dataesr/scientific-paragraphs-categorization huggingface dataset:
As such, results obtained for the K-means algorithm with Euclidean distance on CLR-or logCLR-transformed profiles are very similar to those obtained for the K-means algorithm with χ 2 distance on the original counts. Finally, several extensions of this work could be considered in future work. For instance, rather than selecting a single number of clusters for a given dataset, it could in some cases be preferable to instead construct a hierarchy of clustering for varying K. To do this, one possibility would be to partition the data q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q 48.
SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e. g. , GlycoCT) or quality images (e. g. , svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The "quick mode" allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The "normal mode" integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.
A drawing interface may be useful to query databases or to input structures for further analysis, modelling, or prediction of properties. Conversely, the extent of glycan encoding formats often requires the translation of commonly used formats into images. The intrinsic user-friendliness of the symbolic nomenclature not only meets the glycoscientists' needs but also simplifies access to glycoscience for non-specialists. Over the past decades, the variety of glycan representations used in chemistry, glyco-chemistry and glycobiology gave rise to a series of editing tools. We however, limit our coverage to those that meet three requirements:  (1)  web-based, (2) freely accessible, and (3) exporting structures to standard encoding formats  [2]. KegDraw can be considered as the earliest standalone online graphical glycan editor though it was preceded by a basic tool integrated in GlycoSuiteDB for graphical queries in the IUPAC condensed format used in that database  [4].
KegDraw was designed to perform a similarity search in the KEGG databases where the original CarbBank  [5]  is integrated  [6]. It was a Java application that needed to be installed and could produce low-resolution images where text labels of monosaccharides were connected by lines. GlycanBuilder  [7]  is a more recent java applet developed during the EuroCarb project  [8]. This tool provides an interface to assemble glycan structures using the graphic visualization scheme proposed by the Consortium of Functional Glycomics (CFG) and described in  [9]. GlycanBuilder was upgraded to work in a web environment, but it needs to be installed and connected with a server. Moreover, recent security upgrades of all major browsers seriously challenged the usage of Java applets. This web-based implementation usually involves fairly long time-lags during processing despite a recent upgrade  [10].
However, this drawback can be avoided as demonstrated with the glycan structure builder of the GlycoViewer platform  [11]  a web interface for drawing glycans that pioneered in terms of design, usability and speed. A subjective weak point of this tool is the drag-and-drop implementation that allows computer users to draw a glycan structure easily with the help of a mouse. However, this may become tiresome if many and large structures are drawn on a touch-based device such as a tablet or a smartphone. Also, monosaccharides are displayed in text format like KegDraw neglecting the advantage brought by a symbolic notation. GlycoViewer, like GlycanBuilder, is composed of a client interface and a server written in Ruby on Rails. The drag-and-drop feature is also used in Glycano, a software for drawing glycans entirely written in JavaScript (http://glycano.
cs. uct. ac. za). Glycano is browser-independent and does not require a server. The interface uses SNFG symbols, though not in the proper color scheme and lacks the option of positioning of monosaccharides according to their linkage. It is designed for trained chemists and glycobiologists precluding access for non-experts. Polys  [12]  and DrawGlycan-SNFG  [13]  are the most recent published tools to draw glycan structures. Polys is integrated in the Glyco3D portal  [14]  to mainly serve as an input form for building 3D models. This is also the case of the (unpublished) carbohydrate builder (http://glycam. org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1) of the GLYCAM-Web portal. DrawGlycan-SNFG is standalone and produces high quality and SNFG-compliant depiction of glycan structures but data input is limited to IUPAC linear encoding  [15].
Users cannot draw a structure interactively, but only use a string encoding to generate images. In summary, tools developed in the last decade, are either incompatible with SNFG or rely on complicated and/or slow interfaces or have other format or usability limitations. From a technical viewpoint, these tools require a continuous connection with a server to support consistent and fast drawing. From a scientific viewpoint, we believe glycan drawing should be democratized. With this in mind, we have developed SugarSketcher, an intuitive and fast interface to draw glycans online. This tool is entirely built in JavaScript and does not need a connection to any server. It is supported by the major browsers and is fully compatible with the SNFG nomenclature. The interface has been streamlined to accommodate expert and non-expert usage.
In particular, a "quick mode" allows users with limited knowledge of glycans to build up a structure quickly while the "normal mode" offers a broader range of options regarding the structural features of complex carbohydrates. Its beta-version is currently implemented as another graphic interface for searching structures in CSDB, the Carbohydrate Structure Database  [16]. The GlycoCT  [17]  export feature allows every software project or a database supporting GlycoCT to translate the SugarSketcher user input into the project native notation and to further process the constructed glycan sequences, including piping data to the search engine. Major cheminformatics standards (Simplified Molecular-Input Line-Entry System (SMILES), InChi) are also available for export provided the structure is fully defined (e.
g. , no undetermined linkage or configuration). Furthermore, the code is destined to be shared and hopefully improved by the community of glycoinformaticians. A prototype of SugarSketcher is currently included in the tool collection of Glycomics@ExPASy  [18]  as a standalone application. It can be accessed at https://glycoproteome. expasy. org/sugarsketcher while the code is available on GitHub at https://github. com/alodavide/sugarSketcher.
Results SugarSketcher is divided in two main components: the core JavaScript library and the D3. js (https://d3js. org)-based interface. This division provides two main advantages: (1) the core library can be used standalone or integrated in other web applications that handle information about glycan structures; (2) the interface can be modified by collaborators without changing the underlying core library. In the "Materials and Methods" section we present how the two components have been built using JavaScript and a set of libraries rich in visualization components. The interface of SugarSketcher has been designed to address the increasing popularity of glycans among scientists with only basic knowledge of carbohydrates. Without knowledge of chemistry behind each monosaccharide, average users can quickly draw glycan and derivative structures using the "quick mode".
In this case, the interface presents 12 monosaccharides most commonly found in mammalian glycans as a reflection of the bias in structural data production observed in  [19]  for example. This limited set of monosaccharides is used as LEGO© bricks to sequentially build a structure. Each time a new monosaccharide is added to a structure, the user needs to input only the anomericity of the linkage and the attachment position of the monosaccharide. To depict monosaccharides and glycans, SugarSketcher uses the SNFG icons. Positioning monosaccharides basing on the acceptor linkage only can end up in overlays. For example, this situation occurs when two nodes coming from different branches should be in the same place. We have created a grid system that tracks whether a position is free or already occupied by a monosaccharide.
At present, positioning follows the option of depicting the monosaccharide linkages with embedded type and anomericity  [20]. Figure  1a  shows a galactosylated and sialylated N-glycan core drawn with the "quick mode" option. Molecules 2018, 23, x; doi: FOR PEER REVIEW 5 of 11 InChi) are also available for export provided the structure is fully defined (e. g. , no undetermined linkage or configuration). Furthermore, the code is destined to be shared and hopefully improved by the community of glycoinformaticians. A prototype of SugarSketcher is currently included in the tool collection of Glycomics@ExPASy  [18]  as a standalone application. It can be accessed at https://glycoproteome. expasy. org/sugarsketcher while the code is available on GitHub at https://github. com/alodavide/sugarSketcher.
Selecting optional values at each step (fully described in Supplementary S1-S5) will lead to the placement of the corresponding monosaccharide (alphalinked L-glycero-D-manno-heptose) in main space of the interface. SugarSketcher was benchmarked with currently available web interfaces in terms of speed for drawing a selection of small, middle-sized, and large molecules from several glycan databases. It was also compared to other tools according to a list of qualitative criteria. The results of the speed tests are summarized in S6 in Supplementary Material. Sugar Sketcher functionality and performance are compared to other tools in Table  1. The overall drawing process is a succession of feature selection steps that ends with the display of an SNFG icon. This process is repeated as many times as the target structure contains building blocks.
Discussion We encourage glycoinformatics project holders to integrate SugarSketcher as an alternative structure input tool. Currently it has been incorporated in CSDB  [16]. Ultimately it is also destined to become the graphic interface for querying databases and running software from the glycomics@ExPASy collection. At the moment, SugarSketcher supports the depiction of glycan structures following the standard imposed by SNFG. However, there are various features that we would like to implement in the nearest future:.
• On the fly Copy-Paste of the glycan image • Import structure via the URL • Automatic adjustment of parameters where it is possible to detect their chemically forbidden combinations Several users have asked for the possibility of copying the glycan image from SugarSketcher to other applications via the clipboard. The choice of high-resolution Scalable Vector Graphics (SVG) as the primary image format precludes this possibility since no general-purpose software supports it. Other image formats will be included. Another feature in development is the import of a glycan from the GlycoCT or IUPAC string in the URL parameter for an automatic image generation. As SugarSketcher is developed primarily for non-glycobiologists, one of the main features we are working on is the possibility of automatic preselection of various parameters where it is possible to infer them from the user input.
The Core Library The main assumption behind the core library is that each glycan can be represented as a graph. This concept has already been applied by users of MzJava  [21]  from which the core library is inspired. To avoid reinventing the wheel, the Graph class has been taken from Sigma. js, an established JavaScript library (http://sigmajs. org) which allows the integration of graphs in a web environment. The Graph class, together with GraphNode and GraphEdge classes, form the general data structure that can handle a general graph. Since a glycan structure holds specific chemical information for each node and edge, the basic data structure is extended in the glycomics package to encapsulate glycan-specific information. For example, GraphNode is extended by Monosaccharide and Substituent classes.
The Interface SugarSketcher runs in two different modes: "quick mode" and "normal mode" the application of which is illustrated in the "results" section. In either mode, a collection of pre-built structures can be used as a template amenable to extension. This selection currently mirrors the trend in overrepresentation of animal N-and O-linked carbohydrate moieties in glycoproteins in recent databases and in the literature (except for CSDB  [16] ). All N-and O-linked core structures reported in  [9]  are listed. Additionally, a shortlist of glycan epitopes is provided. For example, to draw a di-antennary core-fucosylated N-linked structure, an N-linked core-fucosylated template can be loaded and the first antenna added manually. Then this antenna is selected and with the copy-paste functionality available on right click, the second antenna can be pasted to complete the structure.
A collection of glycan structures is already encoded in the library and can be directly used to create sugar objects. The input-output section of the library allows the import and export of glycan sequences. Since we are mainly using GlycoCT encoding  [17]  across the tools in Glycomics@ExPASy  [18] , the first implemented parser/writer implements the GlycoCT standard. Parsers and Writers are completely decoupled from the data structure allowing the implementation of adapters for any glycan encoding format. The way the library is built and the Apache license 2. 0 (https://www. apache. org) allow any research group to contribute with their specific import and export adapters. The core library has been designed to facilitate external contributions and encourage further extension. Unless the Graph class, the rest of the code follow the ECMAScript6 (ES6) standard and comes with unit test.
The Interface SugarSketcher runs in two different modes: "quick mode" and "normal mode" the application of which is illustrated in the "results" section. In either mode, a collection of pre-built structures can be used as a template amenable to extension. This selection currently mirrors the trend in over-representation of animal N-and O-linked carbohydrate moieties in glycoproteins in recent databases and in the literature (except for CSDB  [16] ). All N-and O-linked core structures reported in  [9]  are listed. Additionally, a shortlist of glycan epitopes is provided. For example, to draw a di-antennary core-fucosylated N-linked structure, an N-linked core-fucosylated template can be loaded and the first antenna added manually. Then this antenna is selected and with the copy-paste functionality available on right click, the second antenna can be pasted to complete the structure.
Mistakes can be corrected with the "Delete" button that has been enabled to prune the tree-like structure. Once the structure is completed, the depiction can be downloaded in in high-resolution SVG format. As an alternative to images, SugarSketcher provides an export of glycan structures to the GlycoCT machine readable format  [17]. Since several glycoinformatic tools provide the export in GlycoCT, SugarSketcher has an internal engine for parsing and displaying GlycoCT encoded structures. In that respect, GlycoCT encoded structures can also be imported and further modified in the SugarSketcher interface. We also added newly developed converters (unpublished) to extend export options to cheminformatics standards, namely SMILES, InChi (IUPAC International Chemical Identifier) and InChiKey, commonly adopted in major compound databases such as PubChem  [22]  and ChEBI  [23].
At this stage, this export is restricted to fully defined structures, i. e. , cannot be applied to structures with undetermined linkages or residues. The interface is built using HTML5, CSS3 and the JavaScript library D3. js. (V3). To handle all glycan information, the interface is connected to the core library (see Section 4. 1). SugarSketcher works with any browser that supports JavaScript (up to version ES6) and can be integrated in any website. In addition, it can be combined with web-based glycoinformatics tools, that accept GlycoCT as encoding format. For example, GlycoDigest  [24]  that simulates the digestion of glycans by exoglycosidases accepts the structure input in GlycoCT format. The same is true for several modern glycan databases, such as GlyTouCan  [25]  or CSDB  [16].
Funding: This work was supported by the  European Union   FP7 Innovative Training Network  [grant number  316929 ],  IB-Carb  (http://ibcarb. com/)and by the  Swiss Federal Government  through the  State Secretariat for Education, Research and Innovation SERI. ExPASy is maintained by the web team of the  Swiss Institute of Bioinformatics  and hosted at the  Vital-IT Competency Center. Architectural  and interface design testing was supported by  Russian Science Foundation , grant  18-14-00098. P. S. benefits from  RIAT-CZ  ( ATCZ40 ).
Corresponding URLs:[1]https://glycoproteome. expasy. org/sugarsketcher/;[2]http://glycan-builder. cermav. cnrs. fr/;[3]https://glytoucan. org/Structures/graphical;[4]http://csdb. glycoscience. ru/database/core/wizard. html;[5]http://www. glycoviewer. babs. unsw. edu. au/sequence_sets/add. xhtml;[6]http://glycam. org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1.
Acknowledgements We thank  V. Ryazanov ,  V. Gurtovoy ,  F. Debontridder  for fruitful discussions and advice. This work was supported by the  French National Agency for Research ANR  via grants MISTRAL and SUPERSTRIPES, and by the grant of the  Ministry of Education and Science of the Russian Federation , Grant No. 14. Y26. 31. 0007. V. S. S. acknowledges the financial support of the  Ministry of Education and Science of the Russian Federation in the framework of Increase Competitiveness Program of NUST MISiS  (No. K3-2017-042 ). M. Y. K. acknowledges the partial support by the  Program of Competitive Growth of Kazan Federal University. D. R. , V. S. S. , and D. I. K. acknowledge the partial financial support within the framework of the state competitiveness enhancement program of improving the prestige of leading Russian universities among world leading research and education centers.
The grey and white matter volumes are known to reduce with age. This cortical shrinkage is visible on magnetic resonance images and is conveniently identified by the increased volume of cerebrospinal fluid in the sulci between two gyri. Here, we replicated this finding using the UK Biobank dataset and studied the genetic influence on these cortical features of aging. We divided all individuals genetically confirmed of British ancestry into two sub-cohorts (12,162 and 3435 subjects for discovery and replication samples, respectively). We found that the heritability of the sulcal opening ranges from 15 to 45% (SE = 4. 8%). We identified 4 new loci that contribute to this opening, including one that also affects the sulci grey matter thickness. We identified the most significant variant (rs864736) on this locus as being an expression quantitative trait locus (eQTL) for the KCNK2 gene.
Materials-subjects The present analyses were conducted under UK Biobank data application number 25251. The UK Biobank is a health research resource that aims to improve the prevention, diagnosis and treatment of a wide range of illnesses. Between the years 2006 and 2010, about 500,000 people aged between 45 and 73 years old, were recruited in the general population across Great Britain. In this work, we used the data released on January 2018, consisting of 20,060 subjects with a T1-weighted MRI. We included 15,040 in our discovery sample and 5,020 in our replication sample. The subjects were separated according to their availability in NIFTI format. In January 2018, replication sample was available only in DICOM format. The imaging quality control (QC) was performed by UK Biobank following information described until and including the NIFTI conversion stage in  (Alfaro-Almagro et al.
2018). The UK Biobank genetic data underwent a stringent QC protocol, which was performed at the Wellcome Trust Centre for Human Genetics  (Bycroft et al. 2017). We restrained our analysis to people identified by UK Biobank as belonging to the main white British ancestry subset (using the variable in. white. British. ancestry. subset in the file ukb_sqc_v2. txt). Additionally, we excluded from our analysis subjects with high missingness, high heterozygosity, first degree related individuals or sex mismatches. In total 12,162 subjects in the discovery cohort and 3,435 subjects in the replication cohort passed the image processing steps and the genetic criteria filtering (see study design on Figure  S1 ). Both sets include approximately 48% of males and 52% of females.
Functional annotation of the loci To obtain information on the role of the region upstream of KCNK2, we investigated the gene expression QTL using the GTEx database [GTEx Analysis Release V7 (dbGaP Accession phs000424. v7. p2)] (GTEx Consortium 2017). We found that the variants rs864736 and rs14526008, which are in LD, are significant eQTLs for the KCNK2 gene expression, with significant multi-tissue meta-analysis RE2 (random-effects model 2)  (Han and Eskin 2011)  p values of 9. 7•10 -6 and 5. 7•10 -9 , respectively. Figure  S15  presents the effect size in various tissues of rs864736 allelic configuration on KCNK2 gene expression. Even though the association barely reaches nominal significance in single brain tissue due to low sample sizes (~ 80-140 subjects), it overall emphasizes strong effects across brain tissues.
Indeed, when this integrated model becomes available, running it on any given soil sample will require a tremendous amount of microscale information, which may take weeks or even months to gather, not to mention that the integrated model itself will likely take quite some time to run, which means that with this integrated microscale description of soils, only very few soil samples will ever be characterized and modeled. What we need instead is to come up with simple macroscopic measurements that can be carried out routinely. One way to find out what these macroscopic measurements should be is suggested in Figure  1. It consists of expanding the available experimental database by simulating many different scenarios under different conditions of microscale heterogeneity of the soils, and of their properties.