dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of the HBV preS1 region by NGS In this study, we explored a fragment of the HBV genome including the entire preS1 region and the N-terminal end of preS2. The HBV genotype-specific insertions and deletions occurring along the HBV genome change the nucleotide (nt) numbering of the fragment. Hence, the fragment includes nt positions 2844 to 56 (434 bp) in genotype A (genome size 3221 nt), positions 2838 to 56 in genotypes B, C, D, E and H [434 bp in B, C, and H (genome size 3215 nt in all of In order to simplify the variations due to HBV genotype, the numeration of aa positions in both domains and their consensus sequences is presented according to genotype D (reference sequences obtained from GenBank, accession numbers provided in Supplementary Table  1 ). Asterisks indicate positions where the wild-type aa varies according to HBV genotype.
Briefly, molecular amplification was performed by nested PCR. In the final PCR products (amplicons), the technique incorporated M13 universal adaptor sequences (forward and reverse), a unique identifier that enabled grouping of the sequences derived from each sample [multiplex identifier sequences (MID)], and sequences A and B (adaptors for the elements of the UDPS system). The amplicons were purified and pooled at equimolecular concentrations. The pool was UDPS-analyzed following the manufacturer's protocol. The sequencing data underwent a bioinformatics filtering procedure based on an in-house-developed pipeline  [28]  , with all computations done in the R environment and language  [29]. UDPS reads (sequences from each individual amplicon) were demultiplexed according to their MID sequence, and primers were trimmed.
The first step of this analysis was to classify the haplotypes from each patient according to their HBV genotype by phylogenetic analysis in order to differentiate sequence variations from genotype-related polymorphisms. First, we selected 86 full-length HBV genome sequences representative of HBV genotypes A to H, obtained from GenBank (accession numbers in Supplementary Table  1 ) and extracted the region from nt 2837, 2838, or 2844 (depending on viral genotype) to 56. We then determined the maximum genetic distances between sequences from the same HBV genotype in this region and the minimum genetic distances between sequences from different genotypes, in order to set a Positions where the wild-type aa varies according to HBV genotype have been highlighted in bold and red. aa: Amino acid; NTCP: Sodium-taurocholate cotransporting polypeptide.
322 and aa = log2 (20)-4. 322 = 0. These calculations in the regions of NTCP interaction (47 aa) and virion morphogenesis (22 aa) were also represented as sequence logos created using the R language package, motifStack [33]. The statistical and bioinformatics methods used in this study were reviewed by Dr. Josep Gregori from the liver disease-viral hepatitis laboratory (Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron), CIBERehd and Roche Diagnostics SL.
preS1 variability and/or conservation The NTCP-interacting domain (47 aa) and virion morphogenesis domain  (22 aa)  were analyzed in the 18 patients in group A with viremia levels > 4 logIU/mL. In total, 118779 quality-filtered sequences were obtained from the samples, and a median of 5546 (1903 to 13126, interquartile range, 3585) sequences containing both domains were analyzed per sample. In general, aa residues from the NTCP-interacting domain were conserved within each HBV genotype among the different viral genomes examined. Only 12 of 47 (25. 5%) aa positions showed genotypeunrelated changes occurring at > 1% of the HBV quasispecies, a somewhat lower percentage than in the virion morphogenesis domain (7 of 22 aa positions, 31. 8% with genotype-unrelated changes) (Figure  2B ). Interestingly, according to the consensus sequences of HBV genotypes A to H of both domains, obtained from the 86 full-length HBV genome sequences from GenBank, the virion morphogenesis domain had a lower percentage of aa positions with genotype-associated changes (viral polymorphisms) than the NTCP-interacting domain (6 of 22, 27.
Moreover, this latter domain is reported to be highly conserved among Orthohepadnavirus  [31]  , a concept that is supported by the lower percentage of HBV genotype-associated viral polymorphisms in the virion morphogenesis domain than in the NTCP-interacting domain (27. 3% vs 34%, respectively) in consensus sequences of genotypes A to H obtained from the 86 HBV genome sequences downloaded from GenBank. However, in the present study, HBV genotype-unrelated changes above 1% of the quasispecies were found in 25. 5% of NTCP vs 31. 8% of C-terminal positions, with both domains being most highly conserved in genotype C and most highly variable in genotype E (a limited finding because this high variation was observed in 1 of only 2 genotype E patients included). Thus, while the NTCP-interacting domain seems to be more highly conserved within each genotype, the C-terminal virion morphogenesis domain seems more highly conserved between different HBV genotypes.
Research methods We performed two main analyses in serum samples from 246 individuals in 3 groups: patients with CHB, patients with resolved HBV infection, and HBVuninfected individuals. First, the variability/conservation of aa sequences in the NTCP-interacting domain was analyzed and compared to that of a highly conserved preS1 C-terminal domain associated with virion morphogenesis. Comparison between the NTCP-interacting domain and the highly conserved virion morphogenesis domain gave an idea of the magnitude of sequence conservation of the former. To perform this analysis, we developed a highthroughput protocol based on NGS. The raw sequencing data obtained underwent a bioinformatics filtering and analysis procedure based on an inhouse-developed pipeline with all computations done in R environment and language.
Research results High-throughput NGS analysis yielded viral sequences for most HBV genotypes (A to F and H). In general, the NTCP-interacting domain showed a high degree of conservation, which depended on viral genotype, particularly the sequence between aa 9 to 21. In comparison to the virion morphogenesis domain, the NTCP-interacting domain showed a smaller percentage of HBV genotypeunrelated changes, but greater variability between different HBV genotypes, according to consensus sequences from the GenBank patterns of genotypes A to H. Interestingly, proline residues showed a high degree of conservation in both domains, and serine residues were also particularly conserved in the virion morphogenesis domain, where changes above 1% of the quasispecies were always to potentially phosphorylatable aa.
The award-winning media artist Geert Mul (the Netherlands, 1965) has been making computerbased artworks for over twenty-five years. A large portion of his oeuvre, and his more recent work in particular, relies heavily on existing images, often sourced online. With the help of image analysis software, Mul reworks the pictures into new combinations, attracted by the unexpected results that algorithmic operations produce, and the revelatory potential they hold. The artist refers to this work as 'data-based art' -a term revealing not only of his own process as a maker, but also of his take on how people today engage with the world around them and make sense of it. At the conclusion of a large-scale retrospective of his work, Eef Masson spoke with him about some of the key ingredients of his visual practice and the inextricable relations between them: information, databases and collections; randomness and rules; and crucially, makers and audiences or users.
Mul has produced computer-based art throughout his career, which now spans more than twenty-five years. His work comes in different shapes: printed, but also sculptural; installed and performed; self-contained and interactive. His pieces of the past fifteen years in particular also share a key feature: very often, they make use of existing images, reworked into new combinations. Since the early 2000s, the artist has been compiling databases of pictures; first his own, but later also repurposed ones, and increasingly sourced online. Today, he considers those compilations so central to his practice even, that he no longer thinks of the computer but rather of the database as his main medium. He uses the amassed images as starting points for a process involving what he calls 'pixel statistics': a form of advanced image search that allows him to select and (re)combine pictures on the basis of visual resemblance.
3 age 1. Geert Mul  In February of last year, Mul and I took part in an expert meeting organized by Utrecht University (the Netherlands) on artistic and creative forms of data visualization. 4 On this occasion, we engaged in a public exchange on the role of collections and databases in his visual art practice over the years and on his approach to data visualization generally. The talk coincided with the conclusion of a large-scale retrospective of his work, entitled Match Maker, at the municipal museum in Schiedam (also in the Netherlands). 5 The exhibit established the historical significance of this work, demonstrating how over time, it transformed along with the technological developments that it also responded to. Taken together, the works presented attested to a persistent fascination with the possibilities of (visual) recombination -specifically in a formalized, rule-based manner.
Records can be consulted either on site, sometimes in their original form, or remotely, as ( digital) copies, and for various reuse purposes. In most of these cases, users make sense of the overarching theme of a given exhibit. He or she can make different selections, or use the same objects but order them differently in order to tell different stories. A database is comparable to a collection in that it contains discrete objects; however, those objects are not physical but consist of sets of features, expressed mathematically. In addition, retrieval and display do not happen in space but on a flat screen. Like curators, administrators of databases can select, order and reorder the objects within them. However, they can do so at a much higher speed (over 10,000 times a second) and on a much greater scale.
In addition, they can copy and paste -or in other words: manipulate the composition of the databases' contents. Moreover, forms of interactivity can be built in. In the comparison with museum curation, this entails a very different sort of model for the disclosure, or exhibition, of a given set of data or information (a given I also explore in some of my work). 6  light of this difference in generative properties, ingesting a (selection from) an archive or collection into a database inevitably entails a number of fundamental transformations. But in addition, I also tend to repurpose the data I receive. For instance, objects in museum collections often come with metadata, as retrieved from institutional catalogues. In the interactive installations W4 and Horizons, I used some of those labels in selecting images for recombination and visualization.
In the latter case, for instance, I've only pulled those works from the collection that were associated in the museum's database with the keyword 'horizon'. In addition, I also made use of information about the height of this horizon (in a painting's composition), by way of positioning works in relation to each other. In W4, the selection I do is explicated in the work's title, which identifies the fields I used for matching: the 'what', the 'who', the 'when' and the 'where' of the repurposed items. EM: So how would you say does working with metadata in this case affect your process? GM: Essentially, of course, data and metadata are made up of the same 'stuff': they're all strings of numbers. Calling them by different names imposes a hierarchy on them that I prefer to ignore. In my work, I approach data and metadata in the same way: as numbers that can be analysed, and used for purposes of comparison and recombination.
Algorithmic Art EM: Let's talk a bit further about the role of algorithms, in your art but also in your production practice. You just mentioned that in repurposing existing collections, you can sometimes rely on labels that others have assigned to objects, prior to your reusing them. But you often also source images elsewhere, recording them off air or scraping them online. While such images of course have technical specifications, embedded in their so-called 'metadata', they generally have not been subject to re-interpretation -whether by institutional cataloguers, or social taggers -in the same way that annotated collection objects are. Therefore, they lend themselves particularly well to automated image analysis, comparison, and recombination. These are procedures you often use; for instance, in the installation Match of the Day (2004-present, made up of images recorded from international satellite television channels) or the live performance Big Data Poetry (2013, with sound artist Michel Banabila, that makes use of downloaded images).
Can you explain your process further, zooming in specifically on how works that heavily rely on quantitative operations -calculations, measurements -of purely formal image features, can result in products that seem highly meaningful to human observers? Specifically, I am interested here in your role as a maker: your 'editorial intervention', so to speak, in the 'matching' that the computer does. GM: What I like about Match of the Day is that it clarifies some of the relations in my work between images and data, and databases and visualization. But also, between technology (or automation) and meaning -or how such meaning is attributed. As you mention, Match consists of televised images. But in the first instance, the work treats those not as pictures but as mere data. The images are randomly recorded from about thirty international satellite television channels.
GM: The poetry idea is one I have entertained for a while -but recently, I've come to find it particularly useful in discussing my work with a broader audience. During the Schiedam retrospective, for instance, I've regularly taken groups of visitors on guided tours through the exhibit and in doing so, I've increasingly relied upon this metaphor to clarify my approach. A key motivation here was that it could help me subvert the notion that because I work with computers, I am concerned exclusively with the recent or 'new': with new images, new events, new ideas or new perceptions. On the one hand, of course, the database -my main medium -roots my work in the hereand-now, in this particular epoch. For me, the database is not just hardware or software or a combination of those, but a cultural form and a way of seeing things.
It is a mode of perceptionand importantly, one that is dominant in this day and age. Throughout history, we've been able to perceive the world by virtue of the media that we had at our disposal and this shaped our perceptions. Depending on the media available, we've conceived of the world as an organism, a machine, or a brain; of late, we've turned it from a machine into a computer or database. Artistic production illustrates this phenomenon in compelling ways. So, if I call my work 'data-based' art, I do so not only because it relies on data, but also because it explores, and at the same time gives expression to, a kind of data-based mode of thinking that is specific to the here and now, and that affects the way we see the world, comprehend it, and render it. 7 But on the other hand, my algorithmic method also fits into a lengthy tradition.
Obviously, technological media lend themselves to this sort of combinatory practice particularly well. One of the key operations that databases enable is the retrieval of the data within it. Such retrieval involves a (re)combination, in an infinite -or at the very least humanly unknowable -number of aggregations. But databased art also vividly illustrates how closely entwined technology and 'content' are. Considering how much the appearance of a work is determined by the execution of a specific set of rules, which are a function of the technology, the two cannot really be disentangled. This serves to reaffirm my perception that in my work, the database is more than just a tool: it is my medium, in that it shapes every aspect of the ' content' with which it combines to form a 'work'.
Exploring Sites of Information EM: To conclude our conversation, I'd like to return once more to the topic we started off with: the image databases that you subject to acts of 'pixel statistics' when making new work. In doing so, I want to consider this work from the perspective of data visualization. In labelling your pieces as 'visualizations', we arguably align your methods with those in other fields where information in digital form is analysed and visualized -whether for economic purposes for instance, or scientific or scholarly ones. You've previously mentioned that you think of yourself as an artistic researcher, and you've compared yourself to a poet. In doing so, I would say, you implicitly distanced yourself from what practitioners in those other fields do. But we cannot ignore that there is also a certain measure of overlap -especially with the kinds of visualization practice that involve the crunching of abstract data (extracted from image files) but generate results that have a visually recognizable form.
An example here would be instances of 'cultural analytics', as practiced among others by the new media scholar Lev Manovich in the context of his 'lab' by the same name. 12 Not only the However, your practice also diverges in important ways. Most significantly, I would argue, in terms of how you interpret or value both the products of algorithmic operations, and the data they serve to recombine -or more precisely, the cultural objects that those data in turn reference, or even constitute. In the first place, because the visualizations you produce, while sometimes relying on very similar datasets, were never intended as a basis for making scholarly claims. Like the practitioners of cultural analytics, you may be curious to discover large-scale patterns or developments in art or popular culture -but not in order to make empirical statements about them, using computational techniques.
Depending on the type of site I am concerned with in each case -a city, an archive, a database -this information either takes on a material form (and is spatially organized) or is immaterial (and arranged according to some other logic). In conceptualizing how I explore such sites, I take inspiration from the work of the philosopher Guy Debord, co-founder of the Situationist International [a Paris-based, Marxist-inspired movement, involving primarily avant-garde artists and political theorists, that was active between the late 1950s and early 1970s -EM]. The situationists, and Debord in particular, laid out a programme for a so-called 'psycho-geography', which involved procedures for exploring urban environments in playful but also unbiased ways, unaffected by one's pre-existing interests or prior knowledge of the sites in question.
15 The dérive, in this context, is a type of walk -literally 'drift' -that is both arbitrary (for instance, in that one can start it at a random point in the city) and highly structured (in that one follows a predetermined pattern, taking specific turns at a given rate). In my work, I basically apply the logic that structures Debord's city walk to explorations of non-material sites, such as archives and databases. Essentially, the dérive is a very simple algorithm: a mathematical rule, executable also on large accumulations of data, for the purpose of analysing them. Much like in the case of the urban drift, the exploration here generates different outcomes depending on one's particular point of departure within a dataset. Likewise, each outcome is equally valid, as each 'drift' through the data is equally likely to reveal some the specific 'substance' of a particular cultural site -whether this site is a city, or, as in the case of a work like Match of the Day, the domain which, at a specific point in time, we referred to as 'satellite TV' (that is, in the period between 2003 and 2006).
Acknowledgements Authors are grateful to  Dr. Jörn Winter ,  Dr. Ansgar Schmidt-Bleker ,  Dana Sponholz ,  Melanie Schulz  and  Julia Koch  for their help. This work was funded by the  German Federal Ministry of Education and Research (BMBF)  (Grant No. 03Z2DN12 & 03Z22DN12 ), as well as by the  Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern  (Grant No:  AU 15 001 ).
4 ; the complex modulus (G*) is shown in Supplementary Fig. 4. The data suggest gel-like properties for the neat callose solution as the phase angle remained almost independent of the frequency. This is also reflected by the overlap in the storage and loss modulus at low frequency for 100% callose (Fig. 4b ). Steady state viscosity of the mixtures was measured as a function of shear rate at different temperatures. Flow curves demonstrate mostly Newtonian behaviour and a very weak shear thinning, which is more pronounced for 100% callose solutions, likely as a consequence of high molecular weight chains' alignment in the flow (Supplementary Fig. 5 ). The Cross model (Eq. 1)  44  was used to fit the data and calculate the viscosity of the samples at zero shear rate: η ¼ η 0 þ η 1 αγ n 1 þ αγ n ð1Þ where γ is shear rate, ƞ 0 is zero shear rate viscosity, ƞ ∞ is the viscosity at infinite shear rate, n is the flow index and α is the consistency index.
The measurements were carried out in a Diff50 diffusion probe (Bruker Biospin), which can generate a field gradient of up to 20 T m -1. Before each measurement the calibration of the gradient field strength was confirmed by determining the diffusion coefficient of water at 20. 0 ± 0. 1 °C, this has the value of (2. 03 ± 0. 01) × 10 -9 m 2 s -1. The sample environment temperature was also confirmed, by experimentally determining the temperature dependence of the diffusion coefficient for water and comparing those results to data published by Holz et al. 6  To reduce the effect of convection on our results we followed the advice of Annat et al. 6  by keeping NMR tube sample depths to less than 1 cm. The uncertainty in the obtained diffusion coefficients is estimated to be less than 3%. A stimulated echo pulse sequence with bipolar gradients was used, in which the attenuation of the signal intensity follows the following Eq.
66 µM) solution of aniline blue fluorochrome in a 50 mM K 3 PO 4 buffer under vacuum (60 MPa). Direct Red 23 was then added as described above to the aniline blue solution and allowed to stain 2 h more. Roots and leaves were then mounted in a 1:1 vol solution of AF1 antifadent (Citifluor, USA) and 50 mM K 2 HPO 4 or K 3 PO 4 buffer, and subsequently imaged by confocal laser scanning microscopy (Zeiss LSM700). Aniline blue staining was imaged with a 405 nm solid state laser, whose emission was recovered with a short pass 490 nm filter, and Direct Red 23 staining was imaged with a 555 nm solid state laser, whose emission was recovered with a long pass 560 nm filter. Pictures were processed using the deconvolution software Huygens and ImageJ 1. 51 s (for z-stacks projections and contrast). Adobe Photoshop CS5 was used to create the montages.