dataesr/scientific-paragraphs-categorization huggingface dataset:
GO enrichment among CNEEs To test for gene ontology terms (GO) of functional elements enriched in Heliconius-accelerated CNEEs, we used two approaches, i) two permutation approaches to account for possible biases towards particular gene functions; ii) and a genomic fraction approach. In both cases, for each gene in the reference genome (E. isabella) we first assign a regulatory domain implementing the 5 + 1 kb strategy, as implemented in GREAT 164. We then assign to each coding locus a regulatory domain consisting of a basal domain that extends 5 kb upstream and 1 kb downstream from its transcription starting site, which do not overlap between different loci, plus a further extension up to the basal domain of the nearest upstream and downstream locus, up to 1 Mb. For the permutations tests (i) we computed the expected probability (namely the mean of the distribution) of overlap between the regulatory domains of genes of a specific GO term and 10,000 random aCNEEs datasets, using BEDTOOLS SHUFFLE (-chrom -chromFirst -noOverlapping-chrom -chromFirst -noOverlapping) and randomly selecting the same amount of accelerate CNEEs among all CNEEs.
More precisely, all sequences from each of the clade were filtered realigned separately and HYPHY we compute model test and the overall ω (hyphy acd Universal $FASTA MG94CUSTOMCF3X4 Global), while the number of sites under purifying and positive selection using the single-likelihood ancestor counting (SLAC) method  168  as implemented in the HYPHY batch language 139 (P-value threshold 0. 05). Sign of diversifying positive selection was detected by scanning all internal branches of the whole cocoonases phylogeny using adaptive branch-site random effects likelihood (ABSREL) method  137, 138  as implemented in the HYPHY batch language 139 , and correcting for multiple tests using a final P-value threshold of 0. 05. The structural analyses were conducted on 181 full length sequences of the 233 of the entire dataset (~220 aa in length).
For each sequence the N-terminus region was clipped identifying the peptide signal coordinates was identified with SIGNALP v5. 0b 169 , and aligning the resulted sequences with the closest homolog protein for which a crystal structure is available (pdb: 4AG1), identified by HHPRED server 170. The resulting final sequence was then used as input for ROSETTAFOLD v1. 1. 0 171 to predict three-dimensional structures, building five models per sequence using default parameters. A multiple alignment between all the resulting sequences was performed using the PDBALN function of the Bio3D packadge of R project 172. Subsequently, the residue positions of multiple alignment containing more than 170 gaps were eliminated, resulting in a total of 227 residue positions. A graph theory based analysis was performed for each 3D model belonging to the final data set, as implemented in Ruiz-Serra et al.
To consider together the contribution of the first two components, we calculate the product between the two loadings, thus identifying the most crucial residues which are most responsible for separating the groups into essential space. To better interpret the results from a more structural and functional point of view, we map the key residues into best representative 3D structures, which are defined as the closest real sequence to the centroid of each group (calculated through the coordinates of the first two principal components) (Coc1A: Dryadula_Dpha. Dpha1503G76. 2; Coc1B: Silvani-formis_Hpar. Scf0001930G23607b. 6; Coc2: Erato_Hlat. Hel_chr17_2G18 418. 1; Coc2b: Silvaniformis_Hhel. Scf00000159G13686. 1; Coc3: Silva-niformis_Hnum_KU925753. 1_Hmel_cocoonase5a. t4). Finally, to gain insights into the protein mobility 20 resolved x-ray structures of the human chymase were structurally aligned with PYMOL v1.
Acknowledgements This article would not be possible without the great support of the great Heliconius community. We are also grateful to the environmental ministries in Peru and Panama for permission to collect and export samples and the STRI community for assistance in the field. F. C. would like to thank  Ronald Mori Pezo  for his great help in collecting H. aoede and Podotricha telesiphe;  Angel Corpuz  for various informatics support including a great patience;  Ian Fiddes ,  Mark Diekhans ,  Glenn Hichey  and  Marina Haukness  for their great support for Cactus and CAT;  Gregg Thomas  and  Tim Sackton  for they help with PhyloACC-ST, preparation and analysis;  Federica Cattonaro ,  Davide Scaglione  and  Simone Scalabrin  from  IGA (Udine, Italy ) for their fruitful discussion on the best sequencing strategy to perfom.
Data availability The genomic data generated in this study have been deposited in the NCBI database under accession codes: PRJNA686707; PRJNA686708; PRJNA686710; PRJNA686711; PRJNA686712; PRJNA686713; PRJNA686714; PRJNA686715. Short-read data for A. vanillae (Peru; ERR5235460), E. lampeto (ERR5235459), E. vibilia (ERR5235454), E. aliphera (ERR5235452), E. lybia (ERR5235468), E. tales (SRR8883890), H. telesiphe (SRR8883900), H. clysonymus (SRR4032079), H. hortense (SRR4032054), H. hecalesia (SRR8883898), H. erato petiverana (SRR4032055), H. erato etylus (ERR5235453), H. peruvianus (ERR5235458), H. eratosignis (ERR5235467), H. demeter (SRR8883893), H. ricini (SRR4032011), H. leucadia (ERR5235456), H. antiochus (ERR5235455), H. eleuchia (SRR3102171), H. congener (SRR3102172), H. hewitsoni (SRR3102337), H.
hecalesia H. hortense H. clysonymus H. telesiphe E. tales Expanded OGs Contracted OGs E. lybia E. aliphera E. vibilia E. lampeto E. isabella Eueides Dione juno A. v. incarnata Agraulis v. vanillae A. v. maculosa Dione/Agraulis Podothricha telesiphe Dryas iulia Dryadula phaetusa Philaethria dido Other genera Speyeria mormoria Junonia coenia Melitaea cinxia Bicyclus anynana Danaus plexippus 10Mya.
While Dione + Agraulis and Eueides stems have similar proportions of expanded/contracted OGs, Heliconius shows 48 contracted OGs but only eight expanded OGs (Fig. 3c, Supplementary Total intron length Mb [log scale] TE content MB [log scale] Clade Speyeria Podothricha Dryadula Dryas Philaethria Intron type Long Agraulis Dione Eueides Erato Sara/Sapho Aoede Doris Wallacei Melpomene/ Silvaniform Short 25 30 35 GC%.
Dryadula phaetusa, Dione juno, Agraulis vanilla vanillae, were collected from partially inbred commercial stocks (Costa Rica Entomological Supplies, Alajuela, Costa Rica); while individuals of a Melpomene/Silvaniform b Wallacei Doris Aoede Sara/Sapho Erato Eueides Dione/Agraulis Z= 0. 37 + 6 sites Other genera 111 sites Outgroups Branches under diverifying positive selection 0. 2 Z= 0. 23 + 1 sites 116 sites c Z= 0. 14 + 1 sites 175 sites Z = 0. 17 Pos. 216 Thr 33% Ser 17% Pos. 217 Gly 73% Met 7% Pos. 68 Ala 75% Ser 16% Pos. 71 Gly 91% Glu 5% Asp 17% 180º Non-polar Polar + Charge -Charge Pos. 119 Pos. 120 Pos. 122 Ala 46% Ala 32% Gly 33% Pro 33% Ser 23% Ser 17% Asp 22% Asn 16%.
Building of Scenarios The basic structure for the calculations to be done with the NMT is the Scenario. A Scenario represents a certain noise situation at an airport and as such consists of a specific combination of the single events available in the database. Each single event is defined by a unique combination of: The NMT provides several options to create a new scenario. As a first option a scenario can be generated from scratch. In this case the user has to provide all the information on the aircraft operations. This can be done by manually filling in a table like the one presented in Fig. 2 , or, more conveniently, by uploading a file containing the airport flight plan (similar to the time table usually managed at airports, i. e. providing the time of each individual operation) or a so-called operations file (resembling the table shown in Fig.
A strong emphasis has also been set on the ability of the tool to easily change scenarios, i. e. , to quickly analyse various possibilities. We don't know yet whether such a tool could be accepted by decision makers therefore we call our tool the "Demo Virtual Community Tool" (referred as "demo VCT")-as it demonstrates a new approach on evaluating aircraft noise effects. When comparing it to the NMT, it is developed in a computer language, which allows very fast program development, so we can quickly implement whatever we think it could be useful, but it cannot correctly support user right management. Therefore it is good as an experimentation tool to find useful features that could be later on implemented in a more commercial-like software, like the NMT. Please note that all examples presented here serve only to demonstrate the capability and the potential of the tool.
This also supports the notion that annoyance is not just a yearly value and cannot be characterised by a single metric. More and more countries are considering various metrics simultaneously. Here, a good software comes in handy especially for "starting the journey" airports, i. e. airports with less practice in aircraft noise abatement. In the following you will see several scenarios demonstrating the capabilities of the demo Virtual Community Tool. By showing differences in contour-sizes, we definitely don't want to give a position on what is appropriate to use. We just want.
[19]. In all these research efforts, the emphasis was on optimising the aircraft assignment to departure and arrival routes, while dynamic noise maps were created only for one-day scenarios to demonstrate the possibilities of the developed algorithm to reduce noise annoyance and fuel consumption. Furthermore, the calculations of daily population mobility included many assumptions and were based only on data from the census. In this book, different ways of collecting human mobility patterns will be explained in more detail along with the methodology used to incorporate it into dynamic noise maps. Furthermore, a real case study conducted within the ANIMA project, based on the one-year air traffic data, will shed light on the benefits of using this new approach and demonstrate how daily movements influence the estimated population noise annoyance around an airport.
The year 2018 has been selected for this case study based on the availability of data regarding population mobility patterns and air traffic. The yearly traffic at Ljubljana airport for 2018 consisted of 35,512 aircraft performed by 213 different aircraft types, indicating that on average, there were approximately 97 operations per day, or 4 movements per hour. There were several peaks during the day, with the most flights occurring between 5 and 6 PM (nine flights in average), while only 6% of operations were performed during the night hours. The population mobility patterns are assessed using a dedicated national travel survey. The most recent one conducted in Slovenia was the Daily Passenger Mobility Survey (TR-MOB 2017). The data were obtained from the Statistical Office of the Republic of Slovenia through the special request for protected microdata containing detailed information about each trip on an individual level.
The BeWeB Portal: a Virtual Service for Italian Ecclesiastical Libraries  Adriano Belfiore, Francesca Maria D' Agnelli, Valerio Pennasso and Silvia Tichetti 1  BeWeB: a Cross-Portal for Ecclesiastical Cultural Heritage BeWeB1 -'Beni ecclesiastici in web' -is the cross-portal that highlights and displays ecclesiastical cultural heritage that is managed and preserved by entities of the Catholic Church in Italy, providing a cross-sectoral and integrated outlook on cultural heritage with a shared ecclesial identity. Of course, BeWeB is a lot more than just an interface to retrieve survey data on ecclesiastical cultural heritage, since it represents and expresses the identity value of the tangible and intangible cultural heritage of communities whose stories are told by cultural heritage itself.
Its primary aims -on behalf of particular churches, i. e. dioceses7 -include fostering the knowledge and protection of the Church's heritage, which is fundamental for its appropriate and consistent management and development in the future. It provides an overall outlook on issues related to the knowledge, protection, management, and enhancement of both older assets (previously managed by the National Office for Ecclesiastical Cultural Heritage, UNBCE) and newer assets (previously managed by the National Service for Religious Buildings, SNEC The BCE National Office fulfils its mission of service, including to end-point users, and asset enhancement through the BeWeB portal. This project has a solid foundation, since it relies on survey and data collection activities that the BCE National Office coordinates throughout Italy.
The Evolution of BeWeB Portal as a Showcase for Ecclesiastical Cultural Heritage The BeWeB portal was launched in 200024 as a virtual showcase for the survey of the Church's cultural heritage, but with the clear aim of turning it into a popularisation and dissemination portal. 25 Today, it increasingly testifies to the emotional bond that exists between communities and their cultural heritage, emphasising the relationship of faith, devotion, and love between the people of God and the Lord. Starting from the solid foundations given by the pervasiveness and quality of surveys, the BeWeB portal acts as a megaphone for the collections of ecclesiastical institutions and dioceses, by making available not only catalogues, but also tools for their enhancement. Hence, it gives resonance to activities carried out by institutions and works as an editorial tool to publish content stored in its database, with the aim of facilitating, through thematic in-depth analysis, the sharing of resources and information and increasing the understanding and interpretation of diocesan heritage by a broader audience and not only by specialists.
The cross-sectoral and integrated interpretation of cultural resources is achieved thanks to the adoption of an entity-relationship model that integrates book, archival, historical-artistic, and architectural resources (with databases that are constantly being updated and increased); together with glossary entries, descriptive pages of dioceses and ecclesiastical regions, ecclesiastical cultural institutions and person/family/entity authority data. The portal also includes and provides information on events and thematic insights. All of this is the work of an editorial staff that is scattered throughout the Italian territory, and is the result of the description and cataloguing work of ecclesiastical cultural heritage promoted by the BCE National Office and carried out by dioceses and cultural institutions in Italy.
"29 Promotional information about events, exhibitions, or seminars that dioceses and institutions organise in their local area is also provided, via links and in-depth information with descriptions of the cultural heritage showcased in the event and related institutions. The richness of the portal lies in the heritage that is described within it, which is placed at the centre of all additional editorial content, but the way the portal presents data is also important. For example: Search functions that enable queries throughout the database are characteristic and essential features: they include intuitive questions such as What? Where? In which content category? In addition to in-depth geographical and chronological analyses and filtering by person/family/entity. Search results (which can be displayed as a list, gallery, on a map or time line) highlight the many categories in which BeWeB has found results, with the possibility of filtering them by category, geographical location, history and presence of digital images and, where applicable, by the specific filters of individual cultural sectors.
The Inclusion of Different Standards and Different Materials in BeWeB BeWeB does not rely on a common descriptive standard for different cultural domains, but on mapping and data deconstruction systems, to account for each sector's unaltered descriptive approach and, hence, for the richness of original descriptions. This allows each sector to adopt distinctive solutions and keep up with the developments and changes in reference standards. It also allows for the introduction of services and the inclusion of sections, special content and exhibition methods that are peculiar to each type of cultural asset. For book resources, for example, the portal includes specialised sections that are the result of an agreement with the Italian religious publishers' portal, Rebecca Libri. 30 Hence, in addition to multidisciplinary access to resources in the portal's home page, each cultural domain provides advanced sectoral search interfaces, with useful navigation filters that are tailored to specialised users.
32 This is a cluster of equivalent access points that refer to the same entity; it is generated by a clustering system that guides the selection of names found in different description systems according to the relevant cultural domain  (book, historical-artistic, archival, and architectural assets). Managing and controlling authority data requires rigorous and consistent data acquisition and processing, but it offers maximum potential and quality of results by enabling more cross-sectoral queries and the opening to other information systems with which data are exchanged. The controlled access point is displayed in the portal, together with biographical and historical information and links to other external international sources (mainly VIAF and ISNI) or in-depth resources (such as Wikipedia and the Treccani online encyclopaedia), and is enriched by these links with other entities.
The first experience in this sense was made in the bibliographic domain. 33 The bibliographic collections included in BeWeB, as already mentioned, actually come from the ecclesiastical libraries that are part of the National Library Service, regardless of the network to which they belong (therefore also including libraries that are not part of the PBE network), and regardless of the application and bibliographic format they have adopted. 34 Another step in this direction was taken thanks to the agreement35 signed with the Faculty of Theology of Triveneto (FTTr), that enabled BeWeB to add the cataloguing descriptions of materials that are not shared through the SBN Index (i. e. , Bachelor degree and Ph. D. dissertations, but this model can potentially be extended, if quality source data are provided).
A further step towards the unification of collections was made in July 2020, when the BeWeB portal started including descriptions and images of manuscripts preserved in church-owned institutions that are part of the database of the Census of Manuscripts in Italian Libraries36 coordinated by the ICCU. 37 Manuscript descriptions fall under the category of book assets, integrated with ancient and modern bibliographical material. 38 In the portal, the documentary context is enhanced -with the inclusion of the description level of both individual manuscripts and manuscript collections -and hierarchical links are highlighted (between the collections and the preserving institution, or between the collections and the manuscripts contained therein, or even between the composite manuscript and its individual codicological units) as well as horizontal links (e.
g. between manuscripts of the same collection). In order to ensure the greatest possible degree of detail, in addition to the intuitive query functions provided for multidisciplinary searches, the library portal offers both an advanced sectoral search, including modern, ancient, manuscript and audio-visual items, and a dedicated search for manuscript records, whereby the database can be queried with specialised fields and filters. The bibliographical records coming from these separate source systems are brought together and standardised in BeWeB and are enriched by the portal's cross-sectoral structure, which aims to build a network for sharing the complexity of library services.
The system includes an online pre-registration form,40 through which users can input the required data for their reader card, which can then be validated by any of the libraries of the network. Registered readers can: check the availability of a publication in one of the libraries of the PBE from the BeWeB OPAC;41 request to borrow a book; request to consult a publication by indicating the preferred day; check the status of past and current readings in all libraries participating in the network; manage a list of favourite searches; and receive notifications on the availability of new titles they might be interested in. Network librarians can rely on a management system to visualise requests, reservations, and transactions in real time, through which they can capture usage and service data on readers and transactions, which is critical for devising service policies and updating collections.
To determine effects of loss of the Mediator kinases on gene expression, we performed RNA-sequencing analysis of stable populations of single and double Cdk8/Cdk19 knockout organoids. We performed spike-ins with ERCC RNA standards in proportion to genomic DNA content of each sample in case loss of Mediator kinases had global effects on total RNA or mRNA levels. This was not the case since changes were comparable whether samples were library normalised or spike-in normalised (Fig  EV5A ). CDK8 loss had a stronger effect (716 genes upregulated, 575 downregulated) than CDK19 loss (158 up, 151 down), while double knockout organoids  (1, 819 up, 1, 363 down; Fig 3A and B; Dataset EV1)  revealed functional redundancy between CDK8 and CDK19 in regulating gene expression. However, most expression alterations were minor, with only 830 genes deregulated by a factor of two or more.
We next correlated global gene expression changes of double-knockout organoids with mouse single cell RNA-seq data that identify different intestinal cell types  (Haber et al, 2017). Most of the signature genes for each cell type were not significantly deregulated in organoids lacking  CDK8 and CDK19 (Appendix Fig S4) , also suggesting that differentiation is robust in the absence of Mediator kinases. Nevertheless, a subset (227 out of 459) of enterocyte-signature genes were significantly affected, most of which (219 out of 227) were upregulated, while a smaller proportion (43 out of 122) of stem cell signature genes were identified, most of them being downregulated (32 of 43). To investigate this further, we quantified expression of genes characteristic for different intestinal cell-types by qRT-PCR on WT and doubleknockout organoids, and organoids treated with Senexin B to inhibit both kinases.
Taken together, our results show that differentiation into all cell types occurs in the absence of Mediator kinases, but do not rule out minor changes in differentiation or stem cell numbers. Geneset Enrichment Analysis (GSEA) in double-knockout organoids unexpectedly revealed a striking alteration of genes also modulated in intestinal knockouts of the cystic fibrosis transmembrane conductance regulator, CFTR (Fig  4A ), with 98% of intestinal genes deregulated in Cftr knockout also deregulated in Cdk8/19 knockout. Most genes upregulated in the intestine in Cftr knockout (70% in the ileum and 86% in the duodenum) were similarly upregulated in Cdk8/19 knockout, with 22-25% of downregulated genes similarly diminished  (Fig 4B, Dataset EV2). Specifically, in Cdk8/19 knockout, expression of genes involved in mucus production, Muc2, Muc3, Muc13, Nlrp6, Agr2, Gcnt4, Tff1, were upregulated, while Cftr was reduced.