dataesr/scientific-paragraphs-categorization huggingface dataset:
Individual cohort studies may not have the sample size needed to detect clinically important interactions between ZIKV and important cofactors. We will also assess whether a certain interaction is consistent across studies, while not necessarily statistically significant within individual studies. Meta-regression and subgroup analyses have limited power to detect interactions and can only be used to make inference about the relation between the exposure and study-level, average values of participant characteristics. 89 92 Studies that are not willing or able to provide participant-level data may differ importantly from longitudinal studies whose data is included in the IPD-MA. We will apply subgroup analysis to a two-stage analysis of effect estimates from studies included in the IPD-MA and published estimates from studies that did not participate in the IPD-MA to assess whether study-level variation in recruitment and enrolment criteria, exposure and outcome ascertainment and measurement of coinfections and other cofactors are important sources of heterogeneity in the pooled estimates.
Missing data Missing data at the study level, as when confounders are not measured in certain studies, is a well-known challenge of IPD-MA  114 115  and a likely source of residual confounding. In keeping with current recommendations for addressing missingness in IPD-MA, we will apply new methods for multilevel multiple imputation to account for missing values. 116 As a sensitivity analysis, we will impute missing participant-level data in each study separately and use multivariate meta-analysis to combine data across studies that have and have not measured important host-level and environmental-level cofactors. Publication bias IPD-MA may have a lower risk of publication bias than AD-MA because they include data from unpublished studies. 114 We have tried to ensure that the ZIKV IPD Consortium includes representatives from all of the academic and government institutions responsible for planned or ongoing ZIKV-related longitudinal studies of pregnant women and their infants.
58 There have been numerous calls for data sharing  121 122  and cooperation between governments and academic institutions,  54 123  and public and private charities have pledged significant financial support to improve our understanding of ZIKV epidemiology and to develop a vaccine or small molecule prophylaxis to decrease the risk of infection. In the wake of the Ebola epidemic, the global response to ZIKV has been characterised by unprecedented levels of international cooperation. In the absence of a ZIKV vaccine or prophylaxis, international leaders in ZIKV research have formed the ZIKV IPD Consortium to identify, collect and synthesise IPD from longitudinal studies of pregnant women that measure ZIKV infection during pregnancy and fetal, infant and child outcomes. These data will be used to quantify the absolute risk of ZIKV-related pregnancy complications with the goal of aiding women and their families in making difficult reproductive decisions and with helping public health systems prevent and quantify the burden of congenital Zika infection.
EthICs And dIssEMInAtIon This IPD-MA protocol has been deemed exempt from ethical review by the WHO Ethics Review Committee and the Emory University Institutional Review Board. Individual longitudinal studies will provide documentation of ethics review prior to sharing their deidentified, participant-level data. The WHO has developed guidance for data sharing in public health emergencies or in the context of emerging pathogens. 125 Sharing deidentified data for IPD-MA is generally considered exempt from ethical review if the objectives of the IPD-MA are in keeping with the objectives of the original studies. 126 ndividual research studies and consortia will secure additional ethics review and/or legal guidance on the sharing of deidentified, subject-level data as needed. The results of this analysis will be published under the ZIKV IPD Consortium name and will include a list of the names of key investigators from each study that contributed data for that analysis and researchers who contributed to the analysis or writing at the end of the publication.
Acknowledgements The authors would like to acknowledge the valuable contributions of  Liège Maria Abreu de Carvalho ,  Rosangela Batista ,  Ana Paula Bertozzi ,  Gabriel Carles ,  Denise Cotrim ,  Luana Damasceno ,  Lady Dimitrakis ,  María Manoela Duarte Rodrigues ,  Cassia F Estofolete ,  Maria Isabel Fragoso da Silveira Gouvêa ,  Vicky Fumadó-Pérez ,  Rosa Estela Gazeta ,  Neely Kaydos-Daniels ,  Suzanne Gilboa ,  Amy Krystosik ,  Véronique Lambert ,  Milagros García López-Hortelano ,  Marisa Marcia Mussi-Pinhata ,  Christina Nelson ,  Karin Nielsen ,  Denise M Oliani ,  Renata Rabello ,  Marizelia Ribeiro ,  Barry Rockx ,  Laura C. Rodrigues ,  Silvia Salgado ,  Katia Silveira ,  Elena Sulleiro ,  Van Tong ,  Diana Valencia ,  Wayner Vieira de Souza ,  Luis Angel Villar Centeno  and  Andrea Zin  to the review of the  ZIKV IPD Consortium IPD-MA Protocol.
Anthropogenic activities in urban ecosystems induce a myriad of environmental changes compared with adjacent rural areas. These environmental changes can be seen as series of abiotic and biotic selection filters affecting the distribution of plant species. What are the attributes of plant species that compose urban communities, compared with rural communities, as related to their ecological affinities (e. g. , to temperature, humidity), and reproductive traits (e. g. , entomophily, autogamy, floral morphology)? Using a floristic dataset from a citizen science project recording plant species growing spontaneously in the streets, we analyzed the distribution of species according to their ecological requirements and reproductive traits along an urbanization gradient in the Parisian region. We developed an original floral and pollinator typology composed of five floral and four pollinator morphotypes.
, 2018; Fantinato et al. , 2018). The different mechanisms by which competition for pollinators can reduce plant fitness include low frequency of pollinator visits and heterospecific pollen deposition on stigmas, and were described in detail by  Waser (1978). In the present study, we examined the distributions of plant species according to their ecological requirements and reproductive traits along an urbanization gradient. We analyzed a dataset from a French national citizen science project called "Sauvages de ma rue" (literally "wild plants of my street") which aims at recording plant species growing spontaneously in the streets. We focused on the Île-de-France region (around Paris) to benefit both from a high sampling density in a full urbanization gradient and from previously published plant-pollinator studies in the region.
| The "Sauvages de ma rue" protocol The present study was based on data from a French citizen science project called "Sauvages de ma rue" aiming at collecting floristic data in France following a standardized protocol. This scientific and pedagogic project was initiated by the Centre d'Ecologie et des Sciences de la Conservation (CESCO) of the Museum National d'Histoire Naturelle (MNHN) and was promoted by the association Tela Botanica. In this program, volunteers were invited to identify and list all the spontaneous plant species growing in a street of their choice located by the GPS coordinates of the starting point of the inventory (hereafter called a sampling site). An identification guide and a mobile application were available to help the volunteers to identify the plants (http://sauva gesde marue.
mnhn. fr/biodi versit-urbai ne/ cl-diden tific ation-sauva ges-de-paris ). Additional online identification keys and online assistance by botanists from the Tela Botanica network were also provided. The volunteers also recorded the habitat type of each plant in the street and the date of observation. For each species, a confidence degree of identification had to be specified, and pictures could be uploaded for subsequent data validation by botanists involved in the program. The program was launched in 2008 and has been running continuously since then.
| Geographical data A total of 1,161 different sampling sites were available in the "Sauvages de ma rue" database for the Île-de-France region over the years 2008-2017. This region was chosen because (a) it was one of the most densely sampled area, (b) it included seminatural habitats distant from urban influences as well as highly urbanized landscapes, and (c) studies on the distribution of floral visitors  (Desaegher et al. , 2018; Geslin et al. , 2016)  and on plant-pollinator interactions  (Desaegher, Nadot, Dajoz, & Colas, 2017; Geslin et al. , 2013)  in this region were already available. We used 1/5,000 GIS maps reporting land cover over the Île- at http://www. iau-idf. fr/). For every 1,161 sampling sites, we calculated the proportion of impervious surfaces in different radius of 50, 100, 500, and 1,000 meters using a vector layer with Quantum GIS version 2.
| Biological data Based on the identifications made by the volunteers, we established a list of plant species occurring in the study region. Species names were checked, and synonyms were replaced by the currently accepted name (http://www. thepl antli st. org/). The final dataset included a total of 366 plant species. Reproductive traits and affinity indices associated with each plant species were extracted from the online databases BiolFlor  (Klotz, Kühn, & Durka, 2002)  and Catminat (http://phili ppe. julve. pages perso-orange. fr/catmi nat. htm), using the package TR8  (Bocci, 2017)  with R version 3. 3. 2 (R Core Team, 2016). The traits extracted from BiolFlor were as follows: ecological strategy following the system of Grime  (Grime, 1974) , level of vegetative reproduction, level of self-compatibility, and level of autogamy.
The combination of pollen and nectar accessibility allowed us to define five floral morphotypes "pn," "pn+," "Pn+," "Pn," and "PN" (Figure  2 ). Category delimitations of corolla length and width were chosen according to the body width and tongue length of the pollinator morphotypes. Using the morphological plant typology, each entomophilous (at least partially) plant species was assigned to one morphotype, based on botanical descriptions from floras. The theoretical relationships drawn among the plant and pollinator morphotypes (Figure  2 ) were based on physical constraints and on qualitative personal observations. In addition, the presence or absence of a nectar spur and the presence or absence of tubular flowers (two floral features generally associated with nectar production) were scored for every plant species of the dataset.
Three categories of statistical tests were applied depending on the trait variable modalities. Multinomial logistic regressions (MLR) were used with the package nnet  (Ripley & Venables, 2016)  for floral morphotype, Grime's CSR ecological strategy, and dispersal vector, three multinomial variables (Table  1a ). Ellenberg indicator values, soil affinity indices, the level of vegetative reproduction, self-compatibility, autogamy, and entomophily were considered as ordinal variables (Table  1b ) and were consequently treated with cumulative link mixed models (CLMM) with logit link and flexible thresholds using the package Ordinal  (Christensen, 2015a (Christensen, , 2015b)). For both MLR and CLMM, we used a likelihood-ratio test and pairwise comparisons were done using Wald z tests. Both presence/ absence variables ("tubular corolla" and "nectar spur," Table  1c ) were analyzed with generalized linear mixed models (GLMM) using the binomial distribution  (Bolker et al.
| Assembly of the floral dataset The floral dataset used in study included a total of 366 species belonging to 234 genera and 76 families (i. e. , 18% of all flowering plant families). Observations were distributed in 167 spatial clusters of sampling sites, with 16 clusters presenting a mean proportion of impervious areas in a radius of 500 m comprised between "[0, 0. 5]," 44 clusters between "[0. 5, 0. 75]," and 107 clusters between "[0. 75, 1]. " The high number of clusters presenting a high percentage of impervious areas is due to the fact that the program "Sauvages de ma rue" is targeted on plant species growing in streets. On average, 25. 6 species were observed per cluster (see details in Figure  S1 ).
| Reproductive traits and flower morphology Munoz, Violle, and Cheptou (2016) observed recently from a 2,000-species dataset that ruderal species were mostly autogamous, while competitive species were more often allogamous, and stress-tolerant species tended to have a mixed mating system. Our results on species traits along an urbanization gradient are entirely congruent with these findings. The observed interdependence between the ecological strategies and the degree of autogamy (R-strategists being more frequently autogamous or facultative autogamous) probably contributes to the advantage of R-strategists in urban areas over the C and S-strategists. Indeed, urban plant communities are likely more subject to pollen limitation than rural plant communities, which selects for autonomous selfing as a means to ensure reproduction  (Eckert et al.
, 2017; Thompson, Renaudin, & Johnson, 2016). However, for several traits the BiolFlor and Catminat databases specify multiple modalities reflecting plant trait variability (e. g. , level of self-compatibility, level of entomophily). Since we gathered different trait modalities initially recorded in the databases, the information contained in the analyzed variables was conservative regarding the variability of traits along the urbanization gradient. Another potential caveat of our analyses is that we did not formally take into account potential phylogenetic constraints in the distribution of traits along the urbanization gradient, which may bias correlations between trait distributions and the level of urbanization  (Pellissier et al. , 2010). Nevertheless, we verified that the significant frequency reduction of morphotypes "pn" and "Pn" with increasing urbanization was not due to a single family or genus.
Simulation of the optical spectra was obtained using the VMS software. [74] The phosphorescence spectrum of 2 was simulated including vibronic coupling within the Adiabatic Hessian (AH) model. [77] [78] [79] [80]  To ensure a sufficient spectrum progression (> 90 %), normal modes with the lowest energies were neglected in the vibronic treatment. Molecular orbitals (MO) were visualized with the GaussView package. [81].
Acknowledgements C. L. thanks the  "Centre de Calcul Intensif des Pays de la Loire" (CCIPL)  and  Région Pays de la Loire  to support the "CLIC" project, A. B. and J. -F. H. thank the  GENCI-IDRIS  and  GENCI-CINES  (Grant No. 2016-2017-080649 ) for computational resources. T. B. M. is grateful for generous financial support from the  Bavarian State Ministry of Science, Research, and the Arts for the Collaborative Research Network "Solar Technologies go Hybrid " and the  DFG  ( GRK 2112 ). Z. Z. thanks the  Alexander von Humboldt Foundation  for a postdoctoral fellowship.
One presents here a brief outline of previous related works in the same domain. Goland and Reissner worked on the behavior of flexible adhesive using a normal stress  [3]. Hart-Smith studied the shear and peel stresses distributions and gives a simplification for uncoupling shear and peel stresses  [4]. He also developed solutions for stepping a single lap joint  [5]. Bigwood and Crocombe  [6]  presented general elastic, shear and peel analysis for single lap joint using finite element analysis. Chiu and Jones  [7]  applied a finite element method to study a shear stress using a thick adherend test for a single and a symmetrical double lap joint. Pereira and Morais  [8]  conducted an experimental study using a double cantilever beam tests for single and double lap joints measured the critical strain energy-release rate and numerical one with finite element analysis using Abaqus code to explain a strength behavior and peel stresses at the edges of overlap area.
FINITES ELEMENTS MODELS he models are simulated with a three dimensional finite element method analysis using Abaqus software  [17]. A refined mesh is presented at the adhesive layer and plates to determine the maximum stresses which are located at the adhesive interface / adheres to the free edge. Indeed, the refinement of the mesh is of great importance for the analysis of the structure. The linear elements (C3D8R) are used for the mesh of all parts of the models studies. The number of elements over parts of Aluminum plate and the Adhesive layer are respectively 14240 and 1275 for the model 1, 16167 and 1275 for model 2 and 3. The Fig. 5  shows the detail of the meshed models. Each layer is considered as an individual three-dimensional structure under a state of plane-stress and can be connected with adhesive bonds.
1B ). Yeast two-hybrid interactions occur in a reducing environment between proteins that are synthesized without posttranslational modifications typical for secreted mammalian proteins. Such modifications include introduction of disulfide bonds and N-glycosylation. Two disulfide bonds stabilize fibronectin type I modules  (35). The human ADAMTS9 Gon1 module contains 10 cysteines  (11) , which are conserved in other Gon1 modules (http://pfam. xfam. org/family/PF08685)  4  and very likely form disulfides, and two sites of potential N-glycosylation. Therefore, experiments were performed in follow-up of the yeast two-hybrid results asking whether the ADAMTS9fibronectin interactions could be replicated with proteins that had been processed and undergone modification in a eukaryotic secretion pathway.
The dissociation time was 15 min. 50 mM glycine, pH 3. 0 was used for chip surface regeneration at a flow rate of 100 l/min for 30 -60 s after Gon1-binding analysis, whereas 50 mM NaOH was required for regeneration of the ADAMTS9 TSR9 -15 chip surface. All data were corrected with reference to the background binding in the control flow cell. The kinetic constants were calculated assuming a 1:1 (Langmuir) binding model using the BIAevaluation software (version 4. 0. 1; GE Healthcare).
The LC-MS system was a Finnigan LTQ-Orbitrap Elite hybrid mass spectrometer system. The HPLC column was a Dionex 15-cm ϫ 75-m inner diameter Acclaim Pepmap C18, 2 m, 100 Å reversed phase capillary chromatography column. 5 l volumes of the tryptic digest were injected. The peptides were eluted from the column by an acetonitrile, 0. 1% formic acid gradient at a flow rate of 0. 3 l/min for introduction into the source of the mass spectrometer online. The nanoelectrospray ion source was operated at 1. 9 kV. The digest was analyzed using the data-dependent multitask capability of the instrument acquiring full scan mass spectra to determine peptide molecular masses and product ion spectra to determine amino acid sequence in successive instrument scans. The data were analyzed by using all CID spectra collected in the experiment to search the human UniProtKB sequence databases using Mascot (false discovery rate, 0.
This work was supported by the  Allen Distinguished Investigator Program  through support made by the  Paul G. Allen Frontiers Group, American Heart Association  Grant  17 DIA33820024  (to S. S. A. ),  National Institutes of Health  Grant  EY024943  (to S. S. A. ), and a  Mark Lauer Pediatric Research Grant  (to S. N. ). The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Genetic differentiation In this study, we sequenced two genes commonly used to assess the specific status in bumblebees  (Pedersen 2002; Hines et al. 2006; Cameron et al. 2007; Lecocq et al. 2013a,b) : the mitochondrial cytochrome oxidase 1 gene (COI), and the nuclear phosphoenolpyruvate carboxykinase gene (PEPCK). DNA extraction protocol, polymerase chain reaction, amplification reactions, sequencing procedures and alignment of DNA sequences were performed according to the method described in  Lecocq et al. (2015a, c). COI and PEPCK sequences were deposited on GenBank (Table  S1 ). For each gene, we carried out phylogenetic analyses to investigate genetic differentiations between B. lapponicus and B. sylvicola. We performed maximum likelihood (ML) and Bayesian (MB) analyses. For all methods, the PEPCK gene was partitioned into two exons and two introns to explore the best substitution model.
COI fragment and each nuclear exon were partitioned by base positions (first, second, and third nucleotide). For each dataset, we used JModelTest Server 2. 0  (Posada 2008 ) with the corrected Akaike information criterion (AICc) to find the best-fitting substitution models. The models chosen were: (i) for COI : GTR+I (first position), TIM2+I (second position), TrN+G (third position) ; (ii) for PEPCK first intron: TPM1 uf +I ; (iii) for PEPCK exon 1 : HKY+I (first position), JC (second position), TrN+I (third position) ; (iv) for PEPCK second intron : TrN+I ; (v) for PEPCK exon 2: JC (first, second, and third positions). Selected models which are not implemented in MrBayes were substituted by the closest over-parameterized model. For ML analyses, we performed ten independent runs in GARLI 2.
2011). By main compounds, we mean compounds that have the highest relative proportion (RA) among all compounds of CLGSs at least in one individual of the taxon. We extracted CLGS in 400 µl of n-heptane, according to the method described by De  Meulemeester et al. (2011). Samples were stored at -40° C prior to the analyses. For B. lapponicus, B. monticola, and B. bimaculatus, the data of CLGS compositions are the same as those described by  Martinet et al. (2017)  (Table  S2 ). For B. terrestris, we used the CLGS dataset described in  Lecocq et al. (2016). The qualitative composition of the CLGS was determined by gas chromatography-mass spectrometry using a Finigan GCQ quadrupole system (GC/MS) with a non-polar DB-5 ms capillary column [5% phenyl (methyl) polysiloxane stationary phase; column length 30 m; inner diameter 0.
Statistical analyses We performed statistical comparative analyses of the CLGSs using R 3. 3. 2 (R Development Core Team, 2016) to detect CLGS differentiations. We transformed data [log (x + 1)] to reduce the great difference of abundance between highly and lowly concentrated compounds. We used a principal component analysis (PCA, R-package MASS, Venables & Ripley 2002) based on correlation distance matrices, and a clustering method computed with the unweighted pair-group method with average linkage (UPGMA) based on Canberra distance matrices (RA of each compound) (R package ape;  Paradis et al. 2004). We assessed the uncertainty in hierarchical cluster analysis using p-values calculated by multiscale bootstrap resampling with 100,000 bootstrap replications (significant branch supports >0.
85) (R package pvclust,  Suzuki & Shimodaira 2011). We also assessed CLGS differentiations between taxa by performing a multiple response permutation procedure (MRPP, R package vegan,  Oksanen et al. 2011)  based on groups identified by hierarchical cluster analysis. When a significant difference was detected, pairwise multiple comparisons were performed with an adjustment of p-values (Bonferroni correction) to avoid type I errors. To determine specific compounds of each taxon (i. e. indicator compounds), the indicator-value (IndVal) method was used  (Claudet et al. 2006; Dufrêne & Legendre 1997). This value is the product of relative concentration and relative occurrence frequency of a compound within a group. The statistical significance of an indicator compound (>0. 7) was evaluated with a randomization procedure (Dufrêne & Legendre 1997).