dataesr/scientific-paragraphs-categorization huggingface dataset:
Servers Servers are used to provide sophisticated features to clients (Sect. 3. 10. 1. 2). Servers can run databases (database server), they can run the back-end part of application software products (application server), or they can support printing (printer server). Terminal servers run the front-end part of application software products, which traditionally have been implemented on and run by clients. If terminal servers are used, mere terminals (Sect. 3. 10. 1. 2) for displaying output and receiving input are sufficient. Further server types are name servers (for domain name system (DNS) management), DHCP servers (for dynamic IP assignment), mail servers (for email services), and web servers (for website management). There is a strong trend to virtualize servers. A "real" (i. e. , physical) server can simulate lots of the so-called virtual servers.
Extensive security measures are required at the interface between the intranet and the internet to prevent unauthorized access to the physical data processing systems within the intranet from outside the facility. These include, in particular, the so-called firewalls. Firewalls are physical data processing systems on which incoming and outgoing communication is monitored by software. To optimize security, the intranet itself is also partitioned into further security zones. Depending on the need for protection and the permitted user group of application systems, the physical data processing systems on which these application systems are installed are assigned to such security zones. Communication into and out of a security zone is also monitored using dedicated hardware.
Images that are generated by the MRI scanner and all other medical and administrative data from the MDMS, the RIS, and the patient administration system are stored in the Vendor-Neutral Archive PH, an open platform. Thus, these other application systems do not need their own database systems. All three facilities access the central EHR system, a clinical information system, of the health care network. This EHR system comprises patient information such as diagnoses, findings, and discharge letters received from all facilities. To manage the PINs from the different facilities, the health care network uses an MPI that assigns a transinstitutional PIN for the patients and maps the different PINs of the facilities to this transinstitutional PIN. This is a precondition for being able to build the EHRS in the health care network.
3. 12. 6. For the correctness of the model, application systems are only assigned to "leaf functions" but not to superordinate functions such as "execution of MRI diagnostics. " The architecture of Ernst Jokl Hospital (in the left of Fig. 3. 34) can be described as a star-based (DB n , AC n , V n ) architecture. There are at least two major application systems (AC n ), probably from different vendors (V n ), with their own respective database system (DB n ). The application systems-the patient administration system and the MDMS-exchange data via a communication server (star-based architecture) using HL7 V2 messages. Ploetzberg Hospital also features a star-based architecture which is, however, different from Ernst Jokl Hospital's architecture. At the center of Ploetzberg Hospital's (DB 1 , AC n , V n ) architecture, there is a VNA implemented as an open platform based on uniform information models in the openEHR standard.
The hospital's interoperability experts control these information models and stipulate and enforce their use whenever a new vendor system is added. The RIS at Ploetzberg Hospital's radiology department communicates with the MRI scanner using the DICOM standard. The DICOM images generated by the MRI scanner as well as the radiological reports that are documented with the help of the RIS are stored in the VNA. The institutional information system of the specialist medical office has a (DB 1 , AC 1 , V 1 , C n ) architecture because it only consists of a single application system with one database system. The application system combines the functionalities of a patient administration system and an MDMS. It could therefore be regarded as the CIS (or EHRS) of a medical practice (Sect. 3. 4. 15).
This comprehensive application system sends orders for radiological examinations or orders for surgical procedures to Ploetzberg Hospital or Ernst Jokl Hospital, respectively. For this, it uses the HL7 V2 standard. All three care facilities work together in the CityCare health care network, which provides a centralized EHRS that can receive as well as provide patient EHR data on demand. For data persistence, the central EHRS implements the openEHR standard for highly structured EHR data and an additional database system for documents. To receive patient data, the EHRS provides different interfaces for the three facilities in the network: an HL7 FHIR interface for Ernst Jokl Hospital's communication server, an HL7 V2 interface for the specialist medical office, and a native openEHR interface for Ploetzberg Hospital.
For cross-network identification of patients, the CityCare network has implemented an MPI based on an IHE integration profile. In the future, it is planned to implement a portal both for external physicians and for the patients themselves so they can access their data in the central EHRS. If Mr. Russo presents at Ernst Jokl Hospital, the local physician will look for available information on Mr. Russo in the hospital's MDMS. The system can then send a query to the CityCare network, asking for available information on Mr. Russo. The query is sent via Ernst Jokl Hospital's communication server to the network's central EHR system using the unique PIN for Mr. Russo. The central EHR system sends back Mr. Russo's data using the HL7 FHIR standard to the Ernst Jokl Hospital communication server and the data is forwarded to the EJK MDMS.
CityCare The following questions can be answered by reading the text and analyzing the 3LGM 2 figures of the CityCare Example 3. 11. (a) The EHRS and the VNA in CityCare are not linked with any function they support. Which function of the domain layer may (partly) be supported by these application systems? Which functions (as introduced in Sect. 3. 3) that are supported by these application systems could be added at the domain layer? (b) In which database systems shown in the logical tool layer (Fig. 3. 34) should the entity type "patient" be stored? (c) The MPI should receive messages containing PINs (entity type "patient") from all patient administration systems. Why is there no communication link between the MPI and the patient administration system of Ernst Jokl Hospital? (d) According to the matrix view, which functions are supported redundantly in CityCare? Discuss pros and cons of the functional redundancies in this scenario.
We verified the host galaxy assignment and SN type classification via discovery/follow-up papers for each individual SN (see Table  A1 ). We then verified by eye that the SNe indeed lie within the CO (2-1) maps. The PHANGS-ALMA footprint does not cover the outer disk regions of the galaxies surveyed. Because of this, we will miss any SNe that occur in these outer regions. This introduces a bias where fewer SNe will be associated with these lower-density environments. The PHANGS-ALMA survey also cannot "see" all of the molecular gas in the regions that are surveyed. The ∼70% completeness will cause an underreporting of SN-CO interactions occurring in low-density environments. We find 78 OSC objects in 33 galaxies within the PHANGS-ALMA footprint (see Table  A1 ). Of these, we discard a luminous red nova (LRN) reported in the catalog (AT 2020nqq), seven SN candidates  (AT 2018eoq, AT 2019pck, AT 2019npi, AT 2019npd, AT 2020cwh, AT 2020hol, and AT 2020juh) , the second entry of an SN reported by two groups under two different names (SN 2019ehk, which is classified as SN type Ib, and PTSS-19clju, which is listed as unclassified), and two Type II SNe that occurred on the edge of the mapped region of NGC 0628  (SN 2003gd) and NGC 4945 (SN 2005af)  where the CO (2-1) data appeared noisier and the image quality poorer.
(SN 1992eu also falls along the edge of NGC 1097ʼs map, but we keep it in the sample because the map quality appeared fine at its position. ) We also discard PSN +204. 332083-29. 896833 in NGC 5236, which has minimal reported data and is outside of the mapped region of the galaxy. Finally, we remove three SNe  (SN 1997bs, SN 2019krl, and SN 2019qyl)  from our sample because of uncertainty in their type classification and the likelihood that they are instead nonterminal explosions  (Adams & Kochanek 2015; Andrews et al. 2021; Jencson et al. 2021; Ransome et al. 2021). This brings our sample size to 63 SNe within 31 galaxies. We are interested in the coincidence of SNe and molecular gas; this measurement will be limited by the resolution of the ALMA data and the positional accuracy of the SN location determination.
We proceed, noting that this situation could be improved by more ALMA observations focused on modern SNe with welldetermined locations or by simply waiting for more SNe to explode in the PHANGS targets. For each SN in the PHANGS-ALMA footprint, we measure the line-integrated CO (2-1) intensity, I CO expressed in the units of K km s -1 , at the pixel location of the SN in the PHANGS-ALMA "broad" moment-zero map and its associated statistical uncertainty. The "broad" mask is the PHANGS high-completeness data product, expected to include all emission but with somewhat higher noise. Leroy et al. (2021b)  describe the masking scheme and the procedure used to generate uncertainty maps. Briefly, the mask includes any regions of the data cube detected at either coarse or high resolution. The associated uncertainty map is calculated based on a three-dimensional noise model derived from the empty regions of the data cube and then converted into the map following standard error propagation.
The PHANGS-ALMA survey 27  produced broad moment-zero maps at fixed physical resolutions of 60, 90, 120, 150, 500, 750, and 1000 pc, as allowed by the angular resolution of the data and the distance to the targets. We report our CO (2-1) intensity measurements at the pixel location of the SN sites and their statistical uncertainty in Table  A2  at resolutions of 60, 90, 120, and 150 pc. This I CO can be translated to a mass surface density of molecular gas, Σ mol expressed in the units of M e pc -2 , via a S = - - I i cos , 1 mol CO 2 1 CO 2 1 • • ( ) where I CO is the integrated CO (2-1) line intensity expressed in the units of K km s -1 , α CO is the CO (2-1) to H 2 conversion factor, which represents the ratio of the gas mass-to-CO (2-1) luminosity and has units of [M e (K km s -1 pc -2 ) -1 ], and i is the inclination of the host galaxy (see  Sun et al.
Supernova groups, including  Christopher Kochanek ,  Kris Stanek , and  Patrick Vallely , for useful discussions at several stages of the project. This work was carried out as part of the  PHANGS collaboration. Support for this work was provided by the  NSF  through award  SOSP SOSPADA-010  from the  NRAO , which supported the work of N. M. C. The work of N. M. C. , A. K. L. , and J. S. was partially supported by the  National Science Foundation (NSF)  under grants No. 1615105 ,  1615109 , and  1653300. The work of J. S. and A. K. L. is partially supported by the  National Aeronautics and Space Administration (NASA)  under ADAP grants  NNX16AF48G  and  NNX17AF39G. The work of J. S. is partially supported by the  Natural Sciences and Engineering Research Council of Canada (NSERC)  through the  Canadian Institute for Theoretical Astrophysics (CITA) National  Fellowship.
They also acknowledge funding from the  Heidelberg Cluster of Excellence "STRUCTURES"   in the framework of Germanyʼs Excellence Strategy  (grant  EXC-2181/1 ,  Project-ID 390900948 ) and from the  European Research Council  via the  ERC Synergy Grant   "ECOGAL"  (grant  855130 ). K. G. is supported by the  Australian Research Council  through the  Discovery Early Career Researcher Award (DECRA ) Fellowship  DE220100766  funded by the  Australian Government. E. S. and T. G. W. acknowledge funding from the  European Research Council (ERC)  under the  European Unionʼs Horizon 2020 research and innovation program  (grant agreement No. 694343 ). H. A. P. acknowledges support by the  Ministry of Science and Technology of Taiwan  under grant  110-2112-M-032-020-MY3. GAB acknowledges support from the  ANID BASAL.
The  Joint ALMA Observatory  is operated by  ESO ,  AUI/NRAO , and  NAOJ. The  National Radio Astronomy Observatory (NRAO)  is a facility of NSF operated under cooperative agreement by  Associated Universities, Inc (AUI). This work acknowledges the Open Supernova Catalog (OSC; Guillochon et al. 2017), last accessed on 2021 May 25, which included observations and metadata for ∼80,000 SNe and SNRs. This work has made use of  SAO/NASA  Astrophysics Data System, 33 the  NASA /IPAC Extragalactic Database (NED), which is operated by the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration , and the SIMBAD database, operated at  CDS, Strasbourg, France. This work has utilized the following software: Jupyter (Kluyver et al.
2016), Astropy (Astropy Collaboration et al. 2013, 2018), Pandas (Wes McKinney 2010), NumPy (van der Walt et al. 2011;Harris et al. 2020), SciPy (Virtanen et al. 2020),  Seaborn  (Waskom et al. 2017),  Matplotlib  (Hunter 2007), and GitHub. 34.
DIS3 is the major exonuclease regulating lncRNA levels in the cytoplasm To prioritize potential enzymes and co-factors that could regulate lncRNA decay in the cytoplasm, we rst performed differential expression (DE) analyses using public total RNA-seq datasets, including a XRN1 knock-out dataset from HEK293 cells (XNR1 KO)  45  , DIS3 mutants with inactivated RNB and PIN domains  13  (DIS3 PIN RNB mut), and knock-downs (KD) of cytoplasmic RNA decay cofactors HBS1LV1, HBS1LV3 and SKIV2L  46  (supplemental Table  S1 ). Among these, the DIS3 PIN RNB mutation showed the most striking upregulation of 72. 5% of all expressed lncRNAs (Fig. 1A  and Supplemental Table  S2 ). While inactivation of the cytoplasmic factors XRN1 or HBS1LV3, showed moderate percentages of lncRNAs differentially expressed (17.
2% and 19. 1% respectively), XRN1 KO had the higher absolute number of overexpressed lncRNAs (527 from 3059). Thus, we focused our comparative study on DIS3 and XRN1 enzymes. To identify the direct effect of DIS3 and XRN1 in lncRNAs stability, we opted for the existing DIS3 auxindegron cell model (DIS3-AID) and we constructed the XRN1-AID HCT116 cell line with TIR1 controlled by a Tet-On promoter (see materials and methods), which enabled timely removal of the enzymes  47  (Fig. S1A  and S1B). Total RNAs from the cytoplasmic fraction of cells induced or not for degron-mediated DIS3 or XRN1 depletion (Fig. S1C-S1F ) were sequenced (CYTO-seq) and DE analysis was performed. Since DIS3 and XRN1 can degrade cryptic and a priori unannotated transcripts  13, 25  , we quanti ed RNA expression by mapping the read counts on both standard GENCODE v26 annotation, and the de novo annotation generated by Scallop transcript assembler  48.
1C  and Fig. S1G -I and material and methods). The resulting metagene showed that, in contrast to mRNA, the lncRNAs present reads on both exons and introns at similar levels, suggesting that the DIS3-sensitive lncRNAs in the cytoplasm either remain broadly unprocessed or display unknown isoforms. This brought our attention to another group of DIS3 targets, that Scallop pro ling will miss-the intragenic or sense overlapping transcripts, such as enhancer RNAs (eRNAs), a well-known class of nuclear DIS3 substrate  49. Using the recently published annotation of eRNAs  50  , we further identi ed 3025 upregulated eRNAs (Fig 1D  and 1E ), raising a number of DIS3-sensitive transcripts (DISTs) to 5166 out of 8779 (59%) expressed lncRNAs and eRNAs. In conclusion, our analysis showed that in contrast to the minor role of XRN1 in netuning lncRNA steadystate levels (5.
3B  and 3C ). Interestingly, only 4% of DIST-ORFs were also present in cells in which the active exosome was present (Fig. 3D ), suggesting that some but very few of these lncRNAs might escape exosome-dependent degradation and be translated in normal conditions. Moreover, not more than 5% of DIST ORFs were present in different databases based on sequence or gene name analysis  [58] [59] [60]  , further reinforcing the notion that most of the DISTs with translatable ORFs were only found bound by ribosomes upon DIS3 depletion due to their upregulation in cytoplasm and thus, were not characterized in previous studies. The obvious determinant potentially involved in translation is the polyA tail [reviewed in  61  ]. Since eRNAs and lncRNAs are a class of transcripts with a variable status of polyadenylation  62, 63  , we performed polyAenriched RNA-seq on cytoplasmic RNAs followed by a DE analysis, to de ne which of the translated DISTs can be polyadenylated.
Cytoplasmic DISTs are detected in multiple myeloma cases DIS3 is an essential gene and it was shown to be mutated in several cancer types  66. To understand whether DISTs could be found in a disease context, we focused on Multiple Myeloma (MM), presenting various DIS3 mutations in up to 15% of cases  [67] [68] [69] [70] [71] [72]. Interestingly, some of the recurrent mutations in the DIS3 gene have been shown in vitro to impact the activity of its encoded exoribonuclease  73. Thus, we quanti ed DIST expression in the total RNA-seq dataset of bone marrow samples from a cohort of 211 MM patients and 64 healthy controls  74  using kallisto  75  and our custom-made annotation, including GENCODE, eRNAs and Scallop-identi ed transcripts. To identify cases that could accumulate DISTs because of impaired DIS3 activity, we analysed a repertoire of the mutations and single nucleotide polymorphisms present in the MM patients with identi ed mutations in DIS3 gene (33 patients).
MHCI puri cation and analysis of eluted peptides by mass spectrometry (MS) (as depicted in Fig. 6A ) revealed a total up to 9360 uniquely assigned peptides between the 3 experiments. The size distribution of detected peptides showed the most prevalent class of peptides bound by MHCI containing 9 amino acids (Fig. S4 A-C ). Next, we queried these peptides using MSFragger  80  and our database of DIST-ORFs (see materials and methods), ltering out sequences of the UniProt catalogue. In total, 9, 10, and 4 unique DIST-derived peptides were identi ed in DIS3-AID, KMM-1 and KMS27 cell lines, respectively. To assess the robustness of the identi cation of these peptides, we compared the observed retention time (RT) to the RT calculated by the DeepLC algorithm  81  based on peptide sequences. For both proteins and DIST-peptides databases, the Pearson correlation coe cient was between 0.
6D ). The ions predicted by Prosit  83  corresponded well with the ions identi ed in MS. Finally, we assessed the speci city of expression at RNA level of peptide-encoding DISTs in bone marrow samples of MM patients in comparison with healthy controls of the same cohort and 26 healthy tissues from GTEx database for 66 Ribo-seq selected DIST-ORFs and the DIST-ORFs with peptides initially detected in immunopeptidomic analysis (Fig. S5E  and S5F. Expression was quanti ed based on transcripts per million (TPM), only for DISTs with counts above 1 of 90 th percentile values and detected as polyadenylated in our study. This stringent ltering resulted in nal list of 16 DISTs with translatable ORFs and speci c expression only in MM (Fig. 6E ). These lncRNAs encode potential TSAs in MM with DIS3 gene mutations.
DISTs are templates for the immune peptidome Among the potentially translated DISTs, among 3 tested cell lines we detected 18 peptides with high con dence (Fig. S5F  and Table  S8 ) speci cally derived from DIST-ORFs in an immunopeptidomic approach. This proves not only the translation of DIST-derived peptides but also their capacity to be presented by MHCI. However, none of the peptides detected by immunopeptidomic method are among the TSAs prioritized by DIST-ORFs region differential expression (Fig 5B  and 5C ). The reasons could be that the putative peptides would not be good substrates for the MHC class1 presentation, and/or that the mass spectrometry is not sensitive enough to capture these speci c peptides. Mass spectrometry data analysis is based on the prediction of the peptides from the spectra information and can be highly dependent on the type of equipment, sample preparation and dosage.
(2018). The TIMS-MS survey scan was acquired between 0. 70 and 1. 45 Vs/cm2 and 100-1,700 m/z with a ramp time of 100 ms. The 10 PASEF scans contained on average 12 MS/MS scans per PASEF scan with a collision energy of 10 eV. Precursors with 1-5 charges were selected with the target value set to 20,000 a. u and intensity threshold to 2,500 a. u. Precursors were dynamically excluded for 0. 4 s. The timsTOF Pro was controlled by the OtofControl 6. 0 software (Bruker Daltonik GmbH). Ten PASEF scans can contain up to 12 MS/MS scans per PASEF scan. Data were analyzed MS Fragger, integrated in the FragPipe pipeline  80. The build-in "Nonspeci c-HLA" work ow was used. Precursor and fragment mass tolerance was set at 20ppm. Oxidation (M), N-terminal acetylation, pyroglutamine, pyroglutamate and cysteinylation were set as variable modi cations.
The standard database search validation tools from the Nonspeci c-HLA work ow were also used, including MSBooster, which is a rescoring tool that uses deep learning predictions of RT fragment intensities 104. The FDR of peptide and PSM matches was set 1% and probability above 0. 9. Uniprot human reference proteome database was concatenated with the custom lncRNA ORF database. The querry list included all the DIST-ORFs predicted to be actively translated in DIS3-depleted cells in Ribo-seq experiment, combined with the ribotricer prediction of ORF based only on the lncRNA speci c sequences for the remaining 638 lncRNAs that were upregulated in cell line and MM data and not detected by Ribo-seq experiment. smiFISH For smiFISH experiments, cells were passaged at least 2 times after thawing. Two days before experiment, the cells were seeded on coverslips coated with 0.
For each image set threshold (for ZNF674-AS1) or automatic thresholding (for CTD-2371O3. 3) was used to adapt for variable background levels. Two independent replicates of the experiment were performed with DIS3-AID cell line incubated with or without auxin for 1h. For each replicate at least 90 cells were quanti ed. Impact of DIS3 mutations on protein structure/activity Initially, the atomic structures available for the DIS3 protein were analyzed, with the position altered residues, with respect to the de ned catalytic active sites  73. Then a systematic analysis of the structural alterations observed for DIS3 in patients was performed, using a combination of the missense3D software together with the structural analysis of the available atomic structures of the protein 100,106. The atomic model (PDB 6D6Q) 100 was visualized using USCF Chimera 101.
Transcriptomic pro ling Transcriptome assembly was performed on each RNA-seq alignment using Scallop v0. 10. 5, with the following parameters: -min_transcript_length_base 200 -library_type " rst" -min_splice_bundary_hits 5 -min_transcript_coverage 10 -min_single_exon_coverage 20 scheme depicted in Fig. S6A. The obtained GTF annotations of all samples were merged with cuffmerge from cu inks v2. 2. 1 107 , then genes for which the exons overlap GENCODE v26 annotation were ltered out with BEDTools v2. 29  108. The result was nally combined with GENCODE v26 (https://www. gencodegenes. org/human/release_26. html) and eRNAs annotation retrieved from  50  for downstream analysis.