dataesr/scientific-paragraphs-categorization huggingface dataset:
We separately examined the role of CPIs in ESBL-EC and ESBL-KP spread  [9]. Using a Research Program and the Investissement d'Avenir program, Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases" (grant no. ANR-10-LABX-62-IBEID, http://www. agencenationale-recherche. fr/ProjetIA-10-LABX-0062) to DG and from the Ecole des Hautes Etudes en Sante Ṕublique (EHESP, https://www. ehesp. fr/) to AD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. mathematical model, we tested whether CPI information could be useful in designing and organizing control interventions in LTCFs.
For 3 additional episodes, no potential infector was found throughout the network, resulting in a total of 16/35 unresolved episodes. Observed and expected case-to-potential infector distances did not differ significantly based on the remaining 19 resolved episodes (P = 0. 25, Wilcoxon signed rank paired test). Indeed, more direct CPIs (i. e. , distance-1) between cases and their closest potential infectors were found in the permutated data than in the observed data (Fig 1A , 20% and 5% respectively). Conversely, more distance-2 were found in the observed data. Transmission of ESBL-KP. Only 4 of the 20 episodes were not resolved for ESBL-KP i. e. no potential infectors were found. The case-to-potential infector distances differed significantly between observed and simulated datasets for the 16 resolved episodes.
Discussion For this study, contact patterns of patients and hospital staff were combined with weekly carriage data to trace the possible routes of resistant Enterobacteriaceae transmission in an LTCF. We found that the human contact network did not correspond to the spread of ESBL-EC, but supported that of ESBL-KP. Those findings suggested that transmission along CPIs is an important driver for ESBL-KP but that it is not the main driver in LTCF spread for ESBL-EC. This result is consistent with previous studies investigating the role of patient-to-patient transmission in the Enterobacteriaceae spread. Indeed, in a prospective cohort of patients admitted to a tertiary care hospital in the US, patient-to-patient transmission was shown to be an important cause of ESBL-KP but not ESBL-EC acquisition  [23, 24].
66%/week acquisition rate for E. coli, 1% importation rate and 0. 38%/week acquisition rate for K. pneumoniae) were globally higher than those recently reported in a French intensive care unit for ESBL-producing Enterobacteriaceae as a whole (8% importation rate and 0. 29%/week acquisition rate)  [29]. This may be due to differences in patient contact patterns and lengths of stay between intensive care units and LTCFs. We also observed a relatively high prevalence of ESBL-EC and ESBL-KP colonization among patients, which is consistent with previous findings in LTCFs  [30]. The average duration of ESBL-producing Enterobacteriaceae carriage estimated from the collected data was 4 weeks (28. 6 days, 95% CI: 19. 9-37. 3), which is shorter than most published estimates. However, these published estimates are scarce and highly variable; a European study estimated time after clearance for highly resistant Enterobacteriaceae to 42.
Although our approach enabled us to highlight the important dissemination differences between the two bacterial species, between-species gene exchanges within a host's flora were not taken into account, probably contributing to the high unexplained portion of incident-colonization episodes with ESBL-EC. Future studies should be designed to specifically assess that question, which will require detailed data on multiple colonization. In a previous i-Bird CPIs study  [35] , potential "superspreader" professions were identified among the hospital staff. Here, we built a generalized linear model (GLM) to explain the risk, for hospital workers, of having had contact with patients who acquired ESBL-EC or ESBL-KP in the 4 preceding weeks, using hospital worker profession (such as nurses, physicians, hospital porters and so on) as a predictor.
This analysis was performed for the 9 isolates that were found to have been acquired by more than one patient (6 ESBL-EC and 3 ESBL-KP). Hospital worker profession was significantly associated with the predicted risk for 6 of these 9 isolates. Interestingly, hospital porters were found to be at increased risk of having had contact with incident cases for 3 out of 6 isolates (OR from 6. 8 to 10. 3). Being a reeducation staff increased the risk for 2 isolates (OR: 2. 6, 95% CI: 1. 11-6. 05 and OR: 2. 8, 95% CI: 1. 06-7. 49), as were nurses (OR: 2, 95% CI: 1. 06-3. 78 and OR: 2. 3, 95% CI: 1. 22-4. 42). An in-depth investigation of the i-Bird data also allowed us to identify potential "superspreaders" among the hospital workers, although this was not associated to ESBL-EC or KP specifically. For instance, we found a hospital porter with whom all patients who acquired isolate 1 (an ESBL-EC), as well as all patients who acquired isolate 2 (an ESBL-KP), had had earlier contact.
g. horizontal gene transfer, alteration of expression of genes). Studies associating data on ESBL species transmission to genotypic and phenotypic information would probably give more information and will be the next step. Still, we believe that our study already provides some valid insight on ESBL-EC and ESBL-KP transmission in LTCFs. In particular, a part of ESBL-KP cases occurred during an outbreak localized in a single ward, the transmission hypothesis was in this case very likely, despite the lack of genotyping information. Moreover, there is a close relationship between E. coli genotype and phenotype as some studies show a good probability to predict phenotypic resistance through genotypic analysis for this species  [36, 37]. Hence, we can assume that using genotyping information might not affect qualitatively our main results on both ESBL-KP and ESBL-EC.
Therefore, it is important to note that a large part of the ESBL-KP-acquisition episodes that were resolved, had a potential infector at a distance-1 for PVS patients (7/ 13 cases were PVS patients), due to an outbreak of ESBL-KP in neurology ward 1 during the 4-month i-Bird study. More detailed observational data would be needed to fully understand this apparent patient-to-patient transmission of ESBL-KP to PVS patients. In contrast, only 1/ 35 ESBL-EC-acquisition episodes involved a PVS patient. Finally, because the i-Bird study took place in a LTCF, our results may not be generalizable to other healthcare settings, such as acute care hospitals. As mentioned earlier, resistance acquisition rates may be higher in LTCF, due to the specific dynamics of long-term hospitalization. Our results have potentially important implications in terms of infection control.
Our analyses showed that reducing CPIs, especially between patient and staff (through perfect hand hygiene), might decrease the incidence of both ESBL-EC and ESBL-KP, but with a significantly larger reduction for the latter (Fig  2 ). Similar results were obtained under various scenarios regarding intervention compliance (isolation with 75%, 50% or 25% of patient-patient contacts removed, staff hand hygiene with 75%, 50% or 25% of patient-staff contacts removed) even if the carriage duration was extended (S3 and S6 Figs). Those findings confirmed that contact-precaution strategies are bound to be highly effective at controlling ESBL-KP, while additional measures such as environmental decontamination or antimicrobial stewardship, might be needed for ESBL-EC. This study, by jointly analyzing longitudinal ESBL-producing Enterobacteriaceae carriage data with CPI records using radio-frequency identification technology, contributes to our understanding of the dynamics of ESBL-EC and ESBL-KP spread.
Microbiological data Rectal swabs were collected weekly from patients. Briefly, swabs were placed in Stuart's transport medium (500μL; Transwab, Medical 90 Wire and Equipment). Each 100-μL aliquots was plated on selective media for ESBL isolation. The rest of the suspension was then stored at -80˚C for further use. Antimicrobial susceptibility testing was done each week for ESBL-producing Enterobacteriaceae, in accordance with national recommendations  [43].
Based on those results, we assumed that two ESBL-producing Enterobacteriaceae isolates were the most similar when they belonged to the same species and had the same resistancesequence status to the 12 selected antibiotics (allowing for R-I or S-I differences for each antibiotic). Definition of prevalence and incidence. Average weekly prevalence and incidence were determined over the 4-month study period for each ESBL species and each isolate (Section S2). Weekly prevalences were defined as the proportion of colonized patients among swabbed patients during each week of the study period. For weeks with less than 10 swabbed patients the prevalence and the incidence were considered as missing data because of the high uncertainty level in weeks with fewer swabs. We defined an incident-colonization episode for a given week as the isolation from a patient of an isolate or an ESBL species that had not been found in the same patient the preceding week.
Expected distance. For each incident-colonization episode, the expected distance under the null hypothesis was computed through Monte Carlo simulations (Section S4). We randomized all carriage data among the network nodes over the preceding 4 weeks. For each incident-colonization episode, 200 replicates of permutated carriage statuses were obtained. In each permutated dataset, the shortest CPI path was computed as above. The expected distance was then computed by averaging all the shortest lengths of CPI path to this colonization episode. Statistical test. Finally, for all incident-colonization episodes collected, expected distances and observed distances were compared using the Wilcoxon signed rank paired test.
Colonized patients returned to the susceptible state at a rate γ B , equal in average to 1/D B , where D B was the duration of bacteria B colonization. The model was parameterized for ESBL-EC or ESBL-KP independently. All parameter values were directly taken from the observed i-Bird study data, except for the per-contact transmission probabilities p B , which were computed so that the predicted steady-state colonization prevalence reproduced the observed data (Table  1 ). More model details, including model equations and details of baseline parameter computation, are provided in Section S6. We compared the impacts of two simple illustrative control measures with varying levels of compliance, leading to 4 scenarios: scenarios 1 and 2, in which a portion of patient-patient CPIs was removed to simulate patient contact isolation (scenario 1: 100%, scenario 2: 50%); and scenarios 3 and 4, in which a portion of patient-staff CPIs were removed to simulate staff hand hygiene (scenario 3: 100%; scenario 4: 50%).
Acknowledgments  i-Bird Study Group: Anne Sophie Alvarez  ( AP-HP, Paris, France ),  Audrey Baraffe  ( AP-HP, Paris, France ),  Mariano Beiro ( Universidad de Buenos Aires, Buenos Aires, Argentina ),  Inga Bertucci  ( AP-HP, Paris, France), Pierre-Yves Boe ¨lle (Univ. Pierre et Marie Curie, Paris, France ),  Camille Cyncynatus  ( AbAg, Chilly-Mazarin, France ),  Florence Dannet  ( AP-HP, Paris, France ),  Marie Laure Delaby  ( AP-HP, Paris, France ),  Pierre Denys  ( AP-HP, Paris, France ),  Matthieu Domenech de Cellès  ( Univ. Pierre et Marie Curie, Paris, France ),  Eric Fleury  ( ENS Lyon, Lyon, France ),  Antoine Fraboulet  ( Insa, Lyon, France ),  Jean-Louis Gaillard  ( AbAg, Chilly-Mazarin, France ),  Boris Labrador  ( AP-HP, Paris, France ),  Jennifer Lasley  ( Inserm, Paris, France ),  Christine Lawrence  ( AP-HP, Paris, France ),  Judith Legrand  ( Univ.
JPF, PR, FZ are supported by the  French National Research Agency Fighting Heart Failure  ( ANR-15-RHU-0004 ), by the  French PIA  project " Lorraine Université d'Excellence" GEENAGE  ( ANR-15-IDEX-04-LUE ) programmes, and the  Contrat de Plan Etat Région Lorraine  and  FEDER IT2MP. X. R. has received support from the  SEC-CNIC   CARDIOJOVEN fellowship program.
Conclusions The development of a rapid alternative method for screening heterologously produced Arabidopsis enzymes involved in IAA inactivation is described. Our method takes advantage of the fact that recombinant Arabidopsis proteins that inactivate IAA retain their biological activity when produced in bacteria. Our results show that an enzymatic assay can be conducted directly in the bacterial cultures producing recombinant proteins because the expected IAA metabolites are rapidly and abundantly produced upon supplementation of substrate and specific cofactor mixtures to engineered bacterial cultures. IAA metabolites that accumulate in culture media are identified and quantified using UHPLC-ESI-MS/MS by adding corresponding internal standards (Additional file 5: Dataset S1). Prior in vitro methods for assaying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification.
Background: This article describes a bibliometric review of the scientific production, geographical distribution, collaboration, impact, and subject area focus of pneumonia research indexed on the Web of Science over a 15-year period. Methods: We searched the Web of Science database using the Medical Subject Heading (MeSH) of "Pneumonia" from January 1, 2001 to December 31, 2015. The only document types we studied were original articles and reviews, analyzing descriptive indicators by five-year periods and the scientific production by country, adjusting for population, economic, and research-related parameters. Results: A total of 22,694 references were retrieved. The number of publications increased steadily over time, from 981 publications in 2001 to 1977 in 2015 (R 2 = 0. 956). The most productive country was the USA (38.
Identifying the population of study documents For the performance of the study, we opted to identify documents about pneumonia by means of the MeSH thesaurus in the MEDLINE database because this is a detailed instrument for controlled terminology. The thesaurus employs both a human team of specialist indexers to analyze each article and assign medical subject headings to it, plus automated processes to improve indexing; the result is a highly consistent system of classification for research topics  [14] [15] [16]. The pneumonia descriptor was introduced in 1963 as a disease of the respiratory tract and the lung, and it was defined as "infection of the lung often accompanied by inflammation"  [17]. Synonyms of this descriptor (and therefore also included in search results) are "Lung Inflammation" and "Pulmonary Inflammation".
Additional file 1: Table  S1  shows the MeSH tree structure for "Pneumonia". The next step was to identify the documents assigned with the MEDLINE descriptor of "pneumonia" indexed in the WoS. This body of research constitutes the population of documents for the present study. Conceived by Eugene Garfield but now maintained by Clarivate Analytics, WoS is the top scientific citation search and analytical information platform worldwide, serving both as a multidisciplinary research tool supporting a variety of scientific tasks and as a dataset for large, dataintensive studies  [18]. The use of the WoS databases enables the analysis of all institutional affiliations reported in the documents and the calculation of citation indicators. The WoS brings together the most visible literature at a global level.
These qualities justify its choice as the database platform used in this study despite some limitations related to covering non-English biomedical journals  [18]. Although initially no limitations were imposed on our search, to calculate the bibliometric indicators we considered only two types of documents, articles and reviews, as these are the primary references for researchers. The study period was limited to 2001-2015, as delays associated with assigning MeSH descriptors to documents mean that information on the most recent articles on pneumonia is not updated. The searches took place on the Clarivate Analytics WoS platform, which includes MEDLINE database, on March 20, 2018.
Analyzing bibliographic characteristics and standardizing data For each of the retrieved documents, data on the following bibliographic characteristics were extracted: year of publication, journal of publication and WoS subject category, document type, authorship, citations, institutional affiliation(s), and MeSH descriptors. Data were then standardized: institutional affiliations corresponding to England, Northern Ireland, Scotland and Wales were grouped together under "United Kingdom," while affiliations in Overseas France, British Overseas Territories, and island dependencies were also assigned to their ruling countries (for example, the documents signed by authors from French Polynesia, Guadeloupe, Martinique, New Caledonia, and Reunion were assigned to France), although regional designations correspond to geographical rather than political criteria.
Descriptive indicators for the evolution of scientific production We analyzed the evolution of the number of documents by year of publication and according to three  5  Data were obtained from World Development Indicators in the World Bank online databases  [20]. We calculated a mean value for each indicator based on available data from the study period. The analysis was limited to countries participating in the top 30 articles in the field of pneumonia in order to facilitate comparison between countries' scientific production, demographic indicators, and economic development. Results for the top 15 articles are shown in the main text, while those for the top 30 are provided in Additional file 1.
Collaboration indicators and network analysis We calculated the percentage of documents produced in international collaboration and the evolution by quinquennium in order to estimate the scope of cooperative practices at a global level, considering the whole population of documents analyzed (research field) by country and geographic region. To specifically analyze collaboration between countries, collaboration networks were generated for each of the three quinquenniums using Pajek software. To specifically analyze collaboration between countries, collaboration networks were generated for each of the three quinquenniums using Pajek software. The collaboration network is a graphic representation (graph), wherein the nodes represent authors' countries (as determined from their institutional affiliations) and links between the nodes represent coauthorships between countries, that is, an international collaboration in published research.
Analysis of the main topics addressed in research Based on an analysis of MeSH terms, we identified the main research focus of the studies in the area, generating density maps using the VOSviewer program with a spatial description of the main MeSH terms for each type of pneumonia  [22] : (A) "Pneumonia, Aspiration" (B) "Pneumonia, Bacterial," (C) "Pneumonia, Ventilator-Associated," (D) "Pneumonia, Viral," and (E) "Pneumonia, Pneumocystis"). The process of generating and interpreting the maps proceeded as follows: -Determination of the co-occurrence of the descriptors assigned to the documents and generation of a matrix of absolute values. The joint assignment of two descriptors in a single document implies a thematic affinity, as both aspects are addressed simultaneously in the same paper.
The different groupings, in the form of "islands" in red tones, represent the main clusters of the thematic networks, while the chromatic gradation illustrates the areas with a lower density of relations between the MeSH in yellow and green tones. The spatial distribution of the MeSH and their proximity to each other responds to the intensity of co-occurrence between them. All data used to perform the study, including the information downloaded from the database as well as that derived from the treatment of the bibliographic entries, are available in the Dataverse Project, an open access public repository  [23]  (https://dataverse. harvard. edu/, doi: https://doi. org/10. 7910/DVN/02BUNE).
Evolution of scientific production and distribution by country and geographic region The search yielded a total of 33,944 documents published between 2001 and 2015 and assigned with the descriptor "Pneumonia" in the MEDLINE database. Of these, 27,017 (79. 59%) were indexed in the WoS Core Collection Databases; 20,918 (77. 14%) of them were classified as articles and 1776 (6. 57%) as reviews. Thus, the population of study documents was a dataset of 22,694 articles and reviews, which we used to calculate the indicators presented below. Letters (N = 2213; 8. 19%), editorials (N = 1, 998; 7. 39%), news (N = 58; 0. 21%), proceedings (N = 17; 0. 06%) and other document types (N = 31, 0. 11%) were excluded from the analysis. The number of publications rose from 981 in 2001 to 1977 in 2015. The evolution of scientific production by year was fitted to a linear growth model, showing an R 2 value of 0.
g. vaccines)  [25]. Thirdly, increased funding has been directed toward research and particularly "proactive investments for emerging infectious threats"  [8, 9] , and finally, the increase in scientific production could be related to scientific development and international dissemination of scientific research in the WoS databases. This is particularly the case of China and other emerging economies like Brazil, where the rates of growth were highest relative to their respective regions  [26] [27] [28]. We observed a substantial increase in research worldwide, but particularly in some geographical regions and countries of South Asia, East Asia & the Pacific, Latin America & and the Caribbean, and sub-Saharan Africa. To a great extent, this increase is simply a reflection of the limited contribution to global research that these countries made in the first period analyzed  (2001) (2002) (2003) (2004) (2005).
In publications pertaining to the MeSH "Pneumonia, Ventilator-Associated," the main axes of the subject content according to the MeSH terms were the group of epidemiological studies and clinical and treatment protocols in intensive care. "Pneumonia Pneumocystis," is closely related to infection due to HIV and immunodepression. The main areas of research interest for "Pneumonia, Viral," were the epidemiological aspects related to the setting for the infection ("Community-acquired Infections" and "Hospitalization") along with the viruses responsible ("Influenza, Human" and "Orthomyxoviridae Infections"). Finally, for the MESH "Pneumonia, Aspiration" the main research focus is "Deglutition Disorder". The main limitation of this present study is its analysis of only the documents included in the WoS databases and MEDLINE (80% of the documents).
2GHz frequency while the arrangement in H-plane the array elements works well at 7GHz of frequency. In planar arrangement, the operating frequency of antenna elements is shifting as results of the distance among inter elements which increase in wavelength. In H-plane arrangement an antenna elements generate additional gain up to 10. 2 dB with good radiation patterns as compared to the planar plane. The CSTMWS simulation software has been used for antenna structural design and parametric verification.
In the setting of prior myocardial infarction, the oral antiplatelet ticagrelor added to aspirin reduced the risk of recurrent ischemic events, especially, in those with diabetes mellitus. Patients with stable coronary disease and diabetes are also at elevated risk and might benefit from dual antiplatelet therapy. The Effect of Ticagrelor on Health Outcomes in diabEtes Mellitus patients Intervention Study (THEMIS, NCT01991795) is a Phase 3b randomized, doubleblinded, placebo-controlled trial of ticagrelor vs placebo, on top of low dose aspirin. Patients ≥50 years with type 2 diabetes receiving anti-diabetic medications for at least 6 months with stable coronary artery disease as determined by a history of previous percutaneous coronary intervention, bypass grafting, or angiographic stenosis of ≥50% of at least one coronary artery were enrolled.