dataesr/scientific-paragraphs-categorization huggingface dataset:
0081). Using a multivariate Cox model including histological grade (hyperplasia vs dysplasia) and treatment arm, patients suffering from OPMD with a high GIN score had shorter oral-cancer-free survival (HR = 3. 55, IC95  (1. 23;10. 28) , p = 0. 0193, Supplementary Table  S3 ). (B) GIN score was also computed in 86 OPMD from the OPMD-3 dataset. Samples were grouped into low and high GIN according to optimal cutoff for GIN score using the Maxstat r package in order to evaluate the association of the GIN score with oral cancer-free survival (OCFS), using Kaplan-Meier curves. Survival distribution compared between high and low GIN groups using a log-rank test. Lastly, using our previously published molecular classification of OPMD, we found that GIN score was significantly higher in the classical subtype compared to that in the (B) GIN score was also computed in 86 OPMD from the OPMD-3 dataset.
Discussion Oral carcinogenesis is characterized by the accumulation of key genetic events  [15, 16]  leading to overall genomic instability. At premalignant steps, the loss of heterozygosity, which may occur at different microsatellite markers, is the most robust marker of this instability, which is associated with OPMD malignant transformation  [5] [6] [7] [8] 41, 42]. Over the single biomarker approach, we aimed to capture an overall genomic instability phenotype in OPMD. Because genomic instability is an intrinsic property of cancer cells, we first identified a set of 20 genes whose expression was correlated with genomic instability, as defined by the fraction of genome altered, in two independent datasets of HNSCC from TCGA and the CCLE. Using the ssGSEA tool, we computed a genomic instability (GIN) score corresponding to the enrichment score of this set of genes in independent datasets in order to validate the correlation between this score and the FGA.
Lastly, we found that the GIN score was associated with oral carcinogenesis in independent datasets of OPMD. The gene-expression-based surrogate of genomic instability had been proposed in different cancer types, including breast and colorectal cancers  [17] [18] [19] [20] 43]. The CIN70 signature  [20]  is the most robust gene-expression marker of chromosomal instability that is associated with prognosis  [44, 45]. In patients suffering from HNSCC, a significant association was recently observed between this signature and survival  [46]. However, to the best of our knowledge, there is no gene signature associated with genomic instability at premalignant steps of head and neck tumorigenesis. We used a similar approach to identify the specific genes whose expression was correlated with genomic instability, as defined by the fraction of genome altered.
In our study, we showed significant correlation between GIN score and FGA in independent datasets, while correlation between GIN score and mutation count was not significant and consistent across datasets. Thus, the GIN score would allow for capturing a GI related to copy-number variations rather than to the mutational load. Pathway enrichment analysis of our set of 20 genes showed that the most enriched terms were related to chromatin organization involving 3/20 genes (MTA1, SMYD3, CDK4), suggesting that we identified a signature of GI related to chromosomal rearrangements. We observed an increased GIN score at different stages of oral tumorigenesis (normal -dysplasia/OPMD/OSCC) in independent datasets. Moreover, we observed significant association with the GIN score with oral-cancer-free survival (OCFS) in 86 patients with OPMD, while no association was found between CIN70 score and OCFS.
There was no overlapping gene between the GIN and the CIN70 signatures, suggesting that the GIN score could add relevance to the prognostic value of the CIN70 signature, as previously shown in various cancer types. While the CIN70 signature was associated with survival of patients suffering from HNSCC [46], our approach allowed for us to identify specific genes that were associated with FGA during oral carcinogenesis and with the malignant transformation of OPMD. We identified two gene-expression-based molecular subtypes of OPMD using a 400-gene classifier. There were no overlapping genes between GIN signature and this classifier, and we observed that the GIN score was significantly higher in classical OPMD compared to that in immunological OPMD. Moreover, no significant association was found between LOH status, available in 70/86 OPMD from the OPMD-5 dataset, and GIN score, suggesting the need for combining our GI signature with other biomarkers together with our previous molecular classification of OPMD.
Supplementary Materials: The following supporting information can be downloaded at: https: //www. mdpi. com/article/10. 3390/cancers14030834/s1, Table  S1 : Description of the 12 datasets used in our study, Table  S2 : Number of selected genes according to the threshold of correlation, Table  S3 : Multivariate oral cancer-free survival analysis of patients with OPMD from the OPMD-3 dataset (GSE26549). Figure  S1 : Association of the GIN score and HPV status in HNSCC from TCGA (A), GSE39366 (B) and GSE65858 (C). Figure  S2 : Association of the GIN score and survival in HNSCC from TCGA (Samples were grouped into "low" and "high" GI according to the median of the GIN score, in order to evaluate the association of the GIN score with progression-free survival (PFS) (A) and overall survival (OS) (B) using Kaplan-Meier curves.
Characterization of synthesized samples Fourier transform infrared spectroscopy (FTIR) was performed to characterize the chemical functional groups of prepared powders suspended in KBr pellets using a Shimadzu FT-IR 8400S series instrument (Shimadzu, Japan). The FTIR spectra were acquired from 4000 to 400 cm -1 at a data acquisition rate of 4 cm -1. The crystalline phase of synthesized samples was evaluated by Xray diffraction (XRD) using a Shimadzu (XRD Shimadzu 6000) diffractometer with nickel-filtered Cu-K  radiation (1. 5418A ˚). The characterization was operated at 30 mA and 40 kV, with a scanning 2  range between 10°and 60°and a step size of 0. 02°. Thermogravimetric analysis (TGA) was carried out utilizing Shimadzu DTG-60 to evaluate the thermal behavior of the paper powders. Samples were heated up to 900°C with a heating speed of 10°C /min in a nitrogen atmosphere.
The X-ray photoelectron (XPS) analysis were performed on a Physical Electronic PHI Versa Probe II spectrometer via monochromatic Al-K  (49. 1 W, 15 kV, and 1486. 6 eV), and the central signals of the interest elements were analyzed with a hemispheric multi-channel detector. The spectra of the samples were registered with constant passage energy of 29. 35 eV with a circular surface area of 200 m diameter. The resulting XPS spectra were examined by the PHI Smart software and treated by MultiPak 9. 3 software package. The signal of the incidental carbon C 1 s (285. 2 eV) references the binding energy, which is determined from the Background Shirley and Gauss-Lorentz plots. Using this analytical technique, we determined in Table  4  , the binding energies of the major constituents (Ca 2p, O 1s, P 2p, and C 1s) are associated with the superficial layers of our apatite samples and the atomic ratio.
Sample imaging The samples are analyzed within the small animal imaging platform, Animage (CERMEP -living imaging, Bron, France). The samples are passed through an X-ray microscanner (Skyscan 1076 microcomputerized X-ray tomograph, SkyScan, Aartselaar, Belgium). The scanner is used in isotropic mode providing pixels of 17. 6 microns per side. From the raw data, the reconstruction of images makes it possible to obtain isometric images in XYZ mode. The data thus reconstructed is composed of a series of slices of plane images separated by the same distance of 17. 6 microns. In the bone, the presence of titanium implants required special precautions with the parameters of the scanner. These were determined to minimize the disturbance of the images by the presence of the implant. Other precautions have been taken in the reconstruction process, making it possible to obtain from the raw images, images reconstructed in the XYZ plane: smoothing of order 2, "ring artefact reduction" of 20% and "beam hardening" of 10%; the defect pixel mask function has also been used to further reduce the noise caused by the presence of the implant.
Image analysis The analysis is carried out using CtAn ™ software from SkyScan ™ associated with the microscanner, from images in XYZ mode. The bone area surrounding the first third of the implant was studied. This area is considered the region of interest (ROI), which corresponds to an average length of 3. 2 mm (Fig. 4 ). The analysis is performed on a 1 mm circular crown around the implant. Thus, for a diameter of 3. 46 mm of the threaded part of the implant defined from the images, the ossification is studied inside a bone tube with an internal diameter of 3. 46 mm, an external diameter of 5. 46 mm and a length of 3. 2 mm. The bone in this area around the implant is then analyzed after setting two thresholds: a low threshold and a high threshold. The low threshold is set to eliminate all that is too transparent to X-rays to be bony, the high threshold to eliminate all that is too opaque to be bony, essentially the implant.
Results Data is presented in Table  1 , Table  2  and Table  3. BV/TV ration is presented in Table  1. At 42 days, BV/TV ratio is significantly higher on the treated side than the untreated side (42,1 +/-8,76% versus 32,31 +/-10,11%, p < 0,02). Trabecular bone thickness is represented in Table  2. At 42 days, TbTh is significantly higher on the treated side than the untreated side (0,13 +/-0,01 mm versus 0,10 +/-0,01 mm, p < 0,01). The intersection surface is represented in Table  3  according to the distance from the implant surface. At 42 days, it is also significant-Fig. 4. The analysis is carried out using CtAn ™ software from SkyScan ™ associated with the microscanner, from images in XYZ mode. The bone area surrounding the first third of the implant was studied. This area is considered the region of interest (ROI), which corresponds to an average length of 3.
Examining the pangenome of 345 archaea and two nanoarchaea N. equitans  (Waters et al. , 2003)  (GenBank accession number AE017199. 1) and Candidatus N. acidilobi  (Wurch et al. , 2016)  (GenBank accession number CP010514. 1) using the Roary pan-genome pipeline in Galaxy software (https://usegalaxy. org. au. /) (SI Appendix, Fig. S1 ), we determined that the 30S SSU L12 gene conserved among these 347 organisms exhibited a species-specific sequence. More specifically, the 873-bp nanoarchaea 30S SSU L12 gene exhibited sequence similarity < 95% with homologous sequences in methanogenic archaea (here designed as methanogens). A PCR primer pair (forward primer: 5 ′ -TGAAAGCAAAGGGATTTTATTCA-3 ′ ; reverse primer 5 ′ -TTGCATGTGGAACAATACCAG-3 ′ ) (Eurogentec, Seraing, Belgium) was designed using Primer-Blast (https://www.
Automated cluster generation and paired end sequencing with dual index reads were performed in a single 39-hour run in 2 × 250-bp. For each sample/purified nanoarchaea DNA sequence, the quality of each Illumina read was checked by FastQC and trimmed using trimmomatic version 0. 36. 6. Sequence reads were concatenated and assembled using SPAdes version 3. 5. 0 software  (Bankevich et al. , 2012). Finishing was achieved by LongRange PCR (LR-PCR) followed by next-generation sequencing after PCR primers were designed by aligning nanoarchaea on-going genome sequence with Candidatus N. acidilobi reference genome, targeting regions to be finished (SI Appendix, Table  S5 ). Purified LR-PCR products were sequenced using the Illumina Iseq technique as previously described  (Tulloch et al. , 2021). Contigs were identified using Blastn against NCBI database and concatenated reads were mapped using CLCgenomic version 7 against the Candidatus N.
acidilobi genome sequence. The nanoarchaea genome, annotated using Prokka software  (Seemann, 2014) , was added to a nanoarchaea pangenome analysis performed using Roary pan-genome pipeline, as above. Genomic similarity of the on-going nanoarchaea with closely related species was estimated using the OrthoANI: An improved algorithm and software for calculating average nucleotide identity | Microbiology Society (2021) and digital DNA-DNA hybridization (dDDH) performed using Type (Strain) Genome Server (TYGS) (https://tygs. dsmz. de/) (Meier-Kolthoff et al. , 2014). The new nanoarchaea genome was then incorporated into a rhizome representation, using a previously described protocol  (Togo et al. , 2019). Putative encoded protein functions were searched against the Clusters of Orthologous Groups (COG) database using BLASTP (E-value 1e-03, coverage 0.
7 and identity percent 30%). Secretion systems were searched via the Mac-SyDB/TXSSdb database. Further metabolic pathway repertory was established with a RAST server. Lastly, in silico antibiotic resistance profiling of N. massiliensis was determined according to Abricate, Resfinder, Card and Argannot databases with a minimum of 10% identity. Co-culturing nanoarchaea. A dental plaque sample positive for methanogens and nanoarchaea by PCR-sequencing was collected in a Hungate tube (Dominique Dutscher) containing 3 mL of transport SAB medium  (Khelaifia et al. , 2013). As for inoculation, a culture bottle was prepared under a strict anaerobic atmosphere in a BACT/ALERT® blood culture bottle (bioMérieux, Craponne, France) emptied of its original broth and atmosphere, replaced by 30 mL of SAB medium  (Khelaifia et al.
001. The presentation of rhizome was built using Power BI software. f, OrthoANI heatmaps between Nanopusillus massiliensis and other Nanoarchaea genomes. OrthoANI matrix was visualized using MORPHEUS software (https://software. broadinstitute. org/morpheus/). yielded 3125,000 paired end reads and the generated read length is between 1 and 3000 bp, which were assembled and blasted against the nr database. After 12 Methanobrevibacter sp. contigs were detected, remaining reads were mapped against the Candidatus N. acidilobi reference genome using 0. 5 length fraction and 0. 3 similarity fraction as mapping parameters, to recover a 606,947-bp unique contig exhibiting a gap ratio of 19%, with N-bearing regions varying from two bp to 1200pb, representative of a draft genomic sequence of N. massiliensis.
Finishing yielded a unique 606,947-bp long chromosome sequence (WGS accession number: CAKLBW000000000; 16S rRNA gene sequencing accession: Q6268) with 23. 6% GC encoding 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups (COGs) (SI Appendix, Table  S3 ). A nine-nanoarchaea pangenome, including N. massiliensis, incorporated 5294 genes, including 4329 cloud genes and shell genes. Six genes were common to the 9 nanoarchaea genomes; they encoded the 50S ribosomal protein L18, 50S ribosomal protein L23, 30S ribosomal protein S19, 30S ribosomal protein S5, DNA-directed RNA polymerase subunit K and replication factor C small subunit (SI Appendix, Fig. S3 ). We observed that single nucleotide polymorphisms (SNPs) varied from 29 SNPs between the novel nanoarchaea and Candidatus N.
However, only the pellet, but not the supernatant, yielded cocci-like nanoarchaea sized 200-400 nm, either as free cells or located around M. oralis cells, as observed by scanning electron microscopy in parallel to fluorescent in situ hybridization, the observations being enhanced by deglycosylation of the pellet (Fig. 3 ). In parallel, colonies of hosting M. oralis observed at day 10 were firmly identified as M. oralis (strain YH) by PCR-sequencing of the 16S rRNA gene (The 16S rRNA gene sequence accession is OU484279, the Gen-Bank access number of genome is CAJVUI000000000), exhibiting 100% sequence similarity with the homologous 16S rRNA gene sequence of M. oralis strain VD9 (accession NCBI: LN898260. 1). M. oralis strain YH colonies were sub-cultured on liquid SAB medium, and viability and culture of the strain were monitored by CH 4 detection, as described above.
Acknowledgements The authors thank all Hitachi team members in Japan for the collaborative study with  Hitachi High Technology and Institut Hospitalier Universitaire  and for the installation of and service of the TM4000 microscope in our facility. We thank  Mr Louis TSAKOU NGOUAFO  for his help in Nanopusilus Massiliensis genome finishing and  Mrs. Sarah BELLALI  for her help in microscopy analysis.
32) Vitoss (Stryker) I b-TCP granules Bone marrow aspirate Spinal pathologies Putty ultra-porous, NCT03509480; flexible (ref. 33) ChronOS (DePuy I b-TCP granules Autologous blood and/or Tibial plateau Putty NCT02056834; Synthes) bone marrow fractures (ref. 34) ChronOS Inject I Brushite matrix Proximal tibial Injectable, degradable NCT02056834; (DePuy Synthes) and (TCP) fractures (ref. 35) granules CERAMENT s I HA and calcium Tibial plateau Injectable, degradable NCT01828905; (Bone Void Filler) sulfate cement fractures (ref. 36) Norian s Drillable II Carbonated apa- Bioresorbable polylactide/ Tibial fractures Mechanical resistance NCT01132508; (DePuy Synthes) tite cement glycolide copolymer fibres 24 hours after injection (ref. 37) Graftys quickset/ II CDHA cement Powder of HPMC polymer Bone disease, bone Porosity NCT02575352; HBS (Graftys) fractures (ref.
Studied Samples The 121 Individuals included in the study were selected using a nested case-control design. Cases (n = 61) were individuals affected by T2DM based on self-reported physician's diagnosis and/or being on anti-diabetic treatment (oral medication or insulin) at the time of data collection. Controls (n = 60) were selected concurrently and were free of diabetes at the time of data collection. For the present study, we used the following information from each participant: sex, age (years)categorized as old (i. e. , 67-75 year) and oldest old (i. e. , 76-84 y), BMI (calculated as measured weight in kg divided by the square of measured height in m), T2DM status, smoker status (never, former, current), food consumption, and adherence to the MedDiet.
Bioinformatics and Statistical Analysis A total of 3,788,644 raw sequences were obtained from MiSeq Illumina sequencing. The Divisive Amplicon Denoising Algorithm (DADA2) pipeline of R software (version 1. 8. 0) was used for quality-filtering, trimming, error correction, exact sequence inference, chimera removal, and generation of amplicon sequence variant tables (ASV)  (22). The final dataset contained an average of 24,621 sequences per sample, leading to a total 6,840 ASVs. Bacterial taxonomic classification was determined by reference to the Human Oral Microbiome Database (HOMD). Diversity indices such as Observed, Shannon, and Inverse Simpson were calculated using the DADA2 R package and compared by Wilcoxon rank-sum tests. For the ordination plot, multi-dimensional scaling (MDS) was performed using Bray-Curtis distances.
Salivary Microbiome Richness and Diversity in Type-2 Diabetes Mellitus and Non-type-2 Diabetes Mellitus Subjects Following assessment of the quality of isolated DNA, we generated a total of 109 samples of oral metagenomics data based on 16S rDNA amplicon sequencing. Rarefaction curves were plotted to verify the efficiency of the sequencing process (Supplementary Figure  2  and Supplementary Table  2 ). Using the R Dada2 software package, we pre-processed short reads and checked observed amplicon sequence variants (ASVs) by the sequencing depths, observing no increase in the number above our minimal sequencing depth; those samples (n = 5) with less than the minimal depth were excluded from the analysis (Supplementary Figure  2 ). Therefore, the final number of samples for assessment of the microbial community was n = 99.
FUNDING This work was initiated by the  Joint Programming Initiative, A Healthy Diet for a Healthy Life (HDHL). The  SALAMANDER  project was funded by  Agence Nationale de la Recherche, France  (grant no. ANR16-HDHL-0005-01 ),  Biotechnology and Biological Sciences Research Council, United Kingdom  (grant no. BB/R000891/1 ), and the  Ministry of Economy and Competitiveness, Spain  (APCIN grant no. 2016-145 ). SL was supported by a  GIST Research Institute (GRI)   GIST-MIT research Collaboration  grant by the  GIST  in 2022; the " 2020 Joint Research Project of Institutes of Science and Technology" at South Korea ; the  KHIDI-AZ Diabetes Research Program , South Korea; and the  Basic Science Research Program  ( 2021R1C1C1006336 ) of the  Ministry of Science, ICT  through the  National Research Foundation, South Korea.
The storage moduli (G') were also obtained by dynamic mechanical analysis (DMA) using pellets prepared from the hydrogels in a cylindrical mold. For a homogeneous and isotropic material, the moduli measured by tensile tests must be approximately triple, relative to the values obtained via dynamic shear measurement  [31]. This latter trend is in agreement with our data as the values of the modulus determined by tensile tests are, respectively, 3. 8 (for 1) and 4-fold (for 2) higher than those obtained by DMA in shear stress mode (Table  1 ). Markedly, the storage modulus for the hydrogels obtained using Irgacure 2959 was lower, indicating that better mechanical properties were reached with both 1 and 2. Finally, the moduli measured for the materials obtained from 1 and 2 were similar to the value reported for materials obtained using a thermal initiator (Young Modulus 12 MPa)  [32].
SARS -CoV-2 (Severe acute respiratory syndrome coronavirus 2), a virus causing severe acute respiratory disease in humans, emerged in late 2019. This respiratory virus can spread via aerosols, fomites, contaminated hands or surfaces as for other coronaviruses. Studying their persistence under different environmental conditions represents a key step for better understanding the virus transmission. This work aimed to present a reproducible procedure for collecting data of stability and inactivation kinetics from the scientific literature. The aim was to identify data useful for characterizing the persistence of viruses in the food production plants. As a result, a large dataset related to persistence on matrices or in liquid media under different environmental conditions is presented. This procedure, combining bibliographic survey, data digitalization techniques and predictive microbiological modelling, identified 65 research articles providing 455 coronaviruses kinetics.
Studies on coronaviruses persistence were generally conducted by experiments in laboratory consisting in monitoring the virus kinetics under controlled conditions. The reduction of virus infectivity over time could be evaluated by fitting inactivation mathematical models on experimental data. Studying the effects of environmental conditions encountered in food premises requires collecting kinetics data as exhaustively as possible to cover large ranges of values for each condition: inert or food surfaces, temperature, relative humidity, experimental quantification method, virus strain etc. To our knowledge, such exhaustive kinetics dataset are not available yet in the literature. It should also be noted that the gathering of data between different studies is not easy. For example, kinetics are frequently plotted in research articles but raw data are not often provided in all of them as quantitative (numerical) values that can be used for further studies of theirs.