dataesr/scientific-paragraphs-categorization huggingface dataset:
Simulations To understand the theoretic signal and contrast behavior of the sequences used above after gadolinium injection, we performed Matlab (MathWorks, Natick, Massachusetts) simulations of lesion SNR and lesion-WM relative contrast by implementing the signal equation for 2D-SE and 3D-GRE, similar to that of Mugler and Brookeman. 13 We used a T1 value of 1300 ms and a T2 value of 100 ms to define a theoretic MS lesion precontrast at 3T. 26  We used the data of Yu et al  27  to set the relaxivity values of Dotarem at 3T as r1 ϭ 5. 5 mmol Ϫ1 s Ϫ1 and r2 ϭ 6. 25 mmol Ϫ1 s Ϫ1 and varied the gadolinium concentration values from 0 to 5 mmol/L. We simulated 2 scenarios: 1) The lesion is large and occupies the entire voxel in both the 2D and 3D sequences, and 2) the lesion is small and occupies the entire voxel in 3D but not in 2D sequences (ie, 2D lesion volume Ͻ 2D voxel volume and 3D lesion volume ϭ 3D voxel volume).
Moving to 3D datasets for postgadolinium imaging in patients with MS could offer other advantages in addition to its higher sensitivity to enhancing lesions. Such images seem easier to read on the basis of our junior and senior readers' results, with probably less training required to distinguish noise, artifacts, anatomic variants, and true lesions. For example, the pulsatile flow artifacts seen on 2D-SE, even if not fully absent, were reduced on 3D-GRE because of the shorter TEs used in 3D-GRE. Furthermore, with 3D being more amenable to image registration, the 3D images could be easily displayed in a fixed-registration framework, facilitating longitudinal follow-up and standardization. Finally, because noncontrast 3D-GRE is becoming more frequently used in MS to monitor atrophy,  6  it makes sense to use the same sequence after contrast injection for an accurate pre/post comparison.
ACKNOWLEDGMENTS We thank  Alice Doreille  for her implication in this MS imaging study. Disclosures:  Monojkumar Saranathan-UNRELATED: Other : research support from  GE Healthcare. *Aurelie Ruet-UNRELATED: Board Membership: Biogen Idec; Consultancy: Teva; Travel/Accommodations/Meeting Expenses Unrelated to Activities Listed: Biogen Idec , Novartis; OTHER RELATIONSHIPS: I am a recipient of a European Committee for Treatment and  Research In Multiple Sclerosis fellowship research grant. Bruno Brochet-UNRELATED: Board Membership: Biogen Idec, Teva ; Grants/ Grants Pending:  Teva ,  Merck Serono, Bayer , Caridian; Payment for Lectures (including service on Speakers Bureaus):  Novartis ,  Teva ;  Payment for Development of Educational Presentations: Novartis, Genzyme ; Travel/Accommodations/Meeting Expenses Unrelated to Activities Listed:  Novartis ,  Teva.
This work was supported by the  FLI  ( ANR-11-INBS-0006 ) and the  French Agence Nationale de la Recherche  within the context of the Investments for the  Future Program , referenced  ANR-10-LABX-57  and named TRAIL. Paper previously presented in part at: Annual Meeting of the  International Society for Magnetic Resonance in Medicine and European Society for Magnetic Resonance in Medicine and Biology  (.
S2 ); biomass in the remaining samples was too low for accurate quantification. Reaction efficiency was 71. 6% (R 2 ϭ 0. 999), possibly due to high primer degeneracy. While the 783F primer limited chloroplast amplification, it did not prevent 16S rRNA gene amplification from host plant mitochondria. Mitochondrial contamination was minimal in sequenced libraries (Ͻ1% in 47/60 datasets, 1 to 5% in 13/60 datasets) and could be discounted in copy number calculations. Pyrosequencing libraries with a high percentage of chloroplast 16S sequences had lower qPCR copy numbers (R 2 ϭ 0. 3), suggesting that amplification of chloroplast rRNA genes occurred only in the absence of significant bacterial abundance. We estimated operon copy number for each operational taxonomic unit (OTU) using rrndb  (29)  and corrected read counts for each OTU to generate estimated cell counts in each sample (average rrn copy number/sample ϭ 3.
6). We observed a linear correlation between leaf area and rosette dry weight after leaf wash (with trimmed root and stems) across 12 plants (R 2 ϭ 0. 952). We thus used dry weight data to extrapolate leaf area and deduce bacterial densities on leaves, taking into account both adaxial and abaxial leaf area. Microbial population density on leaves was relatively constant between days 45 and 67 (1. 7 ϫ 10 4 to 2. 7 ϫ 10 4 cells per cm 2 ), rising to 4. 8 ϫ 10 4 Ϯ 2. 9 ϫ 10 4 cells/cm 2 on day 73 (see Fig. S2 ). Total estimated cell counts per plant rose from 8. 0 ϫ 10 3 Ϯ 0. 54 ϫ 10 3 on day 19 to 2. 4 ϫ 10 6 Ϯ 1. 3 ϫ 10 6 on day 73, an ~300-fold increase. These results suggest that microbial density on Arabidopsis leaves reached a steady-state density of 10 4 cells/cm 2 roughly 25 days following initial colonization.
Initial plant community richness varied between 79 and 114 at day 19 and increased 6-to 7-fold by day 60, depending on estimation method (see Fig. S3 ). The estimated richness of the airborne colonizing community does not show a time-related evolution and oscillated between 131 and 314 OTUs. Between (beta)-sample diversity was computed using QIIME  (35)  and Vegan (36) software after abundance normalization to the minimum sample depth (896 sequences) and removal of singleton and doubleton OTUs. The resulting abundance matrix contained 261,637 sequences and 397 OTUs over 53 samples, with an average of 4,936 reads per sample. Subsampling and removal of singleton/doubleton OTUs did not affect beta diversity results (data not shown). Establishment of a "mature" phyllosphere community. We analyzed plant and airborne colonizing community structure based on OTU presence/absence, using principal coordinate analysis (PCoA) on pairwise unweighted beta diversity metrics (Jaccard [Fig.
Inserts were placed in plastic trays under shade boxes constructed with wire screens to reduce light levels to those standard for Arabidopsis growth  (28). The first sampling occurred on day 19, 5 days after transfer from plates to soil. Environmental conditions in the shade boxes were monitored using HOBO sensors (temperature/RH [relative humidity] and light as PAR [photosynthetically active radiation]) and a MicroStation data logger (Onset Computer, Bourne, MA). The greenhouse temperature set point was 20°C, and humidity was not controlled. Plants were watered every 3 days and fertilized with 200 ppm 20/10/20 fertilizer 1ϫ per week starting at day 27. Plant and tray positions were randomized at each watering, fertilization, and sampling event. Plants were randomized within each tray, and trays were moved between the two shade boxes, but plants were not moved from tray to tray (Fig.
1 ). Air and phyllosphere sampling. We captured airborne microbes representing the colonizing community using sterilized standard microscope slides coated with the biological adhesive CellTak (BD Biosciences) at a density of 3. 5 g/cm 2. We constructed small platforms to hold slides at the level of plant leaves. Slides were left in place during each sampling interval (~5 days), collected, and replaced at the next sampling event. In preliminary experiments, fluorescent microscopy using 4=,6-diamidino-2phenylindole (DAPI) staining indicated the presence of intact cells on slides exposed to air for ~1-week periods (data not shown). Slides were incubated with trypsin to remove CellTak and detach microbes; the wash solution was collected on sterile 0. 22-m-pore-size filters, and DNA was extracted using the Biostic bacteremia DNA extraction kit (MoBio Labs).
Plant leaf area was calculated based on dissected plant photos using ImageJ software  (62). Plant dry weight was measured on a high-precision scale after overnight drying of the plants at 70°C. It was not possible to obtain wet weights due to the addition of Silwet/buffer to plants in the wash procedure. One of the day 60 plants and all day 45 CellTak slide replicates were omitted after manipulation problems (breakage of the filtration membrane). Sterility tests. During each sampling event, we collected four negative controls to detect possible contamination during plant and air sampling. First, we filtered sterile Silwet wash solution through our Swinnex apparatus onto a 0. 22-m-pore-size filter. Second, we sampled 500 l of Silwet wash solution alone. Third, we filtered 30 ml of the trypsin solution used in CellTak slide extraction onto a 0.
Amplification and 454 sequencing of the v4v6 region of 16S rRNA genes. The v4v6 variable region of 16S rRNA genes was amplified in triplicate with 454 fusion primers containing adapters and bar codes with bacterial primer sequences 518F (5= CCAGCAGCYGCGGTAAN 3=) and 1046R (5= CGACRRCCATGCANCACCT 3=) and sequenced on a 454 GS-Ti instrument at the MBL as previously described  (64). Individual plant samples were separately amplified, but CellTak slides from each shade box were pooled prior to amplification due to low biomass. Bioinformatic analyses. Processing and filtering of v4v6 pyrosequencing reads were carried out using a standard MBL pipeline  (32, 64). Reads were trimmed to the v5v6 region using a conserved anchor sequence due to low quality at the v4 end, and all subsequent analyses were performed on these data set.
Sequences were clustered using a standard Usearch6 pipeline into 97% similarity OTUs  (33). We used the Catchall software  (34)  for both parametric and nonparametric richness estimation. We then used QIIME  (35)  and Vegan (36) software for beta diversity analysis based on a corrected abundance matrix: (i) OTUs containing 1 or 2 reads were discarded in order to further reduce the number of spurious OTUs generated by errors introduced during PCR and sequencing, and (ii) observation counts were subsampled to the number of reads present in the smallest library (895 reads) for calculation of beta diversity indices. We used LEfSE software  (40)  to identify biomarker OTUs. We used oligotyping  (42)  to identify significant sub-OTU-level variation in each of the 20 most abundant genera and analyzed the abundance pattern of oligotypes across sample sets.
ACKNOWLEDGMENTS We thank  M. Sogin ,  Z. Cardon , and  E. López-Peredo  for critical discussions and reading of the manuscript,  Z. Cardon  for use of the MBL greenhouse facility,  H. Morrison ,  J. Vineis , and  S. Grim  for assistance with sequencing,  S. Huse  for assistance with bioinformatic analysis,  A. Aicher  for assistance with greenhouse protocols, and  Norm Pace  for suggesting CellTak as a substrate for capture of airborne microbes. Funding was provided by the  J. Unger Vetleson Foundation  to S. L. S.
The absence of genomic DNA contamination was confirmed by PCR. RT-PCR was performed with 50 ng of RNA as a template, with the Transcriptor one-step RT-PCR kit (Roche, Meylan, France), according to the manufacturer's recommendations. For cotranscription assays, we used the hcp-vgrgF and hcp-vgrgR primers (Table  2 ) for PCR assays. PCR was carried out in standard conditions, as follows: annealing temperature, 57uC; extension time, 15 s; 25 cycles; polymerase: PhusionH High-Fidelity DNA polymerase (NEB). mRNAs of vgrG were quantified by real-time PCR as described by Guyard-Nicodeme and coworkers with minor modifications  [40]. Primers (Table  2 ) were designed with Primer express 3 software and validated by PCR. PCR reactions were performed with the 7500 Fast real-time PCR system (Applied Biosystems).
MFE01 has at Least Two hcp-like Genes PCR primers designed on the basis of the sequence of Pf01 hcp genes  [43]  were used for the amplification of MFE01 chromosomal DNA (Table  2 ). Two amplicons, corresponding to the Pfl01_2328 (462 bp) and Pfl01_2045 (474 bp) primers, were obtained. These two partial sequences were checked by sequencing and subjected to Blast analysis. The gene hcp1 corresponding to the Pfl01_2328 primers displayed 95% identity to hcp Pfl01_2328 (partial sequence hcp1 genBank accession number: KF447439), whereas the gene hcp2 corresponding to the Pfl01_2328 primers displayed 97% identity to hcp Pfl01_2045 (complete sequence hcp2 genBank accession number: KF447438). Partial hcp1 gene sequence (462 bp) displayed 99% identity with hcp2 gene (516 bp) with a query cover of 89%.
Acknowledgments We are grateful to  Sarah J. Coulthurst  from  University of Dundee (Dundee, UK ) for the gift of the plasmids pSUPROM containing or not rap genes. Thank to  Josette Gue  ´rillon and  Gae ¨lle Rossignol , which initiated T6SS research in LMSM lab,  Daniel Sperandio ,  Alexandre Crepin ,  Morgane Cormontagne  and  Mathias Gallique  for technical assistance and discussions. We also thank  Alex Edelman  for linguistic support.
Moreover, it should be noted standard anxiolytics (e. g. , diazepam) sometimes produce counter-intuitive results as well such as the finding in Experiment 2 (see Table  3 ) that the low dose of diazepam was associated with less time spent on the open arms of the EZM than the saline control condition. Given that data for these groups were collected over a time span of 18 months, we postulated that such variations may, in part, be due to circadian rhythm effects. Benzodiazepines, such as diazepam, are thought to act by potentiating the action of the neurotransmitter c-aminobutyric acid, which in turn, has been linked to regulation of the sleep-wake cycle  39. Hence, the variations in responses to diazepam may be the result of the benzodiazepine acting at varying levels of GABA that mediate the generation of circadian rhythms.
c) injection was administered under red light and the animal was placed in a cage measuring 40. 5 3 28 3 12 cm containing only sawdust bedding (i. e. , no food and water). The animal remained in this staging cage for 30 minutes in order to allow adequate absorption of drug, after which time the animal was transferred to the experimental room (again in a darkened box) and placed on the zero-maze at a junction between an open and closed arm, facing into the closed area. Each animal was placed on an alternative side of the maze so as to avoid any bias. All testing was conducted under red-light. After 5 minutes, the animal was removed from the maze and the maze was washed using an ethanol/water solution so as to avoid olfactory cues transferring from one experimental session to the next. Once testing was complete, computer-based event recording and ethological analysis software (Hindsight ver.
Measures Locomotion and maintenance measures. Rearing Frequency was defined as the number of vertical movements against the side or end of walls of the closed arms of the maze or raising up its hind paws sans support in the open area of the maze  26. Rearing Duration measured the time each animal was engaged in rearing behavior. Analysis. Data for each behavioral element were grouped according to treatment and were initially checked for normality and homogeneity of variance. Levene's tests were statistically significant (i. e. assumptions that distributions were normal or variances were equal had to be rejected); therefore, non-parametric tests were conducted (as opposed to data transformation). Data were analyzed using Kruskal-Wallis nonparametric one-way analysis of variance across treatment groups.
5 μl of deionized formamide and 0. 5 μl of a dye-labeled size standard (ROX 500; Applied Biosystems). This mixture was denatured at 100°C for 5 min and then electrophoresed using an automatic sequencer (ABI PRISM 3130xl; Applied Biosystems). The sizes of the alleles in base pairs were estimated using GeneMapper analysis software (version 4. 0; Applied Biosystems).
Acknowledgements The financial support of  Oromia Regional State Rural Capacity Building, Addis Ababa University  and  VLIR-UOS  project no. " ZEIN 2010 PR 372" "promotion of the PhD program  in veterinary public health at the  Faculty of Veterinary Medicine", Belgium  are highly acknowledged. The authors also would like to extend their gratitude to  Mr. Hashim Nuru , owner of HELMIX export abattoir and his employees for their collaboration during sampling.
Light microscopy, Confocal Microscopy and Image Processing Specimens were observed with a confocal laser-scanning microscope Leica TCS STED (Leica Microsystems, Wetzlar, Germany) and a Leica light microscope DM 1000 (Leica Microsystems, Wetzlar, Germany). Confocal image stacks were processed with Leica AS AF v2. 3. 5 (Leica Microsystems) and Imaris 6. 3. 1 (Bitplane AG, Zurich, Switzerland). Light microscopic images were processed using the software Leica AS V3. 6. 0. Final panels were designed using Adobe (San Jose, CA, USA) Photoshop CS3 and Illustrator CS3.
Acknowledgement The 22C10 antibody developed by  Seymour Benzer  (Pasadena, CA) was obtained from the  Developmental Studies Hybridoma Bank developed  under the auspices of the  NICHD  and maintained by The  University of Iowa ,  Department of Biology, Iowa City , IA 52242. We thank the staff of Station  Biologique Roscoff  for providing facilities and support of sampling animals. Maite Aguado  (Madrid) is thanked for commenting on earlier drafts. CH was supported by special funds of the  University of Leipzig  and by the  EU due  to ASSEMBLE grant agreement no. 227799  (http://www. assemblemarine. org).
Data collection All identified PHCPs were interviewed by trained field investigators from a research agency (GfK India) using a semi-structured questionnaire. The respondents were shown photographs of commonly available POC tests, such as pregnancy test kits and glucometer devices, to ensure that they understood what the survey staff meant by POC tests. http://dx. doi. org/10. 5588/pha. 14. 0061 In a cross-sectional survey conducted in 45 districts of India, we assessed 1) use of any rapid point-of-care (POC) tests by primary health care providers, and 2) their willingness to use POC tests for tuberculosis (TB) in future. A total of 767 primary health care providers, including private and public sector practitioners, health workers and chemists, were interviewed. A quarter of the primary health care providers reported using POC tests, with pregnancy tests being the most common.
Patient Selection Transplantation modalities were made as homogeneous as possible using the following inclusion and exclusion criteria: (1) patients older than 18 years referred for first allo-SCT after RIC or NMA according to the standard definition published by Bacigalupo et al. [14]  and (2) source of stem cell was marrow or blood from either a sibling or an HLA-A, -B, -Cw, -DR, and -DQ identical unrelated donor at the allelic level (so-called 10/10). Patients who received allo-SCT from an HLA-mismatched donor, cord blood, or T celledepleted graft and patients with chronic myelomonocytic leukemia were excluded. Participating centers were asked to verify the data recorded for each patient in the French Bone Marrow Transplantation Registry and to provide additional information. Quality of the data was controlled using a computerized search for discrepancy errors and vigorous onsite data verification of each file.
HLA matching was cross-checked with the data from the French Bone Marrow Donor Registry as previously described  [15]. Consequently, 283 consecutive patients with MDS who underwent allo-SCT between January 1999 and December 2009 in 24 French and Belgian centers were identified. Twenty-seven patients were excluded because their files lacked at least 1 of the following: initial French-American-British (FAB)/World Health Organization (WHO) category or International Prognostic Scoring System (IPSS) classification, treatment before transplantation, and disease status at transplant. In addition, we excluded 128 patients who received induction-type chemotherapy or cytoreduction treatment other than AZA. Based on local physicians' decisions, the 128 remaining patients received either best supportive care (BSC group, n ¼ 88), which included blood transfusion, hormones, growth factors (erythropoietin, granulocyte colony-stimulating factor), and immunosuppressive treatment, or AZA alone (AZA group, n ¼ 40) (Figure  1 ).
ACKNOWLEDGMENTS The authors thank  Raja Prince  for collecting and checking data onsite. Special thanks to  Nicole Raus , the  French Society of Bone Marrow Transplantation and Cell Therapy data manager. Ibrahim Yakoub-Agha thanks the "Association Capucine"  for their support in his research. Portions of this article were presented at the  European Bone Marrow Transplantation Congress , April 1-4, 2013, London,  United Kingdom , and at the 12th  International Symposium on Myelodysplastic Syndromes (received Tito Bastianello 's best abstracts' award), May 8-11, 2013,  Berlin, Germany. Conflict of interest statement: Y. B. is on the  Advisory Board of Celgene. M. Mo. and P. F. have received honoraria and research funding from  Celgene. I. Y. A. received research funding from  Celgene. Authorship statement: G.
Sequence of ROAR029 colicin plasmid, colicin R sequence and structure analysis The sequence of the pColR plasmid was deposited in Genbank (accession number KF137578). Sequence alignments. Alignments were performed by MultiAlin software as described in  Corpet (1988). Phylogenetic dendrogram. Colicin sequences were directly obtained from GenBank (http://www. ncbi. nlm. nih. gov/gene). Sequences were aligned following ClustalW standards and further examined in order to create phylogenetic dendrograms with MEGA 5 software developed by  Tamura et al. (2011). Plasmid map. pColR plasmid map was constructed using the SnapGene viewer from GSL Biotech LLC (Chicago, IL, USA). Colicin tertiary structure. Colicin R structure was simulated using the PHYRE software (Imperial College, London, UK;  Bennett-Lovsey et al.
Acknowledgements We are grateful to  Juraj Bosa  ´k and David S ˇmajs for providing colicin U-and colicin Y-producing strains. We thank  Erick Denamur  for the strain ROAR029. We thank  Franziska Stressmann  for critical reading of the manuscript. OR was supported by a fellowship from the  Network of Excellence EuroPathogenomics; European Community  Grant  LSHB-CT-2005-512061. This work was supported by a grant from the  Region Ile-de-France  ( DIM Malinf ) and from the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'  (Grant no. ANR-10-LABX-62-IBEID ).
In order to apply a realistic acceptance correction, the simulation package R3BROOT [16] was used, which contains full geometrical information about the setup, and allows to simulate fragment and proton behaviours. The intrinsic efficiency of proton detection was estimated by analyzing coincidences between the proton-branch detectors. The two-proton efficiency of these detectors was determined to be 55. 9 ± 1. 5%. The required γ-rays were detected in the 4π γ-ray spectrometer. Two groups of 15 O excited states were observed: above 5 MeV and 6 MeV. However, 5% of the events show these excited states, which makes them negligible.
In order to extract informations about the three-body system (core +p + p), energy and angular correlations of internal clusters ([core, p + p] or [core+p, p]) in the Jacobi coordinates should be analyzed. Thanks to these comparisons, the mixture of the s 2 and d 2 configurations can be obtained  [19]. The experimental data are convoluted with theoretical predictions provided by Ref. [20]  using the simulation package R3BROOT. The final conclusion is not obtained yet.
REG-1 negative controls are shown in (E, L). In (F-G) and (M-N), the border of islets is defined by the red dashed line. In Fig. 2N, ''d' ' means ''duct''. doi:10. 1371/journal. pone. 0090045. g002 [32] , but it was very faint in our study; 2) in type 1 nonobese diabetic (NOD) mice and NOD-rat insulin promoter-1-human IFNb mice  [33]. In GK rat pancreas, inflammatory cell levels increase from weaning onwards (1 month of age), reach a plateau between 2 and 3 months and decline thereafter to finally disappear almost completely around/in fibrotic islets  [3]. Diabetic 2-month-old GK  All data were determined under fed conditions. Values (pg/ml) are mean 6 SEM for the number (n) of animals. Statistical analysis used the Student t-test for unpaired data. No significant difference in circulating cytokine levels was observed between 3-and 4-month-old Wistar and GK rats.