dataesr/scientific-paragraphs-categorization huggingface dataset:
Patients and methods Patients and samples. We retrieved samples from patients with HNSCC who underwent upfront surgery at the Curie Institute between 1990 and 2006. We selected patients with complete clinical, histological, and biological data and long-term follow-up. We used samples from two independent cohorts: the cohort #1 consisted of 122 patients with HNSCC from various primary sites: oral cavity (OSCC; n = 61), oropharynx (n = 22), hypopharynx (n = 17), and larynx (n = 22). The cohort #2 consisted of 90 OSCC patients. Finally, we grouped the OSCC patients from the first cohort with the second cohort for analysis (merged cohort). The flow chart of patients is displayed in Fig. 1. The study was conducted in accordance with the ethics principles of the Declaration of Helsinki and GDPR regulations.
Immune-related gene expression analysis by real-time quantitative reverse transcription PCR. The immune-related genes were selected in collaboration with immunologists from our group, consistent with our previous publications  21, 22. Immune-related gene expression levels were normalized on the basis of TBP contents (Genbank accession number NM_003194)  23. We chose TBP, which encodes the TATA box binding protein, as endogenous control because the prevalence of its transcripts is moderate, and because there are no known TBP retropseudogenes (retropseudogenes lead to co-amplification of contaminating genomic DNA and thus interfere with RT-PCR, Cohort #1  despite the use of primers in separate exons)  23. We had previously selected and used the same gene as endogenous control in different cancer types including HNSCC  21, 24.
Results, expressed as N-fold differences in target gene expression and termed "Ntarget, " were determined as Ntarget = 2 ΔCtsample , where the ΔCt value of the sample is determined by subtracting the average Ct value of the target gene from the average Ct value of the control gene. Primers for immune-related genes were designed with the assistance of Oligo 6. 0 computer program (National Biosciences, Plymouth, MN). We searched the dbEST and nr databases to confirm the total gene specificity of the nucleotide sequences chosen as primers and the absence of single nucleotide polymorphisms  25. In particular, the primer pairs were selected to be unique relative to the sequences of closely related family member genes or of the corresponding retropseudogenes  25. Agarose gel electrophoresis was used to verify the specificity of PCR amplicons.
This systematic review aims to identify probiotics and prebiotics for modulating oral bacterial species associated with mental disorders. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guideline, we search the electronic MEDLINE database published till January 2021 to identify the studies on probiotics and/or prebiotics for preventing and treating major oral dysbiosis that provokes mental disorders. The outcome of the search produces 374 records. After excluding non-relevant studies, 38 papers were included in the present review. While many studies suggest the potential effects of the oral microbiota on the biochemical signalling events between the oral microbiota and central nervous system, our review highlights the limited development concerning the use of prebiotics and/or probiotics in modulating oral dysbiosis potentially involved in the development of mental disorders.
Search Strategy To identify studies that met the inclusion criteria, an electronic search was conducted through the MEDLINE (PubMed) database up to January 2021 without restriction. While modulation of the microbiome represents an innovative therapeutic axis to treat or prevent human pathologies  [36] , the impact of probiotics on human health has long been documented  [37]. Consequently, the search was performed without time restriction to identify the studies that explore the application of probiotics and/or prebiotics in preventing and treating major oral dysbiosis potentially involved in mental disorders. The search terms were used in combination with Boolean operator "AND"/"OR" according to the following equations: (("Probiotics"[Mesh]) OR "Prebiotics"[Mesh]) AND "Mouth/microbiology"  [Mesh]  ( (("Probiotics"[Mesh]) OR "Prebiotics"[Mesh])) AND "Dental Plaque/microbiology"[Mesh] (4).
Study Selection The initial studies retrieved from the databases were first selected. We selected 38 studies from 285 studies (Figure  3 ), and we reviewed and analyzed studies that met the eligibility criteria. Each study that met the inclusion criteria was analyzed to identify prebiotic compounds or probiotic strains and their effects on the oral microbial flora or immunological markers involved in mental disorders. Three distinct effects on oral dysbiosis associated with mental disorders emerged: modulation of the oral microbiome  [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] , antimicrobial activity  [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] , and modulation of immunological or inflammatory factors  [43, 44, 46, 56, [70] [71] [72] [73] [74] [75].
Fs Laser Experimental SETUP The synthesized PLA samples were laser processed by Quantronix-Integra-C Ti: sapphire (Hamden, CT, USA) Fs laser system (τ = 150 fs) at a central wavelength of λ = 800 nm and 0. 5 kHz repetition rate Figure  1. For samples positioning perpendicular to the laser beam, a high-precision XYZ translation stage was used. All the experiments were performed in the air by scanning the laser beam over the material surface at precisely defined separation intervals (in the X and Z axis) in order to optimize the PLA surface texturing. All modifications of the PLA plates, performed by the Integra-C laser system were precisely controlled by LabView software. On the basis of previously performed large scale preliminary experiments on PLA, part of which are already published  [36] , the following laser parameters were chosen for surface structuring of the material: fluence F = 1.
WCA Evaluation The water contact angle measurement measurements were performed in air with distilled water drop with volume of 1 µL on control and laser modified surfaces of the PLA samples for the time period of 0. 5-7 s-Figure  2. The samples were positioned on XYZ horizontal translation stage. The measurements were performed according to a contact angle goniometry method-the droplet was deposited by a fixed above the sample micropipette (Dlab, Beijing, China ISO9001/13485 certified -0. 1-10 µL). The process was captured by a high-resolution camera (Huawei P40 pro camera in super macro mode with additional macro lens-Huawei Investment & Holding Co. , Ltd. , Shenzhen, China). For WCA evaluation, the images obtained were analyzed by ImageJ software equipped with contact angle measurement plug-in.
For visualizing clustering of multivariate data, the Clustvis web tool (Nucleic Acids Research, 43(W1):W566-W570, 2015) was employed-each treatment condition of the obtained FTIR spectra was assigned as a variable in PCA, which permits the discovery of changes of the samples characteristics in respect to physico-chemical properties. The obtained variances are 77% and 20. 8% for PC-1 and PC-2, respectively. The results for all sets of data for the first two principal components PC1 and PC2, jointly were calculated to be 97. 8% of the data matrix variance. The scores scatter plot PC1 vs. PC2 (Figure  11a ) showed peaks distribution and scattering along the PC1 axis. The V1, V3, V4, and V5 are positioned on the positive side of PC2. In Figure  11  the tendency for the assembling of scores in a pattern going to negative values of PC2 is monitored.
Funding: This work was supported by:  EUROPEAN UNION'S H2020 research and innovation program  under the  Marie Sklodowska-Curie Grant  Agreement AIMed No. 861138 ; BULGARIAN NATIONAL  SCIENCE FUND (NSF)  under grant number No. KP-06-H48/6  ( 2020-2023 ), "Development of hybrid functional micro/nanoporous biomaterial scaffolds by ultra-fast laser modification"; and  H2020 FET Open METAFAST  Grant Agreement No. 899673. Institutional Review Board Statement: Not applicable.
5. 374 (available at https:// www. meshm ixer. com) and Meshlab free software version 2016. 12 (available at https:// www. meshl ab. net), and then exported again as surface meshes, together with those of the mandible segments (. stl files) into the FORGE NxT 3. 0 finite element software (Transvalor, Biot, France) which has been already validated using different biomechanical models  [18] [19] [20]. An adaptive volume meshing (I-deas Universal File format) of the different parts (mini-plates, screws and bone segments) has been created due to the volumetric mesher included in the FORGE NxT 3. 0 package (GLpre). Mesh boxes were created to limit the number of elements (coarser mesh) in areas where small deformation are expected in order to reduce computing time and to refine the mesh in areas that are likely to have high strain or stress levels, such as around the screw holes in bone segments, and in the fixation devices (Fig.
FORGE NxT 3. 0 uses linear and nonlinear implicit finite element frameworks designed specifically for analysis in computational solid biomechanics. HSOO is a case of computational solid biomechanics and the mathematical model is based on the governing equations of continuum mechanics associated with the boundary and initial conditions. FORGE NxT 3. 0 provides a numerical method of analysis based on the mathematical models which requires numerical discretization, solutions algorithms, and convergence criteria as requested in computational biomechanics  25, 26. Several finite element studies have been carried out using Forge software and have been validated in the literature  18, 20, 27. www. nature. com/scientificreports/ Models were developed from patients previously cared with HSOO technique and achieving a class I level of dental occlusion with improved facial balance and proportions.
Bearing this preexisting inequity in mind, lockdown led to additional barriers: anecdotal evidence emerged of unmet urgent dental needs among people with disabilities, declining access to dental general anesthesia which was open between the 10 th and 31st of July 2020, a time when restrictions were generally eased. -Data Collection and Analysis Questions were entered into Google Forms for electronic distribution and data collection. Data was exported to Microsoft Excel for cleaning and manipulation of variables for further analysis. Analyses were carried out using SPSS v. 26. Demographic data were described using counts and percentages. Responses to questions from the section 'Changes in practice over time related to COVID-19 restrictions' that were "check all that apply"-styled were converted to dichotomous "yes/no" responses to each item on the list using dummy variables.
Additionally, the study involves a large international sample, giving a global perspective, albeit with limited representation from some world regions. However, there are limitations. Given the sampling approach applied, it is impossible to estimate a response rate and therefore to assume external validity. It is possible that those dentists that were most impacted by lockdown responded to our survey, or vice versa. This limits the generalisability of our data and is an acknowledged inherent weakness in our sampling approach. Another weakness arises from the potential for multiple interpretations of the term lockdown, depending on where respondents lived. Lastly, the data collected are based on self-report, a method selected in the absence of comparable international clinical datasets. It is acknowledged that respondents may produce biased data through recall bias and socially desirable responding, to name but two.
To achieve this, coating is not necessary  (Skibo, 1992). Their identification in the archaeological record can be achieved under certain condition, using gas chromatography/mass spectrometry analysis  (Drieu, 2017). These types of studies are rarely applied in the archaeological record although ethnographic investigations regularly highlight the omnipresence of organic materials in pottery surface treatments  (Gosselain, 2002; Livingstone Smith, 2010; Schiffer, 1990). Moreover, distinguishing organic coatings on archaeological vases from organic deposits related to the vases' function remains a challenge. The establishment of a reference database of surface treatments applied to flat clay tablets, aims firstly at identifying signatures of organic and mineral surface treatments at a microscopic scale; secondly, characterising surfaces' performance characteristics depending on their treatments.
We have so far focused on milk, wool, olive oil and beeswax but other materials such as animal fats, birch bark tar, etc. should be considered in the future. Roughness was measured with a confocal microscope and characterised by the method of the continuous wavelet transform, providing, for the first time, a microscopic signature of surface treatments. These reference data must be compared, in the future, with those from the archaeological record. In fact, ceramic surface attrition constitutes one of the major research areas in the field of surface characterisation. Although well developed by a small number of scholars  (Bonaventure, 2010; Fanti, 2015; Forte et al. , 2018; Saurel, 2017; Skibo, 1992; Vieugué, 2014) , the use-wear approach could be strengthened by borrowing methodologies specific to tribology.
Acknowledgements, The authors wish to thank  Alain Giosa  and  Christophe Petit  ( Université Paris 1 Panthéon-Sorbonne, UMR 7041 ) for their kind provision of the kiln that fired the tiles. Their gratitude also goes to the  Société Languedocienne de Préhistoire  for the provision of the clay and to  Euan Wall  and  Marilena Pateraki  for having proof-read the text.
Bacteria were isolated using tryptic soy agar (TSA). Then, identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): MALDI Biotyper®(Bruker, Billerica, MA, USA) and the Bruker Biotyper 3. 0 database for samples of one urban area. They were identified using Gram straining and biochemical analytical profile index (API) test (bioMérieux, Marcy-l'Etoile, France) for samples of the other urban area. Antibiograms were performed in accordance with the guidelines of the European Society of Clinical Microbiology and Infectious Diseases to test the antibiotic susceptibility of bacterial pathogens. Fungi were identified by mycologists according to their macroscopic and microscopic morphology colored with lactophenol and, for samples of one urban area, using MALDI-TOF MS.
Statistical Analysis Data were described as numbers and percentages for categorical variables and as means ± standard errors (SE) or median associated with range (minimum-maximum) for continuous variables. The results were statistically processed with Mann-Whitney U tests or Student's t-tests according to non-normal or normal distributions of variables (analyzed by Shapiro-Wilk test) using RStudio®(RStudio Inc. , Boston, MA, USA) version 1. 1. 456. The statistical significance was set at p < 0. 05. Regarding each organic compound, tests were performed only for most quantified compounds (50% > LoQ). To perform the tests, the maximal value hLoQ (high limit of quantification) replaced a concentration >hLoQ; the minimal value LoQ/2 replaced a concentration <LoQ, i. e. , when the compound was detected but not quantified.
CASE DESCRIPTION A 66-year-old man without previous medical history was referred to our department to undergo a pre-therapeutic 18 F-FDG-PET/CT for the staging of an EMC of the left nasal cavity discovered on the symptomatology of epistaxis. 18 F-FDG PET/CT was performed on a digital Biograph Vision 600 (Siemens Healthineers, Knoxville, TN, United States). The patient fasted 6 h before the intravenous injection of ∼3 MBq/kg of 18 F-FDG. Following the injection, the patient remained in a quiet room for approximately 60 min before acquisition and was then scanned from the top of the skull to the mid-thigh in the arms-down position  (6). Free breath acquisitions were performed for both PET and CT. The PET data were acquired in three-dimensional (3D) continuous bed motion mode. Different scan speeds were set (3 mm s -1 over the head, 2 mm s -1 over the lungs, 1.
Randomized placebo-controlled trials Based on the observational data and on the fact that an oral drug would improve patient comfort, the value of oral alendronate has been tested in a placebo-controlled randomized trial  [29]. With the same premise that in the initial observational studies of IV drugs, the higher Paget's disease of bone dosage has been chosen. Therefore, 40 patients with polyostotic FD were randomized in a single American center to receive either alendronate daily or placebo, over 24 months. Adults were on 40 mg daily for 6 months, followed by 6 months off drug and this cycle was repeated once; children received a lower dose, adapted to their body weight. The primary endpoint was the variation in urinary NTX, whereas bone pain was analyzed as a secondary outcome, in an intent-to-treat analysis at 18 months.
Spectrophotometry The resin color change (∆E) was evaluated and analyzed with the CIELab color system by the formula ∆E 00 (ISO 11664-6)  [47, 48]. ∆E 00 = ∆L k L S L 2 + ∆C k C S C 2 + ∆H k H S H 2 + R T ∆C k C S C ∆H k H S H A black silicon mold was used to accurately reposition the resin samples. Measurements were performed on the polished side, using a spectrophotometer (eXactTM Standard, X-Rite PANTONE ® ) which set-up was: standard illuminant D65, 45/0 • optical geometry, CIE 1964 10 • observer, and 2-mm 2 surface measurement (Color iControl software, X-Rite). Beforehand, the color acceptability threshold was experimentally evaluated. Regarding each sample (n = 48), a first point was defined as the sample color standard (Figure  1 ). From this standard point, eleven measurements were taken every 0.
Statistical Analysis Regarding the microbiological assay, the Shapiro-Wilk test revealed a non-normal distribution for CFU counts. Then, a pair-wise comparison was performed between the independent groups using the non-parametric Wilcoxon-Mann-Whitney test (Prism5, GraphPad Software, San Diego, CA, USA). A P value less than 0. 05 was considered to be "statistically significant". As for the spectrophotometry assay, the Shapiro-Wilk test revealed a non-normal distribution. The independent groups were compared with a Kruskall-Wallis test followed by a Wilcoxon rank sum test (Rstudio Software, 1. 41717, 2021, RStudio, Inc, Boston, MA, USA). A P value less than 0. 05 was considered to be "statistically significant".
Statistical Analysis Regarding the microbiological assay, the Shapiro-Wilk test revealed a non-normal distribution for CFU counts. Then, a pair-wise comparison was performed between the independent groups using the non-parametric Wilcoxon-Mann-Whitney test (Prism5, GraphPad Software, San Diego, CA, USA). A P value less than 0. 05 was considered to be "statistically significant". As for the spectrophotometry assay, the Shapiro-Wilk test revealed a non-normal distribution. The independent groups were compared with a Kruskall-Wallis test followed by a Wilcoxon rank sum test (Rstudio Software, 1. 41717, 2021, RStudio, Inc. , Boston, MA, USA). A P value less than 0. 05 was considered to be "statistically significant".
Materials and Methods The study was conducted in accordance with the World Medical Association Declaration of Helsinki. All participants signed an informed consent. The survey protocol was approved by the Bioethics Committee of the Jagiellonian University. This study was performed on a random subsample of 1008 persons (478 men and 530 women), between 50 and 75 years of age, from the 10,728 Polish participants of the Health Alcohol and Psychosocial Factors in Eastern Europe (HAPIEE) Project. Details of the methodology used in the HAPIEE study, which examined a representative sample of residents of Kraków, the second-largest city in Poland, have been published earlier  [29, 30]. A brief overview of the present study is given below. Baseline information included data on health, lifestyle, diet (food frequency), socioeconomic circumstances and psychosocial factors.
A short examination included measurement of anthropometric parameters, blood pressure, lung function, assessment of cognitive function, and collection of a fasting venous blood sample. Re-examination included collection of data on healthy aging, economic wellbeing, medical history, and current medication status by face-to-face interview  [29]. Additionally, in a subsample, oral examination was performed. Oral examination was carried out at the University Dental Clinic in Kraków, according to WHO recommendations  [31] , by dentists carefully trained in the study methods, and the results of the measurements were subjected to quality control. Standard extraoral and intraoral examinations were undertaken. The intraoral examination was carried out from the first to the fourth quadrant. Data were collected on the number of teeth with caries, extracted teeth, filled teeth, and use of partial and full dentures.
Objectives: A better understanding of the microstructure and mechanical properties of enamel and dentine may enable practitioners to apply the current adhesive dentistry protocols to clinical cases involving dentine disorders (dentinogenesis imperfecta or dentine dysplasia). Data/sources: Publications (up to June 2020) investigating the microstructure of dentine disorders were browsed in a systematic search using the PubMed/Medline, Embase and Cochrane Library electronic databases. Two authors independently selected the studies, extracted the data in accordance with the PRISMA statement, and assessed the risk of bias with the Critical Appraisal Checklist. A Mann-Whitney U test was computed to compare tissues damage related to the two dentine disorders of interest. Study selection: From an initial total of 642 studies, only 37 (n = 164 teeth) were included in the present analysis, among which 18 investigating enamel (n = 70 teeth), 15 the dentine-enamel junction (n = 62 teeth), and 35 dentine (n = 156 teeth).
Search strategy and selection criteria Studies that involved participants of any age with dentinogenesis imperfecta or dentine dysplasia were included. Studies which assessed the microstructure of enamel and/or dentine were also included. Three online databases were used to identify relevant references: Medline via PubMed, DOSS via EBSCO and the Cochrane Library. In addition, a manual search through the reference lists of selected studies was performed. The terms (dentinogenesis OR (dysplasia AND dentine)) AND (structur* OR composition OR microstructur* OR ultrastructur* OR anatomopathology OR properties) were entered into the search fields. The search was limited to English language articles. The title and abstract of identified studies were screened by two reviewers for eligibility. Consensus was obtained by discussion or consultation with one other reviewer.
Data extraction Data extraction was performed by two reviewers using spreadsheets (Excel 2007, Microsoft©, CA, USA). Disagreements were discussed and a consensus reached. The aim, country, study design, patient characteristics (country of residence and age), and sample size of each eligible study were collected. The following items were collected: years of publication, diagnoses, affected and control tooth samples, methods, outcomes (mineral densities, chemical composition, microstructure, mechanical properties) and results.
Sequencing reactions were carried-out using the Big-Dye Terminator, version 1. 1, cycle sequencing kit DNA according to the manufacturer's instructions (Applied Biosystems, Foster City, CA, USA). Nucleotide sequences were assembled using CHROMAS PRO software, version 1. 7 (Technelysium Pty Ltd. , Tewantin, QLD, Australia) and compared with the GenBank database by similarity search using the BLASTN program (http://www. ncbi. nlm. nih. gov/blast/).