dataesr/scientific-paragraphs-categorization huggingface dataset:
In other words, deletion on some an identical distance. threads is more prominent than on others. We continue by calculating the Wasserstein distance metric between the observed and the random distribution, with an obtained distance of 0. 036 on the MMC dataset and a distance of 0. 010 on the STY dataset. Similar to the previous measurements on the percentage of users' deleted content, a stronger difference between the two distributions is again observed on the MMC dataset, showing the deletion on that dataset to be less random. Furthermore, the distances obtained on the thread-dependent distributions are almost half the size of the distances calculated on the userdependent distributions, showing that comments of specific users are deleted more often than comments on specific threads, which is an interesting result.
027 and the p-value of 1. 448 * 10 -199 on  the MMC dataset, while the test statistic on the STY dataset is 0. 017 and the p-value 3. 26 * 10 -39. The differences between the observed and the random distribution are still highly significant, but less than with the other analyses. Again, the STY dataset appears more random-like than the MMC dataset. We double-check these observations by calculating the Wasserstein distance between observed and random distributions. On the MMC dataset the distance is 0. 018, while on the STY dataset it is 0. 011. On the MMC dataset this is the smallest distance measured, while on the STY distance this distance is similar to the one calculated on the thread-dependent distribution. The distance to a random distribution is, again, smaller on the STY dataset than on the MMC dataset.
Discussion Regarding the three analyses performed, namely the analysis of content deletion among users, threads and relative locations in threads, we can conclude that on the MMC dataset all the distributions are further away from random distributions than on the STY dataset, hinting at a more careful supervision of comments on that dataset. However, we must be careful about drawing such a conclusion because a less random behavior might also point towards targeting specific users (e. g. , previously misbehaving users), threads (e. g. , threads on specific topics) or locations of the comment in the thread (e. g. , the beginning of the thread). With these three levels of analysis we have shown that the user-dependent distribution of deleted comments is the least random, followed by the thread-dependent distribution, with the location of the comment in the thread being closest to random.
Data availability Both datasets are published on the CLARIN. SI repository with all the metadata pseudoanonymised, and the text encrypted via a simple character replacement method using a random, undisclosed bijective mapping to comply with the terms-of-use of our data providers as well as to mitigate propagation of inappropriate content. The Slovene dataset, published together with the baseline model described in the following subsection, is available from http://hdl. handle. net/11356/1201, while the Croatian counterpart is available from http://hdl. handle. net/11356/1202.
Model availability Given that the distributed datasets are encrypted, because of which only in-vitro experiments on inappropriate content identification can be run, but the final systems cannot be applied on real data, we have also published baseline models trained on the non-encrypted data. While these models are capable of identifying potentially inappropriate content, by sharing them we do not propagate inappropriate content above the token level. For building the baseline models, we split each dataset into training, development and testing portions in a 8:1:1 distribution, and trained, tuned and evaluated fastText  (Joulin et al. , 2016)  classification models on that data split. The published fast-Text models were trained on the full datasets. When splitting the data into train, dev and test, we randomly shuffled on the thread level, ensuring that there is no spillover between threads, i.
e. , text representation procedure. By adding character n-grams of length 3 to 7 we lower the error rate on both datasets by 18%. Adding word n-grams longer than 1 does not have a positive impact on performance of fastText. Optimizing the number of epochs has a slight positive impact as long as other hyperparameters are kept default. If we combine optimal character ngram and epoch hyperparameter values (last row in Table  3 , there is no significant difference to using optimal character n-grams only. This is why we decided to use for our final setting all default hyperparameters, except for the character n-gram lengths that we set between 3 and 7. We evaluate our final system setting on the test set and obtain a ROC AUC result of 0. 794 for the MMC dataset and 0. 793 for the STY dataset. These results are more than half way from random to perfect, which is still far from satisfying.
Conclusions In this paper we have introduced two new large on-line news comment datasets annotated for inappropriate content by the content providers for Slovene and Croatian, languages typically rarely represented in similar datasets, making them all the more valuable for the research community. We have performed a small manual analysis of the kinds of comments that get deleted in each of the datasets. The Croatian deleted comments contain more severe types of inappropriate content, such as insults, as well as more swearing. The Slovene ones, on the other hand, are more covert, formulated as irony, and are frequently aimed at the broadcaster or are off-topic, which indicates differences in the policy of handling user comments by the two media outlets. The initial statistical analysis of the distribution of filtering among users, threads and locations in threads, has shown that all the distributions are less random on the MMC dataset than on the STY dataset, which is probably caused by more constant and vigilant moderation on the MMC RTV portal.
Regarding the three levels of analysis, we showed that the distribution of deleted content among users is the least random, followed by the distribution of that content among threads, with the location of the deleted content being closest to random. This shows that specific users seem to be the most deleted, followed by specific threads, with specific locations in the thread being least prone to deletion. Finally, by building baseline models on the new datasets, we have shown that fastText classifiers can be improved most easily by adding character n-gram information to the text representation. The obtained results are promising, but still far from production-ready, at least for most usages. However, we have published not only the datasets with metadata pseudo-anonymised and texts encrypted, but also the baseline models trained on the nonencrypted full text of each dataset.
Genomic Characterization and in silico Typing Mucoidy and mucoviscosity are typically conferred by expression of extracellular polysaccharide materials. To identify and characterize potential polysaccharide loci, genome sequencing was carried out on both short-read and long-read platforms as described in "Materials and Methods" section. From a hybrid assembly, three contigs were obtained, the largest of which was 4. 72 Mb in length with 27× coverage. The two smaller contigs were 84,087 bases and 50,597 bases long, with coverages of 43× and 64×, respectively. Each of these were resolved into circular contigs by use of Circlator software  (Hunt et al. , 2015). The assembled genome was confirmed as E. coli through sequence comparison (BLAST) of the entire chromosome sequence. Assembled contigs were submitted to the PlasmidFinder1.
3 database  (Carattoli et al. , 2014)  which returned matches (>98%ID) for plasmid replicons FIA, FIB, and IncQ1 to the 84,087 base contig and a 100% match for IncFII to the 50,597 base contig. Submitting contigs to the ResFinder tool  (Zankari et al. , 2012)  which identified blaCTX-M-14 on the larger plasmid and blaTEM-1, aph(3 )-Ib/strA, aph(6)-Id/strB, aph(3 )-Ia, sul2, and tetA(B) were carried on the smaller plasmid. Assembled sequence indicated that catA1 was chromosomally encoded and that this isolate is also resistant to quinolones (nalidixic acid, enrofloxacin and ofloxacin) via substitutions in GyrA (S83L and D87N) and ParC (S80I). This in silico characterization of resistance genotype corresponded with previously reportedly resistance phenotype  (Dahmen et al. , 2013)  and specifies 26561 as a multidrug-resistant (MDR) isolate as defined by  Magiorakos et al.
The genomic region of 26561 from galF to ugd (∼24,500 bp) was used to search NCBI nucleotide collection and whole genome shotgun contigs (WGS) databases (last searched November 2017) resulting in no extensive matches to E. coli (40% coverage at most) yet identifying four matches to Klebsiella with >90% identity over >90% of sequence. Hence, this CPS locus is rare in E. coli and appears to have been a relatively recent horizontal acquisition of capsule from Klebsiella. The matching Klebsiella capsule typed as K10 and the extent of identity between the 26561 locus is presented in Figure  3. The terminology KP_K10 will be used to distinguish from E. coli K-types.
O-Antigen Locus Submission of the complete 26561 nucleotide sequence to the SerotypeFinder database returned a result of serotype O89 by matching of the wzt and wzm genes by 93. 49 and 94. 10% identity, respectively. In the region encompassing galF-gnd, the O89 locus is highly similar to O101 and O162 loci  (DebRoy et al. , 2016 : Iguchi et al. , 2015)  and the wzm and wzt sequences of 26561 show 92. 6% and 93. 4% identity, respectively, to those of both O101 and O162. Locating the chromosomal position enabled comparison of the O-antigen genomic region of 26561 to those in the reference sequence for the O89-serotype locus. From an initial inspection of the 26561 locus in Artemis, the first nine genes (from galF) conformed to the published composition of the O89 locus, although we noted that the 26561 sequence retained a partial wcaM (the final gene of the colanic acid locus) and the gnd gene was severely truncated (henceforth gnd#), both being disrupted by insertion sequences.
To examine differences further, the whole genome reference sequence for O89 strains (strain NCTC9089; European Nucleotide Archive SAMEA3403041) was aligned with the corresponding region in 26561. From the alignment (Figure  4  and further elaborated in Supplementary Presentation 1) it became clear that there were additional differences between these loci. Specifically, the two genes preceding gnd#, annotated as a methyl-transferase and a glycosyl-transferase, share only 47% and 42% amino acid identity to their counterparts in NCTC9089 whilst BLAST searches with the 26561 sequences show 100% matches to other proteins with the same function in the NCBI database. Closer inspection of the protein annotated as Gnd# in 26561, indicated that it is only 33 amino acids long, compared to 468 residues in the reference.
Expression of Polysaccharide Biosynthetic Proteins The atypical organization and location of polysaccharide biosynthetic loci led us to conjecture whether LPS and CPS were expressed. Corroboratory evidence was sought in a protein expression dataset from 26561 (to be reported in full separately) and direct analysis of cell-associated polysaccharide components (see following section). As described in "Materials and Methods" section, a Tandem Mass Tag (TMT) mass spectrometry approach was used to assign and quantify protein expression. In matching peptides to the 26561 protein database, we used only those which matched uniquely to a given protein such that paralogs (e. g. , two GalF variants) could be distinguished from each other. This proteome analysis detected a total of 53% (2451 of the 4577) potential proteins encoded by 26561 genome, providing coverage similar to the upper range in other LC-MS/MS analyses of unrelated E.
coli clinical isolates (e. g. ,  Pettersen et al. , 2016 Pettersen et al. , , 2018;; Møller et al. , 2017). In E. coli 26561 we see that a partial wcaM (the final gene in the colanic acid locus) is present but interrupted by an insertion sequence at its 5 end (pink arrow: IS-1). The furthermost match is to the beginning of the gnd gene. The protein coding sequences for the two genes preceding gnd, a methyl transferase and glycosyl transferase, are 47% and 42% identical, respectively, but are a 100% match to other proteins with the same function in the NCBI database. The genes which flank the insertion sequences marked IS-1 and IS-3 in E. coli 26561 are nfsB and ybdK. The bottom sequence illustrates that these genes are usually separated by two small hypothetical genes, ybdF and ybdJ, in E.
coli K12_MG1655 (ybdJ is not labeled in the diagram). Evidence for expression of both capsular and O-antigen loci from the proteome dataset is convincing; as illustrated in Figure  5A , reporter intensities for the data as a whole span ∼5 orders of magnitude (range 3. 1 × 10 6 -3. 6 × 10 11 ), with the average value for CPS (Figure  5B ) and O-antigen (Figure  5C ) biosynthesis proteins (9. 4 × 10 9 ) being toward the upper end of this range. Of 38 coding sequences between the two loci, 11 are not detected as proteins. Of these, two are annotated as 'hypothetical' proteins (1664 and 3126), four are transposon proteins  (1665, 3141, 3129, and 3125)  and two are known to be truncated (3140 -wcaM and 3130 -gnd). Of the three that remain, (1667 -wzy, 1678 -AT, and 3135 -wzm) two are small transmembrane proteins which are known to be difficult to identify as they may be poorly solubilized and digested in the sample preparation stages.
Tandem Mass Tag data were also examined for evidence of expression of G4C (O-antigen capsule) system which comprises seven gene products and has some similarities to G1C. Of the G4C proteins, GfcE, Etp, and Etk (which are paralogous to G1Cencoded Wza, Wzb, and Wzc, respectively) were detected by only 3, 2, and 3 peptides. This observation suggests that G4C makes negligible -if any -contribution to the mucoid phenotype of E. coli 26561 despite this locus being intact. Hence, we can postulate that O-antigen and CPS biosynthetic loci are functional and are presumably responsible for the observed mucoid or mucoviscous phenotype. We further investigated expression of LPS and CPS by several strains.
Characterization and Distribution of O89 O-Antigen and G1C Loci Among Representative Complete E. coli Genomes An initial BLASTp search (December 2016) of the NCBI nr database with the 33 amino acid Gnd# sequence of 26561 returned only one 100% match with the human intestinal isolate E. coli MS-175. This had been assembled by short read data which made it difficult to accurately compare to 26561. A contemporaneous search with the corresponding nucleotide sequence returned five 100% matches (to strains Sanji, H8, Y5, 6409, EC590) which had been sequenced by PacBio to generate complete genomes. Genome sequences were downloaded and submitted to SerotypeFinder: in each case the O-type result returned was identical to that obtained for 26561, i. e. , serotype O89 with 94. 10% ID to wzm and 93. 49% ID to wzt indicating that the 26561-like O89 locus may be present in these strains.
Characteristics of LPS and CPS Expressed in 26561 and Other O89 E. coli Strains Given the atypical organization of O-antigen and capsular loci, and the novel combination of O and K types in E. coli 26561 and other O89m strains for which complete genomes are available, we speculated whether both LPS and CPS were produced by strains of this type. As indicated above, proteomics identified biosynthetic proteins for both loci in prototypic strain 26561. We sought corroboratory evidence by examining cellular and extracellular polysaccharide production by a panel of O89 strains. Specifically, we surveyed genome sequences from our strain library and identified in our collection five additional strains all possessing the same composition of O89m genes as 26561; none of our isolates possessed a conventional O89 locus (summary information for all O89 and O89m strains is provided in Supplementary Data Sheet 1).
Characterization of Clade of O89-and G1C-Positive E. coli Strains Reports on E. coli O89 are rare, therefore we conducted a survey (March 2018) of publicly available E. coli genome sequences using nucleotide sequences representing entire O-antigen loci from 26561 and NCTC9089 as well as individual coding sequences and protein sequences from these strains. From this survey, a total of 212 E. coli complete or WGS genomes were identified (Supplementary Data Sheet 1). Surprisingly, among these genomes, only ten (including NCTC9089) possessed a region encompassing all 20 genes from wcaM to ugd whilst the remainder terminated with a truncated gnd. Interestingly, the 26561 region encompassing galF-gnd also matched at 99% identity over 99% of the sequence to a genome identified as Citrobacter braakii strain FDAARGOS_290 (GenBank accession CP022049.
Further exploration by in silico typing of O89 strains identified phylogenetic relatedness based on in silico prediction of STs -157 of 202 O89m strains were identified as members of the ST10 complex (encompassing ST10, ST167, ST617, ST34, ST44, ST209, and ST48; full information provided in Supplementary Data Sheet 1). Despite close phylogenetic relatedness, these O89m isolates originate from disparate geographic settings and include commensal/fecal isolates as well as clinical isolates. Where information is available regarding clinical status, 37. 5% (63 of 168) were assigned an extra-intestinal origin (most frequently blood, urine, and mastitis with ten further sites of origin). Since prototype strain 26561 was originally identified as ESBL-positive, multidrug resistant strain, all O89 strains were assessed for carriage of transmissible resistance factors through ResFinder.
Interrogation of this locus identified it as encoding a G1C which was distinct from the prototypic K30 G1C. Consistent with previous reports  (Amor and Whitfield, 1997) , our initial survey indicated that G1C-positive strains were commonly O9 (32%) or O8 (16%) and a further 11% of strains comprised other O-types or for which O-type could not be categorized. Significantly, the most frequent O-type associated with G1C was O89m which represented 41% of all G1C-positive E. coli strains. Searching the sequence databases with the nucleotide sequence of the 26561 G1C locus matched with Klebsiella capsule type KP_K10. Intriguingly, many of the O89m genomes matched with high confidence to Klebsiella capsule types with various combinations of insertion sequences bracketing wzi to ugd. Among O89m strains, the G1C gene cluster (regardless of K-type) was located between yegH and his genes, the region which is normally considered the location of colanic acid together with O-antigen genes or G1C together with O-antigen genes (as exemplified by E.
coli strain 26561 to an extensive genomic survey identified that E. coli serotyped in silico as O89 are more frequently O89m than conventional O89 serotype. Extensive population genomic analysis of O89m/O89 strains will be undertaken and reported separately. Only O89m strains also possessed G1C whereas O89 strains possessed colanic acid, consistent with the mutual exclusivity between these polysaccharide loci. As a group, O89m strains tended to lack conventional virulence factors. Appraisal of available metadata (summarized in Supplementary Data Sheet 1) indicated that a substantial number of O89m strains have been isolated from invasive infections (including urinary tract, pleural cavity, bloodstream, mastitis, wound) or as antibiotic-resistant strains thus circumstantially aligning these O89m:G1C strains to ExPEC pathotype.
Genome Sequencing, Assembly, and Annotation Short-reads Assembly: DNA was extracted from an overnight culture of Escherichia coli 26561 using MasterPure TM DNA Purification Kit from Epicentre. Sequencing was performed by Glasgow Polyomics using the MiSeq platform. Raw data was assessed with FastQC 1. Reads were pre-processed using MyPro  (Liao et al. , 2015)  prior to assembly using SPAdes 3. 1. 1 (Bankevich et al. , 2012). The quality of the assembly was 1 http://www. bioinformatics. babraham. ac. uk/projects/fastqc evaluated using Quast  (Gurevich et al. , 2013). The assembled genome consisted of 96 contigs (NG50 141, 083) with an average coverage ×15 and total length of 4. 76 Mb. Long-reads Assembly: DNA was extracted from a separate culture of strain 26561 and sequenced using the PacBio platform.
Pbh5tools from Pacific Biosciences was installed locally and bashh5tools used to extract subreads from the bax files in fastq format. These reads were used in combination with the raw sequence data from the MiSeq platform mentioned above [which was this time pre-processed using ngsShoRT  (Chen et al. , 2014) ] to produce a hybrid assembly using SPAdes 3. 9. 1. Assemblies were annotated using Prokka 1. 12  (Seemann, 2014)  and visualized in ARTEMIS. Coding sequences in regions of interest were manually checked using BLAST and corrected where appropriate. Visualizations of alignments between 26561 and other genomes were produced using ARTEMIS  (Rutherford et al. , 2000)  and EasyFig 2. 2  (Sullivan et al. , 2011). Escherichia coli 26561 was previously sequenced in short reads format and deposited at NCBI (BioSample SAMN04334740; GenBank assembly accession GCA_001575995.
Protein Identification and Quantification MaxQuant 1. 5. 7. 4  (Tyanova et al. , 2016a)  was used to identify proteins from the raw MS files. The 4577 protein sequences from our 26561 hybrid assembly, together with the contaminant sequences provided by MQ, were used to form the search database. Modifications were selected as 'fixed' for Carbamidomethyl and 'variable' for Oxidation (M) and Acetyl (Protein N-term). Phospho (STY) was added as 'variable' for the files related to phospho-enriched samples. The reporter ion was MS3, TMT10plex, with a reporter mass tolerance of 0. 01 D. The digestion mode was trypsin with two missed cleavages permitted. The PSM and Protein FDR was 1%. Only peptides mapping uniquely to one protein sequence were used for quantification. Data was further processed and analyzed using Perseus 1.
The protein coding sequences for the two genes preceding gnd, a methyl transferase and glycosyl transferase, are 47% and 42% identical, respectively, but are a 100% match to other proteins with the same function in the NCBI database. The genes which flank the insertion sequences marked IS-1 and IS-3 in E. coli 26561 are nfsB and ybdK. The bottom sequence illustrates that these genes are usually separated by two small hypothetical genes, ybdF and ybdJ, in E. coli K12_MG1655 (ybdJ is not labeled in the diagram).
While dedicated libraries provide support for array representation and arithmetic (numpy;  Van der Walt et al. 2011) , a wide variety of functions for scientific computing (scipy;  Jones et al. 2001-) , and publication-quality plotting (matplotlib;  Hunter 2007) , tens of thousands of other high-quality and easy-to-use packages are available, which can help with tasks that are not specific to astronomy but might be performed in the course of astronomical research, e. g. , interfacing with databases, or statistical inferences. More recently, the development and mainstream adoption of package managers such as Anaconda 2  has significantly streamlined the installation process for many libraries, lowering the barriers to entry. The Astropy project aims to provide an open-source and open-development core package (astropy) and an ecosystem of affiliated packages that support astronomical functionality in the Python programming language.
y. z, where "x" is advanced for LTS releases, "y" for non-LTS feature releases, and "z" for bugfix releases. The released versions of the astropy core package are available from several of the Python distributions for scientific computing (e. g. , Anaconda) and from the Python Package Index (PyPI). 9 Effort has been made to make astropy available and easily installable across all platforms; the package is constantly tested on different platforms as part of a suite of continuous integration tests.