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Rapid developments and methodological divides hinder the study of how scientific knowledge accumulates, consolidates and transfers to the public sphere. Our work proposes using Wikipedia, the online encyclopedia, as a historiographical source for contemporary science. We chose the high-profile field of gene editing as our test case, performing a historical analysis of the English-language Wikipedia articles on CRISPR. Using a mixed-method approach, we qualitatively and quantitatively analyzed the CRISPR article's text, sections and references, alongside 50 affiliated articles. These, we found, documented the CRISPR field's maturation from a fundamental scientific discovery to a biotechnological revolution with vast social and cultural implications. We developed automated tools to support such research and demonstrated its applicability to two other scientific fields-coronavirus and circadian clocks. Our method utilizes Wikipedia as a digital and free archive, showing it can document the incremental growth of knowledge and the manner scientific research accumulates and translates into public discourse. Using Wikipedia in this manner compliments and overcomes some issues with contemporary histories and can also augment existing bibliometric research.

X-ray computed tomography (XRCT) imaging allows non-destructive visualization of the structure of various materials. Applied to wooden objects, it allows determination of their morphologies or manufacturing techniques, but also measurement of growth ring widths. We have applied XRCT to a selection of 38 mummy labels. This funerary furniture, made up of endemic or imported tree species, has survived thanks to environmental conditions in very large quantities in regions in Middle and Upper Egypt and is featured now in museum collections across the globe. Mummy labels thus represent a unique and abundant data source to build floating or absolutely dated dendrochronological chronologies for this period. Here we discuss the possible contributions and limitations of XRCT for the analysis of these artifacts and show that the approach allows identification of discriminating markers for the identification of certain species on the transverse plane, but that the insufficient resolution of the tangential and radial planes normally prevents formal identification of species. By contrast, XRCT undeniably enhances the visibility of toolmarks (in terms of numbers and depth), and thereby allows highlighting marks that remain invisible to the naked eye; XRCT also provides key insights into cutting methods and the calibers used and yields new information on silvicultural practices and the knowhow of Egyptian craftsmen. Finally, the measurement of ring widths on XRCT imagery is also more accurate than what can be achieved by traditional dendrochronological measurements, especially in the case of cuts realized on a slab. The approach also confirms the limited potential of local broadleaved species for dendrochronological approaches due to unreadable or poorly visible tree rings and mostly short tree-ring sequences. [ABSTRACT FROM AUTHOR]

The objective of this study was to determine the rates of virological failure (VF) and HIV drug resistance (HIVDR) amongst adolescents on antiretroviral Therapy (ART). A retrospectively designed study was conducted in 10 healthcare centers for adolescents living with HIV (ALHIV) in the two main cities of Cameroon (Yaoundé and Douala), from November 2018 to May 2019. Sociodemographic, clinical, therapeutic and laboratory parameters were collected from medical records. All enrolled ALHIV had viral load (VL) measurements following the national guidelines. All patients with a VL ≥ 1000 copies/ml were called to perform genotyping tests. The chi-square test was used to determine the factors associated with VF. Out of the 1316 medical records of ALHIV, we included 1083 ALHIV having a VL result. Among them, 276 (25.5%) were experiencing VF, and VF was significantly higher in ALHIV with suboptimal adherence (p

We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in Salmonella enterica sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (KanR) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (CamR) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a KanR cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a CamR cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (www.beiresources.org) and publicly available.

BackgroundDespite the fact that an educational programme for parents of youth tennis players has been launched recently, there is a need to empower parents of athletes in sustaining the combination of education and sport careers (i.e., dual career) of their talented and elite athletes across sports. The aim of this study was to explore the parents' view of their role as dual career supporters and their need for educational support in this area.MethodsIn total, 115 parents (F = 49, M = 66) of athletes (14-23 yrs) engaged in full time academic education (high school/university) and competitive (e.g., National, International) sports (individual = 12, team = 9) in five European Member States (e.g., France, Ireland, Italy, Portugal, Slovenia) took part in national workshops. The workshops involved discussing five themes and agreeing statements relevant to assist parents supporting their children as dual career athletes: 1) the athletes' needs; 2) the sports environment; 3) the academic environment; 4) dual career-related policies and services; 5) The educational methods for parenting dual career athletes.ResultsA final list of 80 agreed statements were identified: 25 statements mainly related to the sports entourage; 23 to information on dual career-related policies and services; 22 to the athletes' needs; 17 to the academic entourage, and 8 to the relevant educational resources to parenting dual career athletes, respectively.ConclusionsThis cross-national qualitative research synthesized the parents' perspectives about their needs and the most relevant content of an educational programme for parenting dual career athletes. The findings of this research will help influence the formulation of effective education strategies on parenting dual career athletes to ensure an optimal supportive environment for the successful combination of high-level sport and education careers.

IntroductionWhile use of augmentation of labor (AL) is appropriate for labor dystocia, it is frequently used inadequately and unnecessarily. The objective was to assess at a national level, the frequency and determinants of misuse of augmentation of labor (AL).Material and methodsWomen of the French perinatal survey of 2016 with a singleton cephalic fetus, delivering at term after a spontaneous labor were included. "Misuse of AL" was defined by artificial rupture of the membranes (ROM) and/or oxytocin within one hour of admission and/or duration between ROM and oxytocin of less than one hour. Women, labor and maternity unit's characteristics were compared between the "misuse of AL" and "no misuse of AL" groups by bivariate analysis. To identify the determinants of misuse of AL, a multivariable multilevel logistic regression was performed taking into account the data's hierarchical structure (first level: women, second level: maternity units).ResultsAmong the 7196 women included, 1524 (21.2%) had a misuse of AL. The determinants of misuse of AL were middle school educational level (reference high school), aOR = 1.21; 95%CI[1.01-1.45], gestational age at delivery ≥41weeks (reference 39-40 weeks), aOR = 1.19; 95%CI[1.00-1.42], cervical dilation ≥6cm at admission (reference ConclusionsIn France, one spontaneous laboring woman among five is subject to misuse of AL. The misuse is mostly explained by maternity unit's characteristics. The determinants identified in this study can be used to implement targeted actions in small and private maternity units.

BackgroundThis study aimed to use a concept mapping methodology to develop a European framework of the needs of parents/guardians (P/G) for supporting athletes combining sport and education (dual career, DC).MethodsBy means of a concept mapping methodology, 337 French, Irish, Italian, Portuguese, and Slovenian parents sorted and rated 80 potential statements associated to parenting DC athletes.ResultsFive distinct clusters emerged: 1. P/G' roles, needs and awareness to support athletes, including 22 statements (mean:3.7; range: 3.2-4.2 pt); 2. Requirements for effective planning of DC pathway, including 19 statements (mean:3.7; range: 3.2-4.5 pt); 3. Educational opportunity, including 13 statements (mean:3.5; range: 3.1-4.0 pt); 4. Policy and provision for DC, including 19 statements (mean:3.7; range: 3.1-4.2 pt); and 5. Athletes' lifestyle & self-management, including 7 statements (mean:4.0; range: 3.5-4.5 pt). Estimates of effect size (Partial eta-squared) were calculated for ANOVAs to assess the degree of variability on the statement importance ranking as the dependent variable accounted for by the demographic data. The concept mapping showed good validity (stress value: 0.11) and high reliability (rSHT: 0.99, rSHM: 0.98; rRR:0.98). One-third of the statements indicated differences (pConclusionIn synthesizing the opinions, experience and needs of P/Gs of DC athletes the present framework provided sound theoretical underpinnings to inform the development of an online educational programme for empowering parenting DC athletes (https://edu.empatiasport.eu/eng/), as well as be a foundation for future Pan-European DC research on how these statements interact with each other, in different European contexts.

BackgroundNeuromyelitis optica spectrum disorders (NMOSD) is a primary astrocytopathy driven by antibodies directed against the aquaporin-4 water channel located at the end-feet of the astrocyte. Although blood-brain barrier (BBB) breakdown is considered one of the key steps for the development and lesion formation, little is known about the molecular mechanisms involved. The aim of the study was to evaluate the effect of human immunoglobulins from NMOSD patients (NMO-IgG) on BBB properties.MethodsFreshly isolated brain microvessels (IBMs) from rat brains were used as a study model. At first, analysis of the secretome profile from IBMs exposed to purified NMO-IgG, to healthy donor IgG (Control-IgG), or non-treated, was performed. Second, tight junction (TJ) proteins expression in fresh IBMs and primary cultures of brain microvascular endothelial cells (BMEC) was analysed by Western blotting (Wb) after exposition to NMO-IgG and Control-IgG. Finally, functional BBB properties were investigated evaluating the presence of rat-IgG in tissue lysate from brain using Wb in the rat-model, and the passage of NMO-IgG and sucrose in a bicameral model.ResultsWe found that NMO-IgG induces functional and morphological BBB changes, including: 1) increase of pro-inflammatory cytokines production (CXCL-10 [IP-10], IL-6, IL-1RA, IL-1β and CXCL-3) in IBMs when exposed to NMO-IgG; 2) decrease of Claudin-5 levels by 25.6% after treatment of fresh IBMs by NMO-IgG compared to Control-IgG (p = 0.002), and similarly, decrease of Claudin-5 by at least 20% when BMEC were cultured with NMO-IgG from five different patients; 3) a higher level of rat-IgG accumulated in periventricular regions of NMO-rats compared to Control-rats and an increase in the permeability of BBB after NMO-IgG treatment in the bicameral model.ConclusionHuman NMO-IgG induces both structural and functional alterations of BBB properties, suggesting a direct role of NMO-IgG on modulation of BBB permeability in NMOSD.

Mediterranean wetlands are critical strongholds for biodiversity and the provision of ecosystem functions and services; yet, they are being severely degraded by a number of socio-economic drivers and pressures, including climate change. Moreover, we still lack comprehensive understanding of the extent to which biodiversity loss in Mediterranean wetlands will accelerate change in ecosystem processes. Here, we evaluate how changes in biodiversity can alter the ecosystem of the Camargue (southern France). We collected data on species presence/absence, trends and abundance over a 40-year period by combining observations from the scholarly literature with insights derived from expert knowledge. In total, we gathered more than 1500 estimates of presence/absence, over 1400 estimates of species abundance, and about 1400 estimates of species trends for eight taxonomic groups, i.e. amphibians, reptiles, breeding birds, fish, mammals, dragonflies (odonates), orthopterans and vascular plants. Furthermore, we used information on recently arrived species and invasive species to identify compositional changes across multiple taxa. Complementing targeted literature searches with expert knowledge allowed filling important gaps regarding the status and trends of biodiversity in the Camargue. Species trend data revealed sharp population declines in amphibians, odonates and orthopterans, while birds and plants experienced an average increase in abundance between the 1970s and the 2010s. The general increasing trends of novel and invasive species is suggested as an explanation for the changing abundance of birds and plants. While the observed declines in certain taxa reflect the relative failure of the protection measures established in the Camargue, the increasing exposure to novel and invasive species reveal major changes in the community structure of the different taxonomic groups. This study is the first attempt to assess changes in biodiversity in the Camargue using an expert knowledge approach, and can help manage the uncertainties and complexities associated with rapid social-ecological change in other Mediterranean wetlands.

[This corrects the article DOI: 10.1371/journal.pone.0181780.].

INTRODUCTION:Antimicrobial resistance (AMR) is a substantial threat to public health. Safe and effective alternatives are required to reduce unnecessary antibiotic prescribing. Andrographis Paniculata (A. Paniculata, Chuān Xīn Lián) has traditionally been used in Indian and Chinese herbal medicine for cough, cold and influenza, suggesting a role in respiratory tract infections (RTIs). This systematic review aimed to evaluate the clinical effectiveness and safety of A. Paniculata for symptoms of acute RTIs (ARTIs). MATERIALS AND METHODS:English and Chinese databases were searched from their inception to March 2016 for randomised controlled trials (RCTs) evaluating oral A. Paniculata without language barriers (Protocol ID: CRD42016035679). The primary outcomes were improvement in ARTI symptoms and adverse events (AEs). A random effects model was used to pool the mean differences and risk ratio with 95% CI reported. Methodological quality was evaluated using the Cochrane risk of bias tool; two reviewers independently screened eligibility and extracted data. RESULTS:Thirty-three RCTs (7175 patients) were included. Most trials evaluated A. Paniculata (as a monotherapy and as a herbal mixture) provided commercially but seldom reported manufacturing or quality control details. A. Paniculata improved cough (n = 596, standardised mean difference SMD: -0.39, 95% confidence interval CI [-0.67, -0.10]) and sore throat (n = 314, SMD: -1.13, 95% CI [-1.37, -0.89]) when compared with placebo. A. Paniculata (alone or plus usual care) has a statistically significant effect in improving overall symptoms of ARTIs when compared to placebo, usual care, and other herbal therapies. Evidence also suggested that A. Paniculata (alone or plus usual care) shortened the duration of cough, sore throat and sick leave/time to resolution when compared versus usual care. No major AEs were reported and minor AEs were mainly gastrointestinal. The methodological quality of included trials was overall poor. CONCLUSIONS:A. Paniculata appears beneficial and safe for relieving ARTI symptoms and shortening time to symptom resolution. However, these findings should be interpreted cautiously owing to poor study quality and heterogeneity. Well-designed trials evaluating the effectiveness and potential to reduce antibiotic use of A. Paniculata are warranted.

Opinion evolution and judgment revision are mediated through social influence. Based on a large crowdsourced in vitro experiment (n = 861), it is shown how a consensus model can be used to predict opinion evolution in online collective behaviour. It is the first time the predictive power of a quantitative model of opinion dynamics is tested against a real dataset. Unlike previous research on the topic, the model was validated on data which did not serve to calibrate it. This avoids to favor more complex models over more simple ones and prevents overfitting. The model is parametrized by the influenceability of each individual, a factor representing to what extent individuals incorporate external judgments. The prediction accuracy depends on prior knowledge on the participants' past behaviour. Several situations reflecting data availability are compared. When the data is scarce, the data from previous participants is used to predict how a new participant will behave. Judgment revision includes unpredictable variations which limit the potential for prediction. A first measure of unpredictability is proposed. The measure is based on a specific control experiment. More than two thirds of the prediction errors are found to occur due to unpredictability of the human judgment revision process rather than to model imperfection.

γδ T cells play critical roles in host defense against infections and cancer. Although advances have been made in identifying γδ TCR ligands, it remains essential to understand molecular mechanisms responsible for in vivo expansion of γδ T cells in periphery. Recent findings identified the expression of the inducible NO synthase (NOS2) in lymphoid cells and highlighted novel immunoregulatory functions of NOS2 in αβ T cell differentiation and B cell survival. In this context, we wondered whether NOS2 exerts an impact on γδ T cell properties. Here, we show that γδ T cells express NOS2 not only in vitro after TCR triggering, but also directly ex vivo. Nos2 deficient mice have fewer γδ T cells in peripheral lymph nodes (pLNs) than their wild-type counterparts, and these cells exhibit a reduced ability to produce IL-2. Using chemical NOS inhibitors and Nos2 deficient γδ T cells, we further evidence that the inactivation of endogenous NOS2 significantly reduced γδ T cell proliferation and glycolysis metabolism that can be restored in presence of exogenous IL-2. Collectively, we demonstrate the crucial role of endogenous NOS2 in promoting optimal IL-2 production, proliferation and glycolysis of γδ T cells that may contribute to their regulation at steady state.

OBJECTIVE:Infants from multiple pregnancies have higher rates of preterm birth, stillbirth and neonatal death and differences in multiple birth rates (MBR) exist between countries. We aimed to describe differences in MBR in Europe and to investigate the impact of these differences on adverse perinatal outcomes at a population level. METHODS:We used national aggregate birth data on multiple pregnancies, maternal age, gestational age (GA), stillbirth and neonatal death collected in the Euro-Peristat project (29 countries in 2010, N = 5 074 643 births). We also used European Society of Human Reproduction and Embryology (ESHRE) data on assisted conception and single embryo transfer (SET). The impact of MBR on outcomes was studied using meta-analysis techniques with random-effects models to derive pooled risk ratios (pRR) overall and for four groups of country defined by their MBR. We computed population attributable risks (PAR) for these groups. RESULTS:In 2010, the average MBR was 16.8 per 1000 women giving birth, ranging from 9.1 (Romania) to 26.5 (Cyprus). Compared to singletons, multiples had a nine-fold increased risk (pRR 9.4, 95% Cl 9.1-9.8) of preterm birth (

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual's breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used.In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value.We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental results suggest that tree-based ensemble methods including McRank, Random Forests and Gradient Boosting Regression Trees achieve excellent ranking accuracy. RKHS regression and RankSVM also achieve good accuracy when used with an RBF kernel. Traditional regression methods such as Bayesian lasso, wBSR and BayesC were found less suitable for ranking. Pearson correlation was found to correlate poorly with NDCG. Our study suggests two important messages. First, ranking methods are a promising research direction in GS. Second, NDCG can be a useful evaluation measure for GS.

We analyze two large datasets from technological networks with location and social data: user location records from an online location-based social networking service, and anonymized telecommunications data from a European cellphone operator, in order to investigate the differences between individual and group behavior with respect to physical location. We discover agreements between the two datasets: firstly, that individuals are more likely to meet with one friend at a place they have not visited before, but tend to meet at familiar locations when with a larger group. We also find that groups of individuals are more likely to meet at places that their other friends have visited, and that the type of a place strongly affects the propensity for groups to meet there. These differences between group and solo mobility has potential technological applications, for example, in venue recommendation in location-based social networks.

We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in Salmonella enterica sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (KanR) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (CamR) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a KanR cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a CamR cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (www.beiresources.org) and publicly available.

Chagas' disease is caused by Trypanosoma cruzi, a protozoan transmitted to humans by blood-feeding insects, blood transfusion or congenitally. Previous research led us to discover a parasite proline racemase (TcPRAC) and to establish its validity as a target for the design of new chemotherapies against the disease, including its chronic form. A known inhibitor of proline racemases, 2-pyrrolecarboxylic acid (PYC), is water-insoluble. We synthesized soluble pyrazole derivatives, but they proved weak or inactive TcPRAC inhibitors. TcPRAC catalytic site is too small and constrained when bound to PYC to allow efficient search for new inhibitors by virtual screening. Forty-nine intermediate conformations between the opened enzyme structure and the closed liganded one were built by calculating a transition path with a method we developed. A wider range of chemical compounds could dock in the partially opened intermediate active site models in silico. Four models were selected for known substrates and weak inhibitors could dock in them and were used to screen chemical libraries. Two identified soluble compounds, (E)-4-oxopent-2-enoic acid (OxoPA) and its derivative (E)-5-bromo-4-oxopent-2-enoic acid (Br-OxoPA), are irreversible competitive inhibitors that presented stronger activity than PYC on TcPRAC. We show here that increasing doses of OxoPA and Br-OxoPA hamper T. cruzi intracellular differentiation and fate in mammalian host cells. Our data confirm that through to their binding mode, these molecules are interesting and promising as lead compounds for the development of chemotherapies against diseases where active proline racemases play essential roles.

Using a yeast-based assay, a previously unsuspected antiprion activity was found for imiquimod (IQ), a potent Toll-like receptor 7 (TLR7) agonist already used for clinical applications. The antiprion activity of IQ was first detected against yeast prions [PSI (+) ] and [URE3], and then against mammalian prion both ex vivo in a cell-based assay and in vivo in a transgenic mouse model for prion diseases. In order to facilitate structure-activity relationship studies, we conducted a new synthetic pathway which provides a more efficient means of producing new IQ chemical derivatives, the activity of which was tested against both yeast and mammalian prions. The comparable antiprion activity of IQ and its chemical derivatives in the above life forms further emphasizes the conservation of prion controlling mechanisms throughout evolution. Interestingly, this study also demonstrated that the antiprion activity of IQ and IQ-derived compounds is independent from their ability to stimulate TLRs. Furthermore, we found that IQ and its active chemical derivatives inhibit the protein folding activity of the ribosome (PFAR) in vitro.

We developed an approach for analysing the effects of two crossed factors A and B on the functional, taxonomic or phylogenetic composition of communities. The methodology, known as crossed-DPCoA, defines a space where species, communities and the levels of the two factors are organised as a set of points. In this space, the Euclidean distance between two species-specific points is a measure of the (functional, taxonomic or phylogenetic) dissimilarity. The communities are positioned at the centroid of their constitutive species; and the levels of two factors at the centroid of the communities associated with them. We develop two versions for crossed-DPCoA, the first one moves the levels of factor B to the centre of the space and analyses the axes of highest variance in the coordinates of the levels of factor A. It is related to previous ordination approaches such as partial canonical correspondence analysis and partial non-symmetrical correspondence analysis. The second version projects all points on the orthogonal complement of the space generated by the principal axes of factor B. This second version should be preferred when there is an a priori suspicion that factor A and B are associated. We apply the two versions of crossed-DPCoA to analyse the phylogenetic composition of Central European and Mediterranean bird communities. Applying crossed-DPCoA on bird communities supports the hypothesis that allopatric speciation processes during the Quaternary occurred in open and patchily distributed landscapes, while the lack of geographic barriers to dispersal among forest habitats may explain the homogeneity of forest bird communities over the whole western Palaearctic. Generalizing several ordination analyses commonly used in ecology, crossed-DPCoA provides an approach for analysing the effects of crossed factors on functional, taxonomic and phylogenetic diversity, environmental and geographic structure of species niches, and more broadly the role of genetics on population structures.

Fetal and neonatal mortality rates are essential indicators of population health, but variations in recording of births and deaths at the limits of viability compromises international comparisons. The World Health Organization recommends comparing rates after exclusion of births with a birth weight less than 1000 grams, but many analyses of perinatal outcomes are based on gestational age. We compared the effects of using a 1000-gram birth weight or a 28-week gestational age threshold on reported rates of fetal and neonatal mortality in Europe.Aggregated data from 2004 on births and deaths tabulated by birth weight and gestational age from 29 European countries/regions participating in the Euro-Peristat project were used to compute fetal and neonatal mortality rates using cut-offs of 1000-grams and 28-weeks (2.8 million total births). We measured differences in rates between and within countries using the Wilcoxon signed rank test and 95% confidence intervals, respectively.For fetal mortality, rates based on gestational age were significantly higher than those based on birth weight (p

The role of the Salmonella Pathogenicity Islands (SPIs) in pathogenesis of Salmonella enterica Typhimurium infection in the chicken is poorly studied, while many studies have been completed in murine models. The Type VI Secretion System (T6SS) is a recently described protein secretion system in Gram-negative bacteria. The genus Salmonella contains five phylogenetically distinct T6SS encoded in differentially distributed genomic islands. S. Typhimurium harbors a T6SS encoded in SPI-6 (T6SSSPI-6), which contributes to the ability of Salmonella to colonize mice. On the other hand, serotype Gallinarum harbors a T6SS encoded in SPI-19 (T6SSSPI-19) that is required for colonization of chicks. In this work, we investigated the role of T6SSSPI-6 in infection of chicks by S. Typhimurium. Oral infection of White Leghorn chicks showed that a ΔT6SSSPI-6 mutant had reduced colonization of the gut and internal organs, compared with the wild-type strain. Transfer of the intact T6SSSPI-6 gene cluster into the T6SS mutant restored bacterial colonization. In addition, our results showed that transfer of T6SSSPI-19 from S. Gallinarum to the ΔT6SSSPI-6 mutant of S. Typhimurium not only complemented the colonization defect but also resulted in a transient increase in the colonization of the cecum and ileum of chicks at days 1 and 3 post-infection. Our data indicates that T6SSSPI-6 contributes to chicken colonization and suggests that both T6SSSPI-6 and T6SSSPI-19 perform similar functions in vivo despite belonging to different phylogenetic families.

Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.

The African Hyaenodontida, mainly known from the Late Eocene and Early Oligocene Fayum depression in Egypt, show a very poor diversity in oldest Paleogene localities. Here we report new hyaenodontidans found in the late Middle Eocene deposits of Dur At-Talah (Central Libya), known to have recorded the earliest radiation of African anthropoids. The new hyaenodontidan remains are represented by dental and postcranial specimens comprising the historical material discovered by R.J.G. Savage in the last century and that of the recent Franco-Libyan campaigns. This material includes two apterodontines, in particular a subcomplete skeleton of Apterodon langebadreae nov. sp., bringing new postcranial elements to the fossil record of the genus Apterodon. Anatomical analysis of the postcranial remains of Dur At-Talah suggests a semi-aquatic lifestyle for Apterodon, a completely unusual locomotion pattern among hyaenodontidans. We also perform the first cladistic analysis of hyaenodontidans including apterodontines: Apterodon and Quasiapterodon appear close relatives to "hyainailourines", in particular to the African Oligo-Miocene Metasinopa species. Apterodon langebadreae nov. sp. could be the most primitive species of the genus, confirming an African origin of the Apterodontinae and a further dispersion event to Europe before the early Oligocene. These data enhance our knowledge of early hyaenodontidan diversification into Africa and underline how crucial is the understanding of their evolutionary history for the improvement of Paleogene paleobiogeographic scenarii.

Tumors affect myelopoeisis and induce the expansion of myeloid cells with immunosuppressive activity. In the MT/ret model of spontaneous metastatic melanoma, myeloid cells are the most abundant tumor infiltrating hematopoietic population and their proportion is highest in the most aggressive cutaneous metastasis. Our data suggest that the tumor microenvironment favors polarization of myeloid cells into type 2 cells characterized by F4/80 expression, a weak capacity to secrete IL-12 and a high production of arginase. Myeloid cells from tumor and spleen of MT/ret mice inhibit T cell proliferation and IFNγ secretion. Interestingly, T cells play a role in type 2 polarization of myeloid cells. Indeed, intra-tumoral myeloid cells from MT/ret mice lacking T cells are not only less suppressive towards T cells than corresponding cells from wild-type MT/ret mice, but they also inhibit more efficiently melanoma cell proliferation. Thus, our data support the existence of a vicious circle, in which T cells may favor cancer development by establishing an environment that is likely to skew myeloid cell immunity toward a tumor promoting response that, in turn, suppresses immune effector cell functions.

To improve cancer immunotherapy, a better understanding of the weak efficiency of tumor-infiltrating T lymphocytes (TIL) is necessary. We have analyzed the functional state of human TIL immediately after resection of three types of tumors (NSCLC, melanoma and RCC). Several signalling pathways (calcium, phosphorylation of ERK and Akt) and cytokine secretion are affected to different extents in TIL, and show a partial spontaneous recovery within a few hours in culture. The global result is an anergy that is quite distinct from clonal anergy induced in vitro, and closer to adaptive tolerance in mice. PD-1 (programmed death -1) is systematically expressed by TIL and may contribute to their anergy by its mere expression, and not only when it interacts with its ligands PD-L1 or PD-L2, which are not expressed by every tumor. Indeed, the TCR-induced calcium and ERK responses were reduced in peripheral blood T cells transfected with PD-1. Inhibition by sodium stibogluconate of the SHP-1 and SHP-2 phosphatases that associate with several inhibitory receptors including PD-1, relieves part of the anergy apparent in TIL or in PD-1-transfected T cells. This work highlights some of the molecular modifications contributing to functional defects of human TIL.

In this study we analyze one year of anonymized telecommunications data for over one million customers from a large European cellphone operator, and we investigate the relationship between people's calls and their physical location. We discover that more than 90% of users who have called each other have also shared the same space (cell tower), even if they live far apart. Moreover, we find that close to 70% of users who call each other frequently (at least once per month on average) have shared the same space at the same time--an instance that we call co-location. Co-locations appear indicative of coordination calls, which occur just before face-to-face meetings. Their number is highly predictable based on the amount of calls between two users and the distance between their home locations--suggesting a new way to quantify the interplay between telecommunications and face-to-face interactions.

Salmonella Gallinarum is a pathogen with a host range specific to poultry, while Salmonella Enteritidis is a broad host range pathogen that colonizes poultry sub-clinically but is a leading cause of gastrointestinal salmonellosis in humans and many other species. Despite recent advances in our understanding of the complex interplay between Salmonella and their hosts, the molecular basis of host range restriction and unique pathobiology of Gallinarum remain largely unknown. Type VI Secretion System (T6SS) represents a new paradigm of protein secretion that is critical for the pathogenesis of many gram-negative bacteria. We recently identified a putative T6SS in the Salmonella Pathogenicity Island 19 (SPI-19) of Gallinarum. In Enteritidis, SPI-19 is a degenerate element that has lost most of the T6SS functions encoded in the island. In this work, we studied the contribution of SPI-19 to the colonization of Salmonella Gallinarum strain 287/91 in chickens. Non-polar deletion mutants of SPI-19 and the clpV gene, an essential T6SS component, colonized the ileum, ceca, liver and spleen of White Leghorn chicks poorly compared to the wild-type strain after oral inoculation. Return of SPI-19 to the DeltaSPI-19 mutant, using VEX-Capture, complemented this colonization defect. In contrast, transfer of SPI-19 from Gallinarum to Enteritidis resulted in transient increase in the colonization of the ileum, liver and spleen at day 1 post-infection, but at days 3 and 5 post-infection a strong colonization defect of the gut and internal organs of the experimentally infected chickens was observed. Our data indicate that SPI-19 and the T6SS encoded in this region contribute to the colonization of the gastrointestinal tract and internal organs of chickens by Salmonella Gallinarum and suggest that degradation of SPI-19 T6SS in Salmonella Enteritidis conferred an advantage in colonization of the avian host.

BACKGROUND: Small molecule inhibitors of RNA virus replication are potent antiviral drugs and useful to dissect selected steps in the replication process. To identify antiviral compounds against Tomato bushy stunt virus (TBSV), a model positive stranded RNA virus, we tested acridine derivatives, such as chlorpromazine (CPZ) and quinacrine (QC), which are active against prion-based diseases. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report that CPZ and QC compounds inhibited TBSV RNA accumulation in plants and in protoplasts. In vitro assays revealed that the inhibitory effects of these compounds were manifested at different steps of TBSV replication. QC was shown to have an effect on multiple steps, including: (i) inhibition of the selective binding of the p33 replication protein to the viral RNA template, which is required for recruitment of viral RNA for replication; (ii) reduction of minus-strand synthesis by the tombusvirus replicase; and (iii) inhibition of translation of the uncapped TBSV genomic RNA. In contrast, CPZ was shown to inhibit the in vitro assembly of the TBSV replicase, likely due to binding of CPZ to intracellular membranes, which are important for RNA virus replication. CONCLUSION/SIGNIFICANCE: Since we found that CPZ was also an effective inhibitor of other plant viruses, including Tobacco mosaic virus and Turnip crinkle virus, it seems likely that CPZ has a broad range of antiviral activity. Thus, these inhibitors constitute effective tools to study similarities in replication strategies of various RNA viruses.

6-Aminophenanthridine (6AP) and Guanabenz (GA, a drug currently in use for the treatment of hypertension) were isolated as antiprion drugs using a yeast-based assay. These structurally unrelated molecules are also active against mammalian prion in several cell-based assays and in vivo in a mouse model for prion-based diseases.Here we report the identification of cellular targets of these drugs. Using affinity chromatography matrices for both drugs, we demonstrate an RNA-dependent interaction of 6AP and GA with the ribosome. These specific interactions have no effect on the peptidyl transferase activity of the ribosome or on global translation. In contrast, 6AP and GA specifically inhibit the ribosomal RNA-mediated protein folding activity of the ribosome.6AP and GA are therefore the first compounds to selectively inhibit the protein folding activity of the ribosome. They thus constitute precious tools to study the yet largely unexplored biological role of this protein folding activity.

BackgroundPrion-based diseases are incurable transmissible neurodegenerative disorders affecting animals and humans.Methodology/principal findingsHere we report the discovery of the in vivo antiprion activity of Guanabenz (GA), an agonist of alpha2-adrenergic receptors routinely used in human medicine as an antihypertensive drug. We isolated GA in a screen for drugs active in vivo against two different yeast prions using a previously described yeast-based two steps assay. GA was then shown to promote ovine PrP(Sc) clearance in a cell-based assay. These effects are very specific as evidenced by the lack of activity of some GA analogues that we generated. GA antiprion activity does not involve its agonist activity on alpha2-adrenergic receptors as other chemically close anti-hypertensive agents possessing related mechanism of action were found inactive against prions. Finally, GA showed activity in a transgenic mouse-based in vivo assay for ovine prion propagation, prolonging slightly but significantly the survival of treated animals.Conclusion/significanceGA thus adds to the short list of compounds active in vivo in animal models for the treatment of prion-based diseases. Because it has been administrated for many years to treat hypertension on a daily basis, without major side-effects, our results suggest that it could be evaluated in human as a potential treatment for prion-based diseases.