dataesr/scientific-paragraphs-categorization huggingface dataset:
(55). To assess the agreement between the FM signal and the manually segmented lysosomes in EM, the intersection between the FM and EM segmentations was computed and divided by the number of pixels in the EM segmentation. This measure is also known as the true positive rate (TPR). (B) For dataset EMPIAR-11537, four endosomes were manually segmented and the agreement of the FM signal with the EM volume was quantified as described above. All image visualisations generated with napari. A ROI can also be drawn on the LM image using the 'Shapes' layer in napari to increase registration performance. The plugin also allows users the flexibility to choose between rigid, affine and non-linear registration and tune parameters such as the LM segmentation settings, point cloud sampling density and the maximum number of iterations for the point cloud registration.
ACKNOWLEDGEMENTS This work was supported by  The Francis Crick Institute  which receives its core funding from  Cancer Research UK  ( CC001999 ), the  UK Medical Research Council  ( CC001999 ), and the  Wellcome Trust  ( CC001999 ). D. K. was funded by  The Francis Crick Institute  and the  Pasteur-Paris University   International doctoral program  (PPU). R. F. L. was supported by a  Medical Research Council Skills development fellowship  ( MR/T027924/1 ). R. H. is supported by the  Gulbenkian Foundation (Fundaçaõ Calouste Gulbenkian)  and received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement number  101001332 ), the  European Molecular Biology Organization (EMBO)   Installation Grant  ( EMBO-2020-IG4734 ) and the  Chan Zuckerberg Initiative   Visual Proteomics Grant  ( vpi-0000000044 ).
CONTRIBUTIONS Daniel Krentzel ,  Romain F. Laine ,  Ricardo Henriques ,  Lucy M. Collinson  and  Martin L. Jones  developed the initial idea for this project. Daniel Krentzel  conceived  CLEM-Reg  and directed this project. Daniel Krentzel ,  Matouš Elphick ,  Martin L. Jones  and  Lucy M. Collinson  wrote the manuscript. Daniel Krentzel  and  Matouš Elphick  developed the source-code. Romain F. Laine  collected preliminary CLEM data and  Marie-Charlotte Domart  ( Electron Microscopy Science Technology Platform, The Francis Crick Institute ) and  Christopher J. Peddie  ( Electron Microscopy Science Technology Platform, The Francis Crick Institute ) collected the benchmark CLEM datasets. All authors contributed to the revisions of the manuscript.
//www. ebi. ac. uk/empiar/EMPIAR-11537/) FM (https://www. ebi. ac. uk/biostudies/bioimages/studies/S-BSST1075). Code for CLEM-Reg (under MIT licence) is available on GitHub (https://github. com/krentzd/napari-clemreg). The datasets used in this study have been deposited at EMPIAR and Bioimage Archive. EMPIAR-10819: EM (https://www. ebi. ac. uk/empiar/EMPIAR-10819/) FM (https://www. ebi. ac. uk/biostudies/bioimages/studies/S-BSST707). EMPIAR-11537: EM (https:.
Later, the di-2-pyridylketone TSC Dp44mT (di-2pyridylketone 4,4-dimethyl-3-thiosemicarbazone, see Scheme 1) and its derivative DpC (di-2-pyridylketone 4-cyclohexyl-4methyl-3-thiosemicarbazone), which is currently implicated in clinical trials (NCT02688101), showed higher cytotoxicity (nM range) than 3AP (μM range) and more advantageous pharmacokinetics. The best-known mode of action of anticancer TSCs is iron chelation and the inhibition of the Fe-dependent enzyme ribonucleotide reductase, which is essential for DNA synthesis and cell proliferation, was the first identified target. Since then multiple other effects have been described. [6] [7] [8] [9]  In addition to iron, Cu chelation also emerged as an additional mechanism for some TSCs. In particular, Dp44mT and its derivatives, but not 3AP, have shown a pronounced synergism with Cu II salts, suggesting the involvement of Cu chelation and, possibly, Cu-catalyzed production of reactive oxygen species (ROS) in their mode of action.
5 mW, modulation amplitude of 1 G, time constant of ∼5 ms, and conversion time of ∼12. 5 ms. Every 17 s, a single scan (sweeping time of ∼10 s) was then acquired to obtain the kinetics of TEMPOL reduction over ∼60 min. All spectra were best simulated, and the resulting simulations were doubly integrated to relatively quantify the concentration of remaining TEMPOL. Data analysis and simulations based on experimental data were performed using Xenon (Bruker Biospin GmbH, Germany) and lab-made routines based on Easyspin Toolbox under Matlab (Mathworks) environment. 22  UV-Vis Spectroscopy. UV-vis measurements were carried out in 1 cm path quartz cuvettes using an Agilent Cary 60 spectrophotometer. DFT. The Gaussian16 software package  23  was used to carry out all the calculations in the framework of DFT and its TD-DFT extension.
Results Accurate map of protonation states in substrate-free TthSHMT. SHMTs from prokaryotic sources function as biological homodimers, whereas eukaryotic SHMTs exist as homotetramers composed of a dimer of dimers  17, 18. TthSHMT crystallizes as a dimer with virtually equivalent active sites in protomers A and B, as seen in the cryogenic X-ray structure (PDB ID 2DKJ, unpublished). Similar to the other fold type I PLPdependent enzymes, each protomer of TthSHMT can be divided into large and small domains  1, 65. The large domain (residues 33-284) is composed of a seven-strand mixed β-sheet surrounded by α-helices in an α/β/α sandwich fold (Fig. S4 ). The small domain (residues 7-32 and 285-407) is made up of residues from both the N-and C-termini and the structure is dictated by antiparallel β strands and α-helices in a two-fold α/β sandwich.
The small domain is primarily responsible for establishing intersubunit contacts  54, 66, 67. Each active site is located at the corresponding dimer interface and is constructed from residues of both protomers. To visualize the active site of SHMT at the atomic level of detail, we obtained a 2. 3 Å neutron crystallographic structure of substrate-free TthSHMT in the internal aldimine state jointly refined with 2. 0 Å X-ray diffraction data (Table  S1 , Supplementary Data 1, PDB ID 8SUJ). We were unable to obtain neutron diffraction data from the P6 5 22 crystals of hSHMT2 because they diffracted X-rays at a synchrotron only to 2. 5 Å (Table  S2 ). Therefore, to directly compare hSHMT2 with the joint XN structure of TthSHMT, we also determined a 2. 5 Å roomtemperature X-ray structure of hSHMT2 in the internal aldimine state (Supplementary Data 2, PBD ID 8SSJ), because all previous hSHMT2 X-ray structures were done at cryogenic temperatures  18, 37, 62, 63.
We accurately mapped the H atom positions (observed as D atoms), revealing the active site protonation states, H-bonding networks, water molecule orientations, and consequently electrostatics. Both diffraction datasets were collected at room temperature and pH of 5. 5 from the same H/D exchanged protein crystal (Table  S1 ). In TthSHMT, PLP is covalently bound to Lys226 (Lys280 in hSHMT2) through a Schiff base linkage with the side chain ζ-amino group forming the internal aldimine. Because the active site structures are identical within the experimental coordinate error of 0. 3 Å in the protomers A and B of the TthSHMT homodimer, we selected protomer B for our structural analyses below, unless stated otherwise. The pyridine nitrogen, N1, of the PLP cofactor, is protonated. Thus, it is positively charged (Fig.
S6 ). The Schiff base out-of-plane rotation appears to be the attribute of the N SB neutrality as was also observed in the joint XN structure of AAT  44. Therefore, the above considerations point to the high probability of N SB atom not being protonated in hSHMT2 either. Interestingly, in the high-resolution cryogenic X-ray diffraction structure of TthSHMT (PDB ID 2DKJ) this torsion angle is reduced to 26°and 15°in protomers A and B, respectively. Protonation of N SB promotes the Schiff base to be more co-planar with the pyridine ring due to an H-bond formation with the phenolic oxygen O3′, as demonstrated by previous DFT calculations  9, 44, 71. It is thus reasonable to suggest that N SB may be protonated at lower temperatures, pointing to the possible temperature dependence of the Schiff base protonation state.
The phosphate group makes 1. 8 and 1. 9 Å hydrogen bonds with Ser95 and Tyr51* hydroxyls, but somewhat longer 2. 0-2. 3 Å H-bonds with the main chain amides (Fig. 2e ). The water molecules mediate the phosphate group interactions with the main chain carbonyl of Gly258*, and with the side chain of His122 mentioned above. L-Ser binds as a zwitterion in the pre-Michaelis complex. To obtain a complex with the bound substrate, we repurposed the TthSHMT crystal from the first neutron diffraction experiment by soaking it with the deuterated serine substrate, L-Ser-d 7 at 500 mM concentration. We then collected a 2. 3 Å roomtemperature neutron diffraction dataset on this crystal. Joint XN refinement was performed using 2. 0 Å room-temperature X-ray diffraction data collected on the same crystal immediately after the neutron experiment.
In the pseudo-Michaelis complex, Glu53* was observed within an H-bond distance of 2. 9 Å to the D-Ser hydroxyl. All these H-bonds would probably be retained when L-Ser binds in the Michaelis complex before its nucleophilic α-amino group attacks C4´of the internal aldimine for the reaction to proceed to the external aldimine. Importantly, the H-bonds with the residues corresponding to Arg358, Glu53*, and Tyr61* are also observed in the X-ray structures of the L-Ser external aldimine state for SHMTs from different species (PDB IDs: 4PFN, 6CDI)  [77] [78] [79]  , indicating minimal structural rearrangements upon the external aldimine formation. In the TthSHMT/D-Ser complex, the D-Ser α-amino group is 3. 0 Å away from N SB but is angled away from C4′ at a distance of 3. 5 Å, possibly making the nucleophilic attack unfavorable and producing the stable pseudo-Michaelis complex.
Materials and methods General information. Columns for protein purification were purchased from Cytiva (Piscataway, New Jersey, USA). His-tagged Tobacco Etch Virus (TEV) protease was produced in-house. Crystallization reagents and supplies were purchased from Hampton Research (Aliso Viejo, California, USA). Crystallographic supplies for crystal mounting and X-ray and neutron diffraction data collection at room temperature were purchased from MiTeGen (Ithaca, New York, USA) and Vitrocom (Mountain Lakes, New Jersey, USA). Deuterated L-Ser and hydrogenous D-Ser were purchased from Millipore Sigma (St. Louis, Montana, USA). TthSHMT expression and purification. The glyA gene (Fig. S9 ) encoding SHMT enzyme from the bacterium Thermus thermophilus was codon optimized, synthesized, and cloned into kanamycin-resistance plasmid, pJ411 (ATUM, Newark, CA), in addition to a DNA sequence encoding for an N-terminal polyhistidine-(His 6 )tag with a 34 amino acid long linker.
A TEV protease cleavage tag, ENLYFQS, was introduced at the TthSHMT N-terminus sequence so that after cleavage the enzyme sequence started from Ser3 (Fig. S9 ). This was done because residues Met1 and Val2 are not visible in the electron density maps in the previously deposited TthSHMT structure (PDB ID 2DKJ). The plasmid was transformed into BL21(DE3) competent E. coli cells for expression. Transformed cells were grown in Luria-Bertani (LB) media supplemented with 50 μg/mL kanamycin antibiotic at 37 °C to an optical density of 0. 8-1. 0 and induced overnight with 1 mM isopropyl ß-D-1-thiogalactopyranoside (IPTG) at 22 °C (approximately 16-18 h). Induced cells were harvested by centrifugation at 5660 rpm at 4 °C, producing typical yields of 10 g of cells per 1 L of cell culture. A buffer containing 50 mM sodium phosphate pH 7.
In this approach, only a few, but larger, crystals per drop of TthSHMT grow. A crystal of ~2 mm 3 in volume suitable for neutron diffraction was mounted in a 2 mm-inner diameter quartz capillary with a liquid plug of 40 mM NaOAc pH 5. 5, 1. 0 M (NH 4 ) 2 SO 4 , and 0. 5 M Li 2 SO 4 prepared in 100% D 2 O to perform H/D-vapor exchange. The same crystal was used for both neutron crystallographic experiments, in the absence and presence of substrate L-Ser-d 7. To prepare the crystal for soaking with L-Ser, the quartz capillary was unsealed, and the H/D-exchange liquid plug was removed. The capillary was then filled with 500 mM deuterated L-Ser, 40 mM NaOAc pH 5. 5, 1. 0 M (NH 4 ) 2 SO 4 , and 0. 5 Neutron diffraction data collection. Neutron diffraction was tested at room temperature and a preliminary dataset was obtained on the LADI-DALI beamline  88  at the Institut Laue-Langevin (ILL) in Grenoble.
A complete roomtemperature neutron diffraction dataset for the TthSHMT internal aldimine was collected on the IMAGINE  [89] [90] [91] [92]  single-crystal diffractometer at the HFIR at ORNL using a neutron wavelength range of 2. 8-4. 5 Å. Each neutron image was composed of a 20 h exposure of the crystal held in a stationary position. The crystal was rotated along the vertical axis (Δφ = 8°) before collecting each successive image. The crystal orientation was changed three times by tilting the capillary with respect to the incident neutron beam to improve data completeness. In total, 44 neutron diffraction images were collected. Neutron diffraction data processing was performed with a version of LAUEGEN  93, 94  modified to account for the geometry of the cylindrical image plate detector. The wavelength-normalization curve was determined using the intensities of symmetry-equivalent reflections at different wavelengths in LSCALE  95.
No explicit absorption corrections were applied. The data were scaled and merged in SCALA (Weiss 2001). Room-temperature neutron diffraction data for the TthSHMT-L-Ser pre-Michaelis complex were collected on the instrument MaNDi  96, 97  at the Spallation Neutron Source (SNS) at ORNL. The crystal was held stationary for 20 h exposures and rotated 10°around the φ-axis before collecting the next image. All neutrons between 2 and 4. 16 Å were used to collect the frames, with a total of 25 images collected. Neutron diffraction data collection on MaNDi was processed and integrated with 3D time-of-flight profile fitting in Mantid  98, 99. Wavelength normalization of the data was performed with LAUENORM  94, 100  and the data were scaled and merged in SCALA 101. Neutron data collection statistics for both datasets are shown in Table  S1.
Room-temperature X-ray diffraction data collection and structure refinement. Room temperature X-ray diffraction data collection for TthSHMT crystals was carried out on a Rigaku HighFlux HomeLab instrument equipped with a MicroMax-007 HF X-ray generator, Osmic VariMax optics, and a DECTRIS Eiger R 4 M detector at Oak Ridge National Laboratory. The data were indexed and integrated using the CrysAlis Pro software (Rigaku, The Woodlands, TX), then reduced and scaled with the AIMLESS program in the CCP4 software suite  102, 103. The TthSHMT room-temperature X-ray structures were solved by molecular replacement in PHASER 104 using phases from PDB code 2DKJ. Room temperature X-ray diffraction data collection for hSHMT2 crystals was performed from a single crystal on the ID19 beamline at SBC-CAT using a Pilatus3 × 6 M detector at the Advanced Photon Source (APS).
X-ray diffraction data were integrated and scaled using the HKL3000 software suite 105. To minimize radiation damage to the hSHMT2 crystal, the X-ray beam intensity was attenuated 40 times and the data were collected with 0. 2 sec/frame rate. The radiation damage to the crystal was estimated by the HKL3000 software to be less than 5%. The hSHMT2 structure was solved by molecular replacement using PHASER 104. The cryo-temperature X-ray structure of hSHMT2 (PDB ID 4PVF)  18  was used as a starting model. All the structures were subsequently refined against the room temperature data with Phenix. refine from the PHENIX suite 106,107 and COOT  [108] [109] [110]. Geometry validation was aided by Molprobity 111. All ligand restraints were generated with eLBOW 112 using geometry optimized by quantum mechanical calculations in Gaussian 16 113 at B3LYP/6-31 g(d,p) level of theory.
Final data collection and refinement statistics can be found in Table  S2. Joint XN refinement. Joint XN-refinement of the TthSHMT internal aldimine structure and TthSHMT pre-Michaelis complex were performed using the nCNS 114,115 patch of the Crystallography & NMR Systems (CNS)  115, 116  software suite for macromolecular structure determination. The refinement procedure began with a single rigid body refinement followed by a series of atomic position, atomic displacement parameters, and D atom occupancy refinements. The structures were visualized in the graphics program COOT  [108] [109] [110]  , in between rounds of refinements to inspect side chain modeling and correctly rotate side chain hydroxyl, thiol, and ammonium groups, as well as rotate water molecules to make appropriate H-bonding networks based on both 2F O -F C and F O -F C nuclear scattering length density maps.
Data availability The structures and corresponding structure factors have been deposited into the protein data bank with the PDB accession codes 8SUJ for TthSHMT (Supplementary Data 1), 8SSJ for hSHMT2 (Supplementary Data 2) 8SUI for TthSHMT/L-Ser (Supplementary Data 3), and 8SSY for TthSHMT/D-Ser (Supplementary Data 4). Supporting information is available online.
Acknowledgements This research at  ORNL's High Flux Isotope Reactor (IMAGINE beamline)  and at  ORNL's Spallation Neutron Source (MaNDi beamline)  was sponsored by the  Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy. The  Office of Biological and Environmental Research  supported research at  ORNL's Center for Structural Molecular Biology (CSMB) , a  DOE Office of Science User Facility. ORNL  is managed by  UT-Battelle LLC for DOE's Office of Science , the single largest supporter of basic research in the physical sciences in the United States. X-ray crystallographic data were in part collected at  Argonne National Laboratory using Structural Biology Center (SBC)  beamline ID19 at the  Advanced Photon Source. Use of the  Advanced Photon Source , an  Office of Science User Facility operated  for the  U.
An additional Ti 0. 5 Zn 0. 5 NiSb sample was prepared for Neutron powder diffraction (NPD), with the analysis carried out on a pulverized annealed pellet. All manipulation of powders was done in an argon lled glovebox to prevent exposure to oxygen and moisture. All samples were initially characterized using powder X-ray diffraction (XRD). Data was collected over 30 minutes using a Malvern Panalytical Empyrean diffractometer, with Cu K a1 and K a2 radiation. Room temperature NPD data was collected on ∼3. 5 g of nely ground powder, on the D2B instrument, ILL, Grenoble, France. Rietveld tting of XRD and NPD data were carried out using the General Structure Analysis System II (GSAS-II) of programs, whilst qualitative peak matching was carried out using the Malvern Panalytical Highscore Plus soware and the ICDD database.
50, 51  Scanning electron microscopy (SEM) of the hot pressed Zn 1-x Ti x NiSb disks was performed using a Quanta 650 FEG SEM, equipped with an Oxford Instruments X-max 150 mm detector for EDX spectroscopy. Prior to measurements, all samples were polished rst with SiC sandpaper, then with subsequent 15 mm, 5 mm and 1 mm diamond polish pastes to produce a reective mirror nish. Polished surfaces were thoroughly washed with propan-1-ol to remove any SiC or diamond paste residue. Quantitative analysis of selected areas was performed using the Oxford Instruments Aztec Large Area Maps soware. Total scattering synchrotron X-ray data was collected on the ID15A beamline 52 at the ESRF (European Synchrotron Research Facility, Grenoble, France) using a Dectris Pilatus 2 M CdTe detector. X-ray energy was 68.
5 keV (wavelength 0. 1810 Å) and sample-detector distance 185. 0 mm. Detector images were averaged and azimuthally integrated using pyFAI  53  and the resulting integrated intensities were converted to PDF using GudrunX. 54  Fitting of the XRD dataset was carried out using the GSAS-II soware, whilst the PDF ts were undertaken using the PDFt2 and PDFGui soware. 55  The electrical resistivity r and absolute Seebeck coefficient S were measured using a Linseis LSR-3 instrument on bar-shaped specimens (∼1. 5 × 2 × 10 mm 3 ), under a static He atmosphere. The thermal diffusivity a was measured using a Linseis LFA-1000 laser ash instrument on hot-pressed disks of ∼13 mm diameter and ∼1. 5 mm thickness, under dynamic vacuum conditions. The thermal conductivity k was then calculated from the equation k = aC p r, with C p the specic heat of the  nominal composition estimated from the Dulong Petit Law and r the disk density obtained using the Archimedes method (Table  S3  †).
Acknowledgements The  EPSRC  is acknowledged for funding the research into new half-Heusler materials, through award ( EP/N01717X/1 ) and for a PhD studentship for B. F. K. The ILL is acknowledged for easyaccess beam time on the super-D2B instrument. 48 The ESRF is acknowledged for provision of inhouse beamtime (proposal  IH-HC-3871 ). 49.
Differential Scanning Calorimetry The glass transition temperatures of both the pristine and EB irradiated samples were obtained by utilizing the DSC Q2000 instrument from TA Instruments (New Castle, DE, USA). To prepare the samples, 9 ± 3 mg of polymers were added to an aluminum crucible. The received heat flow data were standardized to the weight of the samples and a heating and cooling rate of 10 • C/min was maintained within the temperature range of -70-+200 • C under a nitrogen flow. The initial step of the program cooled the sample and carried out three cycles of heating and cooling to account for any thermal events that might be linked to the sample's preparation history. The thermograms analyzed in this study were obtained during the second heating cycle. To ensure the reproducibility of the results, at least three experiments were conducted using identical samples with the same composition and independent preparation.
Electromagnetic and Mechanical Modelling The electromagnetic performances of the machine are evaluated using a 2D finite element model. Simulations are performed using an Open Source XFEMM ® integrated into Matlab ®. The electromagnetic performances of the machine are performed using magneto-static evaluations at each angular position of the rotor, which reduces computation time. The latter can be reduced further by using mechanical and electrical symmetries of the machine, which makes it possible to launch the simulations on only one pole of the machine and 1⁄6 of the electrical period. Electromagnetic quantities are reconstructed based on these symmetries, as detailed in  [24]. The machine has three phases and is supplied with sinusoidal current using an ABC model. Two variables are defined for each operating point: current density and control angle.
The initial delay was set at 60 s, and the stirring rate inside the sample cell was set at 300 rpm to ensure the homogeneity of the cell solution during titration. The interval between injections was 200 s to reach the thermodynamic equilibrium. For each ITC experiment, a reference titration was performed by titrating LF solutions directly into 10 mM MES buffer containing the studied NaCl concentration. A negligible signal was associated with this reference injection, which was subtracted from the corresponding experimental signal. The ITC data were fitted using graphical user interface (GUI) of PyTC (version 1. 2. 2, University of Oregon, OR, USA), an open-source python software  [23]. The ITC experiments were performed at least in duplicate.
Statistical Analysis The effect of salt concentration on coacervation yield and turbidity during direct mixing and dialysis experiments and on titration by ITC was tested using analyses of variance (ANOVA) with one factor. When the ANOVA was significant (p < 0. 05), Tukey's multiple comparison test was used for paired comparisons of means with p < 0. 05. Tests were performed using R Studio, a software package developed by a community (version 2021. 09. 1, Boston, MA, USA).