dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The paper is the result of a working group within the  ILSI workshop on "Next generation MRA  ( Microbiological Risk Assessment ); integration of Omics data into assessment" that took place in Athens, Greece, May 13-14th 2016. This workshop was organised with the help of  ILSI-Europe, IAFP  and the ICFMH. This paper forms part of a series of four papers that address the contribution of  NGS  and omics approaches in MRA.
To establish the safety from ingestion of migrating substances, the toxicological data indicating the potential hazard and the likely human exposure data need to be combined. Exposure is estimated from studies on migration into food or food simulants and considering that a person may consume daily up to 1 kg of food in contact with the relevant FCM. As a general rule, the greater the exposure through migration, the more toxicological data is required for the safety assessment of a substance. Currently, there are three tiers with different thresholds triggering the need for more toxicological information as follows: a) In case of high migration (i. e. 5-60 mg/kg food), an extensive data set is needed. b) In case of migration between 0. 05 and 5 mg/kg food, a reduced data set may suffice. c) In case of low migration (i.
Non-toxicological data Chemical formula: Ln 2 Ter 3 (H 2 O) 4 with Ter = terephthalic acid and with Ln=Lanthanides in all combinations of La, Eu, Gd and Tb. According to the applicant, the complexes are solid salts formed by reaction of disodium terephthalate with the corresponding lanthanide chloride (LnCl 3 ) followed by precipitation from aqueous solution. The molecular masses range from 842 Da for La 2 (Ter) 3 (H 2 O) 4 to 882 Da for Tb 2 (Ter) 3 (H 2 O) 4. Purities range from 99. 8% to 99. 99%. Upon heating, the complexes lose water between 150°C and 200°C and are decomposed above 470°C. In water and 50% ethanol, solubility was determined to be ca. 20 mg/L, in 3% acetic acid ca. 100 mg/L. The additive is used as a fine powder with particles largely in the 10 lm range and is not considered a nano material.
Toxicological data The four individual complexes (europium-, gadolinium-, lanthanum-and terbium 1,4-benzene dicarboxylate) were tested in water suspension for gene mutation in the bacterial reverse mutation test using Salmonella Typhimurium strains TA98, TA100, TA1535, TA1537 and Escherichia coli tester strain WP2uvrA(pKM101) up to 5,000 lg/plate in the presence and absence of rat liver S9 following the 471 OECD guideline. The plate incorporation method with the 48 h exposure was applied. No statistically significant increases in revertant colonies were observed with any rare earth salts tested in any Salmonella strains at any test conditions. The mixture of the four individual complexes (25% w/w of each) was tested in the same way using the pre-incubation test in triplicate. No increase in revertants was detected at any concentration.
Acknowledgements D. K. and D. S. would like to acknowledge the financial support of the  Health-Holland TKI  project  NOVAMEM  (project no:  LSHM16059-SGF ). L. D. B. , R. M. , C. L. , and D. S. acknowledge the financial support by the  European Commission  for the  BIOART  project  Marie Curie Initial Training Network , Contract No. FP7-PEOPLE-2012-ITN-316690. S. M. M. , K. G. F. G. , M. C. V. , R. M. , and D. S. would like to acknowledge the financial support of the strategic alliance program entitled: Advanced biomanufacturing, funded by the  University of Twente ,  Utrecht University and University Medical Center Utrecht , project title: Innovative (bio)engineering membranes for improved treatment of kidney failure. P. S. -A. would like to acknowledge the financial support by  Gobierno de Aragón and Fondo Social Europeo  through a predoctoral Fellowship DGA  C066/2014.
N. S. R. would like to acknowledge the financial support by a  POCTEFA/RefBio II  and FGJ research grant. P. B. would like to acknowledge the financial support the  PI15/00563Research  Project from  Instituto de Salud Carlos III, Madrid, Spain. M. P. , U. P. , and C. L. would like to acknowledge the  French PIA  " RHU Ilite Innovations in tissue liver engineering " ANR-16-RHUS-0005. B. B. would like to acknowledge funding from the  ERC , the  European Union   Horizon 2020 research and innovation program  (grant agreement no. 646990-NICHOID ). K. G. F. G. would like to acknowledge the support of the  European Commission   Horizon 2020 research and innovation program , project  WEAKID  (grant agreement no. 733169 ). M. M. and R. M. acknowledge the support by  ZonMW  (project code  114024113 ).
Cloning, Expression and purification of the proteins The expression construct of the full length GST tagged RomA gene lpp1683 (GenBank entry CAH12835) was cloned into pGEX-4T2. 13 The domains or full-length non-histone substrates were cloned by PCR using cDNA isolated from HEK293 cells into the pGEX-6p2 expression vector for bacterial expression. Protein domains were predicted using Scooby domain prediction (http://www. ibi. vu. nl/programs/scoobywww/). 33 The lysine to arginine mutants were introduced by site directed mutagenesis  34  and confirmed by sequencing. Thereafter, the bacterial expression constructs were transformed into BL21 DE3 Codon Plus cells for protein expression. The overexpression of the non-histone proteins was performed in Luria-Bertani medium, which was supplemented with ampicillin.
5 ml Eppendorf tubes. The protein content of each sample was measured using a Bradford assay (ROTI nano-quant) and 200 µg of cleared lysates were put aside as total loading. For pre-clearing, 2 mg of protein were incubated for 6 minutes at 4°C on a spinning wheel with Protein G beads (Dynabeads, Invitrogen) to eliminate non-specific binding of proteins to beads. Pre-cleared lysates were incubated overnight with 2. 5 µg of anti-AROS antibody (HPA042874, Sigma) at 4°C on a spinning wheel. The following day, 30 µl of slurry Protein G beads were added to each sample and incubated at 4°C on a spinning wheel for 3 hours. Samples were washed three times in lysis buffer and resuspended in 1x SDS loading buffer. Samples were electrophoretically separated using a Bio-Rad 5-15 % Criterion Precast Gel, transferred onto a nitrocellulose membrane and blotted for protein analyses.
The following antibodies were used: antipan di/trimethyl-lysine (Abcam, ab23367), anti-AROS (Sigma, HPA042874), anti-Actin (Sigma, A5316), anti-H3K14me (Euromedex, H3-2B10), horseradish peroxidase (HRP)-conjugated secondary antibodies (DAKO). Immunoblots were revealed with a G:Box system (Syngene).
Acknowledgments This work has been supported by the  DFG  ( AJ , project  JE252/7 ). Work in CB laboratory is financed by the  Institut Pasteur ,  the Centre national de la recherche scientifique (CNRS) , the  Agency National de Recherche (ANR)  grant  n°ANR-10-LABEX-62-IBEID , the  Infect-ERA  project  EUGENPATH  ( ANR-13-IFEC-0003-02 ) and by the  Fondation pour la Recherche Médicale (FRM)  grant  N° DEQ20120323697.
Identification of binding partners of Lmo1656 A yeast two-hybrid screen was performed (Hybrigenics) using the predicted mature form of Lmo1656 (amino acids 31-143; fusion N-LexA-Lmo1656-C) as the bait with a human placental cDNA as the source of prey. After screening 56. 8 million interactions, two proteins were identified as "very high confidence" interactors of Lmo1656: SIPA1L1 (GenBank TM accession number AF090990. 1) and SNX6 (GenBank accession number NM_152233. 2).
1% Triton X-100 when required. Samples were mounted in Aqua-Poly/ Mount (Tebu-Bio) and allowed to clear for at least overnight at 4 °C. Image acquisition and analysis-Confocal z-stacks (0. 3-m step size) were acquired on a Zeiss AxioObserver. Z1 inverted fluorescence microscope equipped with an Evolve electronmultiplying charge-coupled device camera (Photometrics) and a Yokogawa CSU-X1 spinning disk confocal system. Images were acquired using MetaMorph with a 100ϫ oil objective with a numerical aperture of 1. 4. Images were visualized using Icy software  (51). When necessary, comparisons of experiments and controls were acquired in the same session with the same image acquisition parameters and data analysis. 3D surface reconstructions of Lm with SNX6 were assembled using Imaris (Bitplane) using identical processing and thresholding when appropriate.
Acknowledgments-We thank  E. Gouin  for help with antibody generation and crucial lab maintenance and  Dr. O. Dussurget  for fruitful discussion. We thank  Dr. P. Cullen  and  B. Simonetti  from the  University of Bristol, UK  for generously providing GFP-SNX plasmids. Note added in proof-In the version of this article that was published as a Paper in Press on April 17, 2018, Tables 1 and2 were inadvertently omitted. This error has now been corrected.
Tibia cortical geometry and trabecular microarchitecture Microcomputed tomography (μCT) imaging of the tibia was performed using a high-resolution (32-µm slice increment) imaging system (Siemens INVEON Micro SPECT/CT, Siemens Medical). The methods used were in accordance with guidelines for the use of μCT in rodents  (36). Scans were acquired using an isotropic voxel size of 0. 0316 mm, a peak X-ray tube potential of 80 kVp with a tube current of 500 µA, and a 600-ms exposure at a medium-high magnification using a bin of 2. In a single rotation, 360 projections were collected at 1°increments and calibration images were collected prior to data acquisition. Images were reconstructed in real time using a Feldkamp cone beam filtered back projection algorithm (2D-FDP). Trabecular bone microarchitecture was evaluated in a 1-mm region of interest that started 1 mm below the growth plate of the proximal tibia.
Cortical bone cross-sectional geometry was evaluated in the tibia mid-diaphysis, between the crest of the tibia and the distal edge of the tibiofibular joint in a 0. 5-mm region of interest 0. 25 mm proximal and 0. 25 mm distal to the midslice. The optimize threshold function was used to delineate mineralized bone from soft tissue. Segmentation thresholds of 214 mg/cm 3 and 570 mg/cm 3 were used for evaluation of trabecular and cortical bone, respectively. Scans were analyzed using BoneJ software  (37) , a subset of ImageJ (ver.
Soy isoflavones preferentially bind to the ER-β subspecies  (44) , and cancellous bone has greater expression of ER-β compared with cortical bone  (55). Additionally, the rate of turnover in trabecular bone is considerably higher than that of cortical bone  (56) , owing to an increase in active surface area  (57). Other researchers have also shown that soy preferentially protects trabecular bone through increases in bone formation  (58) , which would be consistent with our findings. However, the bone markers that we measured represent the whole body, and cannot distinguish between cancellous and cortical bone. Loss of individual trabeculae and thinning of existing trabeculae (59), as well as a lower trabecular bone volume  (60) , significantly contribute to loss of bone strength. Thus, data from the present study suggest that soy protein isolate might increase cancellous bone strength.
Acknowledgements The authors' responsibilities were as follows-JPT, RSR, and PSH: designed the research; RKD,  MWR , and GMM: conducted the research; DNB and ESK: provided the diets; RKD,  MWR , and PSH: analyzed the data; RKD and PSH: wrote the paper; RKD: had primary responsibility for the final content; and all authors: read and approved the final manuscript.
Materials and methods This retrospective analysis of hospital records included data of a consecutive group of patients with advanced esophageal carcinoma, treated between 2008 and 2015 in Department of Thoracic Surgery, Jagiellonian University Collegium Medicum. Demographic and clinical data including age, sex, weight, dysphagia, dyspnea, chemotherapy/chemoradiation, technical success rate, stent migration, complications and survival were evaluated.
Statistical analysis Statistical analysis was performed using the STATISTICA 11 PL software package (StatSoft, Tulsa Oklahoma, USA). The Mann-Whitney test was used to compare two samples. Kruskal-Wallis test was used to compare three or more attempts. In order to evaluate the changes over time (dysphagia before and after stenting, migration), the Wilcoxon signed rank test was applied. To assess the significance of connections between data on nominal scale, the Fisher's Chi-square test or Fisher's exact test was used. The logistic regression model was used to find the risk factors for complications after stenting. If an important factor was found, odds ratio (OR) was calculated along with 95% confidence interval. Survival was calculated using Kaplan-Meier method. Gehena-Wilcoxon test was used to compare survival curves.
Acknowledgments: This work is supported by  Foundation for Science and Technology (FCT)  with the reference project  PTDC/EEI-TEL/5250/2014 , by  FEDER  funds through Projecto 3599-Promover a  Produção Científica e Desenvolvimento Tecnológico e a Constituição de Redes Temáticas  ( 3599-PPCDT ) and by grant  SFRH/BD/100649/2014.
Data Analysis Using CLC Genomics Workbench 8. 5 (CLCbio), we paired and assembled contigs from the raw reads. Next, de novo assembly was performed using CLC Main Workbench (CLCbio) with the following parameters: Mismatch cost = 2; Insertion cost = 2; Deletion cost = 2; Length Fraction = 0. 5; Similarity Fraction = 0. 95. All contigs longer than 200 nt were submitted to National Center for Biotechnology Information (NCBI) for BLAST analysis.
This method resulted in the amplification of the whole genome for samples containing a single virus or mixture and the amplicon products were used for NGS. To validate the proposed primer sets capability of generating whole genome sequencing data, we tested 15-EVA, 40-EVB, 20-EVC, and 2-EVD viruses (Table  1 ). We obtained the full genome sequencing data for all viruses except two (EV-C95 T08-083 and EV-D70), for which we obtained 93. 6 and 87. 5% of the genomic sequences, respectively. In all cases the sequences of the VP1 capsid protein could be used to confirm the type of virus. These results indicated the effectiveness of the proposed primers in conjunction with NGS sequencing to correctly identify the viruses and to reconstruct the whole genome using de novo assembly. Additionally, to evaluate the sensitivity of this assay, we tested a fourfold serial dilution of one representative of each enterovirus species (Table  3 ).
2 Cycle threshold values obtained using a pan-enterovirus real-time RT-PCR assay performed on the extracted RNA. 3 Concentration of DNA amplicons obtained by RT-PCR for each dilution. 4 Total number of reads from NGS sequencing. 5 Number of reads mapped against the known reference (indicated in column one) for each viral dilution with percent identity to total reads. 6 The size of each contig (enteroviruses ∼7500 nb). 7 There was no amplification therefore no threshold was obtained. obtained for the ten isolate samples from stool tested, indicating that the method was sensitive enough to determine the entire genome. The results were different for sewage because mixtures of strains appeared to be more complex (up to 7 different strains) than those present in stools (two strains maximum). Only three of the ten isolate samples resulted in sequencing data for the whole genome.
ACKNOWLEDGMENTS The authors are indebted to  Maud Vanpeene ,  Andrea Alexandru ,  Sobhy Wilhame , and  Vincent Enouf [Institut Pasteur ,  Pasteur International Bioresources network (PIBNET) ,  Plateforme de microbiologie mutualisée  ( P2M ), Paris, France] for performing the sequencing experiments. Thanks to  Deborah Delaune  and  Anne-Lou Pinon  for their assistance with performing some experiments. We would like to thank the staff involved in the sampling collection and isolation from  Institut Pasteur de Madagascar  ( Seta Andriamamonjy ,  Fitahiana Michael Rakotoarison , and  Sandratana Raharinantoanina ). In addition, we are grateful for the isolates used for this study from  Anda Baicus  (Romania) and  Serge Sadeuh-Mba  (Cameroon).
Morphological analysis of neurons. Neuronal diameters of L4, L5, and L6 DRG slice sections were measured after immunohistochemistry. Neurons with distinguishable nuclei were counted and their area was measured using Metaview software. Soma diameters were also determined and three categories of sensory neurons were distinguished: small neurons with a diameter <17 µm, intermediate neurons diameter 17-25 µm, and large neurons >25 µm  46. Five to eight sections from each DRG were analyzed and 3 to 5 animals were used for each condition. Experiments were performed three times. Quantification of microglial surface. Lumbar spinal cord slices were labelled with Iba1 antibody. 4 slices par animal and 3 mice per condition were analyzed. Iba1 positive area of the ipsilateral side of the CFA injection was detected after background subtraction with the ImageJ software and expressed in µm 2.
Fluorescence was excited by illumination with an x20 water immersion objective with a light wavelength switch provided by a DG4 filter wheel. Fluorescence was detected with a CCD camera under the Metafluor software control. Pairs of images were acquired every 2 s. Intracellular calcium is expressed throughout in the figures as the fluorescence ratio F 340 /F 380 , after background subtraction. Experiments were performed at room temperature. Drugs were applied through an 8-channel gravity-fed bath-perfusion system, which allows switching between various solutions. ATP was prepared in distilled water and used at a final concentration of 20 µM. Ivermectin (Sigma) was dissolved in DMSO and used at a final concentration of 3 µM. Western blot. Ipsilateral L4, L5, L6 DRG were homogenized in lysis buffer (20 mM HEPES, pH 7.
Acknowledgements This work was funded by the  Institut National de la Santé et de la Recherche Médicale (INSERM) , the  Centre National de la Recherche Scientifique (CNRS) , the  French Government (National Research Agency, ANR)  through the  "Investments for the Future" Program reference #   ANR-11-LABX-0015-01 , the  Languedoc-Roussillon  " Chercheur d'avenir program ", and  Institut UPSA de la douleur. The Figure 6 has been designed and created by  Dr. V. Juvin  from  SciArtWork  (www. sciartwork. com). We thank  Pr. B. Hempstead  for kindly providing the BDNF-HA mouse strain, the staff of  Réseau des Animaleries de Montpellier (RAM) of the Institute for Functional Genomics  and the  Montpellier Ressources Imaging facility (MRI) of the Institute for Human Genetic.
| Colonyidentification Isolated bacterial colonies identification trials were done first by using MALDI-TOF MS analysis as previously described  (Elsawi et al. , 2017). In case of MALDI-TOF MS identification failure, complete 16S rRNA sequencing was performed for further analysis with the same protocol used in our previous studies  (Elsawi et al. , 2017). Complete 16S rRNA nucleotide sequence are assembled and manipulated using CodonCode Aligner software (http://www. codoncode. com) and blasted in the online PubMed National Center for Biotechnology Information (NCBI) database for phylogenetic analysis. According to  Kim, Oh, Park, & Chun (2014) , a threshold of 98. 65% 16S rRNA gene sequence similarity was used to classify a new species, whereas a threshold of 95% 16S rRNA gene sequence was used for new genus classification.
| Strainidentificationandphylogeneticanalysis The identification of P3236 T strain using MALDI-TOF MS failed due to the absence of its mass spectrum in the current databases. However, a typical spectrum was added to our custom database (Figure  1 ) after performing a complete 16s rRNA gene sequencing. Strain Marseille-P3236 T exhibited a 97. 05% sequence similarity with Parabacteroides gordonii strain MS-1 (NR_112835. 1), the phylogenetically closest species with standing nomenclature (Figure  2 ). Accordingly, with more than 1. 3% sequence divergence from its phylogenetically closest species with standing in nomenclature, we propose the classification of Marseille-P3236 T strain as a new species within the Parabacteroides genus. The protein spectrum of Marseille-P3236 T strain was compared with those of other close species under the same family.
| Comparisonofgenomeproperties The draft genome sequence of Marseille-P3236 T strain was compared to those of Parabacteroides gordonii (P. gordonii) (AUAE00000000), Parabacteroides distasonis (P. distasonis) (JNHP00000000), Porphyromonas canoris (P. canoris) (JQZV00000000), Parabacteroides johnsonii (P. johnsonii) (ABYH00000000), Parabacteroides merdae (P. merdae) (AJPU00000000), and Tannerella forsythia (T. forsythia) (CP003191). Genome of Marseille-P3236 T strain was smaller than those of P. gordonii (6,483 and 6,677 MB, respectively), but was nevertheless larger than those of P. distasonis, P. canoris, P. johnsonii, P. merdae, and T. forsythia  (5,316, 2,203, 4,787, 4,459, and 3,282   johnsonii, P. merdae, and T. forsythia (4,800, 1,612, 4,515, 3,703, and 2,492, respectively). Distribution of functional classes of predicted genes according to the COGs database regarding strain Marseille-P3236 T is presented in Figure  6.
Purpose Acromegaly is characterized by a broad range of manifestations. Early diagnosis is key to treatment success, but is often delayed as symptomatology overlaps with common disorders. We investigated sign-and-symptom associations, demographics, and clinical characteristics at acromegaly diagnosis. Methods Observational, cross-sectional, multicenter non-interventional study conducted at 25 hospital departments in France that treat acromegaly (ClinicalTrials. gov: NCT02012127). Adults diagnosed with acromegaly < 5 years were enrolled. Demographic and clinical data were obtained from medical reports and patient questionnaires. Sign-and-symptom associations were assessed by multiple correspondence analysis (MCA). Results Overall, 472 patients were included in the analyses. MCA was unsuccessful in identifying sign-and-symptom associations at diagnosis.
Data collection and study endpoints Data were collected retrospectively from patients' medical records (transcribed into case report forms [CRFs]; Online Resource 1), and from questionnaires written in lay terms and completed by patients (Online Resource 2). Demographic and disease data were captured, including the signs, symptoms, and comorbidities of acromegaly at diagnosis and the dates of their first occurrence. The study endpoints were to describe the most characteristic sign-and-symptom associations present at the diagnosis of acromegaly (primary endpoint), and to describe demographic and clinical characteristics at the diagnosis of acromegaly (secondary endpoint). Post hoc analyses were conducted to: assess the timing of the occurrence of manifestations in the years prior to diagnosis; report differences in manifestations between men and women; and to examine discrepancies between data captured in the CRF by the physician versus the patient questionnaire.
Multiple correspondence analysis (MCA) MCA is a powerful analytic technique used to detect and represent the pattern of relationships of variables and explore underlying structures in large, complex datasets containing categorical data. MCA has been used been used previously to identify sign-and-symptom associations from clinical datasets  [24, 25]. MCA describes relationships between categorical variables within a dataset and represents the frequency of each variable in terms of the distance between individual variables, and the distance to the average variable profile (explained by the level of inertia), as a cloud of points in a two-dimensional map  [26]. Factorial axes are derived in order to identify which variables differ the most between patients, enabling the differentiation of patient profiles  [26].