dataesr/scientific-paragraphs-categorization huggingface dataset:
results In the ANRS 12174 trial, 1273 mother-infant pairs were randomised and six were excluded due to protocol violations. Of the remaining 1267 participants, 204 were from Ouagadougou, 222 from East London, 278 from Mbale and 563 from Lusaka. In all, 42 were excluded from analysis due to lack of breastfeeding data after inclusion, 7 due to inaccurate feeding duration data and 2 women had no data on weights. The analysis included 1216 subjects. The complete flow chart has been published elsewhere. 27 he mean baseline weight, the percentage of educated and employed women was highest, and the mean EPBF Mean duration of zidovudineregimen post-delivery (days)* 6. 6 (6. 5 to 6. 8) 7 (7. 0 to 7. 0) 6. 8 (6. 7 to 6. 9) 7. 0 (6. 9 to 7. 0) 6. 9 (6. 8 to 7. 0) Mean duration of lamivudine regimen post-delivery (days)* 6.
Acknowledgements We would like to thank all the mothers who agreed to be part of the trial together with their children. Our acknowledgements also go to the different ANRS 12174 site staff for their dedicated effort in this research. We are also very grateful to the  University of Bergen  and the  Centre for International Health  for providing the infrastructure, and the needed supervision and training. We also thank the  UMR 1058 , pathogenesis and control of chronic infections, Montpellier, France, from which we received invaluable support regarding data management. The final typescript has been improved through the help of  BioMedES Ltd, UK  (http://www. biomedes. co. uk).
Data were then converted to percentage of injected dose and to percentage of injected dose per mm 3 of tissue. The CT and SPECT reconstructions were performed using image processing software provided by Bioscan Inc. Eventually, the SPECT/CT fusion image was obtained using the InVivoScope software (Bioscan Inc. ). Each scan was then visually interpreted, and 3D regions of interest corresponding to the tumor and whole body were manually drawn to determine their radioactivity content. In vivo quantification was obtained by accurate calibration of the NanoSPECT/CT γ-camera. Radioactivity contents from image analysis were expressed in Bq/mm 3 , converted to percentage of injected dose, and compared to those determined by ex vivo counting.
Acknowledgements This work was performed within Pharm'image, a regional center of excellence in Pharmacoimaging. Support was provided by the  French Government  through the  French National Research Agency (ANR)  under the program " Investissements d'Avenir"  ( ANR-10-EQPX-05-01/IMAPPI Equipex ) and the  CNRS , the  "Université de Bourgogne" and the "Conseil Régional de Bourgogne " through the  3MIM  integrated project (" Marquage de Molécules par les Métaux pour l'Imagerie Médicale "). This work is also part of the project "pharmacoimagerie et agents theranostiques", supported by the  "Université de Bourgogne" and the "Conseil Régional de Bourgogne"  through the  "plan d'actions régional pour l'innovation (PARI) " and the  European Union  through the  PO FEDER-FSE  Bourgogne  2014/2020  programs.
Data collection and testing protocol Serum samples were obtained from Madagascar's national surveillance system for measles and rubella. Standard protocol requires that when a patient presents for care with symptoms meeting the clinical criteria for measles (fever and rash and either cough, corzya, or conjunctivitis), the patients' serum is collected and sent to the WHO national reference laboratory located at the Institut Pasteur de Madagascar. At Institut Pasteur de Madagascar, the serum is tested for measles-specific and rubella-specific immunoglobulin M antibodies to detect a recent infection. Any remaining serum is stored at Institut Pasteur de Madagascar. In 2016, we tested serum collected between November 2004 and November 2015 for measles-specific IgG antibodies with an indirect ELISA test (Enzygnost Anti-Measles Virus/IgG; Siemens, Erlangen, Germany).
Data sample size We excluded the febrile-rash serum samples collected prior to and during the October 2013 SIA (November 2004-October 2013) in order to estimate the most recent age-specific seroprofile and avoid biasing our estimates of age-specific seroprevalence due to sharp shifts in seroprevalence among the 2013 SIA-targeted age groups. A total of 1,123 samples were collected from November 2013 to December 2015. By grouping the recent 26 months, we assume monotonic increases in immunity (natural and vaccinal) over age during this time; this assumption likely holds for natural immunity given low transmission (2) as well as for vaccinal immunity, because vaccination coverage is unlikely to have declined substantially in this time-frame, so our analysis should be robust to this assumption.
Characterization of the data Identifying sampling biases by age and location is key to understanding the external validity of the data to characterize agespecific seroprevalence. We compared the proportion of samples according to age with the expected proportion according to United Nations Population Division estimates  (25). We also investigated the degree to which the 1,005 febrile-rash samples were generalizable across space, and we assessed the potential of heterogeneous spatial sampling to bias our estimates of measles seroprevalence by comparing spatial variation in sampling with spatial variation in inferred vaccinal immunity. We did not assess potential spatial variation in naturally acquired immunity because: 1) Evidence suggests that recent transmission is low; 2) we removed immunoglobulin M measles-positive cases to reduce this bias; and 3) the immunoglobulin M incidence data is insufficient in sample size to assess spatial differences.
Exploring the effect of measles SIA scenarios We assessed the impact of 16 different SIA scenarios by simulating the administration of each SIA (taking into account vaccination effectiveness) to Madagascar's population, assuming age-specific susceptibility reflected the direct estimates based on the serological data. SIA scenarios differed according to the targeted upper age and the assumed vaccination coverage. We included the age group that was targeted by the 2016 SIA, which was conducted after data collection (ages 9 months through 4 years) (5); a typically targeted age group (ages 9 months through 14 years); and 2 nonclassically targeted age groups (ages 9 months through 9 years and 9 months through 19 years). For each scenario, we analyzed an upper and lower bound of potential vaccination campaign coverage (70% and 95%, based on Madagascar's reported range from WHO  (5) , but setting the maximum to 95% despite reports exceeding 100% due to known overreporting issues using administrative data  (10) ).
Simulated SIAs assumed independence between SIA vaccination and prior immunity (i. e. , all individuals in the target age range had an equal probability of being vaccination by the SIA regardless of immunity status). We assumed that SIA vaccine effectiveness by age followed a logistic function modeled on data from Boulianne et al. (28) , saturating at 97%, and that there was no correlation between prior immunity and SIA vaccination. We used 4 approaches to evaluate the impact of each SIA scenario. First, we compared estimated population susceptibility levels after the SIA with the theoretical susceptibility threshold for elimination. In an unstructured population, the critical immunity threshold ( ) p c required to achieve herd immunity is defined as  29) , where R 0 is the basic reproductive number evaluated at 10, 15, and 20  (30) ; the susceptibility threshold is its complement ( -) p 1 c.
ACKNOWLEDGMENTS Author affiliations:  Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland  ( Amy K. Winter ,  Amy P. Wesolowski ,  Justin Lessler );  Princeton Environmental Institute, Princeton University , Princeton,  New Jersey  ( Keitly J. Mensah );  Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar  ( Miora Bruna Ramamonjiharisoa ,  Andrianmasina Herivelo Randriamanantena ,  Richter Razafindratsimandresy ,  Jean-Michel Héraud); Mathematical Modeling of Infectious Diseases Unit, Institut Pasteur, Paris, France (Simon Cauchemez) ;  Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania  ( Matt J. Ferrari ); and  Department of Ecology and Evolutionary Biology ,  Princeton University , Princeton,  New Jersey (C.
Jess E. Metcalf). This work was funded by the  Bill and Melinda Gates Foundation  (grant  OPP1094793 ) and the  Wellcome Trust  (grant  106866/Z/15/Z ). We thank the staff of the Direction of the  Expanded Program on Immunization  from the  Malagasy Ministry of Public Health , for their dedicated work toward measles immunization, and all staff of the health sector involved in measles surveillance. We also thank all the staff from the  World Health Organization national reference lab at Institut Pasteur de Madagascar  for their work regarding testing and database sharing.
Primer designing Based on the alignment of all available euglenid nSSU rDNA sequences, the regions for primer design were chosen according to the following principles: (i) regions conserved for E. sanguinea (GenBank numbers: strain Argentina JQ281804, Henderson JQ281805, and SAG 1224-30 JQ281806), but dissimilar to any other species of euglenids, were chosen; (ii) intraspecific variations within the region were flanked by the primers; and (iii) the length of the PCR product had to be appropriate for efficient amplification. Two sets of speciesspecific primers were designed manually-the external primers sangF0/R0 (encompassing the region between helix 29 and 45 in the secondary structure of nSSU rDNA; sangF0: C T G Y G G G C G C C A C G C C C C T T G , s a n g R 0 : ACGGACTTGCRGGGTTTCCCAGC) and the internal primers sangF1/R1 (between helix 30 and 45; sangF1: C G C C C C C T T G A C C G A G A A AT C C G , s a n g R 1 : GCCRGGGCCCRCAGAARACGAGG).
Results Designed primer pairs amplified efficiently and specifically the fragment of nSSU rDNA from E. sanguinea strains (length of PCR products with sangF0/R0: SAG 1224-30-921 bp, Henderson, MI-20 and ACOI 1267-743 bp; sangF1/R1: SAG 1224-30-878 bp, Henderson, MI-20 and ACOI 1267-700 bp, MI-51-717 bp, GenBank no. KY928280) in a wide range of annealing temperatures (54-64 °C for sangF0/R0 and 50-66 °C for sangF1/R1). The optimal temperature for the pair of external primers sangF0/R0 was 62 °C. For internal primers sangF1/R1, the optimal temperature was 60 °C. The obtained sequences of PCR products were identical for the strains Henderson, MI-20, and ACOI 1267. Therefore, they were considered as genetically indistinguishable and the latter two strains were not included in subsequent analyses.
Colon tumor of patients contains granzyme B-expressing neutrophils Tumor-infiltrating neutrophils were evaluated in a cohort of 35 patients with colon cancer (all patients for which a tumor sample was available had given its written consent). Using hematoxylin-eosin-saffron (HES) staining, we showed that all tumors were infiltrated by neutrophils at variable rates (Table  1 ). The low number of patients did not allow us to see any significant correlation between the rate of tumor-infiltrating neutrophils and patient's survival. We also determined cytokines and chemokines levels in tumor and normal tissues from 25 patients. We showed no significant differences in IL-2, IL-6, and Il-12b mRNA levels between tumor and normal tissues (data not shown). However, the neutrophil CXC chemokine IL-8 mRNA expression was significantly higher (p < 0.
reported that CD66b+ cell infiltration in colorectal cancer is associated with increased survival  [47]. Our data also showed that GZMB + -neutrophils have anti-tumor activity when activated by a TLR4 agonist unlike those devoid of GZMB, and their infiltration into tumor probably contributed to the LipA-mediated tumor cell death. Our conclusions are supported by results showing that the inhibition of GZMB activity in tumor cells affected the anti-tumor activity of LipA. We noted that colon tumor cells expressing the physiologically inhibitor of GZMB, the serpin B9, grew more slowly in mice as compared to wild type cells (80% reduction  11 (31%) Score of tumor infiltration in polymorphonuclear neutrophils (PMN) was determined as: 0; absence of PMN in tumor zones outside ulceration zones, after careful analysis of the entire cut, 1+; presence of PMN isolated or in small clusters of 2-3 elements in the tumor zones outside ulceration zones.
RT-PCR Total RNA from rat samples was extracted from tumors using the RNeasy kit (Qiagen). RT-PCR were performed with the Qiagen OneStep RT-PCR kit (Qiagen) according to the manufacturer's protocol. The primer list was in Table  2. The PCR products were analyzed by gel electrophoresis (1. 5% agarose) and stained with ethidium bromide (Invitrogen). The amplified cDNA length was evaluated using the 100-bp DNA ladder (Promega). All densitometric analyses were performed with ImageJ software. Total RNA from human samples was extracted from tumors with Trizol (Ambion), qRT-PCR were performed and analyzed with the Sybr Green method (Thermofisher) according to the manufacturer's instructions. Expression was normalized to the expression of human beta-actin using the 2 e-ΔCT method previously described  [57].
Immunohistofluorescence (IHF) and immunofluorescence (IF) For IHF, fixed tumors were embedded in OCT (Labonord) after impregnation with 20% sucrose/PBS. Sections were cut into 5 µm thick and fixed for 10 min in cold acetone. Antigen retrieval was performed (citrate buffer pH 7. 3, 96° C, 20 min) before the blocking of nonspecific sites with 3% BSA. For IF, neutrophils (1 × 10 4 ) were plated in Lab-Tek II (Nalge Nunc), fixed in 4% paraformaldehyde, permeabilized in 0. 2% Triton X-100 and incubated with 3% BSA. Slides for IHF and IF were incubated with primary antibodies in 1% BSA/PBS/0. 1% Tween, then with appropriate secondary antibodies in 1% BSA/PBS/0. 1% Tween. Slides were mounted using Prolong Gold (Invitrogen). Images from rat colon cancer were captured on a Nikon Eclipse E400 epifluorescent microscope at 40x magnification, images from human colon cancer were captured on a Axio Imager 2 microscope with Axiovision software.
Statistical analyses Experimental data are expressed as means ± SEM. Statistical analysis was performed using StatView software. The Mann-Whitney U test was used to compare data between two treatment groups. Differences were considered statistically significant as follows: * P ≤ 0. 05; ** P ≤ 0. 01; *** P ≤ 0. 005, and **** P ≤ 0. 0005.
2 µm Whatman polycarbonate filter with PBS-EDTA, pH 7. 4. Functionalized CNTs (CMC-CNTs) were then resuspended in PBS-EDTA. For oxidized DWNTs, 100 mg of DWNTs were added to 100 mL of HNO3 (3 M) and placed in ultrasonic bath for 30 min and refluxed at 130°C for 24 h. The solution was left to cool at room temperature. The solution was washed and filtered on a polypropylene membrane (0. 45 μm). For electron microscopy, 2 µL of well-dispersed CMC-CNTs were adsorbed onto carbon-coated grids. Micrographs were recorded using a JEOL 2100 FEG-TEM operating at 80 Kv, and the images were processed using Gatan microscopy suite software (Gatan, Inc. ). Surface visualization of CMC-CNTs was performed using a Zeiss Supra 35vP scanning electron microscope operating at 5 kev.
A NanoDrop 2000/2000c spectrophotometer (Thermo-Fisher Scientific) was used to determine the amount and purity (260/280 nm ratio) of RNA. The cDNA was synthesized using High Capacity RNA to cDNA Kit (Applied Biosystems). Primers (Table  1 ) were designed using Primer-BLAST. 1 he qPCR reaction mixture included 5 µL Power SYBR Green MasterMix (Applied Biosystems), 75 nM forward and reverse primers and 500 ng template cDNA in a 10 µL reaction volume. PCR was performed using a Step One Plus Real-Time PCR System (Applied Biosystems). Human 18S rRNA target was used as an endogenous control. Data were analyzed using the Step One software v2. 3 (Applied Biosystems). Ct (cycle threshold) values for each cytokine target gene were calculated. Relative expression of each cytokine target gene was calculated using the relative quantification (RQ) value, using the equation RQ = 2 -ΔΔCt for each cytokine target gene and comparing relative expression with that of the 18S rRNA constitutive gene product.
The expression of cytokines was measured using real-time qPCR, and the data were normalized using as endogenous control; 18S rRNA gene expression assays were conducted in triplicate. Error bars represent ±SEM. A multiple t-test using Holm-Sidak method was performed to determine significance differences in expression between each uncoated and protein-coated carbon nanotubes (CNTs) of different time points. All these comparisons were significant: *P < 0. 05, **P ≤ 0. 01, ***P ≤ 0. 001, and ****P ≤ 0. 0001. Properdin-CMC-CNT as well as TSR4+5-CMC-CNT. GM-CSF is produced by macrophages in response to immune stimuli, which can recruit neutrophils and lymphocytes. IL-1α and IL-1β (Figure  7 ) induce an inflammatory pathway initiated via Myd88 activation and triggered by NF-κB transcription of inflammatory genes.
Observation with IRAM 30 m telescope Observations of the CH 3 OH, C 2 H, and c-C 3 H 2 lines in the 1. 3 mm band were carried out with the Institut de Radio Astronomie Millimétrique (IRAM) 30 m telescope at Pico Veleta. The sources except for NGC 1333-16 (IRAS 4A) and NGC 1333-17 (SVS 13A) were observed in the period from between 2015 January to 2016 May. For these two sources, we use the data taken by the ASAI (Astrochemical Survey At IRAM) project  (Lefloch et al. 2018). The Eight Mixer Receiver (EMIR), E230, was employed in the dual-polarization mode. The system temperatures ranged from 250 to 400 K. HPBW is 10 ′′ at 260 GHz, which corresponds to 2400 au at the distance of 235 pc. The back end consists of eight Fourier transform spectrometers (FTS), whose bandwidth and channel width each are 400 MHz and 200 kHz (velocity resolution of ∼0.
Data analyses Figure  1  shows the observed spectral lines of CH 3 OH (J=5-4, K=1, E -, E u =40 K) and C 2 H (N=3-2, J=5/2-3/2, F =3-2, E u =25 K) for a few selected sources. The relative intensities between CH 3 OH and C 2 H are significantly different among the sources. For instance, the CH 3 OH line is strongly detected toward NGC 1333-1, whereas the intensity of the C 2 H line is weak. In contrast, NGC 1333-6 shows an opposite trend; CH 3 OH is not detected. A similar trend can be seen in B1-5: the C 2 H lines are strong, while the CH 3 OH lines are weak. For B1-3 and L1448-3, both the CH 3 OH and C 2 H lines are moderately intense. To quantify the trend, we evaluated the line parameters for each line by assuming that the line profile is approximated by a Gaussian function. The CH 3 OH lines at 242 GHz would likely trace a relatively dense and warm region rather than a cold ambient cloud because of their upper state energies (e.
Column densities are derived from the CH 3 OH (J=5-4, K=1, E -), C 2 H (N =3-2, J=5/2-3/2, F =3- 2), and c-C 3 H 2 (3 2,1 -2 1,2 ) lines. Error bar are calculated for the rms noise and do not included calibration uncertainty (20 %). As a reference, the column densities of L1527 are derived with the available IRAM 30m/NRO 45m dataset. (d). Data points with an arrow show the lower limits. The correlation coefficient is defined in the caption in Fugure 2. The correlation coefficient is derived excluding the lower limit data. If we include the data point, the correlation coefficient is changed to be 0. 12 for (a), 0. 13 for (b), 0. 28 for (c), 0. 45 for (d) and 0. 58 for (e), respectively. b The wing components are excluded in the Gaussian fit. T MB dv d rms e V LSR J, K [K] [km s -1 ] [K km s -1 ] [K km s -1 ] [K] [km s -1 ] NGC 1333-1 J=5-4, K=2 E - 0.
Methods Animals. Close-up photographs from a total of 16 specimens of African bush elephant (Loxodonta Africana) were acquired for image analysis and qualitative observations. These include data from living animals from zoos or reserves and fixed skin samples held by various institutions (Supplementary Table  1 ). In all cases, the pictures were taken with the consent of the animal's supervisor or the sample's curator. Additionally, we obtained museum formaldehyde-fixed skin samples from seven animals (IDs 3 and 11-16 in Supplementary Table  1 ) that were used, e. g. for histology, micro-CT scanning and statistical analysis of papillae. Stratum corneum regrowth was followed on a patch of skin located on the buttocks of animal 8, Nuanedi (see section 'Evidence for cracking as the patterning mechanism of the skin of the African elephant' in Supplementary Material).
Skin samples were stained with 25% Lugol's iodine for ~48 h prior to imaging, as this procedure has been shown to produce good differential contrast with minimal tissue shrinkage  37. Finally, samples were transferred to phosphate-buffered saline and imaged using a Quantum GX MicroCT Imaging System (PerkinElmer, Waltham, MA, USA) at 6 μm resolution. Raw data were analysed and segmented using Amira 6. 2. 0 (FEI, Hillsboro, OR, USA). The software was also used to produce a rough mesh, which served as the input for a custom mesh regularisation algorithm designed to smooth out the surface kinks and the irregular edge length distribution of the raw micro-CT mesh (see section 'Mesh geometry and regularity' in Supplementary Material). This regularised mesh output was then used in the numerical simulations.
Acknowledgements We thank  Athanasia Tzika ,  Ingrid Burgelin ,  Liana Manukyan ,  Adrien Debry ,  Florent Montange  and  Valérie Haechler  for technical assistance with histology, image acquisition and analyses, as well as Isabelle and  Albert Haechler  for wetting experiments. This work was supported by grants to M. C. M. from the  University of Geneva (Switzerland) , the  Swiss National Science Foundation  (grants  31003A_140785  and  SINERGIA CRSII3_132430 ), the  SystemsX. chinitiative (project  EpiPhysX ) and the  Human Frontier Science Program  ( HFSP RGP0019/2017 ).
Data collection We conducted a retrospective study involving every patient who had received at least one injection of botulinum toxin into masticatory muscles was conducted and whose treatment was carried out at the Stomatology and Maxillofacial Surgery department of the Nantes University Hospital between 2014 and 2016. Patients who were enrolled in the study had been suffering from TMD for more than six months. BTX was used after failure of non-invasive therapies. Patients were informed of the use of their medical records. The study obtained the approval of the regional Ethics Committee (no. 2016/41). All patients answered a series of questions about the history of their disease. The "NFD" criteria were assessed during the clinical examination: myalgia and its location, joint pain and noises, mouth opening range and kinetics.
Epidemiological data Our study included 40 patients. Among them, 34 answered all the questions. Six patients were not followed up. The group was made up of 76. 5% of women (n = 26) with a mean age of 37  at the first injection (Tab. I). The male/female ratio was 3 females for every male. Among the identified TMD risk factors, 53% (n = 18) had a class II deformity. Among them, 17. 6% (n = 6) were class II. 2. Bruxism was identified in 26. 5% (n = 9) of patients. Regarding TMD symptoms, 19 (56%) patients were suffering from myalgia, 18 (53%) from arthralgia and 13 (38%) from headached or cervicalgia. Five patients were followed in a pain treatment centre. Masticatory muscle hypertrophy was observed in 26. 5% (n = 9) of patients. As part of treatment before the BTX injections, 76. 5% of patients (n = 26) used occlusal splint to prevent bruxism, 57.