dataesr/scientific-paragraphs-categorization huggingface dataset:
2% and in our lab = 4. 6%) were determined using the standard enzyme linked immuno-sorbent assay (ELISA) technique. Sera levels of cortisol (R&D Systems inc. Minneapolis, USA. Sensitivity <0. 071 ng/ml; Intra-assay variability as stated by the manufacturers = 7. 0% and in our lab = 7. 1%) were also assessed to confirm that time-of-day was chosen appropriately to distinguish between the acro-and bathyphases of the strength-related circadian rhythm, as well as to represent realistic times for training sessions. The optical density of each well in the 96-wells plate set-up was read using a microplate reader (EL808, Biotek instruments, Winooski, USA), with the IGFBP-3 and cortisol standard curves (four-parameter logistic regressions Y = (A-D)/ (1+(X+C) ^B) +D) drawn using Gen5 version 1. 06 data analysis software (BioTek Instruments, Winooski, USA).
Cells were washed in PBS, counterstained with 10 μl 4', 6-diamidino-2-phenylindole (DAPI) and covered using glass coverslips. Cells were visualised using Nikon TE-2000 inverted fluorescent microscope (Nikon UK Ltd, Kingston upon Thames, UK). Images were captured with a Hamamatsu Orca camera (Hamamatsu Phototronics, Herts, UK) and merged using Image Pro Lab v4. 0 image analysis software (BD Biosciences, Oxford, UK). Diameters in micrometers (μm) were obtained using the measure toolbar on IP lab 4. 0 software. Nuclei numbers per captured image were obtained using Image J v1. 44p (National Institute of Health, USA) with the ITCN plug in (Image-based Tool for Counting Nuclei).
Statistical analysis SPSS version 21. 0 for Windows was used for all statistical analyses. Test-order impact on preexercise blood glucose was carried out using an unpaired t-test on the AM vs PM difference. As cortisol levels and blood volumes pooled data obeyed the assumptions of parametricity, Mixed-Design 4×2 ANOVAs (with Greenhouse-Geisser adjustments where required) were run with within factor as the intervention phase (pre-post training, AM vs. PM) and between factor as the protocol (Exercise vs. Control). Myogenic index (%) data were analysed using a one-way ANOVA performed with a bonferroni post hoc test to run pairwise comparisons. Since the pre-exercise morning IGFBP-3 and blood lactate data were non-normally distributed (as determined by the Shapiro-Wilk test) and logarithmic transformations did not remove the kurtosis in the distribution, Wilcoxon signed-rank and Mann-Whitney U tests were used to determine the pairwise comparison in the trained data sets.
The paper presents empirical research on the quality of the toponyms that can be retrieved from OpenStreetMap (OSM) under the purpose of enriching authoritative toponymic databases and gazetteers. An analysis on the volatility of places and points-of-interest (POIs) is presented. We examine how named features behave and change in terms of type, name and location. The challenge is to understand the behavior and consequently the fitness-for-purpose of OSM data when it comes to a possible use and integration with authoritative datasets. We show that, depending on the OSM feature type, the volatility can vary considerably and we elucidate which feature types are consistent, and thus could be used in authoritative gazetteers despite their grassroots nature and if there are spatial patterns behind the location changes of features during their lifespan.
Introduction Gazetteers are a vital component of any spatial database irrespectively of the level of detail used (i. e. local, national or international). Gazetteers consist of a list of toponyms, a type and their corresponding geography. This geography can be either a point, a bounding box or the footprint of the place. Gazetteers are usually used as an entrance point to a spatial database. People start exploring geographic data by providing a toponym and search for features, relations, maps or events related to that toponym. In other cases, the outcome of a spatial search is accompanied by toponyms that facilitate the understanding of the result. There are also cases where the result of a search is the toponym itself (e. g. reverse-geocoding). Apart from these practical examples, toponyms and gazetteers play a key role in many aspects of everyday life.
Examples can be found in explicit geographic applications like routing, mapping and cartography but also in more general cases such as in government, legislation, security and policing etc. (UN, 2006). However, National Mapping Agencies (NMAs), which are the de facto agencies responsible for creating and updating gazetteers in a national level, are facing difficulties in keeping toponymic databases up to date due to the lack of resources and due to the extensive field work needed for data collection and verification. On the other hand, Volunteered Geographic Information -VGI  (Goodchild 2007 ) can serve as a promising alternative mechanism for collecting toponyms that could enrich and update official gazetteers  (Goodchild & Hill 2008). In this context, the aim of this paper is to examine whether OSM can provide consistent toponymic datasets or the grassroots mechanisms alter constantly the spatial features in such a level that hinder their use in gazetteers.
Related Work The importance of gazetteers and the challenges posed by the nature of VGI data, and especially of toponyms, has drawn the interest of many researchers and there is extensive literature available. Here, we provide few examples of VGI and authoritative data integration efforts so to highlight that VGI quality and stability is an important factor for this task. Such efforts range from creating a gazetteer by harvesting volunteered big geo-data from Web sources (see for example  Gao et al. 2014)  to combining both administrative and VGI toponyms. For example,  Twaroch et al. (2008)  use various web sources to create a surface model of the toponyms' footprints. However, the authors highlight the fact that it is difficult to have crisp boundaries when it comes to VGI data and that there is a need to identify outliers.
Similarly,  Keßler et al. (2009a)  proposed the enrichment of authoritative gazetteers with toponyms extracted from geotags of photos. As the authors support, their approach could benefit from quality indicators of the geotags used. The quality of user-contributed data has been also highlighted as a crucial factor in empirical research with geo-tagged photos (see for example  Hollenstein & Purves 2010). Regarding OSM,  Hahmann and Burghardt (2010)  proposed to link OSM with GeoNames gazetteer using semantic web techniques to produce an enriched, multi-lingual gazetteer and  Smart et al. (2010)  proposed a methodology for the conflation of toponymic data from multiple sources, including both authoritative and VGI datasets, and taking into account the quality differences of each source. However, as  Mooney and Corcoran (2012)  explain, developers of locationbased services should be cautious when it comes to using OSM data as their research on frequently edited features revealed considerable volatility in the naming process.
Moreover,  Keßler et al. (2009b)  underline the importance that gazetteers should cater both for local and small-scale features, as well as timely and user-centric information. In this context, OSM has the potential to become a valuable source of toponyms. Thus the discussion focuses on the nature, the behavior and the evolution of the toponymic datasets that can be retrieved from OSM and how these factors affect quality elements and their use in gazetteers.
OSM Data Extraction Extending this line of research, this paper focuses on the volatility of OSM features. It goes beyond the naming changes that  Mooney and Corcoran (2012)  focused and examines also the location changes of OSM features. The area of scope of the research is Paris region (12. 012 km 2 ). The study area is large enough to have a great diversity of named features, and is quite complete due to the large number of OSM contributors. In order to collect the necessary data, the Geofabrick 3 shapefile download service was used. The datasets for the area of scope were downloaded at the first week of December 2014. Shapefiles include as an attribute the unique OSM_ID of every OSM feature. These IDs were used in combination with the OSM API to collect and store in a Post-greSQL/Postgis database all the versions of each feature.
Descriptive statistics A preliminary analysis on the availability of names for the spatial features (grouped by OSM category) was conducted and the results are shown at Table  1. It can be seen that, depending on the category, there are considerable variations in the presence of names. For example, in the 'Places' category, OSM contributors have assigned a name at almost all (i. e. except from 3) features. Arguably, this behavior meets the expectations of an OSM user (including the 3 www. geofabrik. de Here the percentage of named features is just 27. 6% but, as it will be explained later, this factor is not indicative of the completeness of the dataset in terms of names as for many POIs' subcategories a name tag is not applicable (such as for 'crossing' or 'bench'). Given these results the research focused into two categories that were deemed as the most interesting when it comes to examining the potential to create or enrich a gazetteer: OSM Places and OSM POIs.
OSM Places In terms of changes in type, location and name, a Place point can either remain stable in its entire life-cycle or undergo a change in one or any combination of these three factors. In an effort to understand whether the OSM data can serve as a source of consistent toponyms, the percentage of the features that have been changed or remained stable has been recorded (Figure  1 ). It can be seen that two thirds of the features have never been changed while the most common change that features undergo is in their geographic location. In this context, the next issue of interest was to examine the types of places and their corresponding population versus the location movements that took place for each 'Place' type. This classification was used so to examine which types of features, have been moved by OSM contributors.
For example, motorway junctions seem not to gather consensus among OSM contributors regarding the position of the POI as the average location change is more than 30 m. On the contrary, there are POI types that despite their location change, the distance between various locations remains well under 10 m (i. e. an arbitrary positional accuracy threshold of hand-held GPS devices). Second, this type of analysis can highlight gross errors and outliers in OSM datasets that might downgrade the overall spatial quality of a dataset. The largest the distance between the mean and the upper level of the second Quartile box (i. e. the 50% of the features), the more outliers and gross positional errors exist in each category. For example, 8% of the features for the fuel category have been moved more than 100 m (with a recorded maximum movement of 659 m).
Spatial patterns Finally, for the entire dataset of POIs a hot-spot analysis was calculated based on the location change for each feature. A visualization based on Z-score is shown in Figure  6. Hot-spot analysis (using the Getis-Ord Gi statistic provided in ESRI ArcGIS 10. 2. 2) can reveal whether a phenomenon is random or not. Here it can be observed that there are concentrated hot colors areas (i. e. areas with not random large movements) and cold colors areas (i. e. areas with not random small movements) for POIs. While a first observation can be made that hot colors areas appear in the popular and touristic area of Montmartre (north of map) and the cold colors areas appear at the periphery of Paris (more residential than touristic), further analysis is needed to fully understand the causes of the phenomenon.
Discussion and future work VGI datasets are a dynamic source of spatial information. In particular, OSM datasets, which usually function as a proxy in the research on VGI data, have drawn the interest of researchers regarding their use in helping NMAs to complete or update existing geospatial products or even to create new ones (Antoniou 2011). Improved and enriched authoritative products can be toponymic databases and gazetteers. The importance of gazetteers in acquiring accurate results in spatial searches is paramount and thus the update of official gazetteers with local knowledge should be made with caution and meticulous examination of the VGI quality. Unnecessary changes in the names, types or the geographic position (no matter how subtle or small) can introduce problems to authoritative products or location based services.
However, once successful, the presence of local and community-level named features and landmarks can considerably enrich and improve gazetteers and geospatial services. A first point of consideration is the decision on which types of user-contributed features should be used in a gazetteer. For example, certain types of POIs are possible to serve as landmarks that can help to provide eloquent and easily understandable routing directions. Although this paper does not delve into the subject of feature type importance, it provides evidence that the selection of OSM types and features should be examined from a quality point of view as well. What this paper has examined is the behavior and thus the fitness-for-purpose of OSM data as a source of toponymic data. The aim was to examine whether the OSM datasets are a consistent datasets or the grassroots mechanisms alter constantly the datasets in such a level that in practice hinder the use of OSM data.
The findings show that VGI and authoritative data conflation is not a straightforward process as they differ considerably in nature. While authoritative toponyms are largely static and hard to change spatial entities, a considerable percentage of VGI toponyms undergo changes. Not all OSM types are fit to support the enhancement of administrative gazetteers as the OSM specification and contribution practices might generate an unwanted volatility in the data. This observation generates a number of questions that could be the aim of future work. First, it is important to understand the nature of these changes. For example, do changes in location serve a better mapping outcome, refer to previous mistakes and thus are a spatial quality improvements or are they simply real-life movements that OSM contributors capture? Relating movement to the geographic extent of the named feature, or to some contributor pattern would be useful to understand how and why the changes occur.
Using what  Goodchild and Li (2008)  call the geographic approach to assess named features movement would also be useful: e. g. check whether a Place feature that refers to a town has been move to the centroid of the town hall. Similarly, it could be examined if there are any time patterns in the changes. For example are these changes concentrated at the early period of the creation of a feature and thus it is an indicator of quality improvement (as discussed in  Haklay et at. 2010)  or are they happening during the entire life-cycle of each feature and indicate an endogenous volatility of the spatial feature? Nevertheless, contributors might alter OSM features (no matter what the reason) and this change can either be very small and thus authoritative products and services that have integrated OSM data will not be affected or might be large enough to introduce unwanted volatility.
Methods Observations. A field experiment took place during 5-11 July 2015 near Ansede-Roche in the Saguenay Fjord (Fig. 1 ). Measurements were collected from an 8 m research boat equipped with a towed 120 kHz Biosonics echo-sounder, a towed 500 kHz Teledyne RD Instruments 5-beam acoustic Doppler current profiler (ADCP) and a Sea-Bird Electronics SBE-19plus conductivity-temperature-depth profiler. The ADCP data were acquired in 5 s ensemble averages and 0. 5 m vertical bin size. The data were then averaged to 1. 0 m vertical resolution and 15 s temporal resolution. The ADCP had no bottom-tracking feature. The flow measurements were referenced to ground using global positioning system (GPS) data acquired every second. A 20-megapixel Canon EOS 6D camera with a 60 degree field of view was programmed to take one image every minute during daytime from the balcony of Mrs Simard at 48°13.
Acknowledgements This research was funded by the  National Sciences and Engineering Research Council of Canada , the  Canada Foundation for Innovation , the  Department of Fisheries and Oceans Canada  and is a contribution to the scientific program of Quebec-Ocean. We thank  Teledyne RD Instruments  for loaning us their new V-ADCP Monitor used in this study. We also thank  Alexandre Livernoche  and  Pascal Bourgault  for their assistance in the field and data analysis of the camera data. Finally, we would also like to thank  Louis Gostiaux  ( E ´cole Centrale de Lyon ),  Kraig Winters  ( Scripps Institution of Oceanography ) and  Kevin Lamb  ( University of Waterloo ) for general discussions about internal wave dynamics and for their comments on the manuscript as well as the anonymous reviewers for their constructive critiques.
Methodology/Principal findings A systematic review in according with PRISMA guidelines was conducted. All published articles available in PubMed, Embase, Cochrane library and CINAHL databases before May 20, 2015 were searched without any limits. Two reviewers independently screened, reviewed and assessed all the studies. Cochrane Q and Moran's I 2 were used to assess heterogeneity and the Egger test was used to examine publication bias. The summary odds ratio (OR), summary regression co-efficient (β) and 95% confidence intervals (CI) were estimated using a random-effects model. Out of 2,920 citations screened, 12 articles (five cross-sectional, seven prospective cohort) were eligible to be included in the systematic review and 11 in the meta-analysis. The 12 studies involved 9,337 children in eight SSA countries.
Eligibility criteria All epidemiological studies except case studies which reported prevalence or incidence of P. falciparum infection and/or Plasmodium density stratified by the presence or absence of S. haematobium or S. mansoni infection among children living in SSA were included. Studies that reported immunology of P. falciparum malaria and S. haematobium or S. mansoni co-infection in the general population were also included if they reported the prevalence or incidence of P. falciparum infection in children separately. Unpublished studies, conference abstracts, protocol, gray literature, review protocols, studies that involved only adults or pregnant women, animal or in vitro studies, and studies conducted outside of SSA were excluded after screening the titles and abstracts. Studies were additionally excluded after full text review when children infected with Schistosoma were co-infected with soil transmitted helminths or if they lacked epidemiologic data on P.
Search methods for identification of studies Two authors (AD and DD) independently conducted a search in Pubmed, Embase, Cochrane Library, CINAHL databases using keywords: malaria OR Plasmodium OR "Plasmodium falciparum" OR "Plasmodium vivax" in combination with helminth OR Schistosoma OR "Schistosoma mansoni" OR "Schistosoma haematobium" (S2 Table ) for articles published before May 20, 2015. The search was limited to humans, but no limits were made on language. References of some related reviews  [10, 11, 20, 21]  and African Online Journals database were also searched for relevant studies. Following exclusion of duplicates; abstracts and titles of 2,149 papers were screened for eligibility criteria and 45 were chosen for full text evaluation. Any discrepancies in the choice of articles being included in the review were resolved by third reviewer adjudication.
Study synthesis Heterogeneity was assessed using Cochrane Q (Chi-square) and Moran's I 2 (Inconsistency) using STATA software (Version 11, Texas, USA)  [28]. Publication bias was evaluated using a funnel plot and statistical significance was assessed by the Egger test (bias if p<0. 1)  [29]. Subgroup analyses were conducted for S. mansoni and S. haematobium. Odds ratio, relative risk, regression coefficients, mean differences along with the 95% confidence intervals were used as effect measures. When studies did not report 95% CI for mean differences in Plasmodium density or haemoglobin level, we estimated it using p-values as suggested by Altman and Bland  [30]. The 95% CI for mean difference in haemoglobin level between children co-infected with S. haematobium and P. falciparum and those infected with only P.
Search results and study characteristics A total of 2,920 citations were identified from PubMed (n = 999), Embase (n = 1,847), Cochrane library (n = 50) and CINAHL (n = 24), of which 771 articles were found to be duplicates. All relevant articles identified from reviews on malaria and helminth co-infection  [10, 11, 20, 21]  and African Journal database were similar with the articles found from the four databases. Of the 2,149 articles screened; 2104 articles were excluded after reading the titles and abstracts. Of the 45 full-text articles reviewed, 33 were excluded. A total of 12 articles were considered for the systematic review, of which 11 were included in the meta-analysis (Fig  1). The characteristics of the 12 studies with 9,337 subjects included in this review are summarized in Table  1.
By contrast, crizotinib potency was less impacted by G1202del. Structural data on the G1202del mutation is not available. Based upon structural modeling studies, however, we speculate that deletion of the glycine at position 1202 could shift the aspartic acid at position 1203 into the 1202 position, leading to disruption of TKI binding (T Johnson, personal communication). Importantly, while our functional models suggest that ALK G1202del may be a novel resistance mutation, G1202del appears to be quite distinct from ALK G1202R. Indeed, in Ba/F3 models, ALK G1202R results in much higher degrees of resistance to all currently available first-and second-generation ALK inhibitors (Figure  S1D ). We next evaluated a cohort of 17 ALK-positive patients who underwent repeat biopsies following progression on alectinib.
Given the retrospective nature of this analysis, there is limited clinical data on the therapies patients received after disease progression on ceritinib, alectinib and/or brigatinib. Immediate post-progression therapies are summarized in Tables  S4-6. Patients generally received systemic chemotherapy (25%) or they were enrolled onto clinical trials (31%). Three patients (6%) received commercially available ALK inhibitors, while the remaining 38% of patients did not receive subsequent therapy and/or were lost to follow-up. Thus, we are unable to draw meaningful associations between our findings in post-progression biopsies and clinical outcomes to subsequent therapies. Collectively, across all three biopsy cohorts (N=48), ALK resistance mutations were present in 56% of ALK-positive patients progressing on second-generation ALK inhibitors (ceritinib 54%, alectinib 53%, and brigatinib 71%).
Of note, we were unable to determine whether these mutations were present prior to treatment with second-generation ALK inhibitors due to a lack of baseline tissue for analysis. No KRAS or EGFR mutations were identified. Missense mutations in DDR2 (L610F), BRAF (G15V), FGFR2 (F645L), MET (T992I), NRAS (A155T) and PIK3CA (G106V) were each identified in one (3. 7%) specimen, none of which were overlapping. Mutations in DDR2, BRAF, NRAS and FGFR2 did not occur in known hotspot residues, nor have they been observed in NSCLCs in the COSMIC database (COSMICv76); thus, the impact of these alterations on ALK inhibitor resistance is uncertain. MET T992I was observed in one specimen in this series (MGH040-2). MET T992I has been reported at low frequencies in various malignancies, but functional studies have demonstrated that this variant lacks transformative capacity and does not impact MET phosphorylation status  (34).