dataesr/scientific-paragraphs-categorization huggingface dataset:
QUERY PAGE UPGRADES AND NEW FUNCTIONALITIES The HbVar query page has undergone a major refit in 2006  (7)  to improve the clarity of display. We have now added two additional querying options in the database allowing the user to query for the most recent updates, referring to either new entries or updates of existing entries (or both; Figure  1 ). The user can also specify the date of the new or updated entry in the adjacent drop-down menu. In addition, we have included query options to list all HbVar entries that are also listed in other resources, such as dbSNP (http://www. ncbi. nlm. nih. gov/projects/SNP), Swiss-Prot (8) and OMIM (9; Figure  1 ). In addition to the data querying option changes, we have added new data visualization features. In addition to querying HbVar contents by gene location and globin chain, the user can also pre-select the output of the query results, in different genome browsers, namely the University of California at Santa Cruz (UCSC) Genome Browser  (10)  and the Pennsylvania State University Genome Browsers, using the dedicated HbVar custom tracks (Figure  2 ).
INTER-RELATION WITH OTHER DATABASES AND SCIENTIFIC JOURNALS To maximize querying options and comparative data analysis, we have decided to share HbVar data content with that of other established and internationally renowned genetic data resources. FINDbase (http://www. findbase. org; 11) is a global database documenting allele frequencies of clinically relevant genomic variations, namely, causative mutations and pharmacogenomic markers, in various populations and ethnic groups worldwide. HbVar allele frequency data were initially shared with FINDbase developers in 2006 and made available as an integral part of its data collection. Since then, data collection has been significantly updated with new aand b-thalassemia mutation frequencies data from 28 populations and 27 ethnic groups and/or geographical regions that were extracted from the published literature (Figure  3 ).
Also, the entire HbVar database content has been copied to the Leiden Open-Access Variation database (LOVD; http://www. lovd. nl; 12) V2. 0 platform not only to fulfill the need of comparative analyses with data from other LSDBs that have been developed in the same platform but, most importantly, to allow documentation of hemoglobinopathies-related genome variations in other genomic loci, namely, those leading to a-thalassemia, variations in genes modifying thalassemia disease severity, quantitative trait loci, etc (see later in the text). Finally, HbVar database is inter-related with the scientific journal Hemoglobin such that each variant published in the journal should be first documented in the HbVar database. A user can select a particular gene or genomic region in the human aor b-globin cluster in the HbVar query page (HBB in this example) and the query returns all genomic variants (base changes, small indels and gross deletions) documented in HbVar that are present within the selected region.
IMPLEMENTING MICROATTRIBUTION TO ENCOURAGE DATA SUBMISSION In 2008, the scientific journal Nature Genetics introduced the concept of microattribution in an attempt to establish an alternative reward system for scientific contributions, such as database entries and records and possibly database curation efforts. The principle of microattribution is '. to produce a publication workflow that is open to all journals and that draws on the expertise of all those with a stake in understanding variation at a particular region in the human genome'  (13). In this way, microattribution introduces the concept of individual genome variants curation, so that data submitters and database curators obtain all due credit for their effort and/or contribution. A prerequisite for this is that genomic variants should be deposited in stable, publicly available and well-maintained central repositories that would run independent microattribution services, based on an individual researcher's unique identity, defined by the Open Researcher and Contributor ID consortium (http://orcid.
org), Researcher ID (http://www. researcherid. com), OpenID (http://openid. net) and so on  (14). HbVar data content was used to first demonstrate the use of microattribution in practice  (15). In particular, all causative globin gene variations in the a-like and b-like globin genes, as well as those genomic loci that when mutated lead to (ATRX, KLF1, BCL11A, etc) or modify a hemoglobinopathy-related phenotype (MYB, MAP3K5, PDE7B, etc), their associated phenotypes and allele frequencies, where applicable, were comprehensively documented in the 37 LOVD-based interrelated LSDBs (Table  1 ) and assigned a unique LSDB accession number and IDs of the contributor(s) of the variant. Each genomic variant in these LSDBs included either published variants stored against the PubMed IDs or unpublished variants contributed by individual researchers or research groups involved in hemoglobin research.
Subsequently, the microattribution tables were deposited in the NCBI (http://www. ncbi. nlm. nih. gov) public repository in an effort to measure microcitations for every data contributor or data unit centrally. The microattribution article itself, comprising 51 authors from 35 institutions, was published in 'Nature Genetics' in 2011  (15). According to HbVar data accesses and contribution, microattribution has been found to contribute significantly to the increase in data submission rate, showing an up to 8. 2-fold increase in data submission rate as compared with previous years in which HbVar was active  (15) , even compared with the official HbVar launch year (2001), emphasizing the potential impact of microattribution to genome variation data submission. Also, apart from the increase in data contribution to HbVar, a number of useful conclusions were drawn from this approach, mostly derived from the clustering of HBG2/HBG1 gene promoter variants and the ATRX and KLF1 gene coding variants, from where new mutation patterns have emerged  (15).
PhenCode: CONNECTING GENOTYPE WITH PHENOTYPE LSDBs are key connections between the abundance of genomic information and clinically important issues. In 2006, HbVar and GenPhen databases have been adapted to complete a path from genome sequence to functional analysis, via Encyclopedia of DNA element (ENCODE, http://www. genome. gov/10005107; 18), to human mutations (HbVar) and to clinical phenotypes of groups of patients (GenPhen). The display of clinically relevant locus-specific mutation data on the UCSC Genome Browser makes it readily available to a wide audience, and facilitates viewing of data from many sources in one context. On the other hand, links back to the original databases allow detailed queries within individual loci, which can then be combined and further analyzed accordingly.
FUTURE PROSPECTS HbVar has become, since the year of its launch, a key resource for information about sequence variation leading to hemoglobinopathies and is still considered an exemplary LSDB from the various existing ones. Key factors that have contributed to its success are (i) its constant data update and improvements, mostly driven by the devotion of those researchers involved in this project, (ii) its dynamic data querying and visualization tools, in conjunction with the UCSC and PSU Genome Browsers and (iii) its partnership with other stable and well-respected international databases. The positive impact that HbVar has on the research community is also illustrated by the fact that funding, dedicated or related to other projects, has always been available for keeping this resource alive, in an environment where dedicated funding opportunities for database development and curation are often limited and very hard to find  (20) , frequently resulting in the discontinuation of many useful databases.
The international recognition of HbVar also comes from the fact that although couple of other globin-related databases, such as Deniz [content migrated to the Catalog of Transmission Genetics in Arabs (CTGA) database (http://www. cags. org. ae/ctga_ search. html), 21] or the Ithanet databases (http://www. ithanet. eu/index. php/db), have been developed, HbVar is still considered as the key LSDB for hemoglobin research professionals. To ensure continuous HbVar data enrichment, we plan to implement a broader search strategy that combines manual and electronic search procedures and also tighter links to the scientific journal 'Hemoglobin'. Also, we plan to expand the inter-relation of HbVar with other relevant high quality databases, following the successful example of HbVar and GALA databases (6), the UCSC and PSU Genome Browsers, PhenCode  (19) , FINDbase  (11)  and LOVD  (12).
ACKNOWLEDGEMENTS The authors thank all the HbVar users worldwide for their valuable comments and suggestions, which help us to keep the information as updated and complete as possible and also contribute to the continuous improvement of the database profile and contents. We will always be indebted to the late  Prof. Titus H. J. Huisman  and his colleagues for their detailed compilations of hemoglobin variants and thalassemia mutations. The authors wish to dedicate this work to the memory of  Renzo Galanello  who has much contributed in the field of hemoglobin research. FUNDING  United States Public Health Service  grants  [HG02238  to W. M. and  DK065806  to R. C. H. ];  European Commission  grants  [ITHANET 026539 ,  GEN2PHEN 200754  to G. P. P. ] and financial support from  Tobacco Settlement Funds of the Commonwealth of Pennsylvania , the  Huck Institute of the Life Sciences at Penn State University  and the  Golden Helix Foundation (London, UK).
ACKNOWLEDGEMENTS This work is a part of a PhD research funded by the  Institut Technologique FCBA  and  ANRT  ( Association Nationale de la Recherche et de la Technologie ). Additionally, the authors gratefully acknowledge the financial support of the CPER 2007-2013 " Structuration du Pôle de Compétitivité Fibres Grand'Est" (Competitiveness Fibre Cluster ), through local ( Conseil Général des Vosges ), regional ( Région Lorraine ), national (DRRT and FNADT) and  European (FEDER)  funds.
(2001)  retrieved from their NO y measurements made in 2000. The probably first images of NAT rocks recorded by the greyscale CIP (optical array probe) provide an additional proof of their existence with an optical detection technique other than forward scattering. Those images were observed exclusively when the penetration of NAT fields during a RECONCILE flight was confirmed also by the MAL, MAS, and SIOUX instruments (cf. Table  2 ). The CIP greyscale image data showed mainly 2-4 pixel features which correspond to particles of roughly 15 to 30 µm in diameter. No larger particles were detected. The images recorded during a PSC penetration on 25 January 2010 over a time period of 30 min amount to a number concentration of about 1×10 -3 cm -3 , which is in the same range as measured by the FSSP.
Heterogeneous chlorine activation As expected, the cold vortex temperatures and extensive PSC coverage in December 2009 and January 2010 led to substantial chlorine activation. A broad activated layer of enhanced ClO between 16 and 26 km altitude was detected by MIPAS-B on 24 January  (Wetzel et al. , 2012)  to the vertical extent of PSCs/cold temperatures observed by MIPAS-B in the same dataset, as well as CALIPSO  (Pitts et al. , 2011)  and ground-based lidars  (Khosrawi et al. , 2011)  in the time period preceding the flight. ClONO 2 observations indicate no or very little activation in the air masses below and above this layer. Based on the observations in 2009/10 as well as aircraft data from earlier winters and satellite observations, studies were carried out to better quantify the role of cold binary aerosol in chlorine activation.
Antarctic ozone recovery Using two regression methods (piece-wise linear trend and effective equivalent stratospheric chlorine functions) on three different datasets (ground-based, TOMS/OMI, and multisensor reanalysis data) for the 2000-2010 period that have not been used together for estimating of Antarctic ozone trends before,  Kuttippurath et al. (2013)  have revealed a clear signature of Antarctic ozone recovery, in agreement with a study by  Salby et al. (2011)  based on TOMS/OMI data over the 1979-2009 period. They show a September-November trend of about -4. 6 DU yr -1 over the period 1979-1999, and of +1 DU yr -1 or +2. 6 DU yr -1 (depending on the regression method used) for the 2000-2010 period. Kuttippurath et al. (2013)  also go beyond the  Salby et al. (2011)  work and other previous Antarctic ozone trend studies (WMO, 2011, and references therein) by applying three different vortex definitions to diagnose the strength of the recovery signal and also testing the significance of the recovery signal with respect to the changes in the Antarctic meteorology.
Progress in global chemistry-climate modelling The main objective of the global modelling activity in REC-ONCILE is to assess the impact of results from the process studies described in the previous section on predictions of polar stratospheric ozone loss in a global CCM. This section describes the LMDz-Reprobus model used in RECON-CILE and the implementation of process study results in this model, compares ensemble simulations with the upgraded model to the standard version and to observational records, and exhibits the changes in global spectral properties and temporal correlations of the time series produced by the model of improved chemistry module. In addition to the studies with LMDz-Reprobus described below, scientific findings from the RECONCILE project have been incorporated in the Whole Atmosphere Community Climate Model (WACCM).
The LMDz-Reprobus model and the RECONCILE upgrades LMDz-Reprobus  (Marchand et al. , 2012; Jourdain et al. , 2008)  couples the LMDZ general circulation model  (Hourdin et al. , 2013)  and the Reprobus stratospheric chemistry package  (Lefèvre et al. , 1998 (Lefèvre et al. , , 1994)). The configuration used in RECONCILE extends from the ground up to 65 km on 39 hybrid pressure vertical levels, and the horizontal resolution is 3. 75 • in longitude and 1. 875 • in latitude. The chemical package is comprehensive and includes the usual set of gas-phase and heterogeneous reaction rates -already including those on binaries (cf. Sect. 3. 2) -recommended by the JPL evaluation  (Sander et al. , 2011). For the treatment of polar stratospheric clouds, the pre-RECONCILE version uses a simple equilibrium scheme that predicts the existence of liquid (binary H 2 O / H 2 SO 4 or ternary H 2 O / H 2 SO 4 / HNO 3 solutions) and solid (NAT or H 2 O ice) aerosols from the local thermodynamic conditions in each model grid box.
Model evaluation by spectral weight and detrended fluctuation analyses While the last big cross-validation project CCMVal-2  (Eyring et al. , 2010; Gillett et al. , 2011; SPARC, 2010)  provided comprehensive bias estimates for several models, we extended the methodology by comparing dynamical features of empirical data and time series obtained by the LMDz-Reprobus simulations. The main focus was on a global analysis of spectral properties, two-point correlations determined by detrended fluctuation analysis (DFA, e. g. Derby, 2004) , and detecting higher order correlations by the spectral surrogate method  (Kantz and Schreiber, 2004). Spectral properties were evaluated by extracting the spectral weights (relative strength) of semi-annual, annual, and quasi-biennial oscillations (QBO) with respect to the integrated power spectra.
The spectral weight in a given frequency band provides information about the variance of the original signal, e. g. about the variance explained by an annual oscillation. The method of detrended fluctuation analysis (DFA) has become a standard tool in time series analysis (e. g. Derby, 2004)  for quantifying two-point correlations in non-stationary signals, because the autocorrelation function or the power spectrum can erroneously indicate longrange correlations in the absence of strict stationarity. Higher order correlations were tested by computing the time reversal asymmetry statistics (it is essentially based on timelagged third moments) for the original and surrogate datasets where only two-point correlations are preserved  (Kantz and Schreiber, 2004). In a preparatory study,  Homonnai et al.
The values of precise correlation exponents are hard to obtain over regions where QBO or other strong nonstationarities (ozone hole) are present; however, the missing QBO component in the LMDz-Reprobus data has no demonstrable effects away from the narrow equatorial band. In spite of all the numerical difficulties, significant long-range correlations are detected for total ozone over all geographic locations  (Homonnai et al. , 2013). The results on higher order nonlinear correlations will be reported elsewhere. The three new runs described above (REF, TC, and NMP) are evaluated by the same methodology. Here we show characteristic examples of the results; details will be published in a subsequent paper. Figure  17a  shows the difference in the spectral weights of the annual peak (area under the peak normalised by the integrated total power) between the results of NMP and REF runs.
Conclusions Besides providing the foundation for the advancement of our understanding of processes involved in polar ozone depletion -the overall objective of RECONCILE -the data obtained during the aircraft and Match campaigns have been useful in several ways. The Match sonde data from 2011 have contributed to the quantification of the record-breaking ozone loss in this unusual winter. Measurements of a large number of ODPs made during the Geophysica campaign were used for assessing the trends and lifetimes of these compounds. The dataset is placed at the disposal of the larger scientific community for further scientific exploitation. Future stratospheric campaigns will benefit from technological advances made in the framework of the field campaigns such as enhanced flight-planning tools and the deployment of the novel impactor to collect non-volatile stratospheric aerosol for laboratory analysis.
g. Zhou et al. , 2012). Interactions between the tropics and high latitudes also have influence on the stability of the polar vortex (e. g. Garfinkel et al. , 2012; Holton and Tan, 1980) , and it is indicated that, in a changing climate, major stratospheric warmings will shift towards late winter (e. g. Naoe and Shibata, 2012)  with potentially important consequences for ozone loss in the Arctic. For predicting how climate change will affect the ozone layer in future, it will also be necessary to quantify the contribution of GHG forcing to current and future trends in the atmospheric conditions. Investigations into these issues will be needed to complement the work done in RECONCILE and further advance our understanding of Arctic ozone depletion. Acknowledgements. RECONCILE is funded by the European Commission under the grant number RECONCILE-226365-FP7-ENV-2008-1.
Support for M. C. Pitts is provided under the auspices of the NASA CALIPSO/CloudSat Science Team. Support for L. R. Poole is provided under NASA contract NNL11AA10D. Work at the Jet Propulsion Laboratory, California Institute of Technology, was done under contract with the National Aeronautics and Space Administration. The Atmospheric Chemistry Experiment (ACE), also known as SCISAT, is a Canadian-led mission mainly supported by the Canadian Space Agency. Work at the University of East Anglia was made possible through funding from the UK Natural Environment Research Council (research fellowships NE/F015585/1 & NE/I021918/1). The atmospheric sounding campaign at FMI Sodankylä was supported by the EU through the Lapland Atmosphere-Biosphere Facility (LAPBIAT2) project. The Geophysica flight on 10 March 2010 was funded by the ESA under the PremierEx project.
The goal of this study was to facilitate the modeling process of a building starting from 3D laser scanner data. In order to do this, we wrote two scripts for Rhinoceros 5. 0 based on intelligent algorithms. The first script finds the exterior outline of a building. With a minimum of human interaction, there is a thin box drawn around the surface of a wall. This box is able to rotate 360° around an axis in a corner of the wall in search for the points of other walls. In this way we can eliminate noise points. These are unwanted or irrelevant points. If there is an angled roof, the box can also turn around the edge of the wall and the roof. With the different positions of the box we can calculate the exterior outline. The second script draws the interior outline in a surface of a building. By interior outline we mean the outline of the openings like windows or doors.
The process continues until all reachable edges have been tried. Then the same process is started from another seed triangle, until all points have been considered. The algorithm can be applied to datasets of millions of points representing complex 3D objects, thus not only building surfaces. The BPA requires a relatively small amount of memory, is time efficient and its result has a good quality. (F. Bernardini 1999). Although it is not explicit mentioned, the two previous algorithms seems to be concentrated more on reconstructing surfaces of artifacts than buildings. Just like the algorithm of N. Amenta (N. Amenta 1998) which is based on Voronoidiagrams. A Voronoi-diagram is a mathematical way of dividing space into a number of regions. Also Jenke's and his partners' (P. Jenke 2006) script is more suitable for artifacts than buildings.
g. considering curved structures. (P. Dorninger, N. Pfeifer 2008). In the model driven area, the previous research is done for building reconstruction. But in the data driven area the previous works seemed to be concentrated more on either aerial point clouds or very complex forms, like sculptures or face reconstruction, and not mainly on buildings. That is why we chose to make our own proper new data driven script. And although the final scripts are still restricted we stuck to the data driven approach because with further research, this could lead to the most flexible application. This approach is not based on any previous work and tries to tackle the automation from a new point of view.
Methodology As explained earlier certain assumptions need to be done: Because of the complexity and the diversity of the input data, we started with simplified models in order to gradually make the models more complex. These simplifications limit the input that the scripts can process. As a result, we always can imagine cases for which the algorithms will not work as desired. Despite the fact that in practice the points produced by a 3D scanner are measured with some regularity, the points in a point cloud are typically not assumed to be ordered. The assumption of unordered points allows us to make a script as general as possible, not depending on the type of scanner, on the type of modeling software or the way the object was scanned (Tim Volodine 2007). The idea of the script is based on a thin box rotating around axes in the edges of the wall.
External outlines of the walls In the beginning an interaction with the user is needed. The number of walls has to be given and all points need to be selected. The fact that noise is also being selected will do, in most cases, no harm to the process of the script. After the selection, the script asks to indicate the two outermost points at the base of the longest wall. After entering a thickness, the box can be drawn. The user needs to consider wisely this thickness ass it will operate as the tolerance for the roughness of a wall. The box immediately contains the points of the first wall, so these points can be saved in a special list which will contain all points of all surfaces. All these points will be saved in the same coordinate system. Thereafter the box can rotate around an axis at the corner of the wall.