dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Gipi Schiavo  and  Jernej Ule  for critical reading of the manuscript. We thank  Jernej Ule  for his support with the iCLIP experiments. JH thanks  Ms Shannon Edwards  for her assistance in generating the long intron gene expression plots. PF is funded by an  MRC/MNDA LEW Fellowship , the  NIHR-UCLH Biomedical Research Centre  and the  Rosetrees Foundation. AA-A is supported by the  Miguel Servet Programme of the ISCiii, Spain  ( CP15/00153 ), the  UK MRC  ( MC_UP_A390_1106 ). This work was partly funded by the  Thierry Latran Foundation  (PF, AA-A, EMCF, LG), the  UK Motor Neuron Disease Association (PF, TR, AA-A, EMCF, LG) , the  UK Medical Research Council (PF, PS, AU, MS, EMCF) , the  Rosetrees Foundation (PF, CB, EMCF). National Institute of General Medical Sciences (NIGMS)  of the  National Institutes of Health (NIH)  under Award Number  R01GM118530  (to NLF), a starter grant  17-IIP-342  from the  ALS Association  (to NLF), and an  ALS Research Grant  from the  Judith & Jean Pape Adams Charitable Foundation  (to NLF).
AEC was supported in part by an  NIGMS  training grant to the graduate programme in  Molecular Biology ,  Cell Biology and Biochemistry (MCB) at Brown University  ( T32 GM07601 ) and a  BIBS Graduate Award in Brain Science  from the  Brown Institute for Brain Science Reisman Fund. KAKENHI  nos. 21240043 & 17H00789  ( RF & YG ), EP and PS are supported by the  NIHR BRC GOSH  and by  Great Ormond Street Children's Charity. MH is funded by the  MNDA.
CRITICAL APPRAISAL Since 1991, the Banff classification has undergone several amendments, reflecting the growing body of knowledge in transplant pathology. These amendments have been based on a consensus reached at the biannual Banff meetings. This constant refinement based on emerging data is a strength of the Banff process and has led to the worldwide dominance FIGURE 13. Visual analogue scale for the determination of Banff Lesion Score cv (arterial fibrous intimal thickening). The remaining luminal area is related to the square of the remaining luminal radius. Thus, relatively modest decreases in luminal radius of 13% or 29% translate into relatively large reductions in luminal area of 25% or 50%, reflecting the thresholds for Banff Lesion Score cv. of the Banff Classification for diagnostic practice, research and clinical trials.
C. R. 's and N. S. 's contribution to this research is supported by the  National Institute for Health Research (NIHR) Biomedical Research Centre  based at  Imperial College Healthcare NHS Trust  and  Imperial College London. A. L. is supported by a research grant ATIP AVENIR from the  National French Institute of Research. J. U. B. is supported by the  European Rare Kidney Disease Network (ERKNet)  and by the  Deutsche Forschungsgemeinschaft (DFG, German Research Foundation ) - BE-3801 ). The authors declare no conflicts of interest.
Identification of Brachypodium distachyon and Triticum aestivum PP1 families Genomic, cDNA and protein sequences were retrieved by combining HMMER and Psi-BLAST searches  [24]  using Oryza sativa PP1s as queries on TGACv1 genome (The Genome Analysis Center Version 1) from EnsemblPlant (http://plants. ensembl. org/Triticum_ aestivum/Info/Index) and keyword searches within phytozome database (https://phytozome. jgi. doe. gov). Retrieved sequences were aligned with rice PP1s using MEME (http://memesuite. org/index. html) to search for conserved motifs. FIMO was further used using the N-terminal S/T protein phosphatase motif as query to search for additional PP1 proteins (Pfam PF16981. 4/Interpro IPR 031675;  [4] ). Ultimate searches were done on EnsemblPlant to find orthologs and paralogs of wheat PP1s in Brachypodium distachyon, Oryza sativa, Triticum urartu and Aegilops tauschii.
cDNA sequences of wheat and Brachypodium identified herein are available in S1 Fig. Genomic  and cDNA sequences of Brachypodium, wheat and rice have been used to define PP1 gene structure using GSDS tool (http://gsds. cbi. pku. edu. cn/index. php). Arabidopsis type one protein phosphatases were retrieved using TAIR and phytozome databases. Protein parameters (Molecular weight, pI, Instability Index, GRAVY) have been computed by protparam (https://web. expasy. org/protparam/) and are presented in S2 Table.
Phylogenetic analyses Multiple alignment and phylogenetic analyses were conducted using MEGA6. 06 software  [25]. Multiple alignments of proteins were done using ClustalW and the BLOSUM matrix with default settings. The phylogenetic tree was created using the Neighbor-joining method based on the number of aa substitutions per site and the bootstrap test with 1000 replicates. Ka/Ks calculation was done using MEGA 6. 06 and the Nei-Gojobori method with p-values>0. 05.
TdPP1a isolation and cloning Using cDNA sequences of Oryza sativa OsPP1a and EST sequences of Triticum aestivum available in databases (The Gene Index: http://compbio. dfci. harvard. edu/tgi/) primers were designed for PCR amplification. A first PCR amplification using TdPP1F2 (5'-ACTCCACCGA TCTCTCTCCA-3) and TdPP1R2 (5'-ACTAACCTCAGAGCCTCTAG-3) was done on wheat cDNA of Oum Rabiaa3 Tunisian durum wheat variety by adding 1% DMSO using the following program: 94˚C, 30 s; 50˚C, 30 s; 72˚C 1 min in a final volume of 20 μl. One microlitre of this first PCR product was used for nested PCR amplification using TdPP1F1 (5'-TGCAGCT CTCCGAGTCGGAG-3) and TdPP1R1 (5'-TCAGCAGGTTTGAGAATTTG-3') 1% DMS0 and an annealing temperature of 52˚C. A single band was observed of approximately 1000 bp that was cloned into the pCR2.
Identification of Brachypodium and common wheat PP1 genes Within monocotyledonous species, 5 isoforms of type 1 protein phosphatases have been described in Oryza sativa  [12]  but for other monocots little information was available. We therefore characterized this family in key graminae species, wheat and Brachypodium. Using the 5 different rice isoforms (OsPP1s) as queries for HMMER analyses, we searched for bread wheat and Brachypodium homologous genes and proteins using the Ensembl Plant and phytozome databases (http://plants. ensembl. org/Triticum_aestivum/Info/Index; http://phytozome. jgi. doe. gov). For common wheat, 18 different protein-coding genes could be identified whereas 8 were identified for Brachypodium. The eight Brachypodium PP1 genes were located on chromosome 1 (n = 3), chromosome 2 (n = 3) and chromosome 3 (n = 2) and encoded 8 different proteins.
Isolation of TdPP1a, a durum wheat protein phosphatase type 1 In order to investigate the involvement of PP1s in wheat stress tolerance and knowing the salinity tolerant phenotype of rice plants over-expressing OsPP1a  [23] , we decided to focus here on group PP1a and isolate the durum wheat counterpart of OsPP1a from a Tunisian variety. Based on cDNA sequences available for rice, B. distachyon and mainly T. aestivum, specific sets of primers were designed to amplify durum wheat PP1 sequences. Using cDNA of Tunisian durum wheat Oum Rabiaa3 variety, a 950 bp fragment could be amplified and cloned. Sequence analyses  [24]  revealed that the corresponding ORF is highly similar to type one protein phosphatases and encodes a protein of 321 amino acids with a 36 kDa predicted molecular mass. The cDNA was named TdPP1a for Triticum durum type one protein phosphatase and submitted to GenBank under the accession number KM203893.
Acknowledgments The work has been funded by the  Tunisian Ministry of Science and Higher Education and French and Tunisian PHC-Utique  project ( 15G0902 ). Part of this work was funded by the ' Science by Woman' program  ( Fundacion Mujeres for Africa ) to C. E. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are grateful to  Prof. Joaquin Ariño  ( Universitat Autonoma Barcelona, Spain ) for providing the KT1112 and K2210 yeast strains and  Dr. Greg Moorhead  and  N. Sieben  for providing us the AtI2 constructs. We would like to thank  Miguel A. Botella ,  Araceli Castillo Garriga  and  Vitor Amorim Silva  for help with two-hybrid interactions. We also acknowledge  Aisset Bannannou Silvia Gutierrez Erlandsson  and  Ana Oña Blanco  for help with confocal Laser Scanning Microscopy and  Dr.
This requires fine-grained and possibly 'embedded' research to account for the practices, rationalities and dynamics of public institutions charged with interpreting and enacting broader normative visions. In the last section of this chapter, by way of a conclusion, I make a case for sustained social science research to populate the triangulation imperatives with sound data and analysis. However, this is not enough; we need to think of the role of research as integral to the larger imperatives of fostering new institutional systems of governance, management and rule that strengthen national imperatives to discharge coordination and alignment. At the same time, we need to recognise that alternative local governance and policy processes cannot emerge unless they are connected to experiments, which can generate novel ways of planning, structuring, investing in and running sustainable infrastructures that contribute directly to economic empowerment and socio-spatial inclusion.
Despite its negative position on the overall assessment scores, Luanda was highlighted as an example due to the establishment of an environmental database focusing on the city (supported by the African Development Bank)3, as was Maputo for its environmental education programme in schools (with emphases on tree planting and beach cleaning approaches), and finally Nairobi, where the government was working on an online approach to enable citizens to monitor their water and energy consumption (see for example, World Bank, 2015).
A more recent work by Parnell and Pieterse is concerned with Africa's urban revolution  (Parnell and Pieterse, 2014). South Africa's leading role in Africa's sustainable cities 'movement' is very much assisted by the important role think tanks such as the aac play, but also by the way metropolitan governments in South Africa use information databases to make informed choices on where to prioritise investments in better environmental services (see  Sutherland et al. 2015).
From this perspective, could the growing urban settlements with their constantly moving, negotiated frontier of claims and responses over time provide a laboratory for the development of novel institutional arrangements? Such cities do not seem to be incubators of the same kind of individuation that Weber wrote about in The City  (Weber, 1978 (Weber, , 1212 (Weber, -1372)). What we see in them, rather, is the increasing unmooring of distinct identities, but not necessarily of the logic of mutual dependence. The latter may actually gain further impetus from the erosion of economic mediation through wage labour in Africa. For sure, this mediation never was as pervasive there as in Northern industrial societies. Still, it offered a significant organising principle in postcolonial societies, particularly when linked to the loyalties and obligations of redistribution through kin networks through which salaries lubricated welfare and social reproduction beyond their immediate recipients  (Mbembe, 2001; Roitman, 2007).
Some massive African cities do not appear at all. Even where African cities appear, there are oddities that seem inexplicable to African studies scholars. Between the 2012 and 2016 rankings, for example, Nairobi dropped from Beta+ to the lowest ('Sufficiency') category, when very little of the story of Nairobi in those years would indicate to any scholars of Kenyan urbanisation any reasons for a slip in global significance  (Myers, 2015). The GaWC database is about office networks for advanced producer services-a very narrow economistic understanding of globalisation, even if more recent lists include data on advertising, accounting and law firms. Yet even so it is an inexplicable oddity that the ranking for Nairobi-which any urbanist of Africa would recognise against any measure of globalisation as consistently one of the continent's most globally networked cities for financial services-has fluctuated radically in the GaWC's calculations and plummeted in those four years.
They have equipped themselves with distinct identities and have cultivated the ability to inhabit the identity that a given occasion requires. Young men switch their identities depending on the situation-for example, a young man may be a pious Muslim in traditional raiment on a religious feast, or a Baay Faal wearing ragged motley garments known as Baye Lahat, or a Boy Town dressed up in fancy clothes in line with American trends on a Saturday evening. Thus, in line with  Ferguson's 'performative competence' (1999, 104) , young men in Pikine use their attire, consumption practices and also their speech and discursive practices to position themselves in different fields. This helps them to participate in processes of modernity and globalisation, to be in the world, not as passive spectators but as cosmopolitans with the ability to improvise and ultimately take part in building the nation.
Acknowledgements I am grateful to the organisers of the 7th European Conference on African Studies (ecas 2017) at the  University of Basel  for inviting me to present a version of this paper as a keynote address. I am also grateful for the review comments and continuous discussions with my colleagues,  Sue Parnell ,  Anton Cartwright ,  Gareth Haysom ,  Sylvia Croese  and  Kim Gurney. I am solely responsible for the argument presented here. My research is supported by the  National Research Foundation of South Africa.
Acknowledgements An earlier version of this chapter was published as a working paper on the website of the  African Studies Centre Leiden  (www. ascleiden. nl) as ' Sustainable City initiatives in Africa  and comparison with the oursus approach'. An outline was presented at the igu Congress in Beijing, on 22 August 2016, and benefited from comments by  Qiu Li  and  Brij Maharaj , as well as other people participating at the conference. Additional discussions took place during the annual conference of the Netherlands Association of African Studies, in 2017, and during the 7th European Conference on African Studies (ecas) in Basel in 2017.
Acknowledgements I express my sincere gratitude to all research participants for generously sharing their views and experiences, my research assistants  Kaarina Matti  and  Lukas Nangolo  and the personnel of the  Department of Sociology at the University of Namibia. I also thank  Till Förster ,  Carole Ammann ,  Claire Bénit-Gbaffou ,  Jeremy Gould  and the anonymous reviewers for their comments on the manuscript or earlier versions of this text. The  Academy of Finland  (grants  288998  and  318762 ) provided the funding that made this research possible.
Acknowledgements Funds for the research for this paper have been provided by the  Paul E. Raether Professorship at Trinity College  and the  Luce Foundation  grant to the  Center for Urban and Global Studies at Trinity College  for the study of East Asian urban environments. I thank  Xiangming Chen ,  Mailys Chauvin ,  Jenny Robinson ,  Armelle Choplin ,  Stina Wolff ,  Rosalind Fredericks ,  Jenny Mbaye ,  Tim Mangin , and  Makame Muhajir  for their comments in discussing an earlier version. Acknowledgements I am grateful for the support of the  German Ministry of Research  for the project ' Middle Classes on the Rise ' , which was part of the  Bayreuth Academy of Advanced African Studies , and for the support of the  Volkswagen Foundation  for a postdoc scholarship at the  Center for Cultural Sociology, Yale University.
6 C -23 HS HS 293 S 7. 8 S S S 246 17 S 6. 9 S 225 17 S 7. 6 20 HS S 225 HS HS 8. 8 Luanda Cities in the database C 526 S 526 525 S 315 315 Gaborone C - HS S S S Source: created by author from data available on the website of the Globalization and World Cities Research Group-http://www. lboro. ac. uk/ gawc/gawcworlds. html (accessed on �7 April �0�8).
S1 ) and the spectral sensitivity of mantises  (Rossel, 1979; Sontag, 1971). The blue visual output was 13% that of the green visual output. This ensured approximately equal input of blue and green light to the left and right visual systems after filtering through the glasses and the spectral sensitivity of the mantis. Before each experiment trial, mantises were shown a stimulus to check their motivation. This consisted of a dark disc against a grey background that swirled in from the periphery to the centre as described in Eqns. 1-5 below. This stimulus is known to reliably elicit strikes  (Nityananda et al. , 2016a; Nityananda et al. , 2016b; Nityananda et al. , 2018). Experiments were only carried out if the mantis struck at this stimulus twice in a row. Mantises were also checked for motivation in this way after experimental runs and the data were analysed only if the mantises struck at this stimulus twice in a row after the experimental run.
Since the probability of striking was a binary decision (yes or no) we modelled the data using a binomial logistic link function. All data were analysed with the statistic software RStudio (version 1. 1. 383). Experiment 1: Results from the MID-left and MID-right conditions were pooled as were results from the Constant-left and -right conditions. Motion condition (MID or Constant) was built into the model as a factor as was Disparity. Models were run with or without interaction between these two factors. Models were compared on the basis of the Bayesian Information Criterion (BIC). Experiment 2: Size and Disparity were built in as factors into the model with each having three levels. The three levels for Size were called Loom, Large and Small, each respectively coding the conditions where the stimulus size increased as it loomed towards the mantis or was held constant to subtend an angle of 22.
Data Availability All data will be publically available on publication on figshare. com. Reviewers can access the data supporting this paper using the following private link: https://figshare. com/s/586b4f0e9b06deb8e253. CC-BY-NC 4. 0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted December 20, 2018. ; https://doi. org/10. 1101/502583 doi: bioRxiv preprint.
Indeed, targeting Xf using qPCR appeared inconclusive and did not allow assessing the genetic identity of the strains. In a second step, we compared the results of our molecular tests to the potential range of Xf as estimated using species distribution modelling based on presence/absence tests conducted on plants. In a third step, we collected occurrence data of P. spumarius throughout Europe and estimated its geographical range using species distribution modelling to discuss the interest of using this insect species as a sentinel for the early detection and monitoring of Xf in Europe.
The maps show the sampling sites and the foci of infection. Graphs are plots of distance between each sampling site and the nearest focus of infection. Maps were created using the R package OpenStreetMap  75  with data copyright to OpenStreetMap contributors. to better fit with our experimental conditions. To estimate the sensitivity of the qPCR approach, we used incremental dilution of an inactivated bacterial suspension of known concentration provided by B. Legendre (LSV, ANSES, Angers, France). Two replicates of qPCR were performed on each insect specimen. Nested PCR and Sequencing. Our attempt to amplify the seven loci included in the MLST of Xf using conventional PCR and primers/conditions described in the original protocol  26  , https://pubmlst. org/xfastidiosa/) were unsuccessful, probably because of the low amount of bacteria.
We thus switched to a nested PCR approach. Sequences of the different alleles of each locus were downloaded from, https://pubmlst. org/xfastidiosa/ (last access October 19th 2017) and aligned. Internal primers for each locus were designed from these alignments (Table  S2 ) and primers were M13 tailed to simplify the sequencing reaction. We ensured that the nested PCR approach did not preclude discrimination among genetic entities by comparing maximum likelihood phylogenetic trees obtained from a concatenation of the 7 loci originally included in the MLST of Xf and their reduced sequences as included in the nested PCR scheme (Fig. S2 ). Loci extracted from all genomes available on Genbank (last access October 19th 2017) were used as input. To test for the presence of Xf in the insects, we first targeted holC.
Species distribution modelling of Xf at the Corsican scale. The potential distribution of Xf subsp. multiplex (ST6 & ST7) in Corsica was modelled using BIOCLIM  45, 46  and DOMAIN  47. Methodology followed Godefroid et al. 48. Data collected in France from 2015 to 2017 by the national survey on plant material were used as input. Three different climatic datasets were used to fit the models. The results consisted in a map depicting the percentage of models predicting the presence of Xf subsp. multiplex (ST6 & ST7).
Species distribution modelling of Philaenus spumarius at the European scale. Occurrence data- set. A total of 1323 occurrences were used to model the distribution of P. spumarius in Europe. Off these, 471 originated from the GBIF database (GBIF. org (2017), GBIF Home Page. Available from: http://gbif. org [1rd November 2017]). The remaining 852 occurrences corresponded to our own observation records or were taken from the literature (List of references in Supplementary material, Appendix 3). Modelling framework. We modelled the distribution of P. spumarius by means of Maxent, the most widely used species distribution model  49, 50. Maxent models the potential species distribution based on the principle of maximum entropy. It relates species occurrence records and background data with environmental descriptors to get insight into the environmental conditions that best reflect ecological requirements of the species.
Species responses to environmental constraints are often complex, which implies using nonlinear functions  49. For that reason the parametrization of Maxent involves choosing among several transformations (referred to as feature classes or FCs) of original environmental descriptors i. e. linear, quadratic, product, hinge and threshold  51. The parametrization of Maxent also involves a regularization multiplier (RM) introduced to reduce overfitting  52. Various authors have highlighted that the default settings of Maxent are not optimal in all situations and might lead to poorly performing models in certain cases  [52] [53] [54]  and it is sensible to search for the best parameters given the dataset at hand  53. We built models with RM values ranging from 0. 5 to 4 with increments of 0. 5 and 6 FC combinations (L, LQ, H, LQH, LQHP, LQHPT with L = linear, Q = quadratic, H = hinge, P = product and T = threshold) using the R package ENMeval  55.
This led to 48 different models. The models were fitted using all the available occurrence points and 10,000 randomly positioned background points. The optimal settings corresponded to the models giving the minimum AICc values (see  55  for details). The resulting optimal FC and RM values were used to fit the final Maxent model based on a training dataset constituted by a random subset of 80% of the occurrences and 10,000 randomly positioned background points. The resulting Maxent model was then used to create a map of suitability scores (i. e. habitat suitability) across Western Europe (logistic output of Maxent  51  ). Suitability values were transformed into presence/absence by applying two thresholds a) the value at which the sum of the sensitivity (true positive rate) and specificity (true negative rate) is the highest and b) the lowest presence threshold (LPT)  56.