dataesr/scientific-paragraphs-categorization huggingface dataset:
Mass spectrometry Digested samples were analyzed on a 260 Infinity HPLC stack (Agilent Technologies) and chromatographic separation occurred on a C18 reverse-phase column (Jupiter C-18, 71 μ × 15 cm, 300 Å, 5 μm (Phenomenex)) with an in-line Thermo Orbitrap Velos Pro hybrid mass spectrometer, equipped with a nano-electrospray source (Thermo Fisher). Binary mobile phase solvents were comprised of 0. 1% formic acid (solvent A) and 0. 1% formic acid in 85% acetonitrile (solvent B). All data were collected in CID mode. A parent scan range of 300 to 1200 m/z (at 60 K resolution) was chosen and fragmentation data (MS2) were collected on the top 15 most intense ions. For data-dependent acquisition, charge-state screening and dynamic exclusion were enabled with a repeat count of 2, repeat duration of 30s, and exclusion duration of 90s.
Mass spectrometry data conversion and searches Data acquisition was executed using Xcalibur software. Xcalibur RAW files were collected in profile mode, converted to centroid data, and then converted to mzXML using ReAdW v3. 5. 1 (IonSource). The mgf files were then created using MzXML2Search (included in Trans-Proteomics Pipeline v3. 5) for all scans. The data were searched with a species-specific subset of the UniRef 100 database using SEQUEST (Thermo Fisher, San Jose, CA, USA; version 27), which was set for two maximum missed cleavages, a precursor mass window of 20 ppm, trypsin digestion, variable modification C at 57. 0293, and M at 15. 9949. Peptide filtering, grouping, quantification and statistical analyses Scaffold (v. 4. 8. 4, Proteome Software Inc. , Portland, Oregon) was used to validate MS/MS based peptide and protein identifications.
We also excluded 9,125 dental X-ray procedures (reported by 2,296 subjects) since the fraction of BM in the mandible is close to 0  [33]. Indeed, the dose to the bone marrow from one intraoral dental X-ray is estimated to range from 10 -3 to 10 -5 mGy, depending on the time period  [34]. An additional 52 examinations reported in free text by 51 subjects were also excluded as they were too poorly defined to classify. Cumulative lifetime BM dose was calculated summing doses from all procedures up to the exclusion period. As only age at first and last procedures was available, we attributed: a) to the first and last procedures, the doses in the look-up table corresponding to the time periods and type of procedures. Since there was no data on the precise time period for the remaining "n-2" examinations, we used three different scenarios for attributing dose values, as follows: a) the mean of the dose over the entire time period between first and last exposure for that type of procedure (main analysis); b) the dose corresponding to the time period of the first procedure; c) the dose corresponding to the time period of the last procedure.
Definition of covariates Data on personal and family medical history were collected as part of the study interview by asking if the subject or one of his/her family members had ever suffered from any of a number of medical conditions and, if so, the age at onset. The conditions were grouped as follows: a) family history of lymphoma; b) any autoimmune disease (arthritis, lupus, celiac disease and rheumatic fever); c) any atopic disease (asthma, eczema, allergy, urticaria and sinusitis); d) any infectious disease (mononucleosis, tuberculosis, hepatitis, brucellosis and typhoid fever); e) osteoarthritis; f) cardiovascular disease (diabetes, hypertension). A measure of global health status in childhood was also captured by asking the participants about their level of health during childhood using five questions (having been more sick/absent from school comparing with schoolmates; taking more medicines/antibiotics comparing with siblings; having been a very healthy child)  [25].
Results A total of 2,362 lymphoma cases and 2,465 controls were recruited into the study. The overall participation rates were 87. 7% and 68. 5% respectively for cases and controls (81. 1% for hospital controls and 51. 3% for population controls). The median time between diagnosis and interview was 40 days (Interquartile range: 15 days; 84 days). We excluded 646 participants from analysis who reported: a) a personal history of cancer; or b) immune-depression; or c) had missing values in one of the basic adjustment variables (age, education or SIOPS). We also excluded 307 participants (7. 7% of controls, 6. 8% of cases) for whom data were insufficient to reconstruct their doses. A total of 1,877 cases (1599 NHL; 283 HL; 411 CLL) and 1,987 controls were included in our analyses. Table  2  presents the characteristics of the study population.
Exposure information bias This study is based on self-reported data and it was not possible to check medical records to validate responses. The informed consent signed by the participants allowed the researchers to access medical records only in the hospital where they were recruited, and hence we are unable to validate all of the procedures reported by the patient. In addition, considering the age range of the participants, most of the procedures (in particular those performed in childhood) are likely to have been recorded in paper charts, not in electronic medical records, thus making them very difficult to access. A medical records review that cannot assess the complete lifetime diagnostic exposure of the subjects would be difficult to interpret  [44]. As we based our analyses on self-reported medical radiological history, recall error (random and systematic, differential or not between cases and controls) is likely.
MCT acknowledges the Ramon y Cajal fellowship (RYC- 2017-01892) from the Spanish Ministry of Science, Innovation and Universities and cofunded by the European Social Fund. ISGlobal acknowledges support from the Spanish Ministry of Science, Innovation and Universities through the "Centro de Excelencia Severo Ochoa 2019-2023" Program (CEX2018-000806-S), and support from the Generalitat de Catalunya through the CERCA Program.
Myocardial necrosis quantification. A sternotomy was performed at the end of experimentation. An aortic supra-coronary clamp was placed and Evans blue dye injected at the aortic root to colour the perfused cardiac tissues. The heart was then extracted and sectioned perpendicular to the main axis, to obtain 1 cm-thick sections. The sections were weighed, bathed for 10 min in a 2,3,5-triphenyl tetrazolium chloride (TTC) solution to discriminate infarcted and the area-at-risk (AAR). Both sides of each section were photographed and analysed using NIH Image J software to obtain a planimetric quantification of the infarcted area, expressed as a percentage of the left ventricle AAR and total ventricular mass; values for all sections from each heart were averaged. Myocardial histopathology. One section per animal was used for histologic and protein analyses.
Acknowledgements The authors owe their sincere gratitude to  David Gonthier  and  Virginie Loyer  for the outstanding quality of their technical assistance during the experimental work in the operative setting. This work was financed by the  French Society of Anaesthesiology and Critical Care (SFAR)  through 2017 Research Grants, by  INSERM (French National Institute of Health and Medical Research)  Unit n°1034 through supplemental funding, and the  Association des Anesthésistes-Réanimteurs COeur-THorax et VAisseaux (ARCOTHOVA).
Residual water signal was suppressed by homonuclear presaturation. Proton-decoupled  13  C-NMR spectra were acquired overnight using 60 flip angle, 20 s relaxation delay, 25,063 Hz sweep width and 64 K memory size. Measurements were conducted at 4 C under bi-level broadband gated proton decoupling and D 2 O lock. Relevant peaks in the spectra were identified and integrated using TopSpin 3. 5pl6 software (Bruker Biospin GmbH). Proton-observed carbon-editing (POCE) sequence was used to determine the  13  C-specific enrichment at selected metabolite carbon positions using the ( 13 C- 1  H) heteronuclear multiquanta correlation. 44, 45 he sequence enabled the successive acquisitions of a first scan corresponding to a standard spin-echo experiment without any  13  C excitation and a second scan involving a  13  C inversion pulse allowing coherence transfer between coupled  13  C and 1 H nuclei.
As control, we also performed experiments with oxamate injection alone (HI-O group, Figure  3  (c   3 (b) and (c), respectively). The co-injection of oxamate completely abolished the neuroprotective effect of lactate (lesion volumes, in percentage of total brain volume: 39. 9 AE 2. 9%, 30. 3 AE 2. 6%, and 48. 6 AE 1. 7% in HI-C, HI-L and HI-LO groups, respectively). The deleterious effect of preventing the metabolic use of lactate was also evaluated via the measurement of ROS production, which is a deleterious event concomitant to the HI insult. Analyses of ROS production by oxiblot showed that post-ischemia intraperitoneal injection of lactate led to a significant decrease in ROS production compared to HI-C group; À68% in the cortex and À72% in the striatum (Figure  3(d) ). Conversely, inhibition of lactate metabolism by oxamate prevented the reduction in ROS production compared to the control group in the cortex and in the striatum (moreover, no statistical difference between HI-O and HI-C groups was observed, in both structures, data not shown).
75 7] [78]  Neuroprotection by lactate of long-term memory was assessed with the novel object recognition test. Juveniles that have received at P7, P8 and P9 a daily injection of lactate after the HI event completely recovered. Interestingly, a role of lactate and MCTs was recently demonstrated in memory processes. 53 The authors suggested that astrocytic glycogenolysis leads to lactate production and release from astrocytes via MCT1 or MCT4 and uptake into neurons via MCT2 which appears to be required for the consolidation step of long-term memory. As expected, in our study, rats subjected to HI insult displayed longterm memory deficits. They were, however, completely protected by multiple injections of lactate. These data highlight a therapeutic role of lactate on hippocampaldependent long-term memory in a context of hypoxicischemic stroke.
Funding The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research was supported by the  TRAIL (Translational Research and Advanced Imaging Laboratory) cluster of excellence of Bordeaux University. AKBS has received financial support from the program IdEx and the  LabEx TRAIL, reference ANR-10-IDEX  and  ANR-10-LABX-57. AKBS and LP have received financial support from an  international French (ANR)/Swiss (FNS) grant , references  ANR-15-CE37-0012  and  FNS  n  310030E-164271. LP received financial support from the program  IdEx Bordeaux   ANR-10-IDEX-03-02.
For DNA containing tether and oxoG on the same strand, 50 μM β-me was added to prevent oxidative degradation of 8-oxoG. DNA was purified by 20% urea-PAGE and dissolved in 10 mM Tris, pH 8. 0, 1 mM EDTA, and annealed with complimentary strand 5′-TGGTAGACCTGGACGC-3′. Cross-linked complexes were formed by mixing duplex DNA with 2-fold molar excess protein and incubating at 4 °C for several days. Unreacted DNA and protein were removed by Mono Q chromatography (GE Healthcare). The purified complexes were buffer-exchanged to 10 mM Tris 7. 4 and 100 mM NaCl, concentrated and crystallized by hanging droplet vapor diffusion at 20 °C. For each complex, crystals were allowed to grow for several days, transferred to a cryoprotectant solution containing mother liquor supplemented with 25% glycerol, and frozen in liquid nitrogen for data collection.
For LRC (Y207C/K249Q), diffraction quality crystals appeared with 16. 4 mg/mL complex concentration (protein concentration measured using Bradford assay) within a few days in well solution containing 100 mM sodium cacodylate, pH 6. 5, 200 mM MgCl 2 and 18% polyethylene glycol 8000. For IC (Y207C), diffraction quality crystals appeared with 12 mg/mL complex concentration within a few days in well solution containing 200 mM NH 4 NO 3 , and 20% polyethylene glycol 3350. For EC (Y207C/C253W), diffraction quality crystals appeared with ~17 mg/mL complex concentration within a few days in well solution containing 100 mM sodium cacodylate, pH 6. 1, 200 mM MgOAc, and 17% polyethylene glycol 8000. Structure determination. Diffraction datasets were collected at -170 °C at the 24-ID-C and 24-ID-E beamlines (NE-CAT) of the Advanced Photon Source and processed using the HKL program suites  45.
Initial molecular replacement solutions were obtained by PHASER in the CCP4 suite  46, 47  , using the coordinates of previously determined hOGG1 structure (PDB ID: 1EBM  16  ) but omitting DNA as search models. Each hOGG1-DNA model was built through iterative cycles of manual model building in COOT  48  and structure refinement using REFMAC5  49, 50   and PHENIX  51. The Ramachandran plots, calculated by MolProbity (http:// molprobity. biochem. duke. edu), confirmed no residues in disallowed regions for all structures. Full details on the data collection and structure refinement are provided in Supplementary Table  1. PyMol (The PyMOL Molecular Graphics System, Version 2. 0, Schrödinger, LLC. ) was used to prepare all structure model figures presented in the paper. System preparation for molecular dynamics (MD) simulations.
Then, the HBUILD facility of the CHARMM program  52, 53  was used to assign atomic coordinates of hydrogen atoms. The resulting systems were solvated with a rhombic dodecahedron (RHDO) box of 11,712 TIP3P water molecules  54  and any water molecules 42 within 2. 5 Å from any heavy atom of protein, DNA, and crystal water were removed, leaving, for example, 9554 TIP3P waters for the IC system. Finally, each system was neutralized by adding 50 Na + and 26 Cl -ions at random positions, making its ionic concentration equal to 150 mM. In addition, two additional systems were prepared based on the LRC X-ray structure (PDB-ID: 1YQR)  23  to be used as the reference state of the targeted molecular dynamics (TMD) simulations  55  (see the Supplementary Methods for details). MD simulations. Each system was first energy minimized for 5000 steps and equilibrated for 500 ps at 300 K.
0 Å and 11. 0 Å. All MD simulations were performed with a 2 fs integration time step and SHAKE  60  applied to all bonds involving hydrogen atoms. The Langevin thermostat was used to maintain the system temperature at 300 K. In all simulations, we also applied harmonic restraints to the terminal base pairs to avoid them fraying away from each other. System preparations, trajectory analysis, the TMD simulations, and the string method simulations  36  (see below) were carried out using the CHARMM program (version c37a1)  52, 53  and the 500 ns production MD simulations were performed using the NAMD program  60. String method (SM) simulations. The base extrusion pathways for G and oxoG were determined by applying the string method in collective variables (SMCV)  36. In SMCV, a path connecting two end state conformations (i.
Acknowledgements This work was supported by  National Institutes of Health  ( CA100742  to G. L. V. , and  R01GM132481  to K. N. ), the  University of Texas at Arlington  (K. N. ),  AACR   Anna D. Barker Postdoctoral  fellowship to  U. K. S. , and the  CHARMM Development Project at Harvard  (M. K. ). We thank the staff at the  NE-CAT  at the advanced  Photon Source  for Assistance during data collection. Computer resources were provided by the  Swedish National Infrastructure for Computing (SNIC)  at the  High Performance Computing Center North  ( HPC2N ), by the  National Energy Research Scientific Computing Center (NERSC) , which is supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC02-05CH11231 , and by the  Oak Ridge Leadership Computing Facility (OLCF)  at  Oak Ridge National Laboratory (ORNL) , which is supported by the  Office of Science of the Department of Energy  under Contract  DE-AC05-00OR22725.
𝑆𝑂𝐻 (%) It is important to extend this degradation model developed under specific experimental operating conditions to real-life driving conditions. For this purpose, a similar principle is applied to describe the SOH. It assumes that the variation of the stress factors follows its average values until EOL is reached. In this framework, the idea is to link the battery's entire lifetime to the energy exchanged by the battery until EOL. To cover up the dynamic of the operating conditions, the exchanged energy is weighted by a degradation degree coefficient. This is later deduced from the SOH test dataset. In sum, the reliability assessment is obtained by estimating the residual lifetime, depicted by the weighted of cumulative energy exchanged according to the power density of cycle. Figure  8  shows the different steps of the proposed reliability assessment approach.
To cover up the dynamic of the operating conditions, the exchanged energy is weighted by a degradation degree coefficient. This is later deduced from the SOH test dataset. In sum, the reliability assessment is obtained by estimating the residual lifetime, depicted by the weighted of cumulative energy exchanged according to the power density of cycle. Figure  8  shows the different steps of the proposed reliability assessment approach. where SOHDOD and SOHIc are state of health as a function of DOD and rated current, respectively. NCycle, DOD and NCycle,Ic are number of cycles according to a DOD level and a ratted current, respectively. Crate is charging/discharge current. α, β, γ, δ, ρ and σ are fitting parameters. The study is carried with full range variation of the SOC from 20% to 90%, which leads to a DOD of 70%.
It is important to extend this degradation model developed under specific experimental operating conditions to real-life driving conditions. For this purpose, a similar principle is applied to describe the SOH. It assumes that the variation of the stress factors follows its average values until EOL is reached. In this framework, the idea is to link the battery's entire lifetime to the energy exchanged by the battery until EOL. To cover up the dynamic of the operating conditions, the exchanged energy is weighted by a degradation degree coefficient. This is later deduced from the SOH test dataset. In sum, the reliability assessment is obtained by estimating the residual lifetime, depicted by the weighted of cumulative energy exchanged according to the power density of cycle. Figure  8  shows the different steps of the proposed reliability assessment approach.
Results and Analysis The proposed process is evaluated by extensive simulation using MATLAB/SIMULINK environment (R2018a, MathWorks, Natick MA, USA). A map of different sets of solutions, for different driving cycles (WLTC, US 06 and US Highway), and with various FC dynamics (1 s, 5 s and 10 s: time required to achieve the rated power). To improve design results, different FC dynamics have been introduced. It helps considerably design engineers to set up the best hybridization rate and enables them to practice trade-offs, including reliability aspects, in the early steps of the design.
Results and Analysis The proposed process is evaluated by extensive simulation using MATLAB/SIMULINK environment (R2018a, MathWorks, Natick MA, USA). A map of different sets of solutions, for different driving cycles (WLTC, US 06 and US Highway), and with various FC dynamics (1 s, 5 s and 10 s: time required to achieve the rated power). During the first step, the design optimization results show that the FC sizing is closely linked to the load power average (energy source) while its battery capacity is influenced by the dynamic behaviour depending on transient phases of driving cycle (power source). The FC dynamics are sett using different time responses. The results maps are obtained considering the system's parameters in Table  1. Figure  10  presents sizing solutions considering the reliability effect under WLTC and US highway using the same fuel cell dynamic (10 s).
Similarly, for the genotyping of the B6J-Nemf R487G mice the following primers were used: forward primer specific to wild-type allele: 5′-TGCTGCTAAAAAAACCCGGA-3′; forward primer specific to mutant allele: 5′-TGCTGCTAAAAAAACCCGGG-3′; reverse primer common for both alleles: 5′-AAAGCCCTTGCTGCAAAGCC-3′. The following primers were used for the genotyping of B6J-Nemf D106* strain: forward primer: 5′-CATGGTG AATGGAGAGAACC-3′; reverse primer: 5′-TTGATCCCAGCACTAGGGAG-3′. D106* PCR product was Sanger sequenced and assessed via chromatogram. Phenotypic and behavioral analyses. Mice were weighed weekly from 7 ± 1 days of age to 8 weeks, unless indicated otherwise. Longer surviving animals were additionally weighed at 20 and 55 weeks. For the D106* mouse weight at weeks 1 and 1. 5, it was determined that there were no sex differences on the phenotypes and therefore the data was presented as mixed with similar numbers of males and females.
Inverted wire hang assay was used to assess motor function. It was determined that there were no sex differences in phenotype and therefore the data was presented as mixed sex, with similar numbers of males and females: mice were placed on top of a wire mesh cage cover which was then inverted for a maximum of 60 s, and the latency to fall was measured. Mice were allowed to rest for a minimum for 5 min before repeating the test. The average of two tests was recorded per timepoint. Analysis of myelinated axons. Motor and sensory branches of the femoral nerve, L4 ventral roots or phrenic nerves were dissected and fixed overnight at 4 °C in 2% glutaraldehyde and 2% paraformaldehyde in 0. 1 M cacodylate buffer. Nerves were then post-fixed in 1% osmium tetroxide in 0. 1 M cacodylate buffer and embedded in Embed 812 Resin (Electron Microscopy Sciences, Hatfield, PA).
Sections measuring 1 µm were cut on a Leica RM2265 rotary microtome with a diamond knife, baked onto a glass slide, and heat stained with 0. 5% aqueous toluidine blue. For myelinated axon count and diameter analyses, images were captured using a Nikon Eclipse E600 microscope with 40× and 100× objectives. The total number of myelinated axons in each nerve was counted using an automated threshold method in ImageJ (v1. 52p) with manual confirmation  28. With ImageJ software (v1. 52p), the Threshold function was adjusted in order to only highlight axoplasm on whole nerve sections, and Analyze particle function was then used to quantify the number of myelinated axons and areas of each nerve. The diameter was determined from axonal area. It was determined that there were no sex differences in phenotype and therefore the data was presented as mixed sex, with similar numbers of males and females.
Images of large nerves that could not be captured as a single image at 40× magnification were generated as montages to show the whole nerve, using the ImageJ (v1. 52p) Stitching Grid/Pairwise plugin  29. Histological analysis of gastrocnemius muscle. Mice were euthanized and right hindlimb was extracted and post-fixed in Bouin's fixative. Whole hindlimbs were cross-sectioned through the middle portion of lower and upper legs. The sectioned tissues were then paraffin-embedded, sectioned, mounted, and stained with hematoxylin and eosin for light microscopic analysis according to standard histological procedures. Slides were scanned using a NanoZoomer 2. 0 (Hamamatsu) at 40× magnification. Representative images were taken from the MG region of the lower leg, using NDP. view2 software (U12388-21, Hamamatsu).