dataesr/scientific-paragraphs-categorization huggingface dataset:
DISCUSSION The safety of antimicrobial agents developed to resolve the progression of antibiotic resistance must be studied and compared to reference treatments. In this respect, the direct   11 ) and strain 536  (11)  were cultured in absence (control) or presence of antibacterial agents: phages (LM33_P1 or 536_P1, multiplicity of infection of 5) or antibiotics (8-fold the minimum inhibitory concentration). The viable cells were quantified using an ATP-driven luciferase assay (see Methods). Data are means with standard deviation and the y-axis is in log 2 scale. Abbreviation: RLU, relative luminescence unit. immunogenicity of phage particles involving innate immune response (ie, their own ability to trigger an acute inflammatory response) seems to be negligible  [30] [31] [32] [33]  as long as phage preparations are correctly purified  [34].
Sexual behaviour Each age group consists of persons with low, medium or high sexual activity. Data on sexual behaviour in Italy were scarce or differed in several aspects from the inputs needed to inform the model. The results from the United Kingdom (UK) NATSAL-3 study were used. They were deemed to be applicable to the Italian setting according to experts' opinion as well as being consistent with previously published economic literature  (Haeussler et al. )   [21, 22, 36]. The degree of sexual mixing among members of different age cohorts and sexual activity groups (0 representing no mixing, and 1 representing a maximal mixing) was set up in similar to the US model and adjusted during the calibration process  [19].
Vaccine assumptions (proportion of exposed people avoiding the infection) HPV Overall and age-specific incidence data for cervical, anal, vaginal, vulvar and penile cancers were found in the report from the Institut Catala' d'Oncologia (ICO)-Information center on HPV. The aim of this report was to compile and centralize updated data and statistics from the official Italian registry on HPV and related cancers; age specific values were extracted from the graphs  [55]. The ITACAN database was used for incidence data on cancers in oral cavity, oropharynx and larynx. Overall incidence of genital warts was found in an Italian study  (Baio et al. ). This Italian study provided also overall incidence for CIN 1 and CIN 2-3 incidence. Nevertheless, the reported values were much lower than other available data  (Hartwig).
Therefore, UK data were also considered as a higher bound of plausible data. Since the model studies HPV-induced diseases only, target epidemiological values were calculated by multiplying the incidence or the mortality with the percentage of the disease that can be attributed to HPV infection. The proportion of diseases attributable to HPV infection (for the 2-valent, 4-valent or 9-valent vaccines) were found in the literature  [13, 56]. The model was calibrated to attribute 73% of CIN 2/3 and cervical cancer incidence to HPV 16 and 18 and 17% to HPV 31, 33, 45, 52, and 58. HPV-related head and neck cancers were calculated by weighting HPV-related oral cancers, oropharynx cancers and larynx cancers on their overall incidence. The calibration process involved many rounds of iterations to move model outcomes closer to the targets.
All participants individually generated ideas and returned them by e-mail. For each stakeholder group separately, we collected all statements and removed duplicates to form a final set of statements. In the third phase, participants received all statements from their own peer group online and individually sorted them in groups on the basis of content. They were instructed to sort the statements in a way that made sense to them and to name each group. Next, participants rated the statements both on importance and feasibility on a scale of 1 to 5. In phase 4, clusters were generated by multidimensional scaling and hierarchical cluster analysis, using concept mapping software (Ariadne)  (14). This resulted in a concept map: a two-dimensional graphical representation of the views of the group on the subject, in which closer proximity of clusters represents a stronger perceived relationship between concepts.
Acknowledgements We would like to thank all programme coordinators ( Caroline Bournez  and  Julie Penin , EPODE Flandre Lys coordinators, France;  Dr Ana Rito , MUN-SI coordinator, Portugal;  Helena Stamou  PAIDEIATROFI coordinator, Greece;  Dr Charmaine Gauci , Superintendent of Public Health/ Director General Health Regulation, Malta;  Silvia Bucur , SETS programme coordinator, Romania;  Dr Belén Zorrilla , Salud Madrid coordinator, Spain;  Lucia Polacovikova , SPORTTUBE coordinator, Slovakia;  Mirielle Roillet , VISANO coordinator, Belgium) and scientists ( Prof. Wolfgang Ahrends ,  Prof. Johannes Brug ,  Dr Jeroen Lakerveld ,  Dr Magdalena Kolka ,  Prof. Denise de Ridder , and  Dr Alba Mª Santaliestra Pasías ,) for contributing to the concept mapping sessions. This study is part of the  OPEN  project.
Acknowledgments We thank  Cambridge Biomedical Services  for animal care and husbandry. We are particularly grateful to  Gillian Griffiths  ( Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK ) for aiding with T cell cytotoxicity assays (supported by  Infection and Immunity Immunophenotyping  [3i] grant  100156/Z/12/Z  from the  Wellcome Trust ). We thank  James Warner ,  Betania Mahler-Araujo , and  Sathia Thiru  of the  Cambridge Histology Service  for tissue processing and analysis. JMS was funded as part of the  Wellcome Trust Infection ,  Immunity and Inflammation program. KGCS is funded by the  Medical Research Council (MRC)  ( MR/L019027/1 ) and is a  Wellcome Trust Investigator and NIHR Senior Investigator. DCT was funded by a  Wellcome Trust/CIMR Next Generation Fellowship , an  NIHR   Clinical Lectureship grant , and a  Starter Grant for Clinical Lecturers  ( Academy of Medical Sciences ).
Net survival up to 5 years after diagnosis was estimated after correction for death from other causes. Data were available from 59 countries for almost 5. 5 million women diagnosed with breast cancer. For women diagnosed during 2005-2009, 5-year net survival was 80% or higher in 34 countries, but much lower in India (60%), Mongolia (57%) and South Africa (53%) (Figure  2 ). In the 10 years between 1995-1999 and 2005-2009, 5-year survival from breast cancer increased in Central and South America (e. g. from 66% to 76% in Colombia). Data were available from 61 countries for 602 000 women diagnosed with cervical cancer. The global range in 5-year net survival was very wide. For women diagnosed during 2005-2009, 5-year net survival was 70% or higher in 7 countries, in the range 60-69% in 34 countries, but below 60% in a further 20 countries.
Search Strategy and Selection Criteria Studies were retrieved through systematic searches on the following medical and social sciences electronic databases: EMBASE, Global Health, MEDLINE (OVID), Scopus, Web of Science and Econlit. Variations of search terms related to 'breast cancer', 'cervical cancer', 'low income', 'middle income', 'developing' countries , the individually named countries of relevance, 'economic burden' and 'economic consequence', were combined. We searched Google Scholar, scanned the reference lists of the studies retrieved and hand searched the resources and publications of institutional websites. Searches were limited to studies published in English after 1990 containing original quantitative estimates of economic impact.
The size of the SLNs increased 16 to 22 nm after the addition of LB 509 mAb or OX26 respectively, which corresponds approximately to the diameter of globular mAbs  [48]. The addition of the mAb to the SLN does not significantly affect the zeta potential of the nanocarriers. In order to study the stability of SLN conjugated with the mAb, the size and the zeta potential of carriers were evaluated during 1 month. Over this time, there were no significant variations on these parameters which indicate that the immuno SLN were stable for this period (data not shown). The binding of the mAb to the nanoparticles was also determined by ELISA. Significantly higher absorbance at 405 nm was observed in the nanoparticles conjugated with the two different types of mAbs (1. 6 ± 0. 3) when compared with the nanoparticles without mAb (0.
In order to study the stability of SLN conjugated with the mAb, the size and the zeta potential of carriers were evaluated during 1 month. Over this time, there were no significant variations on these parameters which indicate that the immuno SLN were stable for this period (data not shown). The binding of the mAb to the nanoparticles was also determined by ELISA. Significantly higher absorbance at 405 nm was observed in the nanoparticles conjugated with the two different types of mAbs (1. 6 ± 0. 3) when compared with the nanoparticles without mAb (0. 07 ± 0. 02). Therefore, the antibody used demonstrated bioactivity for the transferrin receptor.
Acknowledgments: This work was supported by  FCT-Fundação para a Ciência e a Tecnologia  and  FEDER  funds through  COMPETE  grant  PTDC/QUI-BIQ/118076/2010 , by Project  UID/EQU/00511/2013-LEPABE , by the  FCT/MEC  with national funds and when applicable cofounded by  FEDER  in the scope of the P2020 Partnership Agreement; by Project  NORTE-07-0124-FEDER-000025-RL2_Environment  & Health, by  FEDER  funds through COMPETE, by the  Programa Operacional do Norte  ( ON2 ) and by national funds through FCT. The postdoctoral grant  FEUP-TRANSCAN/0001/2012  to  J. A. L. is gratefully acknowledged. A. R. N. and C. N. also acknowledge their postdoctoral grants under the project  NORTE-01-0145-FEDER-000011  and  SFRH/BPD/81963/2011. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
The Comorbidities in Rheumatoid Arthritis (COMORA) international study collected recent patient-level data from 17 countries across 5 continents including data on work outcomes. These data offer a unique opportunity to explore the impact of country of residence and specific country characteristics on employment, absenteeism and presenteeism. We hypothesized that higher economic wealth and greater human development of a country is associated with higher employment and lower absenteeism and presenteeism.
Methods COMORA, an international, cross-sectional multicenter study in 17 countries, collected data in patients diagnosed with RA according to the 1987 American College of Rheumatology classification criteria for RA, who were older than 18 years, and had sufficient command of the questionnaire language. The study protocol was approved by one central and all local institutional ethics committees. Written informed consent was obtained from all subjects. Investigators and patients completed a questionnaire on demographics and self-reported health, including questions on work outcome  [8].
Fourth, in the absence of data on levels of income substitution in the case of disability in sickness absence, we considered SPE as a remote proxy in the case of work restrictions due to illness. It must be noted that the personal insurance for work disability may be a potential confounder for which we were not able to adjust. Fifth, work status in the COMORA study only considered employment (yes/no), and therefore no further analyses could be performed to understand reasons for not participating (anymore) in the labor force. Also, information on presenteeism and absenteeism was collected through self-report from patients and comprised a short time span (7 days). However, it should be noted that the WPAI questionnaire and the recall periods are well-validated Specifically for absenteeism, the short time-frame is valid when the sample is sufficiently large, as sick leave likely occurs randomly between different persons over time  [10, [25] [26] [27].
Acknowledgements The authors would like to thank the national principal investigators of the COMORA study:  Gustavo Casado  (Argentina),  Josef Smolen  (Austria),  Bassel Kamal El-Zorkany (Egypt) ,  Martin Soubrier  (France),  Gerd Burmester (Germany) ,  Peter Balint (Hungary) ,  Carlo Maurizio Montecucco (Italy) ,  Masayoshi Harigai  (Japan),  Yeong-Wook Song  (Korea),  Najia Hajjaj-Hassouni (Morocco) ,  Mart van de Laar  (the Netherlands),  Emilio Martin-Mola  ( Spain ,  Shue-Fen Luo  (Taiwan),  Jonathan Kay & Kevin Winthrop (USA) ,  Gabriel Maciel  (Uruguay),  Anna Antunez  (Venezuela); the scientific committee of COMORA study:  Peter Balint ,  Gerd Burmester ,  Paul Emery ,  Jonathan Kay ,  Emilio Martin-Mola ,  Iain McInnes ,  Carlo Maurizio Montecucco  and  Josef Smolen ; and the patients who agreed to participate in this study.
NGS data analysis Data analysis is a time-consuming process and is often considered as the ''bottle-neck" of NGS. Next generation sequencing generates huge amounts of data that often necessitates the use of powerful computing facilities and algorithms. The sequencing data analysis starts from files containing DNA sequences and quality values for each base. Depending on the size and the depth of the sequencing, a FASTQ file size can be several hundred gigabytes. These files need to be transferred from the sequencer into a workstation for analysis and also stored in a dedicated data warehouse. For each NGS project, a custom pipeline must be created to automate the analysis, in order to standardize results and avoid errors. A typical variant calling pipeline includes an assessment of the quality of sequencing, an assembly of the reads (alignment or de novo) and variant detection.
9% NaCl 2 ), seeded onto BHI agar plates and incubated for 48 h at 37 °C. Subsequently, one recovered bacterial colony was cultured in BHI broth. The recovered bacteria were then referred to as Recovered (Rc). For the bacterial virulence assay, we used the freshly recovered bacteria and bacteria that did not contact the murine host as a control, which is referred to as Control (Ct). Groups of five mice were infected with Rc and Ct, via intraperitoneal injection of a suspension containing 10 6 CFU or 10 5 CFU. The animals' survival rates were calculated and represented in GraphPad Prism v. 5. 0 (GraphPad Software, San Diego, CA, USA) using the Kaplan-Meier survival function. The results of 1002_ovis CFU count in the organs were calculated using the two-way ANOVA test.
The Image Master 2D Platinum 7 (GE Healthcare) software was used to analyze the generated images and all spots were matched and analyzed by gel-to-gel comparison. The quantification of the spots was calculated according percentage volume (% Vol) and spots with reproducible changes in abundance were considered to be differentially expressed. Protein spots were excised from the gels, and in-gel digestion was carried out using trypsin enzyme (Promega, Sequencing Grade Modified Trypsin, Madison, WI, USA). The peptides were then desalted and concentrated using ZIP TIP C18 tips (Eppendorf). The samples were subsequently analyzed for MS and MS/MS modes, using an MALDI-TOF/TOF mass spectrometer Autoflex IIITM (Bruker Daltonics, Billerica USA). The equipment was controlled in a positive/reflector way using the Flex-ControlTM software (Brucker Daltonics).
External calibration was performed using peptide standards samples (angiotensin II, angiotensin I, substance P, bombesin, ACTH clip 1-17, ACTH clip 18-39, somatostatin 28, bradykinin Fragment 1-7, Renin Substrate tetra decapeptide porcine) (Bruker Daltonics). The peptides were added to the alpha-cyano-4-hydroxycinnamic acid matrix, applied on an Anchor-ChipTM 600 plate (Brucker Daltonics) and analyzed by Autoflex III. The search parameters were as follows: enzyme; trypsin; fixed modification, carbamidomethylation (Cys); variable modifications, oxidation (Met); mass values, monoisotopic; maximum missed cleavages, 1; and peptide mass tolerance of 0. 005% Da (50 ppm). The results obtained by MS/MS were used to identify proteins utilizing the MASCOT_ (http://www. matrixscience. com) program and compared with the genomic data of the Actinobacteria class deposited in the NCBI nr database.
Multiplexed data-independent (DIA) scanning with additional specificity and selectivity for non-linear 'T-wave' ion mobility (HDMSE) experiments were performed using a Synapt G2-S HDMS mass spectrometer (Waters, Manchester, UK). Following the identification of proteins, the quantitative data were packaged using dedicated algorithms  [27]  and searching against a database with default parameters to account for ions  [28]. The databases used were reversed on-the-fly during the database queries and appended to the original database to assess the false positive rate during identification. For proper spectra processing and database searching conditions, the Pro-teinLynxGlobalServer v. 2. 5. 2 (PLGS) with IdentityE and ExpressionE informatics v. 2. 5. 2 (Waters, Manchester, UK) was used. UniProtKB (release 2013_01) with manually reviewed annotations was used, and the search conditions were based on taxonomy (Corynebacterium pseudotuberculosis).
One missed cleavage by trypsin was allowed be up to 1 and various modifications as carbamidomethyl (C), Acetyl N terminal, phosphoryl (STY) and oxidation (M) were allowed  [29]. The proteins collected were organized by the PLGS ExpressionE tool algorithm into a statistically significant list that corresponded to higher or lower regulation ratios between the different groups. For protein quantitation, we used the PLGS v2. 5. 2 software with the IdentifyE algorithm using the Hi3 methodology. The search threshold to accept each spectrum was the default value for a false discovery rate 4%. The quantitation values were averaged over all samples, and the standard deviations of p < 0. 05, which were determined using the ExpressionE software, refer to the differences between biological replicates.
Bioinformatic analysis The proteins identified in 1002_ovis under both conditions were analyzed using the following prediction tools: SecretomeP 2. 0 server, to predict proteins exported from non-classical systems (positive prediction score greater than to 0. 5)  [30]  and PIPs software, to predict proteins in the pathogenicity islands  [31]. Gene ontology (GO) functional annotations were generated using the Blast2GO tool  [32].
After four weeks of infection in the assay with 10 5 CFU, bacteria were isolated from the spleen, liver, left and right kidney, only in mice infected with Rc (Fig. 1d ). Finally, regarding the clinical signs, in the assay using 10 5 CFU, caseous lesions were detected in different organs (liver, left kidney and right kidney) of all the animals infected only with Rc (data not shown). Altogether, these results showed that the serial passage process in a murine model increased the virulence potential of strain 1002_ovis. In addition, these results confirmed the low virulence of this strain, which was previously suggested based on the composition of its extracellular proteome  [8] [9] [10]. After passage in BALB/c mice, a dramatic change in the virulence potential of strain 1002_ovis was observed.
061860 D9Q7X5_CORP1 Hypothetical protein 38716,45 -1,21 0. 825761 D9Q4T9_CORP1 Hypothetical protein 553,76 -1,28 0. 934591 D9Q6R6_CORP1 Hypothetical protein 1457,62 -1,40 0. 206908 D9Q890_CORP1 Hypothetical protein 1948,52 -1,51 0. 847549 D9Q6M6_CORP1 Hypothetical protein c 1935,68 -1,90 0. 823541 Others D9Q6I3_CORP1 Maltotriose binding protein 5210,9 5,22 0. 864851 D9Q4A3_CORP1 DsbG protein 3101,13 2,06 0. 814366 D9Q6N9_CORP1 D methionine binding lipoprotein metQ 2665,58 1,79 0. 764416 D9Q732_CORP1 Carbonic anhydrase b 689,15 1,66 0. 130559 D9Q6W6_CORP1 Lipoprotein LpqB 1484,31 1,63 0. 670057 D9Q556_CORP1 LSR2 like protein 2714,21 1,49 0. 096802 D9Q5Q0_CORP1 UPF0145 protein 2467,24 1,37 0. 025009 D9Q7W0_CORP1 Hypothetical protein 2467,24 1,26 0. 039678 D9Q701_CORP1 UPF0182 protein 1682,98 1,26 0.
E-mail address: mik. laredo@gmail. com. ablation catheter, using the electroanatomic CARTO 3 mapping system (Biosense Webster, Diamond Bar, CA). Voltage mapping revealed a large endocardial ischemic scar area in the anteroapical and laterobasal walls of the recipient LV (Figure  1B-C ). Hemodynamic tolerance and stability allowed for complete activation mapping of the clinical VT. A critical isthmus containing fragmented, slow-conducting, and prolonged mid-diastolic potentials was identified within the scar (basal to mid segment of the lateral wall, Figure  2A ). Propagation mapping revealed a dual-loop figure-8-type macroreentry with a cycle length of 440 ms (Video 1, available in Online Data Supplement). The clinical VT was terminated after 3 RF applications at 35 W within the protected isthmus (Video 2, available in Online Data Supplement).
OSBPL10 and RXRA candidate genes were identified, with most significant SNPs placed in inferred weak enhancers, promoters and lncRNAs. OSB-PL10 had significantly lower expression in Africans than Europeans, while for RXRA several SNPs may differentially regulate its transcription between Africans and Europeans. Their expression was confirmed to change through dengue disease progression in Cuban patients and to vary with disease severity in a Thai transcriptome dataset. These genes interact in the LXR/ RXR activation pathway that integrates lipid metabolism and immune functions, being a key player in dengue virus entrance into cells, its replication therein and in cytokine production. Knockdown of OSBPL10 expression in THP-1 cells by two shRNAs followed by DENV2 infection tests led to a significant reduction in DENV replication, being a direct functional proof that the lower OSBPL10 expression profile in Africans protects this ancestry against dengue disease.
Besides the haplotype region, the segment immediately 5' to it (within the gene) has some SNPs with significant pvalues in the association test that are also regulatory regions in several cell types  (Table O and Fig R in S1 Text). Although there is no current good database to check eQTLs in African populations, we used GTEx despite its highly European-biased dataset (84. 3%). The six identified OSBPL10 SNPs are not identified in GTEx as eQTLs, but surveying the eQTLs located on that chromosomal region, there is one with frequency differences between African and European populations (rs7642435, at position 32036787; 1000 Genomes frequency in Africa-A = 0. 092, G = 0. 908; 1000 Genomes frequency in Europe-A = 0. 723, G = 0. 277), which presents alternative homozygous genotypes associated with our African/European haplotypes: "African" haplotype with rs7642435_GG and "European" haplotype with rs7642435_AA.
Several other SNPs located on genes (mostly one or two SNPs per gene) reached association p-values of 10 -5. By checking which SNPs are more frequent in Africa (information from the 1000 Genomes database) and which genes would have differential gene expression between dengue patients and control/convalescent subjects (in the whole blood transcriptome obtained in a Thai dengue dataset  [22]  and using a linear discriminant analysis effect size method, LEfSe  [23] , for high-dimensional class comparisons), besides OSBPL10, a few kinases or kinaserelated genes are amongst the most significant genes (.
OSBPL10 and RXRA expression in dengue patients and focused enrichment analysis The genetic evidence collected in this work, summed up in Table  2 , for the involvement of OSBPL10 and RXRA genes in the protection against DHF, led us to check their expression in Cuban patients throughout the infection process (Fig  4 ). The mRNA expression of RXRA was significantly higher during convalescence (day 30) compared to day 3 (p = 0. 027), and also higher than at day 7 after fever onset (not significant). There were no significant differences between days 3 and 7 after fever onset. These results are comparable with the ones for the Thai dataset, where RXRA expression is significantly decreased in DF and DHF cohorts when The mRNA expression of OSBPL10 was significantly increased by day 7 and in convalescence, when compared with day 3 (p<0.