dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of differential H3K27ac across AD regions from genome-wide association studies (GWAS) The summary statistics for the stage 1 GWAS from Lambert and colleagues 8 were downloaded from http://web. pasteur-lille. fr/en/recherche/u744/igap/igap_download. php. These results were clumped (p1 = 1e-4; p2 = 1e-4, r2 =0. 1, window = 3000kb) using plink 66 , which collapses multiple correlated signals (due to linkage disequilibrium (LD)) into regions which represent independent signals. LD relationships were inferred from a reference GWAS dataset (Phase 1) from another study  67. Neighbouring regions located within 250kb of each other on the same chromosome were subsequently merged. After clumping, each region was assigned the minimum P value for all SNPs contained in the region (from Lambert et al), and regions were then filtered to the genome-wide significance threshold (P < 5.
Integrative analysis with DNA methylation and hydroxymethylation DNA methylation and hydroxymethylation data was available (unpublished) from entorhinal cortex DNA for 42 of the samples profiled in this study. DNA methylation and hydroxymethylation profiles were generated on the Illumina Infinium HumanMethylation450 BeadChip (Illumina Inc. , CA, USA) ("Illumina 450K array") using the TrueMethyl Array kit (Cambridge Epigenetix, Cambridge, UK). Profiles for both modifications were pre-processed, normalized and filtered according to a stringent standardised quality control pipeline, as described previously  50  using the WateRmelon 68 package in R. We identified probes on the array within 1kb of differentially acetylated peaks (FDR < 0. 05) using the Bioconductor package GenomicRanges 62. A total of 1,659 of the 4,162 FDR significant differentially acetylated peaks were located within 1kb of at least one CpG probe on the array, with a total of 6,838 probes mapping to the 1kb neighbourhood of these 1,649 peaks.
Acknowledgements This work was funded by  US National Institutes of Health  grant  R01 AG036039  to J. M. S. J. M. and T. R. were funded by the  EU-FP7 Marie Curie ITN EpiTrain (REA  grant agreement no. 316758 ). Sequencing infrastructure was supported by a  Wellcome Trust   Multi User Equipment Award  ( WT101650MA ) and  Medical Research Council (MRC) Clinical Infrastructure Funding  ( MR/M008924/1 ). Generation of DNA hydroxymethylation data was funded by an  Alzheimer 's  Association US New Investigator Research Grant  (grant number  NIRG-14-320878 ) to K. L. , and a grant from  BRACE (Bristol Research into Alzheimer's and Care of the Elderly)  to K. L. The authors acknowledge the help of  Dr Konrad Paszkiewicz  at the  University of Exeter Sequencing Service  for advice on ChIP-seq experiments.
Therefore, in this current study, the EASL criteria (tumor viability and tumor necrosis) was used. According to this guideline a Partial Response (PR) and Disease Progression (PD) were defined as more than 50% reduction or more than 25% increase, respectively, in the size of the contrast enhancement tumor area of the target lesions. The appearance of new lesions at least 1 cm in size consistent with HCC indicated PD. The enhancement analysis was always performed in the CT or MR contrast arterial  [5]  phase. An experienced body diagnostic radiologist performed all evaluations (Figs. 4, 5  and 6 ). Progression-free survival and overall survival were recorded according to imaging studies and clinical outcomes. Statistical analysis was performed by the Kaplan Meyer method and log-rank using S-plus software.
Since 2007 the Telescope Array Project (TA) and Pierre Auger Observatory (Auger) have collected extensive data sets spanning several orders of magnitude of the cosmic-ray spectrum. In both experiments the majority of data is generated from the surface-detector (SD) array as a result of its very high duty cycle. These data are then calibrated for energy with fluorescence detectors using a hybrid approach. The TA and Auger experiments use different SD station designs, giving them different sensitivities to extensive air-shower components. We seek to understand and cross-validate these complementary detectors on a hardware level. In this paper we present an update on the progress of this in-situ cross-calibration program. Presently two Auger water-Cherenkov detectors and two TA scintillator stations are co-located at the TA central laser facility (CLF).
Both experiments utilize SD stations with self-contained electronics, communications, and solar power systems. The detection medium in Auger is used to count air-shower muons but is also sensitive to the electromagnetic shower component, while TA detectors count ionizing particles indiscriminately. The Auger SD station is a water-Cherenkov detector (WCD). Relativistic leptons and highenergy photons generate signals via Cherenkov radiation and pair production, respectively, which are collected by photomultiplier tubes (PMTs). The Telescope Array SD station uses plastic scintillator panels. Fluorescent scintillation light is collected by wavelength-shifting fibers and guided to PMTs in a dual layer setup. To improve understanding of the energy spectrum and origin of ultrahigh-energy cosmic rays (UHECRs), the TA and Auger Collaborations have performed analyses of a joint data set  [4, 5].
Detectors in the field For phase I we are currently collecting data from: one Auger south (AS) WCD, one prototype Auger north (AN) WCD and two TA stations (see Figure  1 ). The AN and AS doublet is formed to study the response between the conventional AS station (used at the Pierre Auger Observatory) and prototype AN station. The AS and AN detectors use a 3. 6 m diameter, 1. 2 m high, reflectively lined (Tyvek R ) tank filled with 12,000 L of purified water. In AS three symmetrically distributed PMTs, each 1. 2 m.
PoS(ICRC2017)395 from the central axis  [1] , are used. Low-gain (AC coupled anode) and high-gain (8th dynode) channels for each PMT are input to the electronics and digitized by 10-bit 40 MHz semi-flash ADCs. These traces are analyzed and time-stamped (GPS synchronized clock) by a programmable logic device running triggering firmware. A data-acquisition (DAQ) system running on a single board computer (SBC) (see section 3. 1) evaluates the timestamps of station-level (T2) events. Coincident time-stamps in a certain geometry surrounding the central laser facility (CLF) generate a physics trigger-the SBC requests the stations to transfer ADC traces for the event. Online calibration data from the previous minute for AS, and the previous 14 minutes for AN, are also retrieved to convert each ADC waveform to an integrated vertical muon-equivalent signal (VEM).
Auger north and south comparison The Auger doublet is used to study the performance of AN and AS observations for the same EAS. From November 2016 through May 2017 we have recorded 1635 coincidences generated by the external local trigger. We show logarithmized data in Figure  3 , along with a fit. No quality cuts or VEM thresholds have been applied. We find a least squares best fit power law of S AS = 1. 18 (S AN ) 0. 92. The ideal expectation is S AS = S AN , however it must be stressed our calibration source is low energy showers with small cores and potentially highly variable particle densities. It is not possible to do any post selection with our current setup-Poissonian fluctuations are included. We will continue to investigate this correlation. To test the responses using a more constrained input, we look at signal correlations for global events where both stations have data.
Numerical implementation We have developed for the global stability analysis the SIREN code (Stability with IneRtial EigeNmodes), freely available at https://bitbucket. org/vidalje/siren. It handles any mechanical forcing and basic flow of uniform vorticity. The matrices N , L and M are first computed symbolically with Sympy (http://www. sympy. org/), a computer algebra system (CAS) for Python, which is used to manipulate the Cartesian polynomials x i y j z k in a symbolic way. Then they are converted to Fortran subroutines with the Sympy fcode function and finally wrapped with f2py  (Peterson 2009)  for fast numerical evaluation inside Python using Numpy  (Van Der Walt et al. 2011). The Jacobian matrix J is computed numerically, because we cannot compute the symbolic inverse N -1 for arbitrary n.
Because of the difficulty to build the Jacobian matrix for an arbitrary forcing, previous global studies have only considered less than 200 basis elements (n 7)  (Kerswell 1993b; Lebovitz & Lifschitz 1996a; Wu & Roberts 2011; Vantieghem et al. 2015; Barker 2016a; Barker et al. 2016). In practice, we have built and solved numerically the stability system (3. 10) for degrees as large as n = 25, yielding more than 6000 basis elements. For the local stability analysis we have also developed the SWAN code (Short-Wavelength stability Analysis), freely available at https://bitbucket. org/vidalje/ swan. It gives sufficient conditions for inviscid instability of any basic flow (not necessarily of uniform vorticity) expressed in Cartesian coordinates. The stability equations (3. 14) are built using Sympy, then converted to a Fortran subroutine with the Sympy fcode function and finally wrapped with f2py for fast numerical evaluations with Numpy.
Both numerical codes use an explicit Runge-Kutta time step solver with adaptive step size (available in the Python library Scipy) to integrate the stability differential equations. Performing a survey in parameter space is an embarrassingly parallel problem, and our implementation takes full advantage of this situation using mpi4py (http://mpi4py. scipy. org/). To validate our codes, we have first considered the precession of a steady spheroid (a = b = c). This benchmark is described in Appendix B. We perfectly recover previous studies  (Kerswell 1993b; Wu & Roberts 2011). We also get a very good agreement between local and global analyses, because we can reach large enough degrees n with the SIREN code. Then we assess the performance of our SIREN code in figure  3 , which shows the evolution of CPU time with n for the tidally driven and libration-driven flows considered below (see §4.
They are quite general and can be applied to several other situations. They are freely available for the community at https://bitbucket. org/vidalje/. On one hand with the SWAN code, local stability analyses of any time-dependent basic flow in unbounded fluids can be performed. On the other hand, global stability analyses of any mechanically driven flow of uniform vorticity in ellipsoids can be carried out with the SIREN code. Unlike previous studies, our code also handles arbitrary (time-dependent) ellipsoidal shapes (not limited to small departures from the sphere). Indeed, it handles ellipsoidal perturbations of unprecedented small wavelengths. We have considered in the present study polynomial degrees as large as n = 25. It corresponds to more than 6000 basis elements. A fork of the SIREN code has been used to compute (i) the tilted hydromagnetic eigenmodes of a fluid in a corotating ellipsoid  (Vidal et al.
The extra computational work per time step makes the code significantly more computationally demanding than a fixed grid version. ALE method has recently been used by  Barker (2016a)  in nonlinear simulations of tidal flows. We have checked that our results are not significantly affected by changing the mesh, the size of the domain or the maximum time step. Figure  19  shows the comparison between the global analysis and direct numerical simulations in COMSOL at β 0 = 0. 3. Formally, the global method cannot predict accurately neither the viscous growth rate nor the viscous unstable flow of a given spatial complexity. However the viscosity selects the spatial complexity of real viscous flows. It mostly enters as a damping term in the stability problem of tidally driven basic flows (e. g. Lacaze et al.
Acknowledgements JV acknowledges the  French Ministère de l'Enseignement Supérieur et de la Recherche  for his PhD grant. This work was partially funded by the  French Agence Nationale de la Recherche  under grant  ANR-14-CE33-0012  (MagLune) and by the  2017 TelluS program  from  CNRS-INSU (PNP)   AO2017-1040353. ISTerre is part of  Labex OSUG@2020  ( ANR10 LABX56 ). Most figures were produced using matplotlib (http://matplotlib. org/). The authors strongly acknowledge the four anonymous referees for their comments, which have strongly improved the quality of the paper.
Mitochondrial Membrane Potential (∆ψm) Estimates To assess ∆ψm of neutrophils, 10 6 cells/mL in RPMI-10% FBS were incubated with either toxin. The cells were stained with JC-1 fluorescent dye (5 µM) for 10 min at room temperature after 3 and 6 h incubations at 37 • C. Positive controls for mitochondrial membrane depolarization were obtained by incubating the cells in a 10 µM CCCP solution for 15 min. Fluorescence intensities were estimated on a FACSort cytometer (Becton Dickinson, Le Pont de Claix, France) equipped with a 15-mW argon laser tuned to 488 nm by recording through the FL1 channel (emission wavelength, 530 nm) and the FL2 channel (emission wavelength, 585 nm). Cell Quest software was used to approximate the percentage of cells analyzed in both populations: the polarized mitochondrial membrane was observed as orange fluorescence and the depolarized membrane as green fluorescence.
Acknowledgments: The authors are particularly grateful to  Daniel Keller  for constant support, recollection of unpublished results in frequent scientific discussions, and for the skillful preparation of leucotoxins. Gaëlle Zimmermann-Meisse was supported by a doctoral award from the  Ministère de l'Enseignement Supérieur et de la Recherche. The experimental work was supported by grants from  Direction de la Recheche  ( University of Strasbourg ) and by funds provided by industrial activity (CONECTUS) of EA-7290. The authors thank the  Institut Fédératif des Neurosciences IFR37/Strasbourg  and the IFR37 imaging facilities. Thanks also to the team of  Christianne Moog  ( Mécanisme de neutralisation du VIH par les anticorps ,  UMR-1110 ) for sharing human neutrophils from buffy coats. The authors are grateful to  Pierre Pothier  ( Sherbrooke, Québec Canada ) for improving the English.
Dendritic spine analysis, segmentation of presynaptic boutons and detection of synaptic contacts from confocal images. Dendritic spine detection was performed using the Neuronstudio software and data were imported into ImageJ for custom 3D automated spine heads segmentation. Segmentation of VGLUT1 objects and detection of synaptic contacts were performed in 3D as described previously  (10). Border to border distance between each spine head and all VGLUT1 objects was computed and the synaptic contact was decided for a distance of zero, meaning that the two objects overlap.
ACKNOWLEDGEMENTS AND DISCLOSURES We would like to thank Jean-Antoine Girault (INSERM, Paris, France) for critical reading of the manuscript. We wish to thank Dr. Haruo Kasai (Tokyo University, Japan) for providing the plasmid coding PPTA-Cre and Alexis Bemelmans (Molecular Imaging Research Center, CEA, France) for producing the AAV virus. The VGLUT2 antibody was a kind gift from Dr. Salah El Mestikawy (NPS, Paris, France). The tdTomato expressing virus was made available by Dr. Hongkui Zeng, of the Allen Institute for Brain Science. We wish to thank the Cellular Imaging facility of the IBPS (Institut de Biologie Paris-Seine) for expert assistance on.
Study design and sample This was an observational prospective cross-sectional study, conducted among a convenient sample of pregnant women during their routine visit to gynecologist clinics in Beyrouth (clinics were randomly selected to be representative of the capital city). Data collection was realized between July 2015 and April 2016. One hundred and forty one Lebanese pregnant women were enrolled after giving their written informed consent. Sample size was set between 100 and 200 participants as described in similar studies  [5, 7]. Exclusion criteria were: age below 18 years, any known chronic medical condition and inability to read and understand the questionnaires.
Data collection The questionnaires were anonymous, confidential and intended to be self-administered. Socio-demographic, anthropometric and clinical data were also collected. The following questionnaires were used: WHOQOL-brief (World Health Organization Quality Of Life scale-brief): it is the short version of the WHOQOL-100. It is a validated instrument to measure quality of life in patients. It was developed by the WHOQOL Group with fifteen international field centers, simultaneously, in an attempt to develop a quality of life assessment that would be applicable crossculturally. This self-administered questionnaire contains two items related to the overall quality of life (question 1) and general health (question 2) and 24 items of satisfaction on the quality of life divided into four domains: physical health (7 items), mental health (6 items), social relationships (3 items) and environmental health (8 items).
Therefore, the reduction of 21% to 36% is made only by reducing the number of library preparation. 2. 3 to 4. 9 million 21-24 nt reads were obtained for the different samples (Suppl Table  2 ). As described in Suppl Fig. 1 , the CLC Genomics Workbench was used for de novo assembly of contigs using RNAs of 21-24 nt and three different word lengths to generate scaffolds and "remainder" contigs (those that did not enter into scaffold assembly). As expected, compared to the contigs, the resulting scaffolds had higher N50, maximum length, and average length values (Suppl Table  2 ). Among the 10 samples, the maximum scaffold length ranged from 466 to 5692 nt. Assembled sequences were compared to the NCBI non-redundant nucleotide sequence database to identify the scaffolds and remainders with similarity to sequences in databases whose description includes "vir", such that all virus and viroid sequences would be retrieved.
The same strategy of read mapping was used to identify which samples bore the sequences identified as belonging to genus Potyvirus in three horizontal and three vertical pools. This was possible because potyviruses are highly diverse, and thus the potyviral sequences observed in the six pools were likely from different members of the genus. For instance, when the reads of pools HBZ-52 -53, -54, -55, and -66 were mapped on the potyviral sequences of pool HBZ-65, reads covering more than 50% of each scaffold were only observed in pools HBZ-52 and -66, thus localizing two potyviruses, one in anemone V089 and a different one in ranunculus V090. In the latter case, the potyvirus sequences could be from the remaining part of the Ranunculus leaf distortion virus (RanLDV) genome, of which there is only a partial sequence in the NCBI database.
Similarly, the potyvirus sequences in alstroemeria V098 and ranunculus V095 may correspond to the remaining parts of Alstroemeria mosaic virus (AlMV) and Ranunculus mild mosaic virus (RanMMV), respectively. That the different viruses were correctly attributed to the right sample was confirmed by sequencing RT-PCR products amplified from RNAs of 10 individual samples; in all cases, using primer pairs specific to the scaffolds examined led to the amplification of the corresponding viral sequences, with the expected levels of sequence identity to reference viral genomes in the NCBI nucleotide database (Table  8 ). It remained to determine which samples were responsible for the presence of the Tomato spotted wilt virus (TSWV) sequences in two horizontal pools (HBZ-47 and -48) and two vertical pools (HBZ-53 and -55).
Acknowledgements We thank  Fabien Robert  of  ASTREDHOR (Association nationale des structures d'expérimentation et de démonstration en horticulture ) for allowing us to contact many of the advisors and producers of the ornamental sector who provided samples for this project, and  Marie-Laure Winocq, AREXHOR (Association régionale d'expérimentation horticole ) who provided particularly numerous ornamental samples. We thank  Gregory Girardot ,  Jonathan Gaudin , and  Antoine Lauvernay  for assistance with sample preparation. We thank  Florian Maumus  for excellent suggestion on the manuscript. The IJPB has benefitted from a  French State grant  ( LabEx Saclay Plant Sciences-SPS , ref. ANR-10-LABX-0040-SPS ), managed by the  French National Research Agency  under an " Investments for the Future" program  (ref.
ACKNOWLEDGMENTS The first author benefited from an  Erasmus-Mundus  fellowship and a grant by  APIS-GENE (Paris, France) , within the framework of the  European Graduate School in Animal Breeding and Genetics (EGS-ABG, Paris, France ). This study was funded by the  French Ministry of Agriculture, Agro-food and Forest , the  French Dairy Interbranch Organization  ( CNIEL, Paris, France ), the  Regional Union of Protected Designation cheeses of Franche-Comté  ( URFAC, Poligny, France ), and the  Regional Council of Bourgogne Franche-Comté (Besançon, France) , under the project FROM'MIR.
By integrating compositional analyses, micro-and macrostructural features, shaping processes, repairs and scales of deformation, she offers new insights into the manufacture and use of helmets, greaves and cuirasses. Mödlinger's broad study not only provides new primary analytical data, but -not less important -also a collection of altogether c. 230 body armour objects between the Mediterranean and Europe. Her detailed discussion of their geographical distribution, chronological position, typological classification and material characteristics leads to a new reference work for a broad scientific community. Thanks to the author's engagement in collecting all available data and in additional sampling a representative group of objects, her results offer sustainable conclusions regarding the use and function of Bronze Age metal body armour.
Barbara Horejs Director of the Institute for Oriental and European Archaeology Vienna, 10 February 2017 First, I would like to thank the Austrian Science Fund (FWF) and the FP7/Marie Curie actions, which supported this research with the Schrödinger-fellowship no. J 3109-G21. This publication received additional financial support from the Austrian Science Fund (project no. PUB 337-G25). Furthermore, my research has also been supported by the European Commission under the 7 th Framework Programme through the Key Action CHARISMA (Grant Agreement n. 228330). Special thanks go to the FWF-Schrödinger team, especially to Reinhard Schmidt and Robert Gass, who helped me with the paperwork of the project. The preparation of this monograph has seen a significant improvement by criticism from (in alphabetic order): Dirk Brandherm (Queen's University Belfast); Albrecht Jockenhövel (Münster); Steven Matthews (Groningen Institute of Archaeology); Barry Molloy (University College Dublin); Tudor Soroçeanu (Berlin); Marion Uckelmann (Durham) and the four anonymous reviewers, although they would not necessarily agree with all herein and whatever remains is my sole responsibility.
The cuirass was allegedly bought by the museum of Székesfehérvár from a private collector in 1982. 997 The cuirass was said to have been found on the east side of the Danube shore at Pilismarót, Kom. Komárom-Esztergom, in the north of Budapest, in the 1960'. Western European Cuirasses Cat. no. 135. Unprovenanced -complete. Measurements: 51 × 39. 4cm -Metropolitan Museum  New York, accession number 09. 41 -Pl. 30. 135. References: Schauer 1982d, 96-97, fig. 2; Mottier 1988, 127, 140-141, figs. 26-28. The cuirass was bought by the Metropolitan Museum in 1909 from D. Reiling, Mainz. Before this it belonged to the Forman collection and was sold at Sotheby's on June 19, 1899 (no. 153). The cuirass is similar to the cuirasses of Fillinges in respect of a number of details, especially to cat. no.