The complex network of global cargo ship movements

Transportation networks play a crucial role in human mobility, the exchange of goods, and the spread of invasive species. With 90% of world trade carried by sea, the global network of merchant ships provides one of the most important modes of transportation. Here we use information about the itineraries of 16,363 cargo ships during the year 2007 to construct a network of links between ports. We show that the network has several features which set it apart from other transportation networks. In particular, most ships can be classified in three categories: bulk dry carriers, container ships and oil tankers. These three categories do not only differ in the ships' physical characteristics, but also in their mobility patterns and networks. Container ships follow regularly repeating paths whereas bulk dry carriers and oil tankers move less predictably between ports. The network of all ship movements possesses a heavy-tailed distribution for the connectivity of ports and for the loads transported on the links with systematic differences between ship types. The data analyzed in this paper improve current assumptions based on gravity models of ship movements, an important step towards understanding patterns of global trade and bioinvasion.Comment: 7 figures Accepted for publication by Journal of the Royal Society Interface (2010) For supplementary information, see http://www.icbm.de/~blasius/publications.htm

Cytotoxic polyfunctionality maturation of cytomegalovirus-pp65-specific CD4 + and CD8 + T-cell responses in older adults positively correlates with response size

Cytomegalovirus (CMV) infection is one of the most common persistent viral infections in humans worldwide and is epidemiologically associated with many adverse health consequences during aging. Previous studies yielded conflicting results regarding whether large, CMV-specific T-cell expansions maintain their function during human aging. In the current study, we examined the in vitro CMV-pp65-reactive T-cell response by comprehensively studying five effector functions (i.e., interleukin-2, tumor necrosis factor-α, interferon-γ, perforin, and CD107a expression) in 76 seropositive individuals aged 70 years or older. Two data-driven, polyfunctionality panels (IL-2-associated and cytotoxicity-associated) derived from effector function co-expression patterns were used to analyze the results. We found that, CMV-pp65-reactive CD8 + and CD4 + T cells contained similar polyfunctional subsets, and the level of polyfunctionality was related to the size of antigen-specific response. In both CD8 + and CD4 + cells, polyfunctional cells with high cytotoxic potential accounted for a larger proportion of the total response as the total response size increased. Notably, a higher serum CMV-IgG level was positively associated with a larger T-cell response size and a higher level of cytotoxic polyfunctionality. These findings indicate that CMV-pp65-specific CD4 + and CD8 + T cell undergo simultaneous cytotoxic polyfunctionality maturation during aging

Age-related changes in global motion coherence: conflicting haemodynamic and perceptual responses

Our aim was to use both behavioural and neuroimaging data to identify indicators of perceptual decline in motion processing. We employed a global motion coherence task and functional Near Infrared Spectroscopy (fNIRS). Healthy adults (n = 72, 18-85) were recruited into the following groups: young (n = 28, mean age = 28), middle-aged (n = 22, mean age = 50), and older adults (n = 23, mean age = 70). Participants were assessed on their motion coherence thresholds at 3 different speeds using a psychophysical design. As expected, we report age group differences in motion processing as demonstrated by higher motion coherence thresholds in older adults. Crucially, we add correlational data showing that global motion perception declines linearly as a function of age. The associated fNIRS recordings provide a clear physiological correlate of global motion perception. The crux of this study lies in the robust linear correlation between age and haemodynamic response for both measures of oxygenation. We hypothesise that there is an increase in neural recruitment, necessitating an increase in metabolic need and blood flow, which presents as a higher oxygenated haemoglobin response. We report age-related changes in motion perception with poorer behavioural performance (high motion coherence thresholds) associated with an increased haemodynamic response

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table 9 published in 10.1371/journal.pone.0017244. Supporting information is attached at the end of the article, and a computer-readable dataset of the ML estimates of selective constraints is available from 10.1371/journal.pone.001724

The clinical features of the piriformis syndrome: a systematic review

Piriformis syndrome, sciatica caused by compression of the sciatic nerve by the piriformis muscle, has been described for over 70 years; yet, it remains controversial. The literature consists mainly of case series and narrative reviews. The objectives of the study were: first, to make the best use of existing evidence to estimate the frequencies of clinical features in patients reported to have PS; second, to identify future research questions. A systematic review was conducted of any study type that reported extractable data relevant to diagnosis. The search included all studies up to 1 March 2008 in four databases: AMED, CINAHL, Embase and Medline. Screening, data extraction and analysis were all performed independently by two reviewers. A total of 55 studies were included: 51 individual and 3 aggregated data studies, and 1 combined study. The most common features found were: buttock pain, external tenderness over the greater sciatic notch, aggravation of the pain through sitting and augmentation of the pain with manoeuvres that increase piriformis muscle tension. Future research could start with comparing the frequencies of these features in sciatica patients with and without disc herniation or spinal stenosis

Finding Direction in the Search for Selection.

Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection. We find that the method to detect diversifying selection also detects directional selection under certain conditions. One method developed for detecting directional selection is powerful and accurate for a wide range of conditions, while the other can generate an excessive number of false positives

Impacts Des Technologies De l’Information Et De La Communication (TIC) Sur Les Rendements Scolaires Des Apprenants De La Ville De Dassa-Zoumé Dans Le Département Des Collines Au Bénin

L’usage des TIC consiste à l’accès et à l’utilisation des technologies de l’information et de la communication dans l’éducation. L’objectif global de cette recherche est de montrer les répercutions socio-éducatives des usages des TIC sur le rendement des apprenants des établissements publics de Dassa-Zoumé. L’approche méthodologique adoptée se subdivise en trois points à savoir : la recherche documentaire, la collecte de données, le traitement des informations et l’analyse des résultats.Les résultats obtenus sur le terrain ont révélé que 37 % des enseignants ont estimé que les TIC facilitent les recherches et 65 % de ceux-ci pensent que cela contribue à l’amélioration des résultats scolaires. L’usage des TIC pour des recherches documentaires est adopté par 65 % des enquêtés. 14 % ont affirmé que cela affaiblit le niveau scolaire des apprenants parce qu’ils l’utilisent pour des fins peu orthodoxes. Malgré les multiples avantages que procurent l’usage des TIC en milieu scolaire, des défis restent à relever à savoir : la non-maîtrise des outils informatiques, le coût d’accès élevés, l’éloignement des lieux d’accès et la privation formelle de l’usage des smartphones par les parents. Enfin 18 % ont énuméré l’indisponibilité des services offerts par les TIC

Longevity Record for a Wild Allegheny Woodrat (Neotama magister) in West Virginia

The Allegheny woodrat (Neotoma magister) is found throughout much of the central and southern Appalachians and adjacent portions of the Interior Highlands. Allegheny woodrats have declined in the northern portions of their range and are state-listed as threatened, endangered or sensitive species of concern in every state where they occur. Until recently, biologists have had to rely on biological data collected from the closely related eastern woodrat (N. floridana) because of limited research on the Allegheny woodrat. We have been studying the ecology and natural history of woodrats in Virginia and West Virginia since 1990. On 8 August 1997 we caught and ear-tagged a juvenile female woodrat. She was caught a total of 24 times in the same outcrop from 1997 through 2002. A conservative estimate of her age on 25 January 2002 was 1,734 days or 57.8 months. This extends the record longevity for a wild Allegheny woodrat by 70 days or 2.3 months. Regardless, her known time alive (from first capture to last) of 1,630 days still surpasses previous estimates of longevity for the Allegheny woodrat

Characterization, reactivity and rheological behaviour of metakaolin and Meta-halloysite based geopolymer binders

The type of aluminosilicate precursor used in the synthesis of geopolymer binders plays a huge role in the resulting performance. Thus, it is critical to understand the properties of precursors and how they influence the corresponding performance of geopolymer binders. In this study, metakaolin and meta halloysite are used as the aluminosilicate precursor in the synthesis of geopolymer binders. These precursors are obtained locally in order to propel the sustainable development and application of geopolymers. The precursors were characterized and the corresponding influence on the reactivity, rheology and setting times of geopolymers was investigated. In addition to the influence of precursor type on the properties of the geopolymers, the effect of two silica moduli (i.e. 1.3 and 1.5) was also evaluated. The results from this study indicated that increasing the activator silica modulus from 1.3 to 1.5 extended the setting times and increased the stress strain of the geopolymer binders. Characterization of the precursors indicated that metakaolin has a higher amorphous content compared to that of meta halloysite. However, the finer particles of meta halloysite embodied it with the ability to participate in a faster geopolymerization and result in more formation of activation products

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software