dataesr/scientific-paragraphs-categorization huggingface dataset:
Dissemination Digital phenotyping can provide detailed knowledge about the non-healthcare aspects of this population, to facilitate the adjustment of prevention strategies. Specific groups of women will be identified based on the huge amounts of individual data collected by the activity tracker for physical activity, heart rate and sleep. This will make it possible to develop prevention programs based on the specific characteristics of the participants. Ultimately, this study will provide public decision-makers with high-quality scientific data to guide policies for promoting healthy behavior. The findings of the NeoFit trial will be disseminated via peer-reviewed publications and conference presentations. The datasets generated and/or analysed during the current study will not publicly available due to personal health data but will be available from the corresponding author on reasonable request at the end of the study.
Reconstruction of the species-specific mutational spectrum for mammalian species Using all available intraspecies sequences (April 2016) of mitochondrial protein-coding genes we derived the mutational spectrum for each species. In brief, we collected all available mtDNA sequences of any protein-coding genes for any chordate species, reconstructed the intraspecies phylogeny using an outgroup sequence (closest species for analysed one), reconstructed ancestral states spectra in all positions at all inner tree nodes and finally got the list of singlenucleotide substitutions for each gene of each species. The pipeline is described in more detail in Supplementary Materials 1. 1. Using species with at least 15 single-nucleotide synonymous substitutions at four-fold degenerate sites we estimated the mutational spectrum as the probability of each nucleotide mutating into any other nucleotide (vector of 12 types of substitutions with a sum equals one) for Nucleic Acids Research, 2022 3 more than a thousand Chordata species.
Four-fold degenerate sites have little or no selective pressure and therefore can be considered the most neutral ones and reflect mutational bias  (22, 23). Moreover, a recent study revealed that synonymous four-fold degenerate sites are highly associated with mutational bias rather than selection  (24). We normalised observed frequencies by nucleotide content in the third position of four-fold degenerative synonymous sites of a given gene. To eliminate the effect of nonuniform sampling of analysed genes between different species, most of our analyses were performed with the Cytb gene--the most common gene in our dataset. Generation length in days (as the average age of parents of the current cohort, reflecting the turnover rate of breeding individuals in a population) for mammals was downloaded from the Dryad data base: https://doi.
Analyses of complete mitochondrial genomes We downloaded whole mitochondrial genomes from Gen-Bank using the following search query: 'Chordata [Organism] AND (complete genome [All Fields] AND mitochondrion [All Fields] AND mitochondrion [filter]'. We extracted non-overlapping regions of protein-coding genes, calculated codon usage and extracted fractions of A H , T H , G H and C H nucleotides in synonymous four-fold degenerate positions. We estimated the G H A H skew as (G H -A H )/(G H + A H ) using only synonymous four-fold degenerate sites for each protein-coding gene of each reference mitochondrial genome of mammalian species.
This suggests that the A H > G H mutations, shaping the G H /A H gradient, can be sensitive to some mutagens associated with gestation time or other life-history traits. Due to the existence of positive correlations between gestation time, body size, and longevity, which in turn are associated with generation length and the level of mitochondrial metabolism  (28) (29) (30)  we can expect differences in mtDNA mutagenesis between species with different life-history traits. To test this hypothesis, we compared datasets of somatic mtDNA mutations of mice and men. To test the potential sensitivity of the two most common transitions to life-history traits, we reanalysed the recent dataset of somatic de novo mtDNA mutations, obtained by the duplex sequencing approach  (19). Sanchez-Contreras et al.
Altogether, using the datasets of somatic mtDNA mutations, obtained by a highly sensitive duplex sequencing approach, we uncovered that A H > G H is more sensitive to age as compared to C H > T H. Assuming a similarity of mtDNA mutagenesis in somatic and germ-line tissues we expect to observe also an excess of A H > G H in aged germ-line tissues. Indeed, recent deep sequencing of de novo mtDNA mutations in aged versus young mice oocytes confirmed that the strongest hallmark of oocyte aging is an increased fraction of A H > G H substitutions  (31). Additionally, we analysed the human de novo mtDNA mutations as a function of the female reproductive age, which is a proxy for oocyte age. It has been shown that the number of de novo mtDNA mutations in children increases with maternal age  (32, 33) , however, no age-related changes in mtDNA mutational spectra have been documented yet due to the low sample size of the de novo mutations.
2 and Supplementary Figure  S4 ). The average mutational spectrum of all mammalian species (Figure  2A ) demonstrates strong excess of C H > T H and A H > G H substitutions which have been shown in previous studies  (4, 5). To focus on the species-specific variation in mutational spectra, we analysed in detail the CYTB gene, which was the most common in our database: it contained 56% of all extracted substitutions  (39 112   Variation in neutral mtDNA mutational spectrum of mammals is driven by the generation length. (A) An average mtDNA mutational spectrum of mammalian species (N = 611). Mutational spectrum is a probability of each nucleotide to mutate to each other based on the observed and normalized frequencies of twelve types of nucleotide substitutions in four-fold degenerate synonymous sites of all available within-species polymorphisms of mtDNA protein-coding genes.
A location of all data points (red and blue circles) near the diagonal shows that mtDNA of mammals is close enough to a neutral equilibrium. However, short-lived species (marked by blue circles) are even closer to the diagonal (horizontal dotted blue line towards the diagonal are shorter than the red dotted lines), suggesting that they are evolving faster towards the neutral equilibrium. (B) Nucleotide frequencies in neutral sites of all 13 protein-coding genes as a function of generation length--fraction of A H is decreasing while fraction of G H is increasing (N = 650). (C) Structure of mtDNA of two mammalian species with extreme generation lengths: a honey possum and a whale. Upper panel: frequencies of A H (red) and G H (grey) nucleotides along the major arc of mtDNA of the most short-lived (honey possum) and the most long-lived (whale) mammalian species from our dataset.
9 × 10 -4 ; see also Figure  3C ). To visualize a contrast in G H A H skew between the shortest-and the longest-lived species in our dataset we plotted A H and G H fractions along the major arc of mtDNA for honey possum (generation length 341 days) and whale (generation length 18980 days) (Figure  3C ). It is evident that on average honey possum mtDNA has an excess of A H (red color in Figure  3C ) while whale has an excess of G H (gray color in Figure  3C ). Fourth, we analyzed how A H > G H mutagenesis affects asymmetry in codon usage. If A H > G H is a strong and uniform mutational force, we expect that most amino acids would demonstrate a deficit of XXA H and excess of XXG H codons. Because the light strand of mtDNA is equivalent to mRNA of 12 protein-coding genes (all except ND6) we analyze codon usage in terms of the light strand notation and thus, A H > G H substitutions are expected to decrease the frequency of XXT L codons (because T L is complementary to A H ) and increase the frequency of XXC L codons (because C L is complementary to G H ).
(B) Nucleotide frequencies in neutral sites of all 13 protein-coding genes as a function of generation length--fraction of A H is decreasing while fraction of G H is increasing (N = 650). (C) Structure of mtDNA of two mammalian species with extreme generation lengths: a honey possum and a whale. Upper panel: frequencies of A H (red) and G H (grey) nucleotides along the major arc of mtDNA of the most short-lived (honey possum) and the most long-lived (whale) mammalian species from our dataset. Each bar represents the nucleotide frequency in a 20-nucleotide window. In both mammals, A H is decreasing and G H is increasing along the major arc of mtDNA: from the bottom left (origin of replication of light strand) to the top right (origin of replication of heavy strand). However, additionally to the gradient, mtDNA of a whale has an integral, genome-wide, deficit of A H and excess of G H -a signature of an increased generation length.
0 version was rolled out in 1990. 7 In some church libraries attempts were also made to use individual personal computers to create catalogue databases or to automate the printing of catalogue cards. It was in these circumstances that the computerisation of church libraries in Poland began, and at the same time the Federation of Church Libraries 'Fides' was founded, primarily for this purpose. This happened thanks to one man -Fr. Krzysztof Gonet, a visionary who was passionate about the use of modern computer technology to automate libraries. 8 From a historical perspective, Fr. Gonet appears to be a man of the moment for the new times. A distinguished graduate of the Institute of Library and Information Science at the University of Warsaw in 1981, he initially began working in the Data Processing Department of the National Library after his graduation, but a year later he left to join the Metropolitan Higher Seminary (Polish: 'Wyższe Metropolitalne Seminarium Duchowne' -WMSD) in Warsaw.
From 2001 the data was partly merged automatically with the inclusion of library symbols. The central catalogue was made available on the Internet as early as 1993, initially on a host server, and then using its own server, Fides. From 1994 the central catalogue was distributed to church libraries across Poland also on CD-ROM and became an aid for copying ready descriptions for libraries beginning computerisation. From that time until 2005 databases in CD-ROM form were issued annually, and from 2001 were equipped with a graphic interface in the form of the MAKWWW program. The latest version of the central catalogue of books in 2005 had 470,742 entries from 30 libraries, while the "FIDES-Magister" database had 29,419 entries from 22 libraries. However, the central catalogue created and made available in the manner described above was never really up to date.
This is why, in 2004, the central catalogue was replaced by a "union catalogue," that is the FIDKAR multibrowser (named after the Fides Distributed Catalogue), working with the Z39. 50 protocol. The software needed to run it was entirely written on commission from the Fides Federation. Its advantage was its ability to simultaneously search any library system and the catalogues and bibliographies available in the Z39. 50 protocol. It could be said to be a very innovative 'discovery service' for those times. At the peak of its existence, FIDKAR offered users simultaneous searches in almost a hundred databases of various types, of which about half were available online and the rest from copies placed on the Fides server. Undoubtedly, this solution was a big step forward and served well both librarians making cataloguing easier, and users looking for up-to-date information.
However, ten years on, FIDKAR slowly became outdated. There arose new possibilities for collaboration and real co-cataloguing, while the said software was no longer developed. The year 2014 saw a new solution, which will be discussed below. The FIDKAR multibrowser itself is still in operation, but has lost much its relevance. Currently, 46 databases are connected to it: 24 library catalogues (including two central ones), 11 bibliographic databases and 11 dissertation catalogues. 14 At this point, speaking about various types of databases which are searched simultaneously in the FIDKAR system, I would like to discuss the issue of creating bibliographies of the contents of journals and collective works. From the very beginning, apart from the creation of a central catalogue, Fr. Gonet and Fides set themselves an equally important goal of creating computer bibliographies of theological writings and related sciences.
Originally, the Polish bibliography of theological sciences was to be modelled on the ATLA Religion Database (earlier name: Religion Indexes), which had been already distributed in the form of a CD-ROM. The Federation's guest at the First General Assembly (19-23 May 1995) was John Bollier, ATLA's development director. The participants discussed possible forms of cooperation and the exchange of databases on optical discs. 15 Although further cooperation between Fides and the American Theological Library Association did not take shape due to the limited capacity of Polish libraries, the innovative publishing of the first database on CD-ROM by Fides in 1995 was appreciated by the American side. From the beginning, therefore, the individual member libraries undertook to create partial bibliographical databases of the contents of the journals published in their theological centres.
After a simple accumulation they became part of a central service on the internet and on CD-ROM. The last version in 2005 of the 'Bibliografia Nauk Kościelnych (fragment)' (Bibliography of Ecclesiastical Sciences [fragment]) database comprised 37,709 entries and was a combination of 17 bibliographical databases of various scope and range, created by libraries belonging to the Federation. Next, the bibliographic databases were connected to the FIDKAR multibrowser, in an analogous way to the connection of catalogue databases. Both solutions were very imperfect due to shortcomings in scope and completeness and due to the heterogeneity of the compilation. In 2011 the Federation managed to solve this problem of the lack of a single, coherent -and reasonably complete -bibliography of the ecclesiastical sciences, for which it had been calling for many years.
The cooperation with the National Library resulted in the project called Electronic Bibliography of Theological Sciences (Polish: 'Elektroniczna Bibliografia Nauk Teologicznych' , EBNT). The National Library made available, free of charge, bibliographic descriptions created by the Department of the Bibliography of Journal Articles, both those included in existing databases from the years 1996-2011 and those newly added in a monthly cycle. This bibliography covers mainly the contents of publications issued by ecclesiastical universities and theological faculties, starting from 1980. A novelty was the combination in one database of both the bibliography of journal contents and the contents of collective works, such as anniversary books and conference materials, modelled on the ATLA bibliographical database.
Those descriptions which were not in the data coming from the National Library -i. e. descriptions of chapters from multi-author monographs and descriptions of articles from non-indexed journal issuescame from the Fides libraries. For this purpose, previously created partial bibliographic databases were used. Many descriptions received from the National Library were also corrected and complemented with abstracts. Author's entries were unified in accordance with authority records in the NUKAT16 union catalogue, and the subject headings language of the National Library was used. Initially, the EBNT database was developed in the MAK program and accessed from the Fides server. In 2013 it was transferred to the Koha system, and these were the first experiences of using this system to computerise the Federation's libraries.
It was launched in 2006, on the 15th anniversary of Fides. The digital library was conceived as a platform where both Church institutions and individual authors could publish their works. Its content was also to be taken care of by the member libraries by providing digitised objects for publication. Due to the weakness of the member libraries of the federation and due to the lack of funds for digitisation, the expectations of the launch of the digital library have not been fully realised and it still has a relatively small amount of content. It is available at: http://digital. fides. org. pl/. the virtually-free MAK program, were in danger of losing access to catalogue databases. The question of which library program would replace the well-deserved MAK was the subject of concern of the Fides Board after the National Library had stopped working on a new version in client-server architecture.
The possibility of using one of the Polish library systems for the whole Federation was analysed, due to their lower prices. There was also no doubt that it was necessary to change the concept and move to the model of co-cataloguing with one central database of bibliographic authority records. This model was adopted in national systems intended mainly for public libraries. However, this very resource of bibliographic authority records, not corresponding to a large extent to the resources of Polish and foreign theological literature in church libraries, constituted one of the most serious obstacles in using the offered solutions. Then the Koha system arrived on the scene, and its adoption resulted in the creation of a central catalogue in the full sense of the word. Already in 2010, thanks to Janusz Kaczmarek, a Dominican, there appeared a Polish implementation of the Koha system, which he used to create a central catalogue of Dominican libraries based on the catalogue of the Library of the Dominican Philosophical and Theological College in Cracow.
2. A common, unified bibliographic record database (one descriptionmany resources). 3. A common interface for the presentation of bibliographic data. 4. A common lending mechanism (but separate readers) and support for inter-library loans. 5. Formal headings in accordance with the NUKAT Union Authority File. 6. Subject description in accordance with the National Library Language File. 7. Inclusion of the catalogue in NUKAT, which implies mandatory active or passive cooperation of member libraries with the NUKAT Centre. 8. The project is to be self-financing: for the necessary IT work, the permanent maintenance of the catalogue and for the salary of the system librarian, the member libraries will pay a fixed monthly contribution to the Fides account. Points 1 to 4 stem from the specificity of the central catalogue.
From the technical point of view, the adopted solution relieves the libraries of the burden of dealing with the IT infrastructure (apart from having working Internet and efficient computers with Internet browsers). Currently the system operates on its own server, Fides, located in one of the member libraries, but it would be just as well possible to give up maintaining one's own server and purchase such a service in the 'cloud' , i. e. from a hosting company. This way, only one IT specialist is needed to operate the system for all libraries. In the case of small and medium-sized church libraries this argument seems to be crucial. Maintaining the catalogue in the MAK system already caused considerable problems with servicing and updating the software, and even more so, no modern library system can be used without professional IT support, which most libraries simply cannot afford.
As far as the use of authority files is concerned, the choice of the formal NUKAT catalogue file seems obvious. It is primarily connected with the decision to establish close cooperation with the NUKAT catalogue and downloading from it the bibliographic authority records as reference records. Most libraries of the Fides Federation are scientific libraries and therefore their cooperation with the university NUKAT centre is natural. Only technical difficulties -using the MAK program -made it impossible to start cooperation earlier. Also, the resources and scope of the literature present in the NUKAT catalogue, co-created from the beginning also by the two largest church libraries in Poland, the Library of the John Paul II Catholic University of Lublin and the Library of the John Paul II Pontifical University of Cracow, correspond to a much greater extent than in other networks to the profile of the collections of the Federation's libraries.
It is also worth mentioning that since 2001 the Fides Federation has been maintaining an updated copy of the NUKAT Authority File in the form of the MAK database, distributing it on commission from NUKAT to several dozen church and non-church libraries. 20 Thus, in many church libraries this catalogue was already in use and the control numbers of formal authority records were added to bibliographic records, which during data migration to the new system allowed for unambiguous linking of entries with the current one. The choice of the language of the subject description was under debate. 21 Subject description of documents in NUKAT records is made with three subject heading systems: KABA Subject Headings (used by academic libraries), National Library of Poland Subject Headings (JHPBN), and the Polish version of Medical Subject Headings (MeSH).
The language of the National Library of Poland, used by very few academic libraries, was chosen for two reasons: this language had already been used by some Fides libraries based on the MAK system, as its authority file was connected to the catalogues of these libraries, and its control numbers were entered into bibliographic records. The second argument, according to the decision-makers, was the greater advancement and simplicity of the language. In particular, the evolution of the JHPBN, which 20 Until 2009, a copy was distributed on CD-ROM, and since then interested libraries have downloaded it from the Fides server as a zipped MAK database. 21 The issue of subject description in the central catalogue Fides is exhaustively discussed by Katarzyna Mituś, "Droga do jednolitego opracowania rzeczowego w Centralnym Katalogu Federacji Bibliotek Kościelnych FIDES," Fides: Biuletyn bibliotek kościelnych 22, no.
With the help of IT tools created by Kaczmarek a coherence check of the database was soon started and errors and shortcomings, mainly concerning the content of field 008 and ISBN numbers, were removed in the MAK system in order to prepare it for importing into the Koha system. After six months of preparation, the project entered the implementation phase. As a result of intensive IT two-week work, 91,214 bibliographic records and lending library data were imported into the Koha system and the new system was configured. The catalogue was officially launched on 16 June 2014, and although it initially contained only the data of the PWT Library in Wrocław, from the beginning it has been called the Fides Central Catalogue of Church Libraries. Since then, it has been available at: https://katalog.
fides. org. pl/. The aim of the project is to transfer all previously created catalogue information about the library's resources as well as the readers' database (and information on loans, if a lending library was opened) to the new system without any losses, and then to consolidate the bibliographic data with the whole catalogue. This process is multistage and depends on the quality of catalogue data of the library being included in the central catalogue. The integration of the local catalogue into the common catalogue is carried out in the following steps: 1. Checking and correcting the original records in the MAK database so that they are consistent with what should be expected of them. This is essentially about the content of fields and subfields, what is already in the records, rather than complementing the records with new information.