dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogeny of the 15 strains isolated in Africa amongst DENV-3 strains A total of 15 African strains from 7 different countries were isolated between 2008 and 2012 from African patients or from imported cases. Their E gene sequences were compared with 101 sequences representative of all five DENV-3 genotypes available in open databases. The phylogenetic analysis highlighted that the 15 African strains clustered within genotype III (Figure  1 ). DENV-3 includes five genotypes numbered from I to V that are mainly described in Asia and the Americas. Little is known about DENV-3 genotypes in Africa that could be explained by a reduced circulation in Africa or a lack of surveillance. In Africa, only genotype III has been reported. This genotype is highly likely to have been introduced in Mozambique in 1985 from India  [17].
4 m/z, and NCE 27, underfill 5%, unassigned and +1 ions excluded, peptide match preferred, isotope exclusion on, dynamic exclusion 30 s, LC solvents A: 0. 1% formic acid with 2% acetonitrile, B: 100% acetonitrile, precolumn: Thermo Acclaim Pepmap 100 75 μm × 2 cm C18 3 μm 100 A (Thermo Fisher Scientific), analytical column: Thermo Pepmap RSLC C18 um 100 A 75 μm × 50 cm, precolumn equilibration 4 μl at 800 Bar, analytical column equilibration 6 μl at 980 Bar, sample loading 6 μl at 980 Bar, gradient 5-10% B in 2 min, to 25% B in 80 min, to 40% B in 8 min, to 90% B in 5 min and held for 5 min. Resulting mass spectral files were searched against the UniProt Mouse database using MaxQuant (http://www. coxdocs. org/doku. php? id = maxquant:start) with the following parameters: partially tryptic, 2 missed cleavages, heavy lysine 6.
Polyclonal rabbit anti-mouse and goat antirabbit secondary antibodies (Dako, Carpinteria, CA, USA) conjugated to horseradish peroxidase (1:3000) were used as appropriate for 1 h. The protein bands were revealed with ECL chemi-luminescence substrate (GE Healthcare, Pittsburgh, PA, USA). For quantification, the blots were exposed to X-ray films or scanned digitally with ChemiDoc Touch Imager. Densitometric analysis was carried out using a BioRad GS-800 calibrated densitometer and Quantity One software or Image Lab software (Bio-Rad, Hercules, CA, USA). Ratios of the optical density of each specific protein were normalized to the corresponding loading control. Contraction-induced myofiber and sarcolemmal injury. After anesthetizing the mice with a mixture of ketamine and xylazine, EDL muscles from the right hind limb of C57BL/6, mdx, and DDKO mice were carefully exposed and 6-0 silk sutures were firmly attached to the proximal and distal tendons.
After removing the excess dye by washing with Ringer's solution, the muscle was frozen using isopentane prechilled in liquid nitrogen. Frozen tissues were sectioned (10 μm) and imaged under red channel using a Nikon Eclipse E800 (Nikon, Sendai, Japan) microscope that was fitted with a SPOT digital color camera with SPOT advanced software (Diagnostic Instruments, Sterling Heights, MI, USA). Representative pictures (×20) were taken and PO-positive fibers/image was quantified for each section. Data are represented as the number of PO-positive fibers per image (mean ± S. D. ). Measurement of inflammation marker. IL-1β inflammatory marker was monitored using real-time quantitative PCR assay as previously described. 29 In brief, quadriceps muscle tissue was obtained from 28-day-old C57BL/6, mdx-52, and DDKO mice.
The excess dye was washed off, and the fibers were transferred to CIM. Myofibers were injured using a pulsed laser and imaged as described above. In cell culture experiments, C2C12 myoblasts were incubated in 100 mM pyruvate for 10 min or 5 μM CCCP for 45 min at 37 °C prior to labeling, and following washes, the cells were transferred to CIM containing the indicated drug for imaging. The fluorescence intensity of MitoTracker dye at the site of injury or in the whole cell (as indicated) was measured and the data are presented as means ± S. D. To assess mitochondrial respiratory activity, muscle tissues (gastrocnemius) were harvested and homogenized in ice-cold H medium (70 mM sucrose, 220 mM mannitol, 2. 5 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7. 4, and 2 mM EDTA). The homogenate was centrifuged at 1500 × g for 10 min at 4 °C.
For pyruvate treatment, biceps muscle from mdx-23 mice were dissected and incubated with pyruvate (100 mM salt, Sigma, St. Louis, MO, USA) for 25 min at 37 °C before laser injury in the presence of FM1-43 dye (as described earlier). The same procedure was carried out for FDB muscles and mitochondria potential measured using MitoTracker Red (CM-H2TMRos) as above. Contralateral muscles were used as untreated controls. Statistical analyses. Statistical analyses were performed using either Student's t-test or one-way analysis of variance (with Bonferroni correction posttest) where appropriate. When data are not normally distributed, non-parametric Mann-Whitney test was used to determine the statistical significance. Calculations were performed with GraphPad Prism version 6 (Graphpad Software, Inc.
Acknowledgements. SR and MCV performed these studies as part of their doctoral studies at the  Institute for Biomedical Sciences at the George Washington University  and the work here from part of their PhD dissertations. We thank  Dr. Isabelle Richard  ( Genethon, France ) for the gift of B6A/J mouse model. Financial support was provided by  NIAMS  ( R01AR055686 ) and  MDA  ( MDA277389 ) to JKJ as well as by  NIH  ( K26OD011171 ;  R24HD050846 ,  P50AR060836 ,  U54HD071601 ) and the  US Department of Defense  ( W81XWH-05-1-0659 ,  W81XWH-11-1-0782 ,  W81XWH-11-1-0330 ) grants to KN. The microscopy core is supported by  NIH  core grant  IDDRC P30HD040677.
The N50 of the contigs was 40. 4 kbp and the N50 of the scaffolds was 664. 0 kbp. The total length of all contigs was 399. 7 Mbp. When the gaps between contigs in scaffolds were included, the total span of the assembly was 419. 4 Mbp. The M. sexta raw sequence, and assembled genome sequence data are available at the NCBI under bioproject PRJNA81037, Assembly ID GCA_000262585. 1, and AIXA00000000. 1.
After end-repair and dA-tailing, the DNA 3. 2. Genome structure and analysis 3. 2. 1. Novel repeats, transposable elements, and repeat masking-Using the automated pipeline RepeatModeler (repeatmasker. org) to scan the genome for repetitive elements, we identified 668 unique, complex repeats, 125 of which were based on structural motifs and sequence similarity to previously described repeat sequences from other species. Among classifiable repeats, we found representatives of 36 repeat families belonging to 5 superfamilies (Table  1 ), and combined this de novo library of repeats with known repeats from arthropods obtained from RepBase  (Jurka et al. , 2005)  to identify repetitive regions in the M. sexta genome assembly using RepeatMasker software (repeatmasker. org). This process identified ~108 Mbp of repetitive sequence, corresponding to 25.
Employing 7988 single-copy M. sexta -B. mori orthologs with chromosomal assignments in B. mori, ~87% of M. sexta genes spanning ~83% of the genome assembly were mapped to their corresponding chromosomes (Fig. S2 ). Assigning M. sexta scaffolds to chromosomes in this manner suggested several genomic rearrangements relative to B. mori, many of which correspond to translocations previously detected using cytogenetic techniques  (Yasukochi et al. , 2009). Contiguous ancestral regions (CARs) were built with the ancestral genomes (ANGES) analysis software  (Jones et al. , 2012)  using 5113 orthologous gene anchors from the outgroup species, the body louse Pediculus humanus, and 16 representative holometabolous species (Table  S5 ). Holometabola, Mecopterida, and Diptera CARs encompassed only 43%-47% of all anchors, the majority of which were found in CARs made up of only two genes, highlighting the large amount of genome shuffling that has occurred over these long evolutionary timescales (Fig.
The total size of the chorion locus and the size of the genomic region between the two chorion clusters exceed 2946 kb and 2760 kb or 1342 kb and 1155 kb, according to configuration b or c, respectively. Thus, the most plausible configuration is c, as the sizes of the chorion locus and of the genomic region between the two clusters are closer to those of B. mori and H. melpomene. To identify the transcription start sites of the genes, the 4 scaffolds that contained chorion protein genes were searched with a lepidopteran chorion protein gene promoter Hidden Markov Model, which was built using a multiple sequence alignment of the promoters of lepidopteran chorion protein genes downloaded from the Eukaryotic Promoter Database  (Dreos et al. , 2013). Gene pairs were numbered according to the order of appearance in the genome, and gene nomenclature was based on their class and the number of the gene pair to which they belonged (i.
melanogaster. One copy of csw in the M. sexta genome contains 11 exons and the other is intronless, suggesting duplication in the genome via insertion of a retrogene from mature mRNA. The elav gene family consists of RNA binding proteins that are restricted to neurons and regulate post-transcriptional processing. These genes are required for embryogenesis and proper neuronal differentiation  (Colombrita et al. , 2013). Two elav gene duplication events were identified. They appear to be lepidopteranspecific, and all four M. sexta genes in this family were intronless. PINTA, which binds the visual chromophore in Drosophila eyes, appears to be missing in Lepidoptera; however, the M. sexta genome encodes 42 other CRAL-TRIO domain-containing proteins (GenBank Accession Nos. KT943537-KT943566)  (Smith and Briscoe, 2015) , far more than other insect genomes examined (D.
Acknowledgments We thank  Sandy Youngeberg ,  Janice Beal , and  Marjolein Schat  for insect rearing. We also thank  Julie Poulain  and  Corinne Da Silva  from the  Genoscope  ( Centre National de Séquencage, Evry, France ) for raw transcript sequence data from fat body and hemocyte libraries, which were used to refine annotation of certain M. sexta genes.
Gas chromatography was performed on a BD-EN14103 capillary column (30 m Â 0. 32 mm Â 0. 25 lm) using helium as carrier gas at a velocity of 33 cm/s. 2 lL of various samples were injected in split mode (split ratio: 1:20) at 250 °C. The oven temperature program was operated as follows: initial temperature 50 °C for one minute, increasing at 20 °C/min to 180 °C and at 2 °C/min from 180 °C to 230 °C, held isothermally at 230 °C for 10 min. Data were collected with Agilent EZChrom Elite software. FAMEs were identified by comparison with purified FAME standards (Sigma Co. , USA). Quantification was performed using internal calibration. The internal standard was glyceryl tripheptanecanoate (Sigma Co. , USA).
For these effects, the p-value was below 0. 05. The results also show that interactions between variables A Á B, A Á C and B Á C were significant, with a p-value lower than 0. 05 (Fig. 4 ). The experimental data obtained from the central composite design allowed the determination of an empirical relationship linking response studied (yield) and key variables involved in the model (in coded units). Thus a third-order polynomial equation was obtained (Eq. (  5 )) where only the significant effects are shown (p < 0. 05): Y ¼ 141:5180 À 1:2819 Á A À 2:4705 Á B À 14:2459 Á C þ 0:0029 Á A 2 þ 0:0029 Á A Á B þ 0:1291 Á A Á C þ 0:0198 Á B 2 þ 0:2231 Á B Á C þ 0:4233 Á C 2 À 0:0014 Á A Á B Á C À 0:0041 Á A Á C 2 þ 0:0 Á B 2 Á C À 0:0041 Á B Á C 2 ; ð5Þ with Y = extraction yield, A = applied ultrasonic power intensity, B = temperature, and C = solid/liquid ratio.
The data required for the calculations are described by Sicaire et al. [39]. As can be seen in Table  4 , there was no difference between conventional and US-assisted extraction in energy consumption for the preparation step, as no solvent was used, and the US treatment was applied during the extraction step. Regarding the solvent extraction step, considering results presented previously, a reduction of one third of total hexane used for conventional extraction is taken for the calculation of the energy consumption of the US-assisted process. The total amount of energy assessed for the distillation step is assessed around 70 MJ/t for US-assisted extraction instead of 139 MJ/t with conventional extraction, which represents a reduction of nearly 50%. As less energy was recovered from the desolventizer, the overall energy consumption of the whole process (preparation + extraction) was 563 MJ/t for the US-assisted process A.
Eventually forty-nine subjects were included in the final analyses: 28 subjects in the NAP group (mean age 21. 5 ± 1. 6 years, 19 females) and 21 in the NONAP group (mean age 22. 1 ± 2. 1 years, 9 females). Task and general experimental design. Subjects were scanned during six separate sessions [note that this protocol is part of larger design including supplemental practice sessions administered after the 6 th session and that are not reported in the present paper] during which they were either trained or tested on a sequential finger tapping task coded in Cogent2000 (http://www. vislab. ucl. ac. uk/cogent. php) and implemented in MATLAB (Mathworks Inc. , Sherbom, MA). The task required subjects to tap on a keyboard, with their (left) non-dominant hand, a five-element finger sequence, while lying in the scanner.
Polysomnographic data acquisition and analyses. Habituation naps, experimental naps and wake periods were recorded with a digital sleep recorder (V-Amp, Brain Products, Gilching, Germany; bandwidth: DC to Nyquist frequency) and were digitized at a sampling rate of 500 Hz. Standard electroencephalographic (EEG) recordings were made from Fz, C3, Cz, C4, Pz, Oz, A1 and A2, with A2 used as the recording reference and A1 as a supplemental individual EEG channel. An electrode placed on the middle of the forehead was used as the recording ground. Bipolar vertical and horizontal eye movements (electrooculogram: EOG) were recorded from electrodes placed above and below the right eye and on the outer canthus of both eyes, respectively. EEG and EOG data were recorded with a 0. 1 Hz low cutoff and a 30 Hz high cut-off filters.
Bipolar submental electromyogram (EMG) recordings were made from the chin, filtered from 10 to 200 Hz to record muscle tone and movements. Electrical noise was filtered using a 50 Hz notch. Polysomnographic data of the diurnal sleep (NAP) and wake (NONAP) recordings were visually scored, with 30-s epochs, by a trained sleep technician according to standard criteria 42 using the fMRI Artefact rejection and Sleep Scoring (FASST) Toolbox  43  (http://www. montefiore. ulg. ac. be/~phillips/FASST. html, University of Liege). To easily visualize the relevant features of sleep and wakefulness, EEG was re-referenced to an average of A1 and A2 displayed from 0. 5 to 30 Hz, EOG below 10 Hz and EMG above 10 Hz using software filters. fMRI data acquisition and analysis. Functional MRI-series were acquired during the 6 sessions of practice of the motor task using a head-only 3T scanner (Siemens, Allegra, Erlangen, Germany).
Multislice T2*-weighted fMRI images were obtained with a gradient echo-planar sequence using axial slice orientation (TR = 2130 ms, TE = 40 ms, FA = 90°, 32 transverse slices, 3 mm slice thickness, 30% inter-slice gap, FoV = 220 × 220 mm 2 , matrix size = 64 × 64 × 32, voxel size = 3. 4 × 3. 4 × 3. 0 mm 3 ). A structural T1-weigthed 3D MP-RAGE sequence (TR = 1960 ms, TE = 4. 43 ms, TI = 1100 ms, FA = 8°, 176 slices, FoV = 230 × 173 mm 2 , matrix size = 256 × 192 × 176, voxel size = 0. 9 × 0. 9 × 0. 9 mm 3 ) was also acquired in all subjects. Head movements were minimized using a vacuum cushion. Only imaging data from the 4 self-initiated test sessions (i. e. , pT, 0 hPT, 8 hPT and 24 hPT) were analyzed [note that 2 additional self-initiated test sessions taking place after the 24 hPT session were also included in the model but the results related to these sessions are not reported in the present paper].
The 3 initial scans for each session were discarded to allow for magnetic saturation effects. Functional volumes were pre-processed and analyzed using SPM8 (http://www. fil. ion. ucl. ac. uk/spm/software/spm8/; Wellcome Department of Imaging Neuroscience, London, UK). Functional scans of each session were realigned using rigid body transformations, iteratively optimized to minimize the residual sum of squares between the first and each subsequent image separately for each session, and a mean realigned image was created. The mean functional image was coregistered to the structural T1-image using a rigid body transformation optimized to maximize the normalized mutual information between the two images. Coregistration parameters were then applied to the realigned BOLD time series. The mapping from subject to MNI space (Montreal Neurological Institute, http://www.
Acknowledgements This study was supported by the  Belgian F. N. R. S. , the  Fondation Médicale Reine Elisabeth , the  Research Fund of Ulg , and  PAI/IAP Interuniversity Pole of Attraction. Financial support for author BRK was provided by the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie grant agreement  (No. 703490 ). We would also like to acknowledge  Luca Matarazzo ,  Ariane Foret  and  Laura Mascetti  for their assistance in data collection.
1 T field was applied and then the data were recorded in heating cycle up to 400 K. Subsequently, the data were recorded in the same field (0. 1 T) by cooling from 400 down to 2 K (FC). The magnetic isotherms, M(H), at 1. 2 K and 257 K have been done in a pulsed fields up to 60 T. The pulsed magnetic field experiments were performed at the Dresden High Magnetic Field Laboratory. Neutron diffraction measurements were done at the D2B high-resolution neutron powder diffractometer (ILL, Grenoble). A vanadium cylinder was used as sample holder. The data were collected at 500 K, 300 K and 3 K using a neutron wavelength of 1. 59 Å in the high-intensity mode. The analysis of diffraction patterns were done with Fullprof software package  [1]. Nuclear structure from neutron diffraction In order case the Pt occupy the 4d (0, 0.
Detailed model description In the following, we provide a detailed mathematical model description, including definitions of the model variables and parameters, their initialisation, the algorithm for computing their temporal dynamics, the general modelling protocol and partial models. The model code is publically available and can be assessed and reviewed here: https://github. com/pik-copan/ pycopanbehave. The implementation is based on the Python complex network software package pyunicorn  70  that is available at https://github. com/pik-copan/pyunicorn.
Acknowledgements The reported research was conducted within the scope of the COPAN flagship project on co-evolutionary pathways at the  Potsdam Institute for Climate Impact Research  (http://www. pik-potsdam. de/copan). The authors acknowledge support by the  German National Academic Foundation. D. E. acknowledges support by an  Amazon  in Education grant. J. F. D. thanks the  Stordalen Foundation  (via the  Planetary Boundary Research Network PB. net) and the  Earth League 's  EarthDoc program  for financial support. The authors gratefully acknowledge the  European Regional Development Fund (ERDF) , the  German Federal Ministry of Education and Research  and the  Land Brandenburg  for supporting this project by providing resources on the high performance computer system at the  Potsdam Institute for Climate Impact Research.
Data collection techniques and tools: This analysis was essentially based on a literature review with counting sheets. This literature review was supplemented by in depth interviews of resource persons with a structured interview guide. The tools used were designed on the basis of the components explored. We used a questionnaire to assess data quality from patients' records. Sampling: All relevant documents available have been used for literature review. We used the activity reports of the department for the three last years, the patient's records, memos and different normative documents available. For a data quality assessment, a sample of patients' records for the 1st semester of 2015 was used. The minimum size n of the sample was calculated by the formula of Schwartz. 2195 cases were registered for the period.
In the current context of the functionality of a national repository for health information (District Health Information Software-DHIS 2) in the national health information system, the interoperability of databases must for example be considered. Moreover, since the hospital itself does not have a hospital information system (HIS), this parameter must be integrated in the feasibility study to design an integrated and scalable system that can meet the needs of the ACED, while taking into account its external environment. A major challenge remains a greater awareness of the administrative authorities of the Hospital about the importance and sensitivity of health information in general and more specifically of health information in the emergency department. This awareness is the starting point for an adherence of the stakeholders to the evolution of the system through a project of implementation of a Health Information System or of the computerization of the data collection system.
M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT Data from twenty consecutive patients treated for lung malignancies were included in this retrospective study. All patients underwent passive scattering proton therapy (PSPT) using two treatment fields with a median dose of 66. 3Gy[CGE] (range:40-66. 6Gy [CGE]) in a median of 1. 8Gy/fraction (range:1. 5-4Gy/fraction). The patient cohort included a variety of tumor sizes, locations and anatomical changes that occurred throughout the treatment course (Table  1 ). The imaging protocol consisted of a 4D PET/CT for treatment planning, CBCT and rescan 4D CT acquired in treatment position for verification during the course of treatment. The proton-gantry mounted CBCT system (Ion Beam Applications SA, Ottignies-Louvain-la-Neuve, BE) has a sourceto-axis distance of 288.
Virtual CT and image correction The CBCT was rigidly aligned to the planning CT (pCT) and the diffeomorphic Morphons deformable image registration (DIR) algorithm available in the open-source REGGUI package was subsequently applied to register the pCT to the CBCT. 21 This method was previously validated for head and neck cancer patients. 16, 17 me anatomical changes in the thorax cannot be modeled by deformation alone. The situations are diverse, but include changes within the lung (such as atelectasis and pleural effusion) and different tumor responses to treatment (such as regression of infiltrating tumors and erosion  22  ). Therefore, a semi-automatic correction step was applied to the vCT for these anatomical modifications. This step consists of a watershed-cuts algorithm  23, 24  combined with an exclusive OR logical operator and a classifier  25, 26  to identify regions showing significant intensity mismatch between vCT and CBCT.
Figure2-Images used and generated by the workflow for PT#1 (atelectasis), PT#2 (large tumor shrinkage) and PT#4 (small tumor shrinkage). A consistent soft tissue window level was used for CT datasets (except the CBCT). For PT#1 and PT#2, the vCT needed the correction step (region defined by the red contour). For PT#4, DIR alone recovered the changes well; however, CBCT truncation affected the similarity between vCT and rCT.
Figure3-Images used and generated by the workflow for PT#3 (lung reinflation), PT#14 (regression of infiltrating tumor) and PT#13 (shrinkage and changes in breathing pattern). A consistent soft tissue window level was used for CT datasets (except the CBCT). For PT#3 and PT#14, correction of the vCT was necessary (region defined by the red contour). For PT#13, DIR was able to recover the tumor shrinkage; however, visible differences in setup occur between vCT and rCT, particularly in the position of the main airways (yellow arrow).