dataesr/scientific-paragraphs-categorization huggingface dataset:
Detection of Genetic Determinants of Antimicrobial Resistance: Detection of Integrons, Resistance Genes, and SXT Element All isolates were negative for class 1, 2, and 3 integrons. A 900 bp PCR product of the intI4 gene was obtained for all isolates. The amplification of SXT integrase revealed an amplicon size of 3 kb in all isolates, different from the expected size, i. e. , 592 bp. The SXT integrase from senegalese isolates was identical to a fragment of V. cholerae KN14, isolated in Kenya GenBank accession number (AB535680). The integration of the SXT element in the chromosome was highlighted by the amplification of the right SXT element-chromosome junction (attP-prf C) which producted a 785 bp PCR product. To identify genes hosted by the ICE circulating in Senegal, PCR analysis revealed the presence of the following antibiotic resistances genes (sulI, floR, strA, and dfrA1), except dfr18 gene.
A Delphi panel meeting was convened in Jakarta on 8 December 2015 comprising 14 experts, including infectious disease physicians and pediatricians, national specialists in dengue treatment guidelines and epidemiology, healthcare system managers, surveillance officers, academics, and laboratory workers, from different geographical areas across Indonesia, invited based on the advice of national-level dengue experts (full list of panelists provided in acknowledgments). The panel was expected to estimate the proportion of symptomatic dengue cases captured in the surveillance system and thus enable calculation of national-level dengue burden estimates. The panel also estimated the percentage of hospitalized and ambulatory dengue cases treated in private and public institutions. A range of epidemiological and clinical data documenting current knowledge and gaps related to dengue in Indonesia was first presented to the panel, to align on recent study results and their methods.
e. ambulatory). Anonymous responses were collected by a moderator who aggregated the data, presented them to the group and facilitated a discussion. Participants were then invited to re-cast their votes in light of the previous results and discussions. The process was terminated after three rounds of voting (two rounds of discussion). Medians of final round votes were used for analysis, and a bootstrapping resampling method (200 samples; SAS software) employed to provide variability based on the theoretical non-parametric distribution of observed values, enabling estimation of medians and their 95% confidence intervals (CIs)  [11]. These medians were used to calculate the total number of symptomatic dengue cases occurring in Indonesia via generation of an overall expansion factor (EF O ): EF O = Total cases Reported cases.
ACKNOWLEDGEMENTS The authors would like to thank the Delphi panelists:  Professor Sri Rezeki Hadinegoro ,  Faculty of Medicine, Universitas Indonesia ;  Dr Rizaldy Pinzon ,  Bethesda Hospital ;  Dr Christiana Trijayanti ,  Gadjah Mada University ;  Dr Harun Hudari ,  Moh Hoesin Hospital ;  Dr Yulia Iriani ,  Moh Hoesin Hospital ;  Dr Savitri L Wina ,  Saiful Anwar Hospital ;  Dr Ni luh Putu Ariastuti ,  Udayana University ;  Dr Komang Ayu Kartika Sari ,  Udayana University ;  Dr Niniek Budiarti Burhan ,  Saiful Anwar Hospital ;  Dr Ari Prayitno ,  Universitas Indonesia ;  Dr Suryadi Tatura ,  Dr Kandao Hospital ;  Dr Mathilda Panggabean ,  Pelni Hospital ;  Dr Suwito ,  SKM, MKes. CDC Indonesia Ministry of Health ;  Dr Tri Yunis Miko ,  Universitas Indonesia. They also thank  Arbovirus Subdirectorate ,  Indonesia CDC ,  Ministry of Health  for collection and sharing of historical surveillance data;  Eri Setiawan  for organizational support and  Alain Bouckenooghe ,  Laure Durand ,  Gee Marsh ,  Christopher B.
Nelson , and  Elsa Sarti  for thoughtful review and comments. This Delphi panel meeting, including travel and accommodation costs of participants, was financially supported by  Sanofi Pasteur. DECLARATION OF INTEREST J. N. , S. B. , S. N. and A. M. are/were employees of  Sanofi Pasteur , a company which produces a vaccine against dengue. A. P. has acted as an investigator for research studies funded by  Sanofi Pasteur. T. Y. M. W. , H. T. and M. N. declared no conflicts.
Behavioral data Behavioral data were collapsed across the male and female runs and were submitted to analyses of variance (ANOVA) and t-tests using SPSS 19. Where appropriate, Epsilon corrections for heterogeneity of covariances  (Huynh & Feldt, 1976)  were performed throughout. Errors of omission were excluded (. 9% of responses). We analyzed recognition performance in signal detection parameters  (Stanislaw & Todorov, 1999)  d-prime (d 0 ) and response bias (C), as well as in accuracy data.
FMRI data Data were analyzed using SPM8 software (Welcome Department of Imaging Neuroscience; http://www. fil. ion. ucl. ac. uk/ spm). During preprocessing anatomical images were aligned to the anterior and posterior commissure (ACePC) and the orientation change was applied to all functional images, i. e. , images from both the experimental runs and voice localizer scan. Functional scans were corrected for head motion by aligning all volumes of the five echo series to the first volume of the first run of the first echo series and, subsequently, to the mean volume. The anatomical scan (T1) was co-registered to the mean volume and segmented. Following the combination of the five echo series for the experimental runs, all functional scans (including voice localizer scan) and the T1 image were transformed to Montreal Neurological Institute (MNI) space using the parameters obtained from the segmentation.
Acknowledgments This research was funded by the  Deutsche Forschungsgemeinschaft (DFG) , grant  ZA 745/1-1  and  ZA 745/1-2  to RZ, and by grants  BB/E003958/1  from  BBSRC (UK) , large grant  RES-060-25-0010  by  ESRC/MRC , and grant  AJE201214  by the  Fondation pour la Recherche M edicale (France)  to P. B. We thank  Leonie Fresz , Achim H€ otzel,  Christoph Klebl ,  Katrin Lehmann ,  Carolin Leistner ,  Constanze Mu ¨hl ,  Finn Pauls ,  Marie-Christin Perlich ,  Johannes Pfund ,  Mathias Riedel ,  Saskia Rudat  and  Meike Wilken  for stimulus acquisition and editing. We are also thankful to  David Fleming  and  Emilie Salvia  for Matlab support,  Francis Crabbe  for assistance in fMRI scanning, and  Stefan Schweinberger  as well as  Marlena Itz  for helpful comments on earlier drafts of this manuscript.
Statistical analysis Data were analyzed using Stata version 13. 1 (StataCorp, College Station, Texas, USA). We estimated the sensitivity, specificity and predictive value for each RDT and simple confirmatory assay by comparing the results of these tests performed at ITM to the results of the reference standard. The analysis was weighted to adjust for the sampling strategy, which underrepresented negative samples. For each participant, the weight was calculated as the inverse of the probability of inclusion in the study. For the total adjusted estimates, the weights were normalized to ensure equal representation of each site. Weighted proportions (e. g. weighted proportion of RDT reactive among all true positives by the reference standard for sensitivity) were calculated using the svy survey prefix command in Stata.
Acknowledgements We are indebted to all study participants. We acknowledge the assistance of health facility staff and the counsellors at each site. We are grateful to the  MSF's laboratory  working group members for the invaluable support during the entire planning and rollout of the study:  Erwan Piriou ,  Charity Kamau ,  Pamela Hepple ,  Pascale Chaillet ,  Monique Gueguen ,  Celine Lastrucci ,  Laurence Bonte , and  Roberto de la Tour. We also thank  Meggy Verputten ,  Karla Bil ,  Annick Antierens , and  Suna Balkan  at  MSF  headquarters for supporting the study. We thank  Patricia Kahn  and  Patrick Adams  for the editing comments. We also thank the  MSF  and the local ethical review boards for the critical review and feedback of the study protocol. Especially we thank the following study team members and local supporters of the study:  J Mashala ,  H Onyango ,  E Oyoo ,  E Abich ,  S Oyugi ,  J Amimo ,  C Mugo ,  N Jaleny ,  F Dwallo ,  S Matiku ,  P Balikagala ,  Z Tu ,  H Elyas ,  S Adega , and  B Kirubi  ( Homa-Bay, Kenya );  S Noubissi ,  F Essomba ,  P Ndobo ,  C Tchimou , and  G Ehounou  ( Douala, Cameroun ),  J Wazome ,  H Nordenstedt ,  P Kahindo ,  JJ Mapenzndahei ,  A Uunda ,  N Amwabo ,  L Byantuku ,  P Tawimbi ,  M Dialo , and  E Castagna  ( Baraka, DRC );  C Gba-Foromo  ( Conakry, Guinea );  P Ongeyowun ,  M Baral-Baron ,  K Kelly ,  C Paye ,  K Chipemba ,  J Sande ,  I Quiles , and  V de Clerck  ( Arua, Uganda );  R Aupal ,  R Olal ,  Shoaib ,  Y Boum  and  S Muhammad  ( Kitgum, Uganda ).
Adult mosquitoes were exposed by tarsal contact for 1 h to the 0. 06 and 0. 08% deltamethrin-impregnated papers. The knockdown (KD) (after 1 h of exposure) and mortality rates (after 24 h) were determined. A kinetic of KD rate during 2 h (by accounting the number of KD mosquitoes every 5 min) was also conducted for each population using 0. 05% impregnated papers to estimate the KDT 50 (Time necessary to affect 50% of mosquitoes) using XLSTAT software (dose-effect option). The KRR 50 is the ratio between KDT 50 of mosquitoes from the field and KDT 50 of mosquitoes from the Bora Bora strain. KRR 50 was scaled as follows: KRR 50 <1 = susceptible, 1≤KRR 50 <10 = low resistance, 10≤KRR 50 ≤30 = moderate resistance, 30<KRR 50 <100 = high resistance, and KRR 50 ≥100 = very high resistance  [21].
Statistical analysis Statistical analyses were performed with STATISTICA 8 software (Statsoft Inc. , Oklahoma, USA) and XLSTAT 2015 software. STATISTICA was used to perform ANOVA Kruskal-Wallis tests (to compare adult KD/mortality rates regarding deltamethrin and amplification gene ratios); Kruskal-Wallis Z tests (to compare larval mortality rates regarding temephos and malathion, adult mortality rates regarding deltamethrin, and expression and amplification genes ratios); and Mann-Whitney U tests (to compare gene expression ratios of Bora Bora strain and each population). XLSTAT was used to perform log-probit logistical regression to investigate the dose-effect relation regarding insecticide larval tests data, as well as to estimate KDT values using adult kinetic data. XLSTAT was also used to perform Spearman's rank correlation tests (between expression and amplification ratios) and the principal component analysis (PCA).
Correlation between overexpression and gene amplification of detoxification genes Correlations between mean values of the expression and amplification ratios were investigated using the Spearman's rank correlation test in XLSTAT software for each gene and all mosquito populations studied (see Additional file 3), however, no significant correlation was found. Nevertheless, the highest levels of association between gene amplification and expression ratios were found for the a b Fig. 2  Histogram of genotype proportions for the six populations studied regarding V1016I (a) and F1534C (b) Kdr mutations. V/V: V1016I wild homozygote genotype; I/V: V1016I heterozygote genotype; I/I: V1016I mutant homozygote; F/F: F1534C wild homozygote genotype; F/C: F1534C heterozygote genotype; C/C: F1534C mutant homozygote; ABY Les Abymes, SF Saint-François, BM Baie-Mahault, SXM Saint Martin, AB Anse-Bertrand, DH Deshaies, BORA Bora Bora susceptible strain Fig.
Acknowledgements We thank the regional health agency of Guadeloupe for its collaboration regarding mosquito sampling. We thank the vector control center of  Martinique  for graciously offering the Bora-Bora susceptible reference strain and for the training of DG on insecticide resistance tests. We thank the  Pasteur Institute of French Guiana  for graciously offering Kdr PCR controls and the  International Division of Pasteur Institute  for supporting DG's training in  Alpine ecology laboratory (LECA Grenoble, France ).
HA influenza A/Puerto Rico/8/34 sequencing Viral RNA (vRNA) was extracted from viral particles collected in 140 ml of cell culture surpernatant with QIAamp Viral RNA Mini Kit (250) (Qiagen, ref 52906). RNA extraction was performed according to manufacturer protocol and eluted in 60 ml AVE Buffer. vRNA of HA and NA proteins were amplified in cDNA by RT-PCR with optimized protocol based on universal primer Uni-12 and AMV RT enzyme. HA and NA cDNAs were then amplified by PCR with optimized protocol using Pfu polymerase, as previously described  [25]. Sequencing was then performed by MWG Eurofins Company on amplified cDNA with these specific primers. Alignment was realized on Bioedit software with PR8 sequence obtained from NCBI database.
The P1-BR (96 hpi) sample showed a more homogenous population. Taken together, these results indicate the generation of biologically active influenza virus. Viral genome extracted from production at P0 and P1 were sequenced to confirm that reverse genetics at large-scale did not induce variation of the viral population, especially on the two major antigens, HA and NA. PR8 HA and NA sequences were aligned using Bioedit software (IBIS Bioscience, Carlsbad, USA) with the original plasmid sequence and with one of the reference sequences obtained from NCBI database for PR8. Sequences from P0 and P1 demonstrate 100% homology with the original reverse genetics plasmid sequences (Supplementary material for HA and data not shown for NA) demonstrating no change of the viral antigen sequences PR8. These results indicate that transfection with eight plasmids for influenza A/Puerto Rico/8/34 can be performed at bioreactor scale using suspension HEK-293 cells generating high amounts of viral particles after only one amplification step.
Acknowledgments The authors would like to thank  Danielle Jacob  for the bioreactor operations,  Shu Zhuang  for the plasmid purification,  Melanie Simoneau  for plasmid sequencing and  Rénald Gilbert  and his team at  NRC  for valuable advises. Also, the authors would like to thank  Micheline Letarte  from  Institut Armand-Frappier  ( Laval, Canada ) for the electron microscopy analyses and  Camille Roesch  from  IZON  company for the TRPS samples analyses. This work was partially funded through  Natural Sciences and Engineering Research Council  Grants  RGPIN-2015-132 ;  STPGP-462995-14  and  Canada Research Chair   CRC-240394.
1 eV/channel. Obtaining spectra in the STEM mode using a camera length of 115 mm and a spectrometer entrance aperture diameter of 5 mm provided a collection semi-angle (β) of 14. 7 mrad. Convergence angle (α) was about 16. 7 mrad. Further spectral processing operations were conducted using digital micrograph (DM, Gatan, CA, USA) software  [21]. LabRAM Raman Spectrometer (LabRAM HORIBA Jobin Yvon, Edison, NJ, USA) excited by the 633 nm coherent line of a He:Ne laser was used to determine the carbon structure of the samples at room temperature. Dynamic mechanical analysis (DMA) was conducted in the tension mode by Netzsch DMA 242C (NETZSCH, Selb, Germany). The measurement was conducted from 25 °C to 150 °C at 1 Hz with a heating rate of 2 °C/min. The size of the specimen was 20 mm × 5 mm × 1.
1 eV/channel. Obtaining spectra in the STEM mode using a camera length of 115 mm and a spectrometer entrance aperture diameter of 5 mm provided a collection semi-angle (β) of 14. 7 mrad. Convergence angle (α) was about 16. 7 mrad. Further spectral processing operations were conducted using digital micrograph (DM, Gatan, CA, USA) software  [21]. LabRAM Raman Spectrometer (LabRAM HORIBA Jobin Yvon, Edison, NJ, USA) excited by the 633 nm coherent line of a He:Ne laser was used to determine the carbon structure of the samples at room temperature. Dynamic mechanical analysis (DMA) was conducted in the tension mode by Netzsch DMA 242C (NETZSCH, Selb, Germany). The measurement was conducted from 25 • C to 150 • C at 1 Hz with a heating rate of 2 • C/min. The size of the specimen was 20 mm × 5 mm × 1.
Discussion The crucial element of our exhaustive picture of the electronic structure of the paradigm half-metallic ferromagnet CrO 2 has been the use of SX-ARPES providing large probing depth and sharp definition of three-dimensional electron momentum. The nontrivial interference effects in the ARPES response of CrO 2 caused by its non-symmorphic space group were described by band structure unfolding onto an effective smaller unit cell using atomic projections. Deciphered with the unfolding, our experimental dataset yields the most complete momentum-resolved description of the electron dispersions and Fermi surface so far achieved for CrO 2. We establish its FS topology as composed of two electron pockets around the Γ and A point and a hole pocket along the Γ-Z direction. At least at low temperature, our theoretical description finds full spin polarization of the states at and close to the Fermi energy confirming the half-metallic nature of CrO 2.
Theoretical calculations The DFT calculations on CrO 2 were performed using the Vienna Ab-initio Simulation Package (VASP)  [62, 63]  with a plane-wave cutoff of 350 eV and 6 × 6 × 9 Monkhorst-Pack grid sampling for charge-density integration. The LDA and the GGA-PBE exchange-correlation functionals were used. In both cases, the on-site Coulomb interaction (U eff ) was tuned to obtain the best agreement with the experimental data, focusing on the most sensitive Γ-Z direction. We adopted the experimental lattice parameters a = b = 4. 421 Å, c = 2. 917 Å and u = 0. 301  [64]. We performed DFT+DMFT calculations  [65]  using a t 2g -only model constructed from DFT via maximally localized Wannier functions  [66, 67]. The DFT in this case was performed using the VASP package with a plane-wave cutoff of 400 eV and a 16 × 16 × 32 Γ-centered Monkhorst-Pack grid to ensure a faithful representation of the hybridization function also at low temperature.
For taking into account the local symmetry of the Cr sites we have used a different local coordinate system on each Cr site. A disentangling procedure with an energy window encompassing the 3d bands of Cr was used, resulting in three t 2g orbitals per Cr site, which agree reasonably well in their shapes and transfer integrals with previous calculations  [17, 68]. The DMFT part was performed using the code W2DYNAMICS  [69]  with a continuous-time quantum Monte Carlo impurity solver  [70]. We used the density-density Hamiltonian for the t 2g orbitals as well as the SU(2)-symmetric Kanamori Hamiltonian. The results in the ordered phase were qualitatively the same in both cases, so only the densitydensity results are shown. The Coulomb interaction was modeled as usual for a three-band problem with the intraorbital interaction U, the Hund's coupling J and the interorbital interaction U-2J.
Acknowledgements We thank  H. Dil ,  J. Minar ,  K. Held ,  Yu. S. Dedkov ,  L. Chioncel , and  O. Gunnarsson  for promoting discussions. The research leading to these results has received funding from the  Swiss National Science Foundation  under the grant agreement n. ° 200021_146890 and European Community's  Seventh Framework Programme  ( FP7/2007-2013 ) under the grant agreement n. °290605  ( PSI-FELLOW/COFUND ). The authors gratefully acknowledge the  Gauss Centre for Supercomputing e. V. (www. gauss-.
Electrophysiologic exploration of oxaliplatin neurotoxicity The sensory and motor excitability was assessed in vivo on mice under isoflurane (AErrane) anesthesia by minimally invasive electrophysiologic methods using the Qtrac software written by Prof. H. Bostock (Institute of Neurology, London, United Kingdom), as described previously  (26). Briefly, an anaesthetized mouse was placed on a heating pad to the maintain body temperature throughout the experiment (between 35. 40 AE 0. 04 and 35. 47 AE 0. 02 C, as determined in 29 mice using a rectal probe) to avoid nonspecific modifications of the measured excitability parameters. For sensory investigation, the compound nerve action potential (CNAP) was recorded using needle electrodes inserted into the base of mouse tail, in response to stimulation of the caudal nerve applied at the distal part of the tail, by means of surface electrodes.
A Zeiss LSM 510 META (Carl Zeiss) multiphoton scanning confocal microscope, mounted on an upright microscope and controlled with the manufacturer's software and workstation, was used for optical sectioning of myelinated axons and subsequent 3D high-resolution digital reconstruction of their structure. Images were collected using a 63Â oil immersion objective with a 1. 40 numerical aperture (Zeiss Plan-Apochromat), following excitation of FM1-43 with the 488-nm wavelength line of an Argon ion laser, and then digitized at 12-bit resolution into a 512 Â 512 pixel array. Images were then analyzed using ImageJ software (NIH, Bethesda, MD). Quantification of morphometric parameters of myelinated axons was performed by measuring the internodal diameter, nodal diameter (D) and nodal length (L). Assuming the simplest geometry in which a node of Ranvier approaches a cylinder, the nodal volume (V) was then determined as V ¼ pL (D/2) 2.
Statistical analysis Statistical analysis was performed using GraphPad Prism 5. Artwork was also created using GraphPad Prism 5, except for electrophysiologic study artwork, which was created using the Qtrac software. Differences between values were tested using the two-tailed Student t test, two-way ANOVA, or the nonparametric Mann-Whitney U test, depending on the equality of variances estimated using Lilliefors test. They were considered significant when P < 0. 05. P values are denoted as follows: Ã , P < 0. 05; ÃÃ , P < 0. 01; ÃÃÃ , P < 0. 001; ÃÃÃÃ , P < 0. 0001; NS, not significant.
B, N2a cells. C, HUVEC. D, THP1 cells. Viability was expressed as percent AE SD versus cells in culture medium alone (100% viability). E, Reduced GSH was also assessed under normal cell culture growth conditions with monochlorobimane. Data from at least three independent experiments have been pooled and were expressed as means AE SD of triplicates. Ã , P < 0. 05; ÃÃ , P < 0. 01 versus oxaliplatin. The oxaliplatin-induced sensory and motor alterations were not detected in mice injected with oxaliplatin plus niclosamide or niclosamide alone (Fig. 3 ; Supplementary Fig. S1 ; Supplementary Table  S1 ). These observations further validate niclosamide as a potentially neuroprotective molecule, as they highlighted the maintenance of the peripheral nervous system functioning by the teniacide. The morphology of myelinated axons of mouse sciatic nerves was examined using confocal microscopy (Fig.
Using the identified E. californica and N. benthamiana predicted protein homologs and the Arabidopsis protein sequences of the SHI/STY/SRS family members we performed comparative sequence analyses, using the Neighbor joining algorithm built into the Mega7 software (Figure  1 ). The resulting tree had an overall topology similar to that of other previously published, although some differences were found mainly affecting less-supported clades and probably due to the use of different tree reconstruction methods and datasets. The clade comprising AtSTY1, AtSHI, and AtSRS8 was related to one formed by five Nicotiana predicted proteins. Four additional Nicotiana proteins grouped in a well-supported clade related to AtSRS5 and AtSRS7, while both EcSRS-L and EscaSTY-L grouped in the same clade as AtSRS3.
Cloning and Sequence Analysis The partial coding sequence of EcSRS-L gene was isolated by RT-PCR on cDNA of flowers of E. californica using the degenerate primers EcSTYdF2/EcSTYdR2 designed from the conserved motifs of SRS homologs from other species. The 3 end of EcSRS-L was then isolated by reverse transcription polymerase chain reaction (RT-PCR) using the primers PoppyRT and RT (sequence added to the oligodT primer used for retrotranscription). To amplify the NbSRS-L genes, we designed primers from the annotated genomic sequences retrieved from solgenomics. net (same pairs as described for cloning the CDS in the previous subheading). The deduced amino acid sequences alignments were analyzed using the MUSCLE tool built in the Macvector 15. 1 software (MacVector Inc. , Cary, NC, United States).