dataesr/scientific-paragraphs-categorization huggingface dataset:
Chlorophyll a fluorescence The chl. a fluorescence is non-invasive technique used to detect damages occurring in photosynthetic organisms before visible damages caused by natural environmental stresses or initiated by biocides. It is widely employed in every fields of biology  (Van Kooten and Snel, 1990; Maxwell and Johnson, 2000; Lazár et al. , 2006) , aquatic pollutants  (Choi et al. , 2012; Dewez et al. , 2018)  and in cultural heritage to monitor the effectiveness of biocides used to eradicate stone dwelling phototrophs  (Tomaselli et al. , 2002; Tretiach et al. , 2010; Pfendler et al. , 2018b). a) Monitoring with Junior PAM fluorometer A handheld photosynthesis yield analyser, Junior PAM Chlorophyll Fluorometer (Walz, Effeltrich, Germany) was coupled to WinControl-3 Software, the device was used with the pulse-amplitude modulated (PAM) in combination with saturating pulse analysis of fluorescence quenching.
Acknowledgements This research was supported by the  Ministerio de Ciencia, Innovación y Universidades (Spain)  Proyecto I + D + i, PID 2019-109333RB-I00 (S. G. M),  Gobierno de Aragón and Programa Operativo Aragón de Fondo Social Europeo   2014-2020  (I. F. C. ) and  Vranken-Pommery Monopole. The authors acknowledge  Rachel Ouvinha De Oliveira  and  Clément Pierlot of Pommery Champagne cellar  for access and support. S. G. M. and S. E. C. would like to acknowledge the  University of Reims Champagne-Ardennes  for visiting professorships.
To keep pace with the rapid advancements in molecular genetics and rare diseases research, we have updated the list of ectodermal dysplasias based on the latest classification approach that was adopted in 2017 by an international panel of experts. For this purpose, we searched the databases PubMed and OMIM for the term "ectodermal dysplasia", referring mainly to changes in the last 5 years. We also tried to obtain information about those diseases on which the last scientific report appeared more than 15 years ago by contacting the authors of the most recent publication. A group of experts, composed of researchers who attended the 8th International Conference on Ectodermal Dysplasias and additional members of the previous classification panel, reviewed the proposed amendments and agreed on a final table listing all 49 currently known ectodermal dysplasias for which the molecular genetic basis has been clarified, including 15 new entities.
We studied a non-consanguineous family of German origin with a total of 5 patients (Figure  3a ). All affected family members showed more or less pronounced abnormalities of teeth, hair, and sweat glands (Figure  3c ). Because family history and pedigree indicated a dominantly inherited defect, we investigated a DNA sample of index patient I by whole exome sequencing. The obtained data set was filtered and analyzed for pathogenic variants of the currently known genes. A heterozygous frameshift mutation, c. 4219dupG (p. E1407Gfs*5), was detected on chromosome 12 in LRP6 (NM_002336. 3; NP_002327. 2), affecting more than 200 C-terminal amino acids of the LRP6 protein. Sanger sequencing of the mutation site revealed the variant's heterozygous presence in each of the affected subjects but not in the unaffected family members (Figure  3b ).
Methods: The search of the primary literature was conducted until [December 31, 2021]. Our search strategy uses the Pubmed/MEDLINE database and was structured around 3 terms ["Development," "Defect," and "Enamel"]. To be included, references had to be primary studies, written in English. Exclusion criteria were reviews, in vitro, animal, genetic or archeology studies, and studies focused on clinical management of DDE. One hundred and twenty three articles were included in this scoping review: 4 Randomized clinical trials, 1 letter, 5 cases reports, 2 fundamentals studies, and 111 observational studies (33 Cross-sectional studies, 68 Cohort study and 10 Case-control study). The quality of evidence was assessed using the PEDro scale for clinical trials, the Newcastle-Ottawa scale for observational studies, and a published tool to assess the quality of case reports and case series.
METHODS To combine the exploratory and systematic nature of our research, we followed the Arksey and O'Malley methodological framework for scoping reviews  (5) , and completed the PRISMA for Scoping review guidelines (see Supplementary Material 1). The search of the primary literature was conducted until  [December 31, 2021]. We focused our search strategy on the Pubmed/MEDLINE database, considering it would include all the major factors identified by biomedical research. We structured our search strategy around 3 terms ["Development, " "Defect, " and "Enamel"], allowing for explosion search, and using the Boolean operator AND (see details in Supplementary Material 2). We did not use terms involving any risk factor for DDE, so as to scan the database broadly without preconceived notions about the factors we were looking for.
The screening process was performed by one author (AMC). To be included, references had to be primary studies, written in English. Exclusion criteria were determined iteratively by a team approach (AMC, JNV, CN), i. e. , as the data were filtered, according to the nature of the studies discovered during the initial screening, in accordance with the methodology of scoping reviews  (5). Thus, excluded articles were reviews, in vitro, animal, genetic or archeology studies, and studies focused on clinical management of DDE. Two raters (AMC, CN) independently assessed the quality of evidence, using the PEDro Scale for clinical trials, the Newcastle-Ottawa scale for observational studies, and a published tool for evaluating the quality of case reports and case series. Agreement on quality ratings of full-text articles was assessed for each, including references, and disagreements were resolved by a consensus-based discussion with a third rater (JNV).
Subsections Relevant for the Subject The initial electronic database search represented a total of 1,096 articles. Considering exclusion criteria, 128 full-text articles were eligible for inclusion. We excluded 5 articles with a quality assessment score of 0 and without published references, or with references that could not be consulted. Finally, 123 articles were included in this scoping review (Supplementary Material 3). Figure  1  describes the flowchart for the entire process. Our explicative model about the mechanisms involved in acquired DDE (aDDE) is presented according to (1) a chronological timeframe of tooth development (Figure  2 ) and (2) putative biological mechanisms (Figure  3 ). All the factors are sorted alphabetically, without any prioritization.
Materials and Methods The experiments were conducted at the Laboratory of Applied Biomechanisms in Aix Marseille University, France. Nine cadaveric heads were acquired and used in the course of this experiment, preserved in Winckler's solution in a cold room. They were de-identified, and no demographic data were available about the cadavers. Approval for the study was not required in accordance with local and national legislation. A standard bilateral mastoidectomy, including a facial recess approach to access the round window, was performed on each head. The edge of the round window niche was slightly drilled to have direct access to the round window membrane. A 1 mm 2 reflector for the laser beam of the velocimeter was placed on the round window on one side (Figure  1 ). optimization of the use of bone implants.
Materials and Methods The experiments were conducted at the Laboratory of Applied Biomechanisms in Ai Marseille University, France. Nine cadaveric heads were acquired and used in the cours of this experiment, preserved in Winckler's solution in a cold room. They were de-identi fied, and no demographic data were available about the cadavers. Approval for the study was not required in accordance with local and national legislation. A standard bilateral mastoidectomy, including a facial recess approach to access th round window, was performed on each head. The edge of the round window niche wa slightly drilled to have direct access to the round window membrane. A 1 mm 2 reflecto for the laser beam of the velocimeter was placed on the round window on one side (Figur 1). The pinna and the soft tissue behind it were removed on each side to adequately expose the mastoid bone and the space needed for the implants.
The implants were fixed in the bone with a measured strength of 45 Newtons. Fifteen linear accelerometers (Bruel and Kjaer 45-17c, Naerum, Denmark) were installed: Five accelerometers were placed at equal distance on the sagittal midline from frontal to occipital, one beside each BAHA™ implant (three on each side) and one in each of the spaces available between the implants (two on each side). To fix all the accelerometers, we exposed the bone by dissecting five squares of soft tissue (2 × 2 cm). The accelerometers were glued directly on the bone for optimal data monitoring. Linear accelerometers, which measure acceleration in only one direction, were used to measure the linear vibration passing through them in the coronal plane from the emitting ear to the other ear. To avoid any damping of the vibrations by external contact and to maintain the head in an upright fixed known position for the duration of the experiment, a stake was placed through the medullar canal of the remaining cervical vertebrae.
The microscope, head, and laser were all placed on anti-vibration tables in an anechoic chamber (Figure  3 ). The implants were fixed in the bone with a measured strength of 45 Newtons. Fifteen linear accelerometers (Bruel and Kjaer 45-17c, Naerum, Denmark) were installed: Five accelerometers were placed at equal distance on the sagittal midline from frontal to occipital, one beside each BAHA™ implant (three on each side) and one in each of the spaces available between the implants (two on each side). To fix all the accelerometers, we exposed the bone by dissecting five squares of soft tissue (2 × 2 cm). The accelerometers were glued directly on the bone for optimal data monitoring. Linear accelerometers, which measure acceleration in only one direction, were used to measure the linear vibration passing through them in the coronal plane from the emitting ear to the other ear.
To fix all the posed the bone by dissecting five squares of soft tissue (2 × 2 cm). T glued directly on the bone for optimal data monitoring. Linea measure acceleration in only one direction, were used to meas passing through them in the coronal plane from the emitting ear t any damping of the vibrations by external contact and to maintai fixed known position for the duration of the experiment, a stake medullar canal of the remaining cervical vertebrae. The microsco all placed on anti-vibration tables in an anechoic chamber (Figure The laser velocimeter (Laser Doppler Vibrometer OFV 534 USA) was oriented so as to send a signal directly on the reflecto on one side. The laser, accelerometers, and BAHA™ implants i matic Ultrasonic Pulse Velocity (UPV) 8-channels audio analyzer boro, MA, USA).
The linear accelerometers' recordings were done randomly with emission from only one side, followed by the contralateral side. The round window response was measured for both the ipsi and contralateral emissions to get data on bilateral stimulations. The data from the UPV were normalized over frequency bins corresponding to 1 / 3 of an octave per data point by MATLAB scripts (The MatWorks, Natick, MA, USA). An Analysis of Variance (ANOVA) was performed on the data sets collected at 500 and 8000 Hz. The Tukey HSD (honest significant difference)  [9]  test that uses the results of the ANOVA to distinguish if the means are different from one another to a significance level p < 0. 05 was applied to all the data sets.
Propagation Properties The propagation properties were analyzed by comparing the results of the different sagittal linear accelerometers. To obtain a reproducible measure from head to head and to account for morphological differences, the recorded signal of each sagittal accelerometer was divided by the sum of the signals from all the sagittal accelerometers (Figure  4 ). This gives the fraction (%) of the initial sound signal stimulating each accelerometer. The signal was sent as a continuous sweep of frequencies, however, the data are presented as the mean value over a scale of 1 / 3 octave against the mean frequency of each 1 / 3 octave. We used the 1 / 3 octave scale because it corresponds to the scale used in acoustic engineering as a match for human perception  [10]. quency sweep response measurements, in addition to one timing measurement (in ral time difference), were recorded.
The linear accelerometers' recordings were do domly with emission from only one side, followed by the contralateral side. The window response was measured for both the ipsi and contralateral emissions to g on bilateral stimulations. The data from the UPV were normalized over frequency bins corresponding an octave per data point by MATLAB scripts (The MatWorks, Natick, MA, US Analysis of Variance (ANOVA) was performed on the data sets collected at 500 an Hz. The Tukey HSD (honest significant difference)  [9]  test that uses the results ANOVA to distinguish if the means are different from one another to a significan p < 0. 05 was applied to all the data sets.
Propagation Properties The propagation properties were analyzed by comparing the results of the d sagittal linear accelerometers. To obtain a reproducible measure from head to head account for morphological differences, the recorded signal of each sagittal acceler was divided by the sum of the signals from all the sagittal accelerometers (Figure gives the fraction (%) of the initial sound signal stimulating each accelerometer. Th was sent as a continuous sweep of frequencies, however, the data are presented mean value over a scale of 1 /3 octave against the mean frequency of each 1 /3 octa used the 1 /3 octave scale because it corresponds to the scale used in acoustic engi as a match for human perception  [10]. Independent of the location of the implant, the low frequencies (100 to 1500 preferentially transmitted via the most frontally located accelerometer (#5).
Cochlear Transmission To calculate the cochlear transmission, the laser velocimeter was used to directly measure the response of the round window to low (100 to 4000 Hz) and high (4000 to 10,000 Hz) frequency sweeps of 220 ms duration. The displacement speed of the window was the value measured. The amplitude of the signal indicates the magnitude of the movement of the cochlear fluids in the internal ear for each frequency. The graph in Figure  6  shows the average for all heads of the frequency response in both ipsilateral and contralateral cases for each of the implant locations. The initial noisy data for each curve was smoothed by performing a moving frequency average over a band of 300 Hz. This smoothed data set was subsequently averaged over all tested heads. For ease of visualization, a normalization factor of 50 was used to multiply the data.
Those parameters confirmed that the data collected are relevant and will be comparable to true clinical features. While the averaged data presented in the results section show strong regularities, there is still a notable morphology-dependent effect on the different heads. This implies that further studies on the different types of morphologies and what they imply in terms of optimal implant location need to be pursued, using the interaural time signals and the ratio of contra to ipsilateral frequency sweeps to obtain individual skull response functions is an example. In the future, a good understanding of the pathways of transmission and the significant morphological features related to them could lead to the possibility of a tailored selection of device and implantation location for each patient.
Their siblings and parents were enrolled as contact cases for longitudinal home follow-up, making up a total of 535 individuals enrolled. The index cases and their families were enrolled as soon as possible, for example, 1-3 days after initial positivity of the index case. Saliva sampling for subsequent SARS-CoV-2 detection by RT-PCR and a SARS-CoV-2 serology was performed on the day of inclusion (D0). Paired NP sampling was performed when accepted. Saliva sampling (and NP if agreed) was performed at 3 (D3), 7 (D7), 15 (D15) and 45 (D45) days post-inclusion, for both index cases and family members. A final SARS-CoV-2 serology was performed at D45. For both campaigns, demographic and clinical data were collected including age, gender, previous vaccination, previous COVID-19 infection (defined by a RT-PCR or a serology positive test at least 60 days before enrolment) and clinical status, for example, asymptomatic or symptomatic, focusing on the initial symptom.
Data analysis To compare the performance of NP and saliva sampling for SARS-CoV-2 detection, we used the RT-PCR results (NPS/saliva) obtained at D0 in the population of the first campaign and from the first NPS/saliva sampling matching pair in the population of the second campaign. As indicated in Table  S2 , 53 out of 449 individuals had their first available saliva-NPS pairs collected either at D3, D7, D15 or D45 from the time of family enrolment. Positivity was retained if SARS-CoV-2 was detected by RT-PCR using either of the two sampling methods. Quantitative data were expressed as medians [interquartile range] (range), and qualitative data as numbers (percentages). The diagnostic accuracy of the tests was evaluated by calculating their respective sensitivities. Confidence intervals were calculated by the exact binomial method.
To achieve a prospective unbiased assessment of sensitivities, we refined our analysis by excluding individuals enrolled with a previous known positive SARS-CoV-2 PCR status, that is, essentially index cases of the second campaign. Hence, results will be presented both for the overall population and for this selected population with no previously documented positive SARS-CoV-2 RT-PCR ('No Prior Positive RT-PCR') subjects. Subgroup analyses were performed according to: (i) age group (ii) serology results performed on the same day when available, (iii) no prior positive RT-PCR group, (iv) presence of symptoms on the day of testing, and (v) the time of enrolment campaign. Quantitative variables were compared with Wilcoxon's test, with a significance level of 5% and qualitative data using Chisquared or Fisher's exact test as appropriate.
ACKNOWLEDGEMENTS The authors thank all the families for their participation and  URC-CIC Paris Centre  for the implementation, monitoring and data management of the study. The later includes  Jean-Marc Treluyer  and  Caroline Elie ,  Mathilde Serpinet ,  Céline Hauw ,  Amel Bouheraoua ,  Victor Bruyère ,  Mégane Ribot ,  Rosa Salhi ,  Gael Plastow ,  Cindy Parent ,  Sonia Lounis ,  Insaf Berrazaga ,  Wafa Atmani ,  Amélie de Haut de Sigy ,  Geovanna Meneses  and  Fabrice Gourmelon. The authors thank  Carl Mann  for careful reading of the manuscript. FUNDING INFORMATION This study was funded by a research grant from the  French Ministry of Health (PHRC)  and sponsored by the  Assistance Publique -Hôpitaux de Paris  ( AP-HP ) and by delegation:  Délégation à la Recherche Clinique et à l'Innovation -DRCI (Clinical Research and Innovation Department).
Preparation of titanium cylinders by additive manufacturing from. stl models The 3D models of both types of cylinders were first imported into a specific software for processing and preparing. stl files for additive manufacturing (Magics ® -Materialise Leuven, Belgium). A support for holding the cylinders was also added to separate them from the built plate of the 3D printer and to evacuate the heat generated locally by the laser during fusion of the powder. The global files containing all the parts and their supports were then imported into the MTT Autofab Marcam ® slicing software (Release 1. 6, Renishaw Benelux, Brenda, Netherland) to virtually slice the parts into thin 30 m layers. The contours were produced at 100 W and 500 mm/s, and the internal hatching at 190 W and 600 mm/s, with a hatching distance of 120 m between passes.
Morphometry of the cylinders The 3D models of the cylinders were used to compute morphometric characteristic and computational fluid dynamics. Morphometric analysis of the cylinders was done with the CTAn software (Bruker nanotomography, Kontich, Belgium) and the following parameters were determined: • porosity (expressed in %) represents the global amount of the cylinder occupied by pores; • pore diameter (in m). Morphological characteristics of the geometric pores was obtained by analysis of images with ImageJ (NIH https://imagej. nih. gov/ij/). The following form factors were derived from measurements of area and perimeters of the pores imaged on 2D microCT scans and theoretical models composed of perfect squares: • circularity (4*area/perimeter 2 ); • solidity (area/convex hull area) is sensitive to indentations of the pores boundaries.
Nanocomputed tomography of the bone blocks The large blocks of bones containing the titanium implants were transferred while in the fixative in a X-ray computed nanotomograph (Nanotom, Phoenix, GE, USA) using polychromatic X-rays to limit artefacts due to titanium. NanoCT analysis was done at 100 kV and 220 A and a copper filter. The rotation angle was 0. 2 • with a pixel size of 12. 82 m. Image reconstruction was done on the projection images with the DATOS software (Phoenix, GE) and a stack of 2D sections was obtained for each specimen. Morphometric analysis of the cylinders was done with the CTAn software (Bruker nanotomography, Kontich, Belgium) and the following parameters were determined: 3D models were obtained with VG StudioMax 3. 2 (Volume Graphics GmbH, Heidelberg, Germany). On the 3D models, re-slicing is possible to expose the different areas of interest and select the most representative 2D sections.
Acknowledgments Mrs. N. Gaborit ,  S. Lemière  and  F. Pascaretti  are thanked for their histotechnical help and microCT analysis and  Mrs I. Pavageau  and  I. Leborgne  for their surgical help. SEM and EDS analysis were performed at  Service Commun d'Imagerie et d'Analyses Microscopiques (SCIAM), Université d'Angers , thanks to  R. Mallet. The 2021 cover image of Morphologie is derived from this study.
Dental impressions are contaminated with potentially pathogenic microorganisms when they come into contact with patient blood, saliva, and plaque. Numerous disinfectants are used; however, no sole disinfectant can be designated as universal for all the impression materials. Thus, the aim of this study is to systemically review the literature to evaluate the effect of the existing disinfection procedures on the bacterial colonization of dental impression materials. This systematic review and meta-analysis was conducted according to the PRISMA statement. PubMed (MEDLINE), Web of Science, Scopus, EMBASE, and SciELO databases were screened up to April 2021. Eligibility criteria included in vitro studies reporting the antibacterial activity of disinfectant solutions in dental impression materials.
Search Strategy The literature search was performed by two independent reviewers (E. C. R. and R. B. ) up to April 22, 2021. The following databases were screened: PubMed (MEDLINE), Web of Science, Scopus, EMBASE, and SciELO. The search strategy was performed according to the keywords defined in Table  1. All studies were imported into Rayyan QCRI platform  [20].
Data Extraction The Microsoft Office Excel 2019 program (Microsoft Corporation, Redmond, Washington, DC, USA) was used to extract the data of interest from the included manuscripts. These were placed on a standardized form. Two reviewers (L. H. and R. B. ), who received training in this software, performed the analysis. The data recovered from each manuscript were author, year, impression material evaluated, disinfection agents used, type of microorganism evaluated, main outcome, and main results.