent structural and dynamical properties of ecological mutualistic networks.Comment: 10 pages, 4 figure

Biology, Methodology or Chance? The Degree Distributions of Bipartite Ecological Networks

The distribution of the number of links per species, or degree distribution, is widely used as a summary of the topology of complex networks. Degree distributions have been studied in a range of ecological networks, including both mutualistic bipartite networks of plants and pollinators or seed dispersers and antagonistic bipartite networks of plants and their consumers. The shape of a degree distribution, for example whether it follows an exponential or power-law form, is typically taken to be indicative of the processes structuring the network. The skewed degree distributions of bipartite mutualistic and antagonistic networks are usually assumed to show that ecological or co-evolutionary processes constrain the relative numbers of specialists and generalists in the network. I show that a simple null model based on the principle of maximum entropy cannot be rejected as a model for the degree distributions in most of the 115 bipartite ecological networks tested here. The model requires knowledge of the number of nodes and links in the network, but needs no other ecological information. The model cannot be rejected for 159 (69%) of the 230 degree distributions of the 115 networks tested. It performed equally well on the plant and animal degree distributions, and cannot be rejected for 81 (70%) of the 115 plant distributions and 78 (68%) of the animal distributions. There are consistent differences between the degree distributions of mutualistic and antagonistic networks, suggesting that different processes are constraining these two classes of networks. Fit to the MaxEnt null model is consistently poor among the largest mutualistic networks. Potential ecological and methodological explanations for deviations from the model suggest that spatial and temporal heterogeneity are important drivers of the structure of these large networks

Dynamic sea level changes following changes in the thermohaline circulation

Using the coupled climate model CLIMBER-3a, we investigate changes in sea surface elevation due to a weakening of the thermohaline circulation (THC). In addition to a global sea level rise due to a warming of the deep sea, this leads to a regional dynamic sea level change which follows quasi-instantaneously any change in the ocean circulation. We show that the magnitude of this dynamic effect can locally reach up to ~1m, depending on the initial THC strength. In some regions the rate of change can be up to 20-25 mm/yr. The emerging patterns are discussed with respect to the oceanic circulation changes. Most prominent is a south-north gradient reflecting the changes in geostrophic surface currents. Our results suggest that an analysis of observed sea level change patterns could be useful for monitoring the THC strength.Comment: Climate Dynamics (2004), submitted. See also http://www.pik-potsdam.de/~ander

A straightforward multiallelic significance test for the Hardy-Weinberg equilibrium law

Much forensic inference based upon DNA evidence is made assuming Hardy-Weinberg Equilibrium (HWE) for the genetic loci being used. Several statistical tests to detect and measure deviation from HWE have been devised, and their limitations become more obvious when testing for deviation within multiallelic DNA loci. The most popular methods-Chi-square and Likelihood-ratio tests-are based on asymptotic results and cannot guarantee a good performance in the presence of low frequency genotypes. Since the parameter space dimension increases at a quadratic rate on the number of alleles, some authors suggest applying sequential methods, where the multiallelic case is reformulated as a sequence of “biallelic” tests. However, in this approach it is not obvious how to assess the general evidence of the original hypothesis; nor is it clear how to establish the significance level for its acceptance/rejection. In this work, we introduce a straightforward method for the multiallelic HWE test, which overcomes the aforementioned issues of sequential methods. The core theory for the proposed method is given by the Full Bayesian Significance Test (FBST), an intuitive Bayesian approach which does not assign positive probabilities to zero measure sets when testing sharp hypotheses. We compare FBST performance to Chi-square, Likelihood-ratio and Markov chain tests, in three numerical experiments. The results suggest that FBST is a robust and high performance method for the HWE test, even in the presence of several alleles and small sample sizes

The HOSTS Survey for Exozodiacal Dust: Preliminary results and future prospects

[abridged] The presence of large amounts of dust in the habitable zones of nearby stars is a significant obstacle for future exo-Earth imaging missions. We executed an N band nulling interferometric survey to determine the typical amount of such exozodiacal dust around a sample of nearby main sequence stars. The majority of our data have been analyzed and we present here an update of our ongoing work. We find seven new N band excesses in addition to the high confidence confirmation of three that were previously known. We find the first detections around Sun-like stars and around stars without previously known circumstellar dust. Our overall detection rate is 23%. The inferred occurrence rate is comparable for early type and Sun-like stars, but decreases from 71% [+11%/-20%] for stars with previously detected mid- to far-infrared excess to 11% [+9%/-4%] for stars without such excess, confirming earlier results at high confidence. For completed observations on individual stars, our sensitivity is five to ten times better than previous results. Assuming a lognormal luminosity function of the dust, we find upper limits on the median dust level around all stars without previously known mid to far infrared excess of 11.5 zodis at 95% confidence level. The corresponding upper limit for Sun-like stars is 16 zodis. An LBTI vetted target list of Sun-like stars for exo-Earth imaging would have a corresponding limit of 7.5 zodis. We provide important new insights into the occurrence rate and typical levels of habitable zone dust around main sequence stars. Exploiting the full range of capabilities of the LBTI provides a critical opportunity for the detailed characterization of a sample of exozodiacal dust disks to understand the origin, distribution, and properties of the dust.GMK is supported by the Royal Society as a Royal Society University Research Fellow. AS is partially supported by funding from the Center for Exoplanets and Habitable Worlds. The Center for Exoplanets and Habitable Worlds is supported by the Pennsylvania State University, the Eberly College of Science, and the Pennsylvania Space Grant Consortium. JMS is supported by NASA through Hubble Fellowship grant HSTHF2-51398.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555

Violence witnessing, perpetrating and victimization in medellin, Colombia: a random population survey

<p>Abstract</p> <p>Background</p> <p>The burden of injury from violence and the costs attributable to violence are extremely high in Colombia. Despite a dramatic decline in homicides over the last ten years, homicide rate in Medellin, Colombia second largest city continues to rank among the highest of cities in Latin America. This study aims to estimate the prevalence and distribution of witnesses, victims and perpetrators of different forms of interpersonal violence in a representative sample of the general population in Medellin in 2007.</p> <p>Methods</p> <p>A face-to-face survey was carried out on a random selected, non-institutionalized population aged 12 to 60 years, with a response rate of 91% yielding 2,095 interview responses.</p> <p>Results</p> <p>We present the rates of prevalence for having been a witness, victim, or perpetrator for different forms of violence standardized using the WHO truncated population pyramid to allow for cross-national comparison. We also present data on verbal aggression, fraud and deception, yelling and heavy pranks, unarmed aggression during last year, and armed threat, other severe threats, robbery, armed physical aggression, and sexual aggression during the lifetime, by age, sex, marital and socioeconomic status, and education. Men reported the highest prevalence of being victims, perpetrators and witnesses in all forms of violence, except for robbery and sexual violence. The number of victims per perpetrator was positively correlated with the severity of the type of violence. The highest victimization proportions over the previous twelve months occurred among minors. Perpetrators are typically young unmarried males from lower socio-economic strata.</p> <p>Conclusions</p> <p>Due to very low proportion of victimization report to authorities, periodic surveys should be included in systems for epidemiological monitoring of violence, not only of victimization but also for perpetrators. Victimization information allows quantifying the magnitude of different forms of violence, while data on factors associated with aggression and perpetrators are necessary to estimate risk and protective factors that are essential to sound policies for violence prevention formulation.</p

Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions