dataesr/scientific-paragraphs-categorization huggingface dataset:
Although most CDI toxins characterized to date have nuclease activities, there is a considerable range of substrate specificities. [56]  We recently determined the high-resolution crystal structure of a novel CDI toxin-immunity protein complex from the nosocomial pathogen S. marcescens BWH57 (Figure  4 ). The CdiA-CT BWH57 region is $280 residues in length and is composed to two domains. The Nterminal domain of CdiA-CT BWH57 shares 69% sequence identity with the corresponding domain in CdiA-CT o11 EC869 from Escherichia coli EC869 (PDB: 4G6U). 51 This N-terminal domain is required for toxin translocation into the cytosol of target bacteria,  57  but this region is not resolved in the CdiA-CT•CdiI BWH57 complex structure as it was cleaved off by in situ proteolysis prior to crystallization.
coli K-12 (PDB: 3HI2),  59  BrnT from Brucella abortus (PDB: 3U97),  60  isoacceptor-specific CDI tRNase toxins from Klebsiella pneumoniae 342 and E. coli NC101 (PDB: 6CP9, 5I4Q),  55, 56  and the C-terminal nuclease domains of colicin E5 (PDB: 2DJH)  61  and colicin D (PDB: 1V74). 62 In contrast, DALI identified only very distant structural homologs of CdiA-CT BWH57 , suggesting that it may represent a new protein fold. The CdiA-CT BWH57 nuclease domain includes three α-helices and one 3 10 helix, four antiparallel β-strands arranged in a small concave β-sheet and two β-strands that form a hairpin. The β-sheet and β-hairpin wrap around α4, which serves as a core of this fold. Helix α3 has a significant kink and helix α1 interacts with the β-hairpin. CdiI BWH57 has a simple α/β fold with two α-helices, three negatively charged patch on the immunity protein (Figure  4B ).
| The J-base binding domain of JBP3 (CASP: T1068, PDB:N/A). Provided by Athanassios Adamopoulos, Tatjana Heidebrecht, and Anastassis Perrakis The modified DNA nucleotide β-D-glucopyranosyloxymethyluracil (base J) replaces 1% of the thymine (T) nucleotides in kinetoplastid protozoa. 99% of base J is found in telomeric repeats; the remaining 1% has a functional role in transcription termination. 86 Base J is specifically recognized by JBP1, a protein central to the epigenetic replication and biosynthesis of base J. JBP1 recognizes base J by a short ($150 residues) J-base DNA-binding domain (J-DBD), which adopts a helix-turn-helix (HTH) fold that we previously described. 87 JBP1 binds base J DNA, and preferentially hydroxylates a T 13 base pairs downstream (but not upstream) on the complementary DNA strand.
To our surprise, most groups and servers did a very good job at predicting this new variant of the coiled-coil fold. It is likely that several predictors have benefitted from the structure of the first representative that we had published for this fold previously, from the fungus Serendipita indica (PDB: 5LOS). 105 This instance has 23% sequence identity to Tuna, 15% to Nitro and 19% to Meio. However, it was not identified as a template by the CASP prediction center for either of the three targets, and also sequence searches with HHpred 109 using the standard settings of the MPI Bioinformatics Toolkit (as of March 2021)  110  do not identify it as a template for every target. Nevertheless, each of the three targets was predicted with a GDT-TS > 50 by more than 100 groups and with a GDT-TS > 80 by more than 30 groups.
One detail, however, was only predicted correctly by AlphaFold2: actually unrelated to the histidine zipper fold, the N-terminal extension of Tuna, seen just in a few homologs from Methylobacter species, forms a polyproline-II helix that buttresses the N-terminal α-helix, similar to an interaction engineered by Woolfson and colleagues into a stable miniprotein, PDB: 5LO3. 112 11 | Duck hepatitis B core protein (CASP: T1099, PDB: 6YGH). Provided by Cihan Makbul and Bettina Böttcher Worldwide more than 250 million people are chronic carriers of hepatitis B virus (HBV) and have an increased risk for developing liver cancer or liver cirrhosis. Despite vaccination programmes, about 900 000 people die each year from HBV infection and related complications. HBV is an enveloped virus that belongs to the family of Hepadnaviridae.
However, in the experimental structure of DHBc the N-terminal helix is not a part of this dimer interface and points toward the capsid interior (Figure  13 ). In conclusion, many predictions recapitulated key-features of the fold of DHBc but failed to predict changes in the oligomerization interfaces that deviated from huHBc. 2. 12 | Cancer biology and the ASCC1 alkylation response protein structure by Naga Babu Chinnam, John A. Tainer, and Susan E. Tsutakawa (CASP: T1101, PDB: N/A) Originating from medical studies on the warfare use of mustard gas in World War I, alkylation chemotherapy is among the most widely used forms of systemic therapy for cancer today. 121, 122 Its damage to DNA and subsequent disruption of replication in cancer cells was thought to the primary reason for its efficacy against cancer.
Bacteriophage T5 tail tip complex (CASP: H1060 and T1061, PDB: N/A). Provided by Romain Linares and Cécile Breyton Bacteriophages are the most abundant biological organisms on Earth. As bacterial viruses, they have an utmost impact on the regulation, diversity, evolution, and pathogeny of all bacterial populations. The large majority of bacteriophages are composed of a capsid, which protects the viral double stranded DNA, and a tail, which serves to recognize the host, perforate its cell wall, and safely deliver the viral genome into the bacterial cytoplasm. The mechanism of cell wall perforation is relatively well documented for Myoviridae, phages with a long contractile tail, and related contractile injection bacterial systems. 34 Much less is known in the case of Siphoviridae, phages that bear a long, flexible tail, which represent 60% of all phages.
BIL2: Holo structure from apo sequence (CASP: T1034, PDB: 6Y75, 6TMM). Provided by Valerio Chiarini and Andrea Ilari Inteins are invasive protein domains translated together with Nterminal and C-terminal host protein fragments, called N and C exteins, respectively. Upon translation, they are able to catalyze a reaction known as protein splicing, which allows the intein to escape from the homing protein while joining the two exteins without leaving any trace of the intein insertion. This mechanism does not compromise the host protein functionality, and inteins are maintained and passed down as harmless genomic elements.
I G U R E 6 Structure superposition of the 3D model from AlphaFold2 (salmon) with the BIL2 experimentally determined structures (cornflower blue and magenta). The catalytic residue H69, as well as the Zn coordinating residues H125 and H148 residues, are highlighted in sticks. Labels indicate per-residue RMSD values over backbone and side chains (calculated with CHIMERA). Global RMSD values (calculated with Superpose) over alpha carbons, backbone, and side chains atoms are reported in the bottom part of the figure Structure of BonA from A. baumannii (CASP: T1054, PDB: 6V4V). Provided by Rhys Grinter.
Structure of C. bescii N4-cytosine methyltransferase (CASP: T1057, PDB: 7M6B). Provided by Markus Alahuhta, Vladimir V. Lunin, and Yannick J. Bomble C. bescii α-class N4-cytosine methyltransferase (M. CbeI) is a thermostable DNA restriction enzyme that is required for transformation of E. coli DNA to C. bescii. 82 The ability to genetically engineer this thermophilic and naturally cellulolytic organism is important for consolidated bioprocessing (CBP) of biomass to biofuels and biochemicals. M. CbeI is structurally somewhat similar (RMSD 2. 64 Å and secondary structure similarity of 43% by PDBeFold [https://www. ebi. ac. uk/msd-srv/ssm/]) to E. coli DNA adenine methyltransferase (PDB: 4RTR) but shows no sequence similarity with any characterized N4-cytosine methyltransferase. We determined the structure of M.
coli DNA adenine methyltransferase structure (PDB code 4RTR) where the S-adenosyl methionine (SAM) cofactor is bound in a different conformation compared to M. CbeI. The authors of this model likely mainly relied on structure comparison and did not minimize their model with SAM as part of their model. The second ranked model T1057TS335 also had a very similar overall structure (GDT-TS 89. 23, all atom RMSD 0. 759 Å) as the F I G U R E 7 Comparison of the BonA experimental structure and CASP14 model. (A) The X-ray crystal structure of BonA-27N, showing the symmetrical dimer observed in the crystal structure. (B) One molecule of the BonA-27N dimer shown in Panel A, with α-helix 1 of BON1 (αH1 of BON1), which is disordered in the crystal structure, modeled as an unstructured polypeptide in orange.
Histidine zipper coiled coils (CASP: T1083, T1084, T1087; PDB: N/A). Provided by Marcus D. Hartmann and Andrei N. Lupas α-Helical coiled coils are among the most ubiquitous and bestunderstood protein folds. 105 They are bundles of at least two α-helices with a specific and repetitive packing and architecture, in which the interface between helices is typically dominated by F I G U R E 1 1 (A) Superposition of the Tsp1 monomer crystal structure (golden yellow) with top two CASP14 models T1078TS427_2-D1 (blue) and T1078TS314_1-D1 (pink). Also, given here is the plot of CA-CA distance (in Å) between crystal structure and CASP14 model T1078TS427_2-D1. (B) Comparison of dimeric structure of Tsp1 (golden yellow) with the best predicted multimeric model (T1078TS177_3o, cyan).
Single chain of the Tuna (T1087) crystal structure (yellow) superimposed with exemplary predictions (red: AlphaFold2; cyan: FEIG-S, green: BAKER-ROBETTA). Tuna forms two coiled-coil interfaces, one intra-chain and one for homo-dimerization with another chain. Although only the monomer was a prediction target in CASP 14, several residues of the inter-chain interface were predicted in the correct rotamer by the top-ranking groups and servers. The N-terminal extension containing a polyproline-II helix is only shown for AlphaFold2, which predicted it most precisely in conformation and position F I G U R E 1 3 Structures of DHBc PDB: 6YGH 114  and huHBc PDB: 6HTX. 115 (A) View of the huHBc monomer perpendicular to the dimer axis. The approximate position of the capsid shell is indicated to mark the protruding part of the spikes.
ACKNOWLEDGMENTS CASP experiment and open access fees for this article are supported by the  US National Institute of General Medical Sciences (NIGMS/ NIH) , grant number  GM100482. H1036  and  T1036 : We thank the  Stanford-SLAC Cryo-EM Facility , the  Stanford Bio-X   Interdisciplinary Initiatives Program  and  NIH  grants  P41-GM103832  (WC),.
2. 3 | 3 Structure of polymorphic CDI toxin-immunity protein complex from S. marcescens (CASP: H1065, T1065s1, T1065s2, PDB: 7M5F). Provided by Karolina Michalska, Youngchang Kim, William (Sam) Nutt, Lucy Stols, Christopher S. Hayes, and Andrzej Joachimiak.
2. 4 | 4 BIL2: Holo structure from apo sequence (CASP: T1034, PDB: 6Y75, 6TMM). Provided by Valerio Chiarini and Andrea Ilari Inteins are invasive protein domains translated together with Nterminal and C-terminal host protein fragments, called N and C exteins, respectively. Upon translation, they are able to catalyze a reaction known as protein splicing, which allows the intein to escape from the homing protein while joining the two exteins without leaving any trace of the intein insertion. This mechanism does not compromise the host protein functionality, and inteins are maintained and passed down as harmless genomic elements.
F 2. 5 | 25 I G U R E 6 Structure superposition of the 3D model from AlphaFold2 (salmon) with the BIL2 experimentally determined structures (cornflower blue and magenta). The catalytic residue H69, as well as the Zn coordinating residues H125 and H148 residues, are highlighted in sticks. Labels indicate per-residue RMSD values over backbone and side chains (calculated with CHIMERA). Global RMSD values (calculated with Superpose) over alpha carbons, backbone, and side chains atoms are reported in the bottom part of the figure Structure of BonA from A. baumannii (CASP: T1054, PDB: 6V4V). Provided by Rhys Grinter.
2. 6 | 6 Structure of C. bescii N4-cytosine methyltransferase (CASP: T1057, PDB: 7M6B). Provided by Markus Alahuhta, Vladimir V. Lunin, and Yannick J. Bomble C. bescii α-class N4-cytosine methyltransferase (M. CbeI) is a thermostable DNA restriction enzyme that is required for transformation of E. coli DNA to C. bescii. 82 The ability to genetically engineer this thermophilic and naturally cellulolytic organism is important for consolidated bioprocessing (CBP) of biomass to biofuels and biochemicals. M. CbeI is structurally somewhat similar (RMSD 2. 64 Å and secondary structure similarity of 43% by PDBeFold [https://www. ebi. ac. uk/msd-srv/ssm/]) to E. coli DNA adenine methyltransferase (PDB: 4RTR) but shows no sequence similarity with any characterized N4-cytosine methyltransferase. We determined the structure of M.
2. 10 | 10 Histidine zipper coiled coils (CASP: T1083, T1084, T1087; PDB: N/A). Provided by Marcus D. Hartmann and Andrei N. Lupas α-Helical coiled coils are among the most ubiquitous and bestunderstood protein folds. 105 They are bundles of at least two α-helices with a specific and repetitive packing and architecture, in which the interface between helices is typically dominated by F I G U R E 1 1 (A) Superposition of the Tsp1 monomer crystal structure (golden yellow) with top two CASP14 models T1078TS427_2-D1 (blue) and T1078TS314_1-D1 (pink). Also, given here is the plot of CA-CA distance (in Å) between crystal structure and CASP14 model T1078TS427_2-D1. (B) Comparison of dimeric structure of Tsp1 (golden yellow) with the best predicted multimeric model (T1078TS177_3o, cyan).
F I G U R E 1 2 2 Single chain of the Tuna (T1087) crystal structure (yellow) superimposed with exemplary predictions (red: AlphaFold2; cyan: FEIG-S, green: BAKER-ROBETTA). Tuna forms two coiled-coil interfaces, one intra-chain and one for homo-dimerization with another chain. Although only the monomer was a prediction target in CASP 14, several residues of the inter-chain interface were predicted in the correct rotamer by the top-ranking groups and servers. The N-terminal extension containing a polyproline-II helix is only shown for AlphaFold2, which predicted it most precisely in conformation and position F I G U R E 1 3 Structures of DHBc PDB: 6YGH 114  and huHBc PDB: 6HTX. 115 (A) View of the huHBc monomer perpendicular to the dimer axis. The approximate position of the capsid shell is indicated to mark the protruding part of the spikes.
42 to 1. 5 mm whereas the vented gas velocity ranged from 7 to 14 cm. s-1) on intermediate scale experiments to meet the efficiency criterion of the aerosol filtration (Decontamination Factor (DF) > 10 for Cs2CÜ3 aerosols tested with 0. 6 < MMAD < 1. 5 |im (Mass Median Aerodynamic Diameter)). Following Chernobyl accident (1986), sand filters have been implemented on French Nuclear Power Plants (NPPs) from 1987 to 1989 to avoid any loss of the containment integrity (by the pressure increase) and limit the ground long-term contamination (especially by 137Cs) in case of accident. FUCHIA program (1990)  [3, 4]  was then performed within the aim to validate the filtration requirements (DF > 10 for aerosols with MMAD ~ 1 |im) of the installed sand bed filters (a scale 1 of the filter was tested).
It was recently found that gaseous I2 (and CH3I) are not well retained neither by the MF (DF(I2) ~ 10, DF(CH3I) = 1) nor by the sand filter (DF(I2, CH3I) ~ 1  [6]. Another result from FUCHIA program  [3]  (on a scale 1 sand bed filter) was that, even though I2 is not trapped by the sand itself, it could be adsorbed on the steel surfaces of the line and on the deposited aerosols on the steel/sand surfaces, leading to an estimated DF(I2)line ~ 10. It is thus expected that any gaseous inorganic and organic iodine compounds coming either from the containment or from the decomposition of iodine aerosols trapped on the MF or the sand filter would be partially or totally released to the environment though the venting line. The quantification of how much gaseous iodine could be released from the MF and the sand filter to the environment is thus crucial for the source term determination.
Acknowledgments Authors acknowledge the  French Government  through the  "Investissements d'Avenir" program  managed by the  National Research Agency (ANR)  for supporting  MIRE  project (grant agreement N°  ANR-11-RSNR-0013-01 ) and the MIRE partners for their support ( Aix-Marseille Université ,  Framatome ,  CNRS ,  Electricité de France ,  IRSN ,  Université de Lorraine, ARMINES, Université Lille 1). Authors also want to thank the  European Atomic Energy Community (Euratom)  for supporting the  PASSAM  project in the frame of the 7th framework program FP7/2007-2013 under the grant agreement n°  323217  and the PASSAM partners (AREVA,  CIEMAT ,  CSIC ,  Electricité de France ,  IRSN ,  PSI ,  RSE ,  VTT  and  Université de Lorraine ).
Adenocarcinomic human alveolar basal epithelial cells (A549 cells) and the ecotoxicology model Saccharomyces cerevisiae were selected as unicellular eukaryotic systems to assess the cytotoxicity of the nanomaterials. Cell viability and reactive oxygen species (ROS) determinations demonstrated different toxicity levels depending on the cellular model used. While both 2D WS 2 suspensions showed very low toxicity towards the A549 cells, a comparable concentration (160 mg L À1 ) reduced the viability of yeast cells. The toxicity of a nano size 2D WS 2 commercialized in dry form from the same provider was also assessed, showing ability to reduce yeast cells viability as well. Overall, the presented data reveal the physico-chemical properties and the.
X-ray photoelectron spectroscopy The surface analysis measurements were performed in a UHV chamber (P~5 Â 10 À10 mbar) equipped with a SPECS Phoibos 100-1D-DLD hemispherical electron analyzer and a nonmonochromatized dual-anode Mg/Al x-ray source for XPS. The spectra were recorded with AlKa at 1486. 6 eV photon energy using analyzer pass energy of 10 eV which results to full width at half maximum (FWHM) of 0. 85 eV for Ag3d5/2 line. The analyzed area was a rectangle with dimensions 7x15 mm 2. Spectra were accumulated and processed using SpecsLab Prodigy (Specs GmbH, Berlin) software. The XPS peaks were deconvoluted with mixed Gaussian e Lorentzian functions after a Shirley background subtraction. The WS 2 -ACS-M and WS 2 -ACS-N samples were prepared by drop casting the dispersion on Si wafers, whereas powder of the WS 2 -ALK-N was pressed on Indium foil.
(45. 72 cm) layer, denotes a Wasatchian 7 North American land mammal age. The holotype of Proxyelia pankowskii gen. et sp. nov. is housed in the collection of Fossil Butte National Monument, Wyoming, USA, under the collection number FOBU14313. Photographs have been taken with a FUJI GFX 50S camera. The figures were composed with Adobe Illustrator CC2019 and Photoshop CC2019 software. Wing venation terminology is adapted from  Goulet and Hubert (1993). Published work and nomenclatural acts are registered in ZooBank (http://zoobank. org/, last access: 5 November 2021), with the following life science identifier (LSID) (reference): urn:lsid:zoobank. org:pub:578A65E0-4FE8-4852-A840-AAC4FAA2A5F7. urn:lsid:zoobank. org:act:7F15690A-0437-4F67-AF19-D9FFE1F3CD18.
Acknowledgements. We give our sincere thanks to  Michael Pankowski  for his time scouring the internet looking for scientifically significant fossils being offered for sale. Without his effort and generosity (and support) this paper would not be possible. We are grateful to  Talia Karim  ( University of Colorado Museum of Natural History ) for the photographs of  Paleoxyela nearctica gen. et sp. nov. (Specimen UCM 18643). We warmly thank the two reviewers  Alexandr P. Rasnitsyn  and  Lars Vilhelmsen  for their constructive and useful comments on the early version of the manuscript. We also thank  Florian Witzmann  for managing the article during the editing process. Text and images by  Arvid Aase  were completed as part of his official duties and as such are considered to be a US Government publication.
Therefore the spacecraft observes the GRS (20   16 ), to these we add the GRS overflights data from PJ18 and PJ21. Figure  1  shows the Juno tracks over Jupiter's reference surface during the latter passes. Figure  1 : Geometry of the Juno GRS gravity observations. The GRS velocity field (black arrows) at the time of Juno's PJ21  (17)  and Juno tracks during PJ18 and PJ21 (cyan and green lines), superimposed on JunoCam imaging of the GRS collected between PJ7 and PJ21  (18). The spacecraft altitude during the GRS closest approach was 13,000 km and 19,000 km, with eastward longitudinal offsets of 11 • and 2 • , during PJ18 and PJ21, respectively. We combine the Juno gravity measurements using a least-squares multiarc filter implemented in the orbit determination software MONTE  (19) , which was also used for trajectory integration and data analysis.
The range-rate integration time was 60 seconds and the typical noise Root Mean Square (RMS) was between 5 and 10 µ ms -1 (oneway). The filter requires the accurate reconstruction of the Juno trajectory, including every acceleration acting on the spacecraft, gravitational and non-gravitational  (5, 16). We searched for the GRS gravity signature in the Juno overflight data by processing the range-rate residuals while solving for the zonal gravity field of Jupiter. Previous analyses (  16 ) have discussed the difficulty of fitting the Juno range-rate data from multiple perijoves without allowing for longitudinal or temporal variations of the gravity field. The range-rate residuals for PJ18 and PJ21, after removing the effect of the zonal gravity field, show non-negligible signals over time scales of ±1 h around closest approach to Jupiter (fig.
3A. The density profile resembles a dipole, with a positive mascon mass, labeled as GM A (where G is the gravitational constant), in the upper levels and a negative mass (GM B ) at depth. The sum of the two masses is zero, to first order  (20). The relationship between the mass and the separation between the positive and negative anomaly is injective (fig. S3 ), therefore the depth (H) can be inferred from estimating the mass using MONTE (13). In the orbit determination software, we model the vortex as a pair of flat disk mascons, whose masses are constrained to be equal and opposite in sign. Deeper winds entail a larger mass involved in the circulation of the GRS and an increasing vertical distance between the mascons. A sign inversion between the upper and deeper levels was also observed in MWR measurements during Juno's seventh perijove  (3).
Acknowledgments We thank  David J. Stevenson ,  Andrew P. Ingersoll , the  Juno Interiors and Atmospheric Working Groups  for useful discussions. We thank citizen scientist  Björn Jónsson , who processed the background image in fig. 1 as part of  Juno's JunoCam outreach program. We thank  Nimrod Gavriel  for helping with the graphics of fig. 1. Funding: This research was carried out at the  Jet Propulsion Laboratory, California Institute of Technology (MP, SML, DRB, WMF, KO) , under contract number  80NM0018D0004  with the  National Aeronautics and Space Administration (NASA) ; at the  Weizmann Institute of Science (WIS)  in Israel (EG and YK) with support from the  Israeli Space Agency  and the  Helen Kimmel center for Planetary Science at WIS ; at  Sapienza University of Rome  (DD and LI) under contract number 2017-40-H.