dataesr/scientific-paragraphs-categorization huggingface dataset:
Principal Component Analysis Principal component analysis (PCA) enables us to condense information from interdependent variables to a smaller set of factors  (Jolliffe, 2002). Before running PCA, the dataset is checked for appropriateness. I used the Kaiser-Maier-Olkin measure (KMO) of sampling adequacy to test whether the variables were largely independent or correlated very closely. The numbers were all above 0. 5, which justified the use of principal component analysis. The purpose of this exploratory method was to synthetize the information contained in a dataset by reducing the number of dimensions of the dataset, in order to identify and uncover latent patterns. PCA uses orthogonal transformations to convert a set of possibly correlated variables into a set of linearly uncorrelated variables (called principal components).
Hierarchical Cluster Analysis PCA enabled us to extract essential information from the dataset and express latent structures within a few variables (principal components). Combining a hierarchical cluster analysis (HCA) with our PCA allowed us to group our counties in relevant clusters based on their (socio-economic, demographic, and cultural) characteristics. as distance measure and Ward's computation method as agglomerative clustering. The dendogram 12  resulting from this method illustrates the sequence in which the counties were partitioned into clusters (Figure  7 ). A choice of six clusters was retained. This number of clusters appeared the most appropriate and presented the most meaningful association of counties. Class 6, comprising one single county, is very different from the rest of the sample and appears as a clear outlier.
Blanket first wall Mockup High heat flux test Helium cooling loop Materials technology Engineering A B S T R A C T A major part in the EUROfusion materials research program is dedicated to characterize and quantify nuclear fusion specific neutron damage in structural materials. While the majority of irradiation data gives a relatively clear view on the displacement damage, the effect of transmutationi. e. especially hydrogen and helium production in steelsis not yet explored very well. However, few available results indicate that EUROFER-type steels will reach their operating limit as soon as the formation of helium bubbles reaches a critical amount or size. At that point, the material would fail due to embrittlement at the considered load. This paper presents a strategy for the mitigation of the before-mentioned problem using the following facts: • the neutron dose and related transmutation rate decreases quickly inside the first wall, that is, only a plasma-near area is extremely loaded • nanostructured oxide dispersion strengthened (ODS) steels may have an enormous trapping effect on helium and hydrogen, which would suppress the formation of large helium bubbles • compared to conventional steels, ODS steels show improved irradiation tensile ductility and creep strength In summary, producing the plasma facing, highly neutron and heat loaded part of blankets by an ODS steel, while using EUROFER97 for everything else, would allow a higher heat flux as well as a longer operating period.
A major part in the EUROfusion materials research program is dedicated to characterize and quantify nuclear fusion specific neutron damage in structural materials. While most irradiation data give a relatively clear view on the displacement damage, which is mainly responsible for the observed irradiation hardening, the effect of gas transmutationi. e. , especially helium production in ferritic/martensitic 9Cr-steelshas not been explored yet sufficiently. Nevertheless, available results indicate that EUROFER-type steels (the selected base and reference material within the European Fusion Project) will reach their operating limit when the formation of helium bubbles reaches a critical amount or size, which then leads to brittle fracturing  [9] [10] [11] [12] [13] [14]. Even though ferritic/martensitic steels show only a small tendency for swelling, this beneficial behavior might change significantly in the presence of helium, as observed in many studies on austenitic steels  [15].
The readings of the camera were calibrated at the beginning of each experimental session by adjusting the camera parameters while maintaining the mock-up at constant temperature (300 • C). This is done by heating-up the mock-up only by using the coolant flow and controlling the helium temperature until a steady state is achieved. The camera measurement accuracy is ±1 %. Past experiments have shown that, for EUROFER97 or similar materials, the changes in surface emissivity with temperature have a marginal impact on the measurements within the expected temperature range (300 • C-600 • C). For the flow measurements orifice flow meters have been chosen. The sensor transducers, Siemens Sitrans P DSIII / P410, were set and calibrated in the factory to provide directly the volumetric flow rate. The mass flow rate was calculated during the data acquisition process by the National Instruments data acquisition and control system cRIO-9025.
The width of the Cr diffusion zone (from the ODS ferrite into the EUROFER martensite) is comparable in both, the hot and the cold area. The density of Cr-rich precipitates in the ODS ferrite is increasing towards the interface. The Ti-K map shows Ti-rich precipitates in the ODS ferrite, likely at grain boundaries. The overall precipitation structure in the ODS ferrite is similar in both areas. Furthermore, we could successfully determine the involved phases by performing a principal component analysis (PCA) on both SEM-EDX datasets. The results are presented in Fig. 23. In both areas, three phases (factors) were found: the Fe/Cr matrix, (Cr/W) carbides, and Ti carbonitrides. A noteworthy finding is that coarse Cr carbides precipitates are located in the ODS steel part of the interface. Their density increases towards the ODS/EUROFER interface.
Acknowledgments We want to thank  Daniel Bolich  and  Rainer Ziegler , both from  Karlsruhe Institute of Technology (KIT, IAM ), for their support regarding organization and dealing with infrastructural tasks like coordination of machining, photographing, and sample preparation. We are also grateful to the  KIT CN  workshop team with a special thanks to Tanja for the excellent EDM performance. Many thanks go to the group of chemical analysis headed by  Thomas Bergfeld ,  KIT , IAM. Generally, we wish to express our gratitude to all colleagues who were involved the one or other way in this project. This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training program 2014-2018 and  2019-2020  under grant agreement No  633053.
ACKNOWLEDGEMENTS We acknowledge the support from  STACE, MITACS and Quebec Ministère de l' Economie, de la Science et de l'Innovation. LN2  is a joint  International Research Laboratory (IRL 3463 ) funded and co-operated in Canada by  Université de Sherbrooke (UdeS)  and in France by  CNRS  as well as  Université de Lyon (UdL , especially including ECL and  INSA Lyon)  and  Université Grenoble Alpes (UGA). It is also supported by the  Fonds de Recherche du Québec Nature et Technologie (FRQNT).
We review epidemiological models for the propagation of the COVID-19 pandemic during the early months of the outbreak: from February to May 2020. The aim is to propose a methodological review that highlights the following characteristics: (i) the epidemic propagation models, (ii) the modeling of intervention strategies, (iii) the models and estimation procedures of the epidemic parameters and (iv) the characteristics of the data used. We finally selected 80 articles from open access databases based on criteria such as the theoretical background, the reproducibility, the incorporation of interventions strategies, etc. It mainly resulted to phenomenological, compartmental and individual-level models. A digital companion including an online sheet, a Kibana interface and a markdown document is proposed.
In Section 4, a synthetic summary of the epidemic models is proposed, as well as the methods used to estimate the parameters, the various approaches to take into account possible intervention strategies are discussed with some insights on data-related aspects. Finally, Section 4. 7 gathers a set of tabular views with complete mapping of the reviewed articles, followed by a conclusion in Section 5. A digital companion of the present review including an online sheet, a Kibana interface and a markdown document is accessible on the github page: https://github. com/MyrtoLimnios/covid19-biblio.
The following equations describe the evolution of the system:              dS dt (t) = -βS(t)I(t) dI dt (t) = βS(t)I(t) -γI(t) dR dt (t) = γI(t) (2) Individuals' heterogeneity and inter-individuals' heterogeneous interactions may be modeled through the partitioning into subpopulations. Usually, numerical schemes are used to fit and/or simulate the model. Individual-level models explicitly define a state for each individual in the population. Therefore such models can incorporate more refined heterogeneity and stochasticity than population-level models, possibly at the expense of computational complexity, collecting appropriate datasets, and the increased number of parameters. As a result, parameter estimation may be difficult  [14]  and simulation running times may be slow compared to other models  [15].
Search strategy The initial step relied on a search over article bases using specific and predefined keywords. We decided to include articles regardless of their submission type and and/or status to provide an historical perspective of the proposed models. We intentionally refer to the first version available of the articles even though updated releases could exist and/or have been published. The search strategy encompasses two main source types. First, to establish the main corpus of the review, the process was based on an extended search based on a set of keywords applied on the three main online open access archives: arXiv, biorXiv, medrXiv. Precisely, motivated by mathematical-based models and as both biorXiv and medrXiv do not provide such filters, our main focus led to the database arXiv.
Results The first subsection 4. 1 reports the number of articles that have been found during the search procedure. We then sequentially present a comprehensive analysis of the articles reviewed as follows. Subsection 4. 2 presents the propagation models proposed in the selected papers for the disease, in particular categorized through either phenomenological, compartmental or individual-based models. In Subsection 4. 3, the intervention strategies are summarized when introduced in the aforementioned modelings. Then the estimation methods for the set of epidemic parameters, defined in Subsection 2. 2, are discussed in Subsection 4. 4. Finally, Subsection 4. 5 gathers the characteristics of the real datasets used.
Main data-driven estimation methods Most of the articles indexed in this review are based on simulations learned from clinical datasets, and when clearly mentioned, three main categories of methods are outlined through: (exact) deterministic methods (13 articles), estimators obtained either by descriptive statistical (5 articles) or by inferential methods (42 articles) combined with sampling techniques. Briefly, the following paragraphs give details on each of these categories. Note that there are at least as many methodologies as papers, considering that often multiple techniques are employed. First, the deterministic methods enclose the derivation of close-formed systems of equations, e. g. the next-generation method  [76, 77]  or the Euler-Lotka equation  [26, 82]  for the computation of R 0.
Characteristics of the data used In this section, we identify the types of data used for each article. We only consider real datasets and do not report simulated data. The variety of data types in the categories used reflects the diversity of the approaches. Clinical data. Most of the articles use clinical data such as the number of reported infected or death cases and some models are validated on simulated data,. In many cases, they are used to evaluate the epidemic parameters implied in the model or to tune the key dates of the spreading dynamics (e. g. arrival, peak, end). Typical clinical datasets are the daily recorded numbers of infections, recoveries, deaths, admissions in hospital, transfers to intensive care units. Those records can be considered at different scales: region, country, world; and at different levels of details: age, gender.
These data often come from either the World Health Organization, or the Johns Hopkins University or the Centers for Disease Control. More disease-related specific datasets, often gathered in hospitals, are sometimes used such as temporal recordings of viral shedding  [92] , time from symptom onset and reporting, and from symptoms onsets to death. Finally, to forecast health service needs, data relating to hospital resources are used  [28] , e. g. ICU beds capacity  [32, 74]. Mobility data. In many articles, various datasets related to geographical mobility are exploited to model individual/population flows. It is of intereset as to quantify possible impact of behavioural change on the spread of the disease. A wide spectrum of sources was employed, that includes information and timing of intervention strategies  [49] , time spent at home versus at work, changes of influence of public places  [31] , day-night locations  [41]  and estimated reduction in mobility from GPS data  [28].
This data often comes from SafeGraph or Baidu. Additionally, some articles deal with the effect of airline suspensions or the role played by exported cases. They involve data containing the travel history of infected people  [23]  and more generally a large volume of information related to air traffic  [78]  (e. g. from International Air Transport Association). Moreover, in  [77]  meteorological data are processed to assess its impact on migration. Lastly, individual-based models required high-resolution population density data, distribution of workplace sizes  [70]  or the locations of major transportation hubs  [78]. Economic data. Economic data were also considered in some studies in order to assess the cost of intervention strategies. Among them, there are daily costs of various interventions (tracing, testing), economic costs per (non-)fatal cases  [38]  or country vulnerability indexes  [93, 94].
Methods/design Study design STEP has been designed as a national, multicentre, open-label, prospective, non-randomized, phase-II trial to evaluate the efficacy and toxicity of preoperative SRT for patients with brain metastases. The experimental plan will be run using Fleming's single-stage design without interim evaluation. This study has been registered on Clinicaltrials. gov (NCT04503772). Seventy patients are expected to be enrolled. The study was started in February 2021 with an 18-month enrolment period and an estimated completion date by July 2023.
Intervention: preoperative stereotactic radiosurgery Patient positioning and data acquisition All patients will be irradiated in supine position. Immobilization devices such as stereotactic customized masks will be used to ensure the accuracy and reproducibility of patient positioning during SRT. For all patients, a dosimetric MRI will be required. The dosimetric MRI sequences of interest will be matched with the planning Computed Tomography (Planning-CT). The maximum time lapse between dosimetric MRI and the first fraction of SRT is 7 days.
Data management and monitoring The data collected for the study will be entered on an eCRF (Ennov Clinical) by each centre. The people with access to the data will be the investigators, the clinical research associates, the project leaders and the biostatisticians. They are authorized professionals and are subject to professional secrecy. The investigator will ensure the accuracy, completeness, and consistency of the data recorded (pseudonymized patient data) and of the provision of answers to data queries. Monitoring reviews will be regularly carried out by a clinical research associate mandated by the sponsor. The objectives will be to ensure the correct conduct of the study in each centre, the recording of data generated in writing, its documentation, recording and reporting, in accordance with the legislative and regulatory provisions in force.
Independent data monitoring committee (IDMC) The IDMC will composed of three experts: a radiotherapist, a neurosurgeon and a methodologist. The objective of the IDMC will be to review all safety data from the study. Grade-4 toxicity is expected to remain under 5%. The IDMC will meet on the basis of 2 grade ≥ 4 toxicity notifications (NCI CTCAE v5. 0).
However, a detailed mechanism of the efficacy has yet to be investigated. Considering the same mechanism, a few clinical trials are ongoing (NCT04353596, NCT04330300, NCT04367883, NCT04345406). Apart from the therapeutics/drugs mentioned in the table, other diversified drugs including antimalarial drugs, antibiotics, antioxidants (α-Lipoic acid)  [71] , angiotensin-II type 1 receptor antagonists, vasodilators, and anti-coagulants are being explored in clinical trials (reviewed elsewhere  [72] ).
Preclinical studies have shown its potency by eliciting anti-spike IgG antibodies with hACE2 receptor blocking, and virus neutralization capacity. Besides, it induced both T and B cell responses  [99]. By considering the above merits, the vaccine candidate has been taken for clinical evaluation (Phase 1-2; NCT04368988). The safety and immunogenicity studies of this vaccine was conducted on 131 healthy adults  [101]. Results revealed that the vaccine is safe and induced optimal immune responses. Preferably, the said adjuvant should enhance a Th1 polarized response. The vaccine benefited from the adjuvant in terms of dose sparing and enhanced immune response  [101]. Huan et al. studied the CoVaccine HT TM adjuvant effect against the SARS-CoV-2 spike S1 protein in mice  [102]. The CoVaccine HT TM is an oil-in-water emulsion type, which is composed of negatively-charged sucrose fatty acid sulphate ester and squalene (source: plantderived)  [103].
Acknowledgements JB acknowledges the support of  Agence Nationale de la Recherche, France  under the call "Flash  COVID-19 " ( ANR-20-COVI-0093-COVIMUNE ) and the  European Union Horizon   H2020  programme under Grant Agreement No. H2020-SC1-2019-874653-INDIGO  and the  Department of Biotechnology (DBT), Government of India. RB is supported through the  Irish Research Council  under the  Government of Ireland Postdoctoral fellowship  grant  -GOIPD/2017/1283. NK, RB and YR also acknowledge the research grant from  Science Foundation Ireland (SFI)  cofunded under the  European Regional Development Fund  under grant Number  13/RC/2073. The figures were created with the support of  BioRender. comunder a paid subscription.
Search Strategy First, we reviewed the drugs used for the treatment of breast, gynecological, gastrointestinal, brain, and lung cancers as well as melanomas and sarcomas from the latest European Society for Medical Oncology (ESMO) guidelines  [17]  and the third consensus of the International Network on Cancer Infertility and Pregnancy (INCIP)  [5]. Second, we carried out a systematic review of the literature by searching the PubMed and Web of Knowledge databases and the bibliography sections of relevant publications. The search terms were "drug name AND pregnancy," "drug name AND placenta," "drug name AND human perfused cotyledon," "drug name AND transplacental transfer," "drug name AND placental passage," "drug name AND amniotic fluid," and "drug name AND cord blood".
In humans, there are limited data on the capacity of cyclophosphamide to cross the placenta. To date, only one human study has documented the transplacental transfer of cyclophosphamide in vivo  [71]. A 33-year-old pregnant woman diagnosed with Hodgkin's lymphoma was treated with cyclophosphamide from 29 WG. The level of cyclophosphamide in amniotic fluid collected via amniocentesis at 34 weeks, 1 h after the last injection, was equivalent to one quarter of the maternal plasma level.
A report of nearly 14,000 RA patients on etanercept recorded ILD as one of the most frequent developments, and importantly it was later demonstrated that concomitant methotrexate therapy could reduce this risk. To date there are 11 studies reporting pulmonary outcomes in patients with RA-ILD treated with rituximab, which include a total of 278 patients whose results can be adequately evaluated. In total, improvement was reported in 17%, stability in 76% and deterioration in 7% over a period of at least 12 months. The single largest study showed that rituximab halved the risk of functional impairment  [41]. Data pooled from the three next largest studies demonstrated a significant reduction in mortality in RA-ILD patients over five years among those who received rituximab as their first biologic as compared to those initially treated with anti-TNF agents  [42, 43, 44].
An ongoing phase Ib study combines the anti-PD-L1 antibody atezolizumab with 223 Ra (NCT02814669) in metastatic castration-resistant prostate cancer. Another attractive field actually supporting a more integrated view of radiobiology is the use of TAT to overcome resistance to medications of fungal or bacterial infections  (81) (82) (83) (84). Although bacteria do not present a nucleus as eukaryotic cancer cells, 213 Bi-MAb D11 directed against pneumococcal capsular polysaccharide 8 (PPS8) was able to efficiently kill Streptococcus pneumoniae in vitro and to reduce bacterial load in C57BL/6 mice (81). Moreover, TAT was also efficient against fungal pathogen such as Cryptococcus neoformans by using 213 Bi-18B7 mAb against capsular glucuronoxylomannan  (81). TAT was associated with changes in concentration of the cytokines interleukin (IL)-2, IL-4, IL-10, tumor necrosis factor-α, and interferon-γ, suggesting that the therapeutic effects of TAT may result from changes in the inflammatory response  (82).
demonstrated that the absorbed dose delivered to the tumor is critical. Indeed, at doses higher than 12 Gy, cytosolic dsDNA is cleared by three prime repair exonuclease 1 (TREX1), precluding the activation of the cGAS pathway to induce type I interferon, and abolishing the radiotherapy-induced anti-tumor immune response  (95, 96). Based on these preclinical results, a phase II clinical trial was started in 2014 in patients with non-small-cell lung carcinoma who progressed after chemotherapy and with at least two measurable disease sites to determine whether radiation (6 Gy × 5 fractions) and immunotherapy (ipilimumab within 24 h of radiotherapy initiation) can stimulate the immune system and stop the growth of tumors that are outside the field of radiation (NCT02221739).
FUNDING This work was supported by  SIRIC Montpellier Cancer Grant INCa_Inserm_DGOS_12553 , by  French National Research Agency  as part of the  Investissements d'Avenir program  ( ANR-10-LABX-53-01 ), by  AVIESAN PCSI  [grant number:  ASC20025FSA ], and by  Fondation ARC pour la Recherche.
Methods In our 18-bed intensive care unit, we prospectively collected data from adult patients admitted for SARS-CoV-2 infections with persistent AF. When heart rate was over 120 bpm, Landiolol was started at a minimum dose of 0. 2 µg/kg/min and progressively increased by steps of 0. 2-0. 4 µg/kg/min every hour to achieve 20% reduction in heart rate, without bolus. Hemodynamic parameters were recorded every 2 h during the first 24 h of drug infusion.