dataesr/scientific-paragraphs-categorization huggingface dataset:
Search Strategy and Information Sources A computerized search was conducted for the last time on 29 May 2021 without time restriction on several databases including PubMed, Scopus, Cochrane Central Register of Controlled Trials (CENTRAL), and Embase in order to identify eligible published studies. A search strategy combining keywords, Medical Subject Headings (MeSH) terms and Boolean operators was done and then adapted for each database (Table  1 ). Search on the Scopus database was limited to articles regarding dentistry. Additionally, a manual search was performed in the bibliography of each included paper in order to identify articles that were not found by the electronic search. Embase, Cochrane ("removable appliance" AND "orthodontic") AND ("biofilm removal" OR "biofilm adhesion" OR "decontamination" OR "disinfection" OR "dental plaque" OR "antimicrobial" OR "antibacterial" OR "clean*").
Study Selection To establish their eligibility, evaluation of the selected articles was staged in a two-step progression after the removal of duplicate records between databases using a reference management software (Zotero version 5. 0. 96. 2). First, the selection procedure was performed by reading the title and then the abstract, independently by two reviewers. Afterwards, a verdict for final eligibility was performed based on full-text assessment by the same reviewers. In case of disagreements, a third reviewer was consulted.
Data Collection Procedure Data were extracted independently in duplicate by two reviewers from the included studies that satisfied the inclusion criteria, according to the PICO approach. The following information was extracted from each included paper: first author's name, year of publication, country, study design, inclusion/exclusion criteria for subjects, description of intervention protocol, comparison, and results. As the included studies showed heterogenic methods, methodology analysis, and outcomes, performing a meta-analysis was not possible. Therefore, the analysis of the articles was qualitative and descriptive.
Study Selection The search strategy initially revealed 2491 records across the four databases: 140 duplicates were eliminated and 2304 records out of 2351 remaining were discarded based on their title and language. The 47 remaining articles were assessed on their abstract, in accordance with the eligibility criteria. Further evaluation was conducted on 25 full-text articles, which led to eight articles eligible for this systematic review. The flow diagram retracing the search strategy is detailed in Figure  1.
Acknowledgments: The members of the MEDIQAI study group are:  Alexandre Baudet  ( Université de Lorraine, CHRU, Nancy, France ),  Estelle Baurès  ( Université de Rennes, EHESP, Rennes, France ),  Olivier Blanchard  ( Université de Rennes, EHESP, Rennes, France ),  Arnaud Florentin  ( Université de Lorraine, CHRU, Nancy, France ),  Jean-Pierre Gangneux  ( Université de Rennes, CHRU, Rennes, France ),  Hélène Guegan  ( Université de Rennes, CHRU, Rennes, France ),  Monique Guillaso  ( Université de Lorraine, Nancy, France ),  Pierre Le Cann  ( Université de Rennes, EHESP, Rennes, France ). The authors thank the healthcare professionals who participated in the survey.
The incorporation of Mg and K offers the advantage of reducing the glass ability to be crystallised during heat treatment: crystalline structure only started to appear after heat treatment at 680 °C, while crystallisation was much more obvious in 45S5 fibres even at 600 °C  [111]  and probably occurred at lower temperatures (data not provided). Unfortunately, the cellular study reported for these 13-93 glass fibres lacks controls  [115]  and no cellular assay was performed on composites created by electrospinning a PCL solution containing dispersed fibres of 13-93 glass  [116]. Due to their low ability to crystallise and to their reactivity higher than 13-93, borosilicate glasses were also evaluated as electrospun fibres. The chosen system had a composition of 47SiO2-23B 2 O 3 -25CaO-5P 2 O 5 (mol%)  [117]  and tributyl borate was used as a boron precursor.
Acknowledgments We apologize for any omission in citation of primary reports owing to space limitations. We thank the members of the  Cascales laboratory  for insightful discussions, and  Dukas Jur  _ enas and  Thierry Doan  for critical reading of the manuscript. Work on the T9SS in the Cascales laboratory is funded by the  Centre National de la Recherche Scientifique , the  Aix-Marseille Universite , and by grants from the  Agence Nationale de la Recherche  ( ANR-15-CE11-0019 ), and from the  Excellence Initiative of Aix-Marseille Universite , a  French "Investissements d'Avenir" programme (A*MIDEX   AAP-ID-17-33 ). The PhD thesis of I. L. S. has been funded by the  ANR  grant.
The relation between the gut microbiota and human health is increasingly recognized. Recently, some evidence suggested that dysbiosis of the oral microbiota may be involved in the development of digestive cancers. A systematic review was conducted according to the PRISMA guidelines to investigate the association between the oral microbiota and digestive cancers. Several databases including Medline, Scopus, and Embase were searched by three independent reviewers, without date restriction. Over a total of 1654 records initially identified, 28 studies (2 prospective cohort studies and 26 case-controls) were selected. They investigated oral microbiota composition in patients with esophageal squamous cell carcinoma (n = 5), gastric cancer (n = 5), colorectal cancer (n = 9), liver carcinoma (n = 2), and pancreatic cancer (n = 7).
Introduction Digestive cancers include cancers located in the esophagus, stomach, liver, pancreas, colon, and rectum. Their incidence and related mortality are increasing worldwide, but with some characteristic geographical differences  [1]. According to the GLOBOCAN, i. e. , Cancer Incidence in Five Continents, and the World Health Organization (WHO) mortality databases in 2018, the majority of new cases of digestive cancers (63%) and related deaths (65%) occurred in Asia, followed by Europe and North America. Moreover, esophageal, gastric, and liver cancers appear to be more prevalent in Asia, whereas colorectal and pancreatic cancers are more common in Europe and North America  [2]. Most of these cancers are considered sporadic and are influenced by several potentially modifiable environmental factors, such as tobacco smoking, diet, alcohol consumption, physical inactivity, obesity, and immunosuppressive drugs  [1].
Protocol Development and Literature Search The present systematic review was performed according to the Cochrane collaborationspecific protocol  [32]  and was reported following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) checklist (Table  S1 )  [33]. Studies that investigated the association between oral microbiota and digestive cancers were searched in the following databases without date restrictions: Medline (through PubMed), Scopus, Embase, Cochrane Library and Google Scholar. A specific research equation was used for each database, using the following keywords and MeSH terms: oral microbiome, oral microbiota, mouth microbiome, gastrointestinal neoplasms, gastrointestinal cancers, gastrointestinal carcinoma, digestive cancer, digestive neoplasms. According to the PICOS schema, the following criteria were used to construct the literature search and to select the pertinent articles: Population: adult patients with a diagnosis of digestive cancer (all types of cancers located in the digestive apparatus).
Xu, J. et al. [52]  focused on the landmark flora of the four common tongue coatings in GC patients. The samples were collected from the middle section of tongue dorsum using a toothbrush and put into the test tube with saline. By describing the oral microbiota composition, the authors concluded that these data could be useful for future standardization of GC diagnosis based on tongue microbiota. Tongue coating is a common sampling method in Chinese medicine. However, its biological and molecular bases are not completely validated, and thus it is not a widespread sampling method in the Western world  [80]. Han, S. et al. [39]  showed a relationship between the risk of PC and the tongue coating microbiota collected by scraping the front and middle section of the tongue with a sterile spoon and put into a test tube with saline (repeated three times and centrifuged (2000 r/min) for 5 min).
Each plaque sample arrived in the laboratory accompanied by a patient card containing information about the patient's age, sex, date of recruitment, tooth number and sampling site where the sample was taken, along with the depth of the periodontal pocket (PPD) and any presence of bleeding on probing or pus at the time of sampling. The primers and probe oligonucleotides were designed based on 16S rRNA gene sequences of the Human Oral Microbiome Database (HOMD 16S rRNA RefSeq Version 10. 1), totaling 845 entries. All the sequences were aligned in order to find either a consensus sequence or less conserved spots. Three real-time polymerase chain reaction (RT-PCR) runs were performed for each sample. The first reaction quantified the total amount of bacteria using two degenerate primers and a single probe matching a highly conserved sequence of the 16S ribosomal RNA gene.
Plasmids containing synthetic DNA target sequences (Eurofin MWG Operon, Ebersberg, Germany) were used as a standard for the quantitative analysis. Standard curves for each target were constructed in a triplex reaction by using a mix of the same number of plasmids in serial dilutions ranging from 101 to 107 copies. There was a linear relationship between the threshold cycle values plotted against the log of the copy number over the entire range of dilutions (data not shown). The copy numbers for individual plasmid preparations were estimated using the Thermo NanoDrop spectrophotometer. The absolute quantification of the total bacterial genome copies in the samples allowed for the calculation of a relative amount of red complex species. To prevent sample and polymerase chain reaction contamination, plasmid purification and handling were performed in a separate laboratory with dedicated pipettes  [28].
Operational Protocol The selected patients received information and instructions, both oral and written, on the modality and purpose of the study. Patients were given the opportunity to ask questions for further clarification. The duration of the study was a total of 9 months. In the first session, all the patients recruited to the study had the following data collected: anamnestic data, radiographic and orthopantomography status, intra-and extraoral photographic collection, charting and intra-and extraoral examination. The visit also included, through the use of periodontal probes (PC-PUNC and NABERS), the detection of the following information and the following periodontal biometric parameters: plaque index (IP), depth of the periodontal pocket on probing (PPD), clinical attack level (CAL), gingival recession (REC), bleeding on probing (BOP), mobility of dental elements (MOB), involvement of furcation and the presence of exudate.
The hypothesis of an infectious connection from the oro-pharyngeal sphere to the brain underlines the interest in analyzing the link between periodontal disease and Alzheimer's disease. The aim of this systematic review was to examine the link between Alzheimer's disease and periodontal disease in patients aged 65 and over. Databases (PubMed (MEDLINE), the Cochrane Library, and Embase) were analyzed for relevant references up to 21 June 2021. The authors independently selected the studies and extracted the data. The quality of included studies was checked using the National Institutes of Health's quality assessment tools. Five studies were included. The selected studies described in their results an increase in F. nucleatum in Alzheimer's disease patients (adjusted p = 0. 02), and its incidence was linked to C.
Information Sources and Search Strategy The bibliographical research was performed through the following electronic databases: PubMed (MEDLINE)/the Cochrane database (Cochrane Library)/Embase. The keywords used were "Alzheimer", "Alzheimer disease", "periodontal disease", "periodontitis", "calculi", "calculus", and "dental plaque". Keywords were mixed using Boolean operators, and MeSH terms (for MEDLINE and Cochrane) or Emtree (for Embase) were used depending on the database. For example, the search strategy used for PubMed (MEDLINE) database was ("Alzheimer's disease" (MeSH) or "Alzheimer") and ("Periodontal disease" (MeSH) or "Periodontitis" (MeSH) or "dental plaque" (MeSH) or "calculi" (MeSH) or "calculus").
Some studies have used a combination of several tests  [27, 28, 31]. One study, using database results  [30] , selected patients based on their membership of the category of people with AD according to the codes of the International Classification of Diseases (ICD), version nine, for the diagnosis of AD, and the ICD, version 10, code G30, for the underlying cause of death  [42, 43]. Three studies used DSM-IV  [27] [28] [29]  in combination  [27, 28] , or not  [29] , with other diagnostic tests. Only one study  [27]  refers to the use of MRI in the diagnosis of AD. One study  [29]  considered the stage of major NCD, but did not associate it with a specific type of major NCD, and moreover did not really use it to assess the presence of PD, but to assess oral hygiene. We wished to study non-genetic forms, and because genetic aetiologias are considered rare after this age  [44] , we chose to include in our review only studies targeting people over 65, or to study only this age group when the study included several, for more homogeneity.
It is also worth noting the multiplicity of criteria used to define PD in the selected publications. Moreover, three studies (Beydoun et al. [30] , Panzarella et al. [27] , and Noble et al. [28] ) used existing databases. Thus, the investigators did not collect the data themselves, and this could have led to selection biases such as misclassification of participants  [27] , underdiagnosis of AD, or underestimation of the severity of periodontal disease  [30] , due to the lack of specific data  [28]. Both aspects make a strict comparison between the different results difficult. The use of more stringent and standardized methods seems to be necessary to obtain a more reliable diagnosis. For PD, a systematic integration of a clinical and a microbiological component may be needed. Calibration of dental examiners prior to the data collection period has been described as weak by Syrjälä et al.
[29] , with furthermore a lack of assessment of the reliability of oral examinations between and within examiners  [29]. The database studies  [27, 28, 30]  did not mention this problem; nevertheless, it may exist, leading to bias in the selection of those with and without PD. The other study  [31]  which did not use a database evokes a collection of periodontal clinical parameters carried out by a research dental hygienist, which assumes a minimum of calibration, but does not state this. It should be noted that some of the variables used in the selected studies correspond to common risk factors for both periodontitis and major NCD, and may induce errors in the interpretation of the relationship between these two processes. The measurable socioeconomic covariates provide a limited range of socio-economic status over the course of life and could lead to residual confusion.
The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25. 9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28. 4) (p = 0. 028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration number: NCT04578509. The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on the healthcare system and socioeconomic activity. Early diagnosis is critical for prompt actions regarding patient management, infection control and public health control measures 1.
In addition, patients should have a valid nasopharyngeal SARS-CoV-2 RT-PCR test. Eligible persons received detailed oral and written information, adapted to their age. Data on sociodemographics, past medical history, presence of symptoms, consumption of alcohol, coffee, food, smoking and tooth brushing in the hours before testing were collected. NPS samples were sent to the Assistance Publique Hôpitaux de Paris APHP high throughput platform for RT-PCR testing as part of routine care (reference method). Participants were asked to self-collect saliva samples after after swishing saliva around in their mouths for 30 s. Saliva samples were tested directly in the screening center (see below) and then centralized for RT-PCR testing and frozen at -80 °C within 24 h. Virology methods. Nasopharyngeal RT-PCR.
For the RT-PCR technique, the Ct values reported are those for the ORF1a gene, and if not amplified, of the N gene (and of the S gene if the N gene was not amplified). Quantitative data were expressed as medians [interquartile range], and qualitative data as numbers (percentages). The diagnostic accuracy of the index tests was evaluated by calculating sensitivity and specificity. Confidence intervals were calculated by the exact binomial method. Subgroup analyses were performed according to (1) the presence of symptoms on the day of testing, (2) the Ct value of the nasopharyngeal RT-PCR, expressed as low (at least one of the 3 targets with Ct ≤ 28, i. e. high viral shedding), or high (all 3 targets with Ct > 28, i. e. low viral shedding) and (3) the consumption of alcohol, coffee, food and smoking or tooth brushing before sample collection.
Acknowledgements The authors thank the following members of the scientific committee for insightful comments on the study protocol and results:  Bruno Lina ,  Anne-Geneviève Marcelin ,  Catherine Paugam-Burtz ,  Astrid Vabret ,  Etienne Voirin-Mathieu ,  Michel Vidaud  and  Claire Poyart , as well as the staff involved in data collection:  Claire Kappel ,  Guiseppina d' Anna ,  Elisabeth Velin ,  Abdulai Jalloh ,  Caroline Du Song ,  Philippine Treluyer ,  Mathilde Bayle ,  Lucie Daveau ,  Marine Hellegouarch ,  Suzie Zhu ,  Pénélope Travailleur ,  Matthieu Kapry ,  Adeline Huet ,  Aurélien Gibaud ,  Emeline Hermel ,  Céline Goy  and  Louise Lavancier.
Cancers of unknown primary (CUP) are metastatic cancers for which the primary tumor is not found despite thorough diagnostic investigations. Multiple molecular assays have been proposed to identify the tissue of origin (TOO) and inform clinical care; however, none has been able to combine accuracy, interpretability, and easy access for routine use. We developed a classifier tool based on the training of a variational autoencoder to predict tissue of origin based on RNA-sequencing data. We used as training data 20,918 samples corresponding to 94 different categories, including 39 cancer types and 55 normal tissues. The TransCUPtomics classifier was applied to a retrospective cohort of 37 CUP patients and 11 prospective patients. TransCUPtomics exhibited an overall accuracy of 96% on reference data for TOO prediction.
Rheological Properties The rheological properties of the calcium hydroxide formulations are shown in Figure  4. The frequency sweep tests (Figure  4a ) and the amplitude sweep tests (Figure  4b ) were performed to determine the rheometric parameters. One preview test was performed for each sealer to analyze the setting pattern and to determine the rheometer settings (angular frequency of 2. 5 rad/s) using a strain amplitude of 0. 01% and the data analysis method. For both formulations, G' and G″ increased over time. On the time sweep analysis curves (Figure  4c ), the storage moduli (G') were very close to the loss moduli (G″) (G' = G″ approximately) for both formulations. For the CHX-free formulation, after 6 min, G' The frequency sweep tests (Figure  4a ) and the amplitude sweep tests (Figure  4b ) were performed to determine the rheometric parameters.
One preview test was performed for each sealer to analyze the setting pattern and to determine the rheometer settings (angular frequency of 2. 5 rad/s) using a strain amplitude of 0. 01% and the data analysis method. For both formulations, G' and G" increased over time. On the time sweep analysis curves (Figure  4c ), the storage moduli (G') were very close to the loss moduli (G") (G' = G" approximately) for both formulations. For the CHX-free formulation, after 6 min, G' became higher than G". In the presence of 1% CHX, the two moduli (G' and G") distanced themselves from each other: G" was first higher than G' then, after 9 min, G" became lower than G'. The amplitude sweeps showed that the moduli were lower with 1% CHX than without CHX. For both formulations, the flow point was 0. 06%. The G points were 3.
49, 50 inally, γH2AX is part of the DNA damage response, a signaling cascade that results in the recruitment of multiple proteins to the vicinity of DNA DSBs. 2] [53]  The γH2AX assay has been used frequently to assess IR-induced DNA damage. 5] [56] [57] [58] [59] [60]  Results from these assays will be discussed (if data are available) for CT scans, CBCT scans, and plain radiographs. Attention will be given to dentomaxillofacial imaging applications. In this literature review performed between January 2019 and March 2021, Web of Science was searched using the following key words: computed tomography, radiology, cone beam computed tomography, biological effects, health effects. These were filtered to only include publications who followed-up patients from the medical examination up to the point of testing (prospective studies).
They found no evidence that children are more radiosensitive than adults. 118  On the other ha d, there are reports showing that there is a significant correlation between the age of subjects (mean age: 25. 21 ± 12. 67) and micronucleus count, contradicting previous results from Ribeiro et al. 125, 128  Note that these studies found this age correlation in an adult patient group and that these results might not be extrapolated to children. Comet assay data suggest that a radiography scan results in a significant increase in DNA DSBs in adults. 131 Similar data were obtained from children. 50 o our knowledge, these are the only two studies that reported on this and therefore should be interpreted with caution, given the many observed contradictions from the other assays that are described in this section.
Both assays showed a significant increase in DNA DSBs shortly after a radiograph was taken. Unlike the data from CT scans where mostly yH2AX assays were performed, data from radiographs mainly rely on the MN assay (performed in 21 studies) to assess genotoxicity following exposure. Although all studies agree that radiographs cause an increase in cytotoxicity, mostly through increases in the frequency of karyorrhexis, there is a lot of disagreement on whether or not the MN frequency is also increased after radiography. While 10 studies report no increase in MN frequency, there are 6 studies that do report an increase after radiography. These data illustrate the controversy and difficulty of low dose research and also show why it is important to study the effects of low doses of IR thoroughly.