dataesr/scientific-paragraphs-categorization huggingface dataset:
To analyze SiR-actin labeling, an ImageJ macro was used. To quantify actin fluorescence intensity, the user identifies the mitotic spindle poles at each frame over the metaphase duration and the macro draws a line along the mitotic spindle crossing the cell membrane and finds the perpendicular to this line. The user draws lines along actin staining, crossing the line drawn between the mitotic spindle poles and the line drawn at the perpendicular. Fluorescence intensity along each line is calculated and related to the length of the line. Statistics. Statistical analyses were performed using GraphPad Prism software. Data are presented as mean ± SEM. No exclusion criteria were used. The distribution of data (Shapiro-Wilk normality test) and the homogeneity of variances (F test) were tested before performing the statistical tests.
The numbers of independent experiments and the statistical tests performed for all of the quantitative data are indicated in the figure legends. Data, Materials, and Software Availability. Raw data corresponding to Fig. 2B  and Fig. 3  B and C have been deposited in Dryad (https://doi. org/10. 5061/dryad. ns1rn8pvv)  (40). Some data are very large (videos of Fig. 1F ) and will be made available upon request.
ACKNOWLEDGMENTS. We thank  Jacques Mazzega  and  Alexei Grichine  for their assistance with the microscopy studies at the  Institute for Advanced Biosciences Cell Imaging facility (MicroCell). C. G. is supported by grants from the  Agence Nationale de la Recherche  ( ANR-13-JSV1-0008 ) and from the  European Research Council (ERC)  under the  European Union 's  Horizon 2020 research and innovation program  ( ERC Starting Grant   639300 ).
An allele was retained if supported by at least 3 reads, and a single-cell variant allelic frequency (scVAF) ≥15% for an scDP between 20-100× or ≥10% for an scDP >100x, or considered noninformative otherwise. infSCITE was used to infer phylogenetic trees from mutation matrices as published  [7]. Inferred clonal architectures (Fig. S1A ) were used to correct raw cell genotypes. Cells with insufficient genotype information or with a genotype violating the clonal hierarchy owing to cell doublets or sequencing errors were excluded for downstream analyses (Fig. S1B ). Protein data was analyzed using Seurat package V4. 0  [9]. ADT counts were transformed using centered log-ratio transformation and differential expression was tested using ALDEX2  [10]. Bulk and single-cell DNA-Seq will be available at European Genome-phenome Archive (EGA) under accession code EGAS00001006565.
Recent clonal phylogenies inference and single-cell protein expression normalization tools will also need to be benchmarked across various single-cell proteogenomic datasets  [12]. Clone-specific immunophenotypes might allow the study of clone-specific drug sensitivity in phenotype-based ex vivo drug screening experiments  [13] [14] [15]. Our study paves the way for single-cell multi-omics deciphering of the genetic and non-genetic contributions to differentiation blockade in AML and provides a proof of concept for precision oncology instructed by singlecell resolution of the genetic and phenotypic diversity of leukemic cells.
For example, the micro-channels configuration of a porous medium may increase the apparent stiffness of the tissue in the case of confined consolidation compared to the unconfined one  [13]. Computational validation issues could be treated by several approaches. Multi-objective optimization and the use of huge experimental databases could be suggested. However, these solutions tend to complicate the studies and raise their time-memory cost. Different approaches, based upon the exploitation of quantitative MRI for the construction and the validation of FE models were introduced  [11, 14]. This technique seems efficient but is limited by the MRI resolution and needs to be clinically validated. Recent studies introduced probabilistic and deterministic deep learning approaches to reduce the cost of complex behavior tissue models including porous media, hyperelastic anisotropic tissue, and multiscale models.
Finite element model The unknowns of the equation system were the hydrostatic pressure p and the three-component displacement field. We have used Lagrange quadratic (P2) and linear (P1) polynomial functions for the interpolation of the displacement and the pressure, respectively. For this study, we have developed a three-dimensional finite element model of human C6-C7 IVD. We have constructed a parametric geometry based on six experimental studies conducted on the cervical spine morphology  [36] [37] [38] [39] [40] [41]. The geometry is composed of a central elliptical nucleus pulposus (NP) representing 26% of the total volume, a peripheral annulus fibrosus (AF) surrounding the NP and two cartilaginous endplates (CEP) (Fig. 1 ). The geometry was meshed using the software Gmsh  [42]. A mesh refinement study was performed using 4 20-node hexahedral element meshes with different element number to check the convergence of our quantities of interest against element size.
Microbial sequence analysis Bacterial and fungal sequences were processed using the FROGS pipeline in the Galaxy project Version 3. 1  (37). The reads were merged with a minimum overlap of 20 bp (FLASH). The minimal sequence length was 350 bp for bacteria and 120 bp for fungi and the maximum sequence length was 450 bp for both kinds of amplicons. The primer sequences and sequences where the two primers were not present were removed and the sequences were dereplicated. The chimeras were removed using the VSEARCH tool with the UCHIME de novo method combined with a cross-sample validation  (38, 39). Clustering was performed using the Swarm method with a distance difference of 3 and OTUs with a relative abundance below 5. 10 -6 were removed (40). The taxonomic affiliations were done using BLAST (NCBI, USA) with the Silva_132_16S database for bacteria and the Unite_Fungi_8.
Data analyses Statistical analyses were done using R version 3. 4. 2. Graphs were created with the ggplot2 package (https://github. com/ tidyverse/ggplot2). The a-error of 0. 05 was used except for (i) correlations between soil physico-chemical properties and microbial community composition and (ii) correlations between necrosis extents and OTUs abundances for which a a -e r r o r o f 0. 0 1 w a s c h o s e n t o f o c u s o n h i g h l y significant relations. To study the a-diversity by calculating species richness and Shannon diversity index [package Phyloseq  (41) ], the number of sequences was rarefied to 3 758 and 172 sequences per sample for bacteria and fungi respectively (Figure  S1 ). These thresholds were motivated to keep as many technical replicates as possible and limit removing soil and rhizosphere samples.
Nonparametric Dunn's Kruskal-Wallis multiple comparisons were applied to study the variability of microbial diversities (species richness and Shannon index, calculated with estimated richness function of package Phyloseq) in bulk soils and rhizosphere soils across sites and between the rhizosphere and its associated bulk soil. To study the variability of OTUs composition within and across sites, for both bulk and rhizosphere samples the unrarefied dataset was used. A core analysis (microbiome package, https://github. com/microbiome) was performed and complemented by Venn diagrams [VennDiagram package  (42) ]. To study a possible site effect on the composition of microbial communities in the bulk soil, we studied the bacterial community similarities between sites with a permutational multivariate analysis of variance [i.
e. PERMANOVA) (function Adonis package vegan  (43) ] on weighted unifrac distances when the beta-dispersions were similar. When the beta-dispersions were not similar, we applied an analysis of similarities (i. e. ANOSIM) [function anosim, package vegan  (43) ] on weighted unifrac distances using 1000 permutations. The correlations between bulk beta diversity (weighted unifrac distances) and soil physico-chemical properties were performed [envfit function of vegan package  (43) ], significantly autocorrelated soil properties were previously removed. Bacterial and fungal communities and the significant soil properties were represented with a non-metric multidimensional scaling (i. e. NMDS) [package Phyloseq  (41) ]. Finally, for each sampling site, Pearson correlations (package stats) were done between the relative abundance of microbial OTUs and the necrosis extent of each plant for OTUs that had a mean relative abundance higher than 0.
Restricted and cosmopolitan soil microbiomes of the Kerguelen Islands A large proportion of the fungal sequences (up to 48%) could not be assigned to any phylum and corresponded to unknown fungi in the database. This proportion of unknown fungi stood across a similar range as observed in soils from Antarctica (~40% detected from ITS2 region analysis)  (3, 58, 59). These unknown fungal communities might be related to fungi with restricted distribution due to the remoteness of the Kerguelen Islands. These fungi might have a valuable role in soil functioning as observed in the Antarctic, where, based on RNA analyses, endemic fungi were identified as more active than cosmopolitan ones  (65). A soil core microbiome shared between the five fellfield sites was identified. It was only composed of bacterial OTUs that belonged to both widespread and more narrowly distributed taxa  (66).
Objective: This systematic review aims to answer the following focus question: "Is there an association between atypical swallowing and malocclusions?". Methods: Appropriate word combinations were chosen and tailored specifically for each of the following electronic databases: EMBASE, Latin American and Caribbean Literature in Health Sciences (LILACS), LIVIVO, PubMed/Medline, Scopus, Web of Science, and gray literature, without any restrictions, up to February 2021. According to the selection criteria, only cross-sectional studies were included. The following inclusion criteria were considered: a sample composed of children, adolescents, and adults; patients clinically diagnosed with atypical swallowing; patients with normal swallowing; and outcome of interest of atypical swallowing in patients with malocclusion.
INFORMATION SOURCES AND SEARCH STRATEGY Appropriate word combinations and truncations were adapted for each of the six electronic databases chosen as information sources: EMBASE, Latin American and Caribbean Literature on Health Sciences (LILACS), LIVIVO, PubMed/Medline, Scopus, and Web of Science. In addition, gray literature was also a source of information through Google Scholar, Open Gray, and ProQuest Dissertation and Thesis (Appendix 1). Manual reference consultation was performed from the references section of all studies included and with experts, in order to improve the search results and following the recommendations of Greenhalgh and Peacock. 7 Searches on electronic databases and gray literature were performed on July 10, 2020 and updated on February 26, 2021. References were managed, and duplicate studies were removed using appropriate software (EndNote ® X7 Thomson Reuters, Philadelphia, PA).
DATA COLLECTION PROCESS Two reviewers (FMG and KVMT) independently collected information from the studies included. The information was discussed with two experts in the field. The data collected consisted of study characteristics (author, year of publication, country, title, and study design), sample characteristics (sample size, control group, form of diagnosis of malocclusion and atypical swallowing), outcomes, and results (Table  1 ). When data were missing or incomplete, attempts were made to contact the authors for important unpublished information. The authors were contacted by email for three consecutive weeks whenever more information was needed.
SELECTION OF STUDIES A total of 6,361 references were retrieved in the six electronic databases, remaining 4,750 references after the removal of duplicates. After reading the titles and abstracts (step 1), 80 articles were selected for full reading (step 2), of which 76 were excluded (Appendix 2). Following a throughout article review, four articles were later included (Fig  1 ). No additional articles were included from the reference lists, gray literature, and consultations with experts.
Database Search (July 10 th 2020; updated on February 26 th , 2020) LIVIVO TI=("Deglutition Disorders" OR "Deglutition Disorder" OR "Swallowing" OR "swallowed" OR "swallowings" OR "swallowable" OR "swallower" OR "swallowers" OR "swallows" OR "swallow" OR "Swallowing Disorders" OR "Swallowing Disorder" OR "atypical swallowing" OR "atypical deglutition" OR "Myofunctional") AND TI=("Malocclusions" OR "malocclusion" OR "dental position" OR "dental positions" OR "tooth crowding" OR "crossbite" OR "crossbites" OR "cross-bite" OR "cross-bites" OR "cross-bite" OR "cross-bites" OR "open-bite" OR "openbite" OR "open-bite" OR "deep bite" OR "Overbites" OR "overbite" OR "deep bite" OR "deep bites" OR "deep bite" OR "deep bites" OR "Over Bite" OR "Over Bites" OR "Angle's Classification" OR "Angle Classification" OR "Angles Classification" OR "angle class I" OR "angle class II" OR "Angle Class III" OR "Class I" OR "Class II" OR "Class III" OR "malocclusion, angle class III" OR "angle class III malocclusion" OR "skeletal class III malocclusion" OR "class III malocclusion" OR "maxillofacial development" OR "angle class II" OR "angle class II malocclusion" OR "skeletal class II malocclusion" OR "class II malocclusion" OR "angle class I" OR "angle class I malocclusion" OR "skeletal class I malocclusion" OR "class I malocclusion").
Scopus ("Deglutition Disorders" OR "Deglutition Disorder" OR "Swallowing" OR "swallowed" OR "swallowings" OR "swallowable" OR "swallower" OR "swallowers" OR "swallows" OR "swallow" OR "Swallowing Disorders" OR "Swallowing Disorder" OR "atypical swallowing" OR "atypical deglutition" OR "Myofunctional") AND ("Malocclusions" OR "malocclusion" OR "dental position" OR "dental positions" OR "tooth crowding" OR "crossbite" OR "crossbites" OR "cross-bite" OR "cross-bites" OR "cross-bite" OR "crossbites" OR "open-bite" OR "openbite" OR "open-bite" OR "deep bite" OR "Overbites" OR "overbite" OR "deep bite" OR "deep bites" OR "deep bite" OR "deep bites" OR "Over Bite" OR "Over Bites" OR "Angle's Classification" OR "Angle Classification" OR "Angles Classification" OR "angle class I" OR "angle class II" OR "Angle Class III" OR "Class I" OR "Class II" OR "Class III" OR "malocclusion, angle class III" OR "angle class III malocclusion" OR "skeletal class III malocclusion" OR "class III malocclusion" OR "maxillofacial development" OR "angle class II" OR "angle class II malocclusion" OR "skeletal class II malocclusion" OR "class II malocclusion" OR "angle class I" OR "angle class I malocclusion" OR "skeletal class I malocclusion" OR "class I malocclusion") Appendix 1: (Continuation) Database search strategy.
Database Search (July 10 th 2020; updated on February 26 th , 2020) Web of Science TS=("Deglutition Disorders" OR "Deglutition Disorder" OR "Swallowing" OR "swallowed" OR "swallowings" OR "swallowable" OR "swallower" OR "swallowers" OR "swallows" OR "swallow" OR "Swallowing Disorders" OR "Swallowing Disorder" OR "atypical swallowing" OR "atypical deglutition" OR "Myofunctional" AND TS=("Malocclusions" OR "malocclusion" OR "dental position" OR "dental positions" OR "tooth crowding" OR "crossbite" OR "crossbites" OR "cross-bite" OR "cross-bites" OR "cross-bite" OR "cross-bites" OR "open-bite" OR "openbite" OR "open-bite" OR "deep bite" OR "Overbites" OR "overbite" OR "deep bite" OR "deep bites" OR "deep bite" OR "deep bites" OR "Over Bite" OR "Over Bites" OR "Angle's Classification" OR "Angle Classification" OR "Angles Classification" OR "angle class I" OR "angle class II" OR "Angle Class III" OR "Class I" OR "Class II" OR "Class III" OR "malocclusion, angle class III" OR "angle class III malocclusion" OR "skeletal class III malocclusion" OR "class III malocclusion" OR "maxillofacial development" OR "angle class II" OR "angle class II malocclusion" OR "skeletal class II malocclusion" OR "class II malocclusion" OR "angle class I" OR "angle class I malocclusion" OR "skeletal class I malocclusion" OR "class I malocclusion") Google Scholar ("atypical swallowing" OR "atypical deglutition") AND ("Malocclusions") Open Grey ("atypical swallowing" OR "atypical deglutition") AND ("Malocclusions") ProQuest ("Deglutition Disorders" OR "Deglutition Disorder" OR "Swallowing" OR "swallowed" OR "swallowings" OR "swallowable" OR "swallower" OR "swallowers" OR "swallows" OR "swallow" OR "Swallowing Disorders" OR "Swallowing Disorder" OR "atypical swallowing" OR "atypical deglutition" OR "Myofunctional") AND ("Malocclusions" OR "malocclusion" OR "dental position" OR "dental positions" OR "tooth crowding" OR "crossbite" OR "crossbites" OR "cross-bite" OR "cross-bites" OR "cross-bite" OR "crossbites" OR "open-bite" OR "openbite" OR "open-bite" OR "deep bite" OR "Overbites" OR "overbite" OR "deep bite" OR "deep bites" OR "deep bite" OR "deep bites" OR "Over Bite" OR "Over Bites" OR "Angle's Classification" OR "Angle Classification" OR "Angles Classification" OR "angle class I" OR "angle class II" OR "Angle Class III" OR "Class I" OR "Class II" OR "Class III" OR "malocclusion, angle class III" OR "angle class III malocclusion" OR "skeletal class III malocclusion" OR "class III malocclusion" OR "maxillofacial development" OR "angle class II" OR "angle class II malocclusion" OR "skeletal class II malocclusion" OR "class II malocclusion" OR "angle class I" OR "angle class I malocclusion" OR "skeletal class I malocclusion" OR "class I malocclusion") Gonçalves.
3 The incidence of GM1 gangliosidosis is estimated at 1 in 100,000-200,000 live births, but it is higher in certain ethnic groups and countries. 1 urrently there is no treatment for GM1 gangliosidosis. Pre-clinical studies using murine and feline models of GM1 gangliosidosis have demonstrated that adeno-associated viral (AAV) vectors can be used to deliver the normal GLB1 cDNA and restore b-gal activity in the brain and spinal cord via several routes of administration: intraparenchymal,  [4] [5] [6] [7]  intra-cerebrospinal fluid (CSF),  8, 9  or intravenously. 10, 11 Restoration of b-gal activity in the CNS led to partial or complete reversion of disease phenotypes in these animal models, even with restoration of only $20% of normal activity levels. 11 ngoing clinical studies to treat GM1 gangliosidosis by gene therapy use AAV9 for intravenous delivery (ClinicalTrials.
gov identifier NCT03952637) and AAVrh10 or AAVhu68 for CSF-mediated delivery via the cisterna magna (NCT04273269 or NCT04713475, respectively). The aim of the present study was to evaluate the impact of AAVrh. 10 vector carrying species-specific GLB1 on enzyme activity and lysosomal storage in the CNS of mouse and feline disease models of GM1 gangliosidosis. Different routes of CNS delivery were investigated, including intraparenchymal and intracerebroventricular (i. c. v. ) in GM1 gangliosidosis mice and i. c. v. , intra-cisterna magna (i. c. m. ), and intrathecal lumbar (i. t. l. ) in the GM1 gangliosidosis cat model. In addition, we investigated in a good-laboratory-practice (GLP) study whether the clinical vector (LYS-GM101) carrying human GLB1, administered into the cisterna magna of nonhuman primates (NHPs), was able to safely achieve therapeutically relevant b-gal expression and broad enzyme distribution in a brain with an architecture and size more close to human, to confirm the scalability of this approach.
While i. t. l. delivery produced elevations in b-gal enzyme activity in spinal cord, this route was ineffective at delivering b-gal to the cerebrum and cerebellum. In general, the highest b-gal enzyme activity in both the brain and spinal cord resulted from i. c. m. infusion, ranging from 0. 08-to 0. 62-fold normal (WT) levels in the brain and 0. 47-to 2. 0-fold normal levels in the spinal cord. Although no statistical difference in b-gal activity existed between i. c. m. and i. c. v. delivery routes, i. c. m. produced the highest mean b-gal activity in 15 of the 16 blocks of the CNS. b-gal activity was also measured in peripheral organs (data not shown), where the highest level was measured in the liver, with mean values similar across injection routes and ranging from 0. 72to 1. 1-fold normal.
35 en though the histopathologic findings observed with LYS-GM101 in NHPs were asymptomatic, they warrant careful monitoring for signs of sensory neuron toxicity in the first-in-human P1-GM-101 clinical trial (ClinicalTrials. gov identifier: NCT04273269) that was recently initiated to assess the safety and efficacy of LYS-GM101 in children with GM1 gangliosidosis. Even though T cell responses against the transgene product were not analyzed in the NHP toxicology study, histology did not reveal signs of cytotoxic immune responses. Nevertheless, to mitigate against potential T cell-mediated toxicity, immune suppression is used in the clinical trial. The dose of LYS-GM101 tested in the clinical trial, which is 2-fold lower than the high dose tested in NHPs (i. e. , 2. 0 Â 10 12 vg/mL of CSF), is expected to restore greater than 20% of normal b-gal activity in the brain and spinal cord of patients with GM1 gangliosidosis.
ACKNOWLEDGMENTS We thank  Kimberley S. Gannon  for her participation in the design and implementation of these studies. We thank the  ERBC team  for their help in the NHP GLP study, the  Genosafe team  for qPCR and b-gal enzyme activity analysis, the  Gene Therapy Immunology Core team  for the anti-b-gal and anti-AAVrh10 antibody assays, and the  Lysogene team  for their continuous support and discussions.
10 -3 m to easily recover the cooling energy stored inside the PCM. In this work, a CFD tool was used to carry out the numerical simulations. A quadrilateral grid was applied to construct the computational domain using a meshing tool. The hot air is introduced into the cavity via an inlet opening of 0. 018 m with a fixed velocity of 0. 57 m s -1 leading to a Reynolds number of Re = 683, and extracted naturally through an outlet opening measuring 0. 024 m. A User-Defined Function (UDF) was employed to use real and time-dependent ambient temperature (Ta) extracted from METEO-NORM software, of three Moroccan cities (Fez, Ifrane and Marrakech) as free stream temperature of convective walls and as inlet temperature of the 2D cavity shown in Fig. 1. In this study, the 24th day of July with 10 h of simulation is considered (from 06h to 16h) to compare the performances of the cooling ceiling with PCM and without PCM in the three different Moroccan climates classified as Csa, Csb and BSh by the Köppen-Geiger climate classification for Fez, Ifrane and Marrakech, respectively (Fig.
Terrestrial laser scanning (TLS) data acquisition The TLS data were acquired using a RIEGL VZ-400i instrument. For this study, we used a vertical and horizontal scan resolution of 40 mdeg, which results in a point spacing of 34 mm at 50 m distance from the scanner. The beam divergence of the instrument is 0. 35 mrad. The laser pulse repetition rate used was 600 kHz, allowing a measurement range of up to 350 m and up to eight returns per pulse. To ensure a full 3D representation of the canopy, each transect consisted of three scan lines parallel to each other (Fig. 1  and 2a ). The scans were spaced by 5 m. This spacing is much smaller than the 10-40 m usually applied in previous studies  (Wilkes et al. , 2017) , to minimize data uncertainties due to occlusion in a dense tropical forest, as well as to maximize the acquisition of data in the upper canopy.
Given that the VZ-400i scans within the zenith angle range of 30-130 • , one additional measurement was acquired at each sampling position with the scanner inclined at 90 • from the vertical. This resulted in a sampling of the full hemisphere in each scan location. No co-registration targets were used in the data acquisition and the final co-registration was done in the RiSCAN PRO software version 2. 9, provided by RIEGL.