dataesr/scientific-paragraphs-categorization huggingface dataset:
8. Generation and consolidation of formal and partial subject headings found in records that are not replaced or merged. The most important part of the whole process of inclusion of each new catalogue database is the exchange of local records into unified NUKAT records, which constitute a reference point for all local catalogues included in the central catalogue. The first stage of the process is automatic exchange with the use of scripts, which are the solution developed by Kaczmarek, based on multicriteria analysis of records, with one hundred percent certainty of bibliographic descriptions matching. The success rate of automatic exchange depends on the quality of the local catalogue, but also on the nature of the collection. Most important, however, is the fact that in the collections of church libraries there are still many rare publications, local or foreign theological books which have not yet been included in the NUKAT catalogue because large academic libraries do not have them, so there are no equivalents for them.
Consolidation is therefore a continuous process: it also takes place e. g. on the occasion of cataloguing new items or browsing the catalogue, during consolidation work carried out by administrators, or by means of periodical automatic comparison of the database with newly created NUKAT records. In addition to the main catalogue, libraries included in the Central Catalogue often have other databases -for journals, old prints, textbooks or theses. Ultimately, these should all be integrated in a single catalogue. The consolidation of journals -very desirable from the readers' point of view -does not entail major difficulties. However, the consolidation of catalogues of old prints seems much more interesting. In 2016, the catalogue of the PWT Library in Wrocław, with 9893 records, was imported as the first one.
It was created on a different basis -a separate record for each print. Moreover, in this case each copy is provided with individual information on provenance and binding, so record-merging is more difficult. It was decided, for example, to multiply fields 561 and 563 for old prints, containing, apart from the content of notes, also information on the library and the signature (in sub-fields 5 and 3). Two additional local authority files were created for provenance -individuals and corpora -which control the content of fields 900 and 910 assigned for standardised provenance. Descriptions of old prints from other libraries are slowly being added to a common database together with the local catalogue. They are also catalogued on an ongoing basis, so the consolidation between libraries in this respect is also becoming a reality.
Results of Cooperation Within almost seven years of its launch in June 2014 until the end of April 2021, twenty-six libraries were included in the Fides Central Library Catalogue in this way. The catalogue is growing and changing dynamically. As of 30 April 2021, the statistics of the database were as follows: -603,125 bibliographic records, including 384,870 records retrieved from the NUKAT catalogue (64%); -16,084 analytical records with descriptions of chapters in monographs; -495,200 authority records, including 438,400 from NUKAT authority file (89%); -2,033,330 copy records including: -more than 1,817,500 volumes of books published since 1801; -more than 176,500 volumes of periodicals; -16,462 old prints (including 1,116 incunabula); and -more than 16,900 dissertations. It is interesting to compare the current quantitative data of individual libraries participating in the Central Catalogue with the data obtained in the BETH survey conducted among Fides libraries in 2010 (although note that not all libraries returned the survey at that time).
Another important effect of the participation of libraries in the Central Catalogue Fides, combined with the shared cataloguing in a single database, is the creation of a kind of single virtual library. The collections of this 'library' are very rich and varied (about half a million different works). It has become very easy to find the library that holds the item you are looking for and to access it through interlibrary loans or by ordering a digital copy. The cataloguers at these member libraries communicate with each other by e-mail and telephone, e. g. , to uniquely identify the items catalogued or to request the exchange or merging of records. The modification of a local record created by another library also requires prior approval. Modifications to subject descriptions are analogous.
As long as they were using the MAK program, cooperation was impossible for technical reasons. Now downloading descriptions to local catalogues provides NUKAT end-users with one-stop access to information on the resources available in church libraries. The cataloguer downloads a selected bibliographic record to the local database and adds the library symbol to the original description in the NUKAT database. The symbol is displayed to the end-users as the name of the library hyperlinked to the copy of the given description in the local catalogue. As a result, the end-users are provided with information on which libraries hold a selected document and what its current circulation state is. This information can be accessed world-wide via the Internet. Bibliographic records from NUKAT are also uploaded into the largest international union catalogue, WorldCat.
Since November 2019, the NUKAT database can also be searched with the KVK virtual catalogue. The NUKAT Centre uploads authority records from NUKAT into the Virtual International Authority File (VIAF). Among them are a (relatively small) number of records made by church cataloguers. This all means that information on holdings of Polish church libraries is available throughout the linked data world. The cooperation of the member libraries of the Fides Central Catalogues with NUKAT can be summarised by the following figures (as of 30 April 2021). The total number of bibliographic records downloaded by particular libraries from the NUKAT database, or rather records to which their symbol is added in NUKAT, is 1,187,225. The percentage share of NUKAT records in the total catalogue of each library, related to the progress of consolidation and the nature of the collection, ranges from 50 to 99 percent.
Challenges and Prospects After ten years of using the Fides central catalogue in the form of the MAK database on CD-ROM, and after another ten years of using the 'union catalogue' , i. e. the FIDKAR multi-search engine, seven years ago the Federation started to create its central catalogue in the full meaning of the term. It is to be hoped that this pursuit of progress will serve readers and librarians well for years to come. With that said, however, it is important to face current challenges and think about the future. First, it should be noted that more than thirty libraries of the Federation, most of which are large academic libraries of diocesan and religious seminaries, are still using the outdated MAK program. In their case, the problem of data security and access to catalogue information is still not solved.
The cataloguing of these valuable historical books and the study of their provenance would be a very important contribution to the preservation of the cultural heritage of the Church. At the same time, however, it is an extremely difficult task because correct and complete cataloguing of old prints according to these standards requires very high qualifications and a lot of experience. Only a few church librarians are able to meet these expectations and undertake this task. It seems that the only possibility would be to obtain external funds within the framework of projects financed by the state, and to employ appropriate people. As far as full bibliographical information is concerned, the Central Catalogue alone, by its very nature, does not provide access to data on the contents of books and journals in the form of descriptions of separate chapters and articles.
For the time being, two compatible Fides databases must be used, the other being the Electronic Bibliography of Theological Sciences (EBNT) discussed earlier. Attempts have already been made to enrich the Central Catalogue with the so-called analytical records for collective works, which currently number about 16,000. They are downloaded automatically from the NUKAT catalogue for those books whose descriptions were entered into the catalogue. For IT reasons it is difficult to download such records from other sources, especially from the catalogue of the National Library. Work is underway to transfer another 10,000 records from the EBNT database to the NUKAT catalogue (enriching its content in the field of theology), and to then download them back to the Central Catalogue. With regard to the descriptions of journal articles, of which there are many more, a decision has still not been taken to include them in the Fides catalogue, which is used simultaneously for lending to all member libraries.
This is problematic from the point of view of the reader, who might feel confused when encountering the catalogue descriptions of journal articles that are not available in his/her library. There are also technical and organisational difficulties. Both the NUKAT catalogue and the catalogue of the National Library contain numerous analytical records for journals. However, many more journals are indexed completely by the National Library, from which we can download descriptions to the EBNT database. In the NUKAT catalogue descriptions are created by individual libraries according to their own criteria and needs, so the indexing is not at all methodically structured. However, downloading data from the NUKAT catalogue does not present any technical difficulties and can be automated, while downloading them from the National Library database to the Central Catalogue would require much more work due to the inconsistency of authority files.
Thus, the connection between the Central Catalogue Fides and the EBNT bibliographic database remains an open question. This is not all. First there is the task of creating a full theological bibliography on an ongoing basis, based on criteria developed by the Polish theological community, which needs to be solved. At present, due to the lack of funds for employing personnel to carry out this work, we rely only on descriptions from the National Library in expanding the EBNT. Moreover, the aspirations of the theological community reach further, towards the modernisation of the whole database and linking it with the repository of full texts of articles and books. Therefore, the University Library of the Catholic University of Lublin, in agreement with the Federation Fides, undertook to develop a project of such a knowledge base, which would easily provide access to the scientific output of theologians through access to full texts of studies in a digital version.
After possible funding from the Polish Ministry of Education and Science, the transformation of the EBNT into a modern information system could begin. One of the aims of this project is also to shape the database in such a way that it can be searched by discovery services used in Polish academic libraries. A further issue is the software for the Central Catalogue. Currently, this role is fulfilled very well by the Koha system, which is still being developed by an international community of volunteers. The launch of the Fides catalogue was one of the first Polish implementations of this integrated library system and at the same time a successful attempt to use it for cooperation with the NUKAT catalogue. In recent years there has been a significant increase in the number of libraries in Poland using this software, which could also be partly due to the success of the Fides project.
The increasing popularity of the Koha system guarantees greater IT security of the project and even better adaptation of the software to Polish conditions. This also bodes well for a possible future change of the Koha system to a new generation open system. As long as the bibliographic data is consistent and of high quality, which is the goal of all current activities of the Fides librarians, transferring it to the new system will not present any difficulties. Finally, in the context of the BETH anniversary, it is worth noting that the next step in the integration of catalogues and bibliographic databases could be the creation of multilingual international systems, for example at a European level. At the moment there is only a very simple search for information on books in services such as KVK or WorldCat, while bibliographic and full-text databases from different providers -mostly licensed -are available from different addresses.
Molecular docking Molecular Docking was performed using Glide 47 from the Schrödinger suite. All ligands were docked to the recently solved cryo-EM structures of LAT1 (PDB: 6IRT 8 , 7DSL  10  ). These structures were prepared for docking with the Glide Protein Preparation under default parameters. The ligand binding site was defined based on the coordinates of the respective ligand in each published structure. The receptor grid for docking was generated via Glide Receptor Grid Generation panel. The small molecules used in molecular docking were prepared for docking using LigPrep of the Schrödinger suite using default parameters. The docking results were visualized via PyMOL  48.
Enrichment analysis Docking and enrichment calculations were performed with Glide as described above. 8 known ligands of LAT1 were selected from the literature, using available IC50 data and ability to dock into the inwardopen conformation as selection criteria. 635 decoys were then generated with the DUD-E server 49 using these ligands. This set of 643 molecules was then screened against both inward-open (6IRT) and outward-occluded (7DSL) structurers, at the substrate binding site for LAT1. The results were evaluated by calculating the AUC (Area Under the Curve) and LogAUC, representing the ability of the virtual screening to discriminate known ligands among the set of decoys  64, 65. The corresponding plots (Fig. 1 ) show the percentage of known ligands correctly predicted (y-axis) within the top ranked subset of all database compounds (x-axis on logarithmic scale).
A 30 ns-long equilibration was performed using GROMACS  57  following the standard CHARMM-GUI protocol consisting in multiple consecutive simulations in the NVT and NPT ensembles. During these equilibration steps, harmonic restraints on the positions of the lipids, ligand, and protein atoms were gradually switched off. In the metainference simulation, a Gaussian noise model with one error parameter for each voxel of the cryo-EM map was used. 16 replicas of the system were used, and their initial configurations were randomly selected from the last 10ns-long step of the equilibration protocol. The metainference run was conducted for a total aggregated time of 10. 8 μs for 6IRT, 30 μs for the 7DSL and 20. 5 μs for 7DSK. All simulations were carried out using GROMACS 2020. 1 and the ISDB module  81  of the open-source, community-developed PLUMED library  80  [GitHub ISDB branch; https://github.
Docking of known ligands to LAT1 structures We applied molecular docking and ligand enrichment calculations to examine the pharmacological relevance of different conformations of LAT1's binding site and ligands, as well as key interactions between them (Fig. 1 ). This analysis was also conducted to evaluate the optimal parameters for rational design of new LAT1 ligands. Specifically, we analyzed the ability of molecular docking and the cryo-EM structure to distinguish between known ligands of LAT1 and decoy compounds, which have similar physical properties to the known ligands but possess different topological properties, to reduce likelihood of binding  46. Compounds were docked against two different conformations of LAT1: an inward-open conformation bound to the inhibitor BCH (PDB identifier: 6IRT)  8  and an outward-occluded conformation bound to the inhibitor JX-078 (PDB identifier: 7DSL)  10.
Virtual screening and functional testing of novel compounds for LAT1 Next, we computationally screened a library of purchasable compounds from the ZINC20 lead-like database (3. 8 million compounds) and amino-acid like compounds from Enamine (8,137 compounds), against the outward-occluded conformation. The top scoring compounds from each screen were prioritized for further analysis (Methods). Specifically, we prioritized compounds for experimental testing based on the following considerations: (i) Compounds contain both carboxy and amino group that make critical interactions with binding site residues. (ii) Compounds are predicted to make hydrogen bonds with S66, G67, G255 and F255. (iii) Compounds have a hydrophobic tail that extends deeper into the binding site, preferably to sub-pocket C or D (Fig.
Acknowledgments Funding for this work was provided by the following grants:  R01 GM108911  (A. S. ),  T32 GM062754  (K. H. ), and  R15 NS099981  (A. A. T. ) This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the  Icahn School of Medicine at Mount Sinai. M. B. acknowledges the support of the  French Agence Nationale de la Recherche (ANR) , under grant  ANR-20-CE45-0002  (project  EMMI ).
, 2015). We checked by simulation that the value of τ had no impact on the separation of the peaks, which are important for the interpretation of the spectra (Fig. S9 ). The spectra were recorded with 256 × 256 data points for the t1 and t2 time domains. The unmodulated part of the echo was removed by second-order polynomial subtraction. Final HYSCORE spectra were obtained by 2D Fourier transformation of the data set, using a Hamming apodization window function. EPR and HYSCORE spectra were simulated with the EasySpin toolbox for MATLAB (version 5. 2. 28)  (Stoll and Schweiger, 2006).
5 ). This procedure raises the question of the origin of all other correlation peaks and ridges present in the HYSCORE spectra (Fig. 5 ). To test the validity of the proposed analysis, the whole 14 N HYSCORE spectra of VO-P1 and VO-P2 complexes recorded at the m I = +3/2 ⊥ field setting were simulated with EasySpin software  (Stoll and Schweiger, 2006)  by adjusting the values of a iso , T and Q zz (the z component of the quadrupolar interaction). The result is shown in the middle of Fig. 5b  and in Fig. S10. Except for peak intensities, which are not correctly accounted for in the simulations, the main features of experimental HYSCORE spectra are well reproduced, taking into account the fact that the shape of the simulated spectra is very sensitive to the values of a iso , T and Q zz parameters.
Code availability. The Easyspin package for EPR simulation is available at https://www. easyspin. org/download. html (Stoll and  Schweiger, 2006). Matlab is a commercial software from Math-Works. Data availability. EPR raw and processed data have been deposited in Mendeley data repository available at https://doi. org/10. 17632/bnb9jsjs5r. 1  (Dutoit et al. , 2022). Supplement. Samples; EPR spectra; ENDOR spectra; derivation of Eq. (1); HYSCORE spectra; estimation of second-order contributions to the 14 N parameters from dq-dq and sq-dq correlation peaks. The supplement related to this article is available online at: https://doi. org/10. 5194/mr-3-111-2022-supplement.
Flow cytometry Immune cell phenotyping Cells were incubated with mouse serum to saturate the Fc receptors, and then with the appropriate antibody cocktail diluted in staining buffer: 1XPBS (Gibco), 0. 2% BSA (Sigma), 0. 02% sodium azide (Prolabo) and 2 mM EDTA (Invitrogen Life Technologies). Red blood cells were lysed in Optilyse C Solution (Beckman Coulter) according to the manufacturer's instructions. Cells were fixed in Cell Fix solution (BD) according to the manufacturer's instructions. Data were acquired in an LSRFortessaX20 flow cytometer. The FCS3. 0 files obtained were exported from BD FACSDiva software and imported into FlowJo v. 10. 5. 2 (BD Biosciences). Automatic compensation was calculated with FACSDiva software and single-stained compensation beads. This compensation matrix was analyzed in detail in FlowJo, with the N-by-N view feature and by investigating the pairwise expression of all proteins stained in this study.
Binding assay Purified human NK cells or Raji cells were incubated for 4 hours at 4 C with various doses of ANKET molecules in RPMI 1640 medium without phenol red (Gibco) supplemented with 1% heat-inactivated fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco) and 1 mM sodium pyruvate (Gibco). Cells were washed once in staining buffer and stained by incubation with a goat anti-human APC antibody (Jackson Immunoresearch, 109-136-088) for 20 minutes at 4 C. Cells were washed once and data were acquired on a LSRFortessa X-20 (BD) flow cytometer.
NHP monitoring Animals were observed daily, by trained staff, throughout the study period. For all procedures (handling, blood collection and treatment), animals were sedated by an intramuscular injection of ketamine (Imalgen 1000, 10 mg/kg) and medetomidine (Domitor 0. 03 mg/kg). Antisedan was administrated to reverse anesthesia (atipamezole, 0. 03 mg/kg). Body weight and temperature were followed throughout the study. Heart rate and oximetry data were recorded with a tensiometer (Vismo Bedside Monitor PVM-2701/ PVM-2703, Nihon Kohden). Behavior scores were determined on the basis of stereotypy, the appearance of the fur, body posture, e7 Cell Reports Medicine 3, 100783, October 18, 2022 Article breath, hydration, interaction with the observer and clinical symptoms (diarrhea, vomiting, mydriasis).
NHP cytokine and chemokine assessment Cytokines and chemokines including IFN-g, IL-1b, IL-10, IL-6, IL-8, MCP-1, MIP-1b and TNF-a were measured in serum of cynomolgus monkeys with multiplex assay kit from MILLIPLEXâ (#PRCYTOMAG-40K, Merck Millipore). Detection was performed using a magnetic Luminex instrument (MagPix). The results were analyzed using xPONENT 4. 2â software (provided by Luminex with MagPix instrument) using a 5-parameters fitting.
The sections were counterstained with hematoxylin, washed, dehydrated, cleared, and finally mounted in Epredia TM ClearVue TM Mountant XYL (Thermo Fisher Scientific) with a Shandon Clearvue Coverslipper (Thermo Fisher Scientific). Slides were scanned with a NanoZoomer S60 digital slide scanner (Hamamatsu). Positive staining for each marker was assessed visually, taking staining intensity and localization into account. Representative snapshots of regions of interest (ROIs) were taken with NDPView. 2 viewing software (Hamamatsu).
RNAseq analysis Sequencing data containing unique molecular identifiers (UMIs) were demuliplexed according to IDT guidelines. Briefly, sample barcodes were extracted for every read in every sequencer lane, each lane of bcl files was demultiplexed and per-sample unaligned BAM including UMI data were created, BAM files were converted to FASTQ files, FASTQ reads were mapped and the sorted aligned BAM files were then merged with sorted unaligned BAM files with UMI data. Picard software suite v2. 18. 29 was used (Broad Institute 2019). The reads were mapped onto the human genome (GRCh38) and the mouse genome (GRCm38) with STAR v2. 7. 0. 50 PCR replicates were removed with the Picard UmiAwareMarkDuplicatesWithMateCigar program (Broad Institute 2019). Gene expression was assessed with featureCounts in SubReads package v1.