dataesr/scientific-paragraphs-categorization huggingface dataset:
Background. To date, there is no clear consensus on the superiority of shoulder hemiarthroplasty (HSA) or reverse shoulder arthroplasty (RSA) for the treatment of acute proximal humeral fractures (PHF). Objectives. The aim of this study was to review the relevant literature for level I and II studies reporting clinical outcomes and revision rates for HSA or RSA in the treatment of acute PHF. Methods. Two electronic databases (PubMed, and Embase) were systematically searched for level I and II studies published after 1998 reporting clinical and/or radiographic outcomes of primary HSA or primary RSA as treatments for acute PHF.
Search strategy An electronic literature search was conducted using the Medline (PubMed)      A total of 148 articles were duplicates, 569 were excluded by reading their titles and/or abstracts, and a further 15 articles were excluded by reading their full text, because they were not level of evidence I or II studies. No additional relevant articles were identified from citations in the full-text articles. This left a total of nine articles from which data were extracted for this review (. Fig. 3 ;  [2, 3, 6, 8, 11, 22, 28, 32, 37] ).
Data extraction and quality assessment Two investigators (LN and AM) independently tabulated and verified the following data from each article: first author, study design, etiology, treatment, cohort size, age atsurgery, follow-up, clinical and radiographic outcomes, reported complication, and revision rate. In cases of discrepancies between abstract and full text, data were extracted from the most comprehensive source. Disagreements were discussed until consensus was reached. Level I studies were evaluated for bias using the Jadad Scale [20] as modified by Gummesson et al. [19] , which evaluates randomization method, blinding, and description of dropouts/withdrawals with preset scores for each question from -1 to 1 point. Total scores range from -2 (lowest quality) to 5 (highest). Level II studies were evaluated for quality using the Methodological Index for Non-randomized Studies (MINORS) checklist  [35] , which assesses articles on 12 methodological items.
Given the distinct risks (loss of reduction, screw cutout, intraarticular screw penetration, and avascular necrosis) and benefits (bone stock preservation, anatomic healing) of ORIF  [29, 36, 38] , this technique is usually preferred for younger patients, which renders comparison difficult  [13]. However, a recent study of 1791 surgically treated patients with PHF, from the National Surgical Quality Improvement Program database [12], reported that, compared with HSA and with RSA, ORIF is an independent protective factor against complications, although patient comorbidities remain stronger predictors of short-term complications than surgical treatment. While there is general consensus on the surgical treatment of displaced fourpart fractures in younger patients, some controversy pertains to elderly patients, who are more likely to be osteoporotic, have low functional demands, and slow recovery.
Methods Five centers specializing in shoulder surgery participated in this study. Portions of this data have recently been used in published articles  [14, 15, 18, 24, 26]. However, the current analysis is unique and has not previously been published. All cases treated between September 1991 and October 2004 were included in this study if the following inclusion criteria were all fulfilled: 1. Diagnosis of primary osteoarthritis of the glenohumeral joint 2. Absence of rotator cuff tears 3. A minimum follow-up of 5 years 4. Treatment with the same 3rd-generation total shoulder arthroplasty with a cemented keeled glenoid component 5.
Danksagung Diese Arbeit wurde durch die DFG im Rahmen des SPP1784 (HE3397/8-1, HE3397/13-2, to M. H. ,SCHA750/20-2 to R. S. , KL2937/1-2 to R. K. ,R O4681/6-1 to J. -Y. R. ,L E3260/2-1 to S. A. L. ) unterstützt. Y. M. wurde durch das ANR-DFG-Stipendium HTRNA-Mod ANR-13-ISV8-0001 und Forschungsmittel der Region Lothringen (Frankreich) unterstützt. Die Zusammenarbeit erfolgte im Rahmen des COST EPITRAN Netzwerks. U nterstützung durch die IMB Core Facility wird anerkannt.
Because the landscape had already undergone strong anthropogenic changes before, the recorded impact of the Walser was ultimately less prominent than could be expected. Data availability. The geochemical data underlying this study are given either in the tables of the article or in the Supplement published with this article. The pollen data can be requested by contacting the first author. Supplement. The supplement related to this article is available online at: https://doi. org/10. 5194/egqsj-68-13-2019-supplement. Author contributions. As corresponding author, CvS was responsible for planning and carrying out field work, geochemical analyses, data processing, and designing and writing of the paper. The pollen analyses were conducted by AL, whereas FDV contributed to sample preparation, geochemical analyses and designing of the paper.
Microarray and Experimental Design The DNA microarray was designed using the published genome sequence for S. Enteritidis strain NCTC13349 2. The microarray, consisting of probes matching 3971 ORFs (representing 94. 4% of S. Enteritidis gene composition), was designed using Agilent's e-array software 3. Note that 235 ORFs were not included due to restricted design parameters of the e-array program. The custom oligonucleotide microarray was manufactured by Agilent Technologies using an 8 × 15 K format and included each probe in duplicate. Microarray hybridization and data analysis were performed by the Pasteur Institute (Transcriptome and Epigenome Platform PF2, Paris, France). S. Enteritidis exposed for 45 min to EWF at pH 9. 3 was compared to a reference (0 min incubation, i. e. , S. Enteritidis washed with EWF at pH 9.
3). For each time point, three arrays were hybridized with three independent biological replicates in duplicate (giving three biological replicates and two technical replicates). Cy3 and Cy5 dye-swap design was included in order to reduce dye-specific effects. The data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE144179 4. To compare the genes differentially expressed between EWF and EWMM, the data obtained from a previous study for exposure of S. Enteritidis to EWMM (at pH 9. 3 for 45 min) were used  (Baron et al. , 2017)   5.
Data Acquisition and Pre-processing of Microarray Data Images of the microarrays were scanned using an Axon 4000a scanner (Axon, Instruments, CA, United States) and intensity data were extracted using the GenepixPro 6. 1 software. Raw microarray data were first normalized using the LOWESS (Locally Weighted Scatter Plot Smoother) regression option in the R software suite, version 2. 10. 1 6  , to correct for dye-bias within the array, followed by median normalization to normalize across all arrays.
Differential Expression Analysis of Microarray Data Changes in gene expression upon incubation were recorded as fold changes (ratio at 45 min cf. 0 min, in EWF; ratio in EWF cf. EWMM, at 45 min). Statistical significance was estimated with a moderated t-test using the LIMMA package  (Smyth, 2004)  of the R software suite (version 2. 10. 1). Genes that exhibited change in expression (with respect to the control) with P ≤ 0. 05 were considered as differentially regulated. Differentially expressed genes were initially categorized by function according to the Clusters of Orthologous Groups 7  designations and categorization was subsequently optimized manually.
RNA extractions were performed on S. Enteritidis incubated in EWMM or EWF at 45 • C for 0 and 45 min. RNA extracts thus obtained was subjected to qRT-PCR, in triplicate, for each selected gene. Standard curves were generated to calculate the copy number of each gene in each sample. The three most stable control genes under the conditions used here were determined by geNorm 9  from five potential genes. qRT-PCR data were normalized by geometric averaging of three internal control genes (asmA, emrA, orf32; primers in Table  1 ). Changes in gene expression upon incubation were recorded as fold change (ratio at 45 min cf. 0 min, in EWF; ratio in EWF cf. EWMM, at 45 min). To highlight the differential gene expression in the two media, the ratio between the fold change at 45 min in EWMM and the fold change in EWF was calculated for each selected gene.
In order to identify those genes that are differentially expressed in response to the presence/absence of EW proteins, microarray data obtained from our previous study (S. Enteritidis exposure to EWMM for 45 min at 45 • C;  Baron et al. , 2017)  was compared to that obtained with EWF at 45 min. A statistical comparison between the fold changes obtained for each gene after 45 min exposure to either EWMM or to EWF at 45 • C showed that only 64 genes exhibited a significant difference of greater than 2-fold (Table  2 ).
Enteritidis was compared in EWMM, EWF and EW at 30 and 45 • C (Figure  4 ) using the diSC3(5) fluorescent dye method  (Epand et al. , 2010). The results show that the relative fluorescence intensity was not affected by temperature (30 vs. 45 • C) under any of the Up-regulated, down-regulated, and non-regulated genes are represented in red, green or black, respectively. Genes with a ≥4-fold change in expression are in bold. The metabolites predicted to be increased are underlined. Up-regulated, down-regulated and non-regulated pathways are represented by thick, broken, or fine arrows, respectively. Genes with different expression levels between the incubation in EWMM (from  Baron et al. , 2017)  and in EWF are boxed in pink. Metabolic pathway data were obtained from KEGG (www. genome. jp/kegg).
Calculation of fold change by qRT-PCR was determined from the number of RNA copies after 45 min of incubation divided by the number of RNA copies at 0 min of incubation. Data were normalized using values for three internal control genes  (asmA, emrA, orf32). Standard deviations data are in parentheses. Highlighted fold changes correspond to significantly (p = 0. 05) up-regulated (dark gray) and down-regulated (light gray) genes. The ratio between the fold change at 45 min in EWMM and EWF was calculated from microarray data (from  Baron et al. , 2017  for EWMM and this study for EWF) and from qRT-PCR analysis (this study) for each selected gene. affected (highlighted in Figure  3 ), and the degree of expression change achieved (average difference of 3-fold by microarray).
72 and 0. 48 mL delay volumes, respectively). The mobile phase pH was systematically adjusted using a Seven-Multi S40 pH meter (Mettler Toledo, Greifensee, Switzerland). Data processing and instrument control were performed by Empower Pro 3 software (Waters). For data transfer and calculations, Python programming language (v. 3. 7, Anaconda Python Distribution, https://anaconda. com ) using NumPy package was applied.
The typing data are expressed as a combination of group, variable VR1 and VR2 of PorA, variable region of the protein FetA and clonal complex. Furthermore, because of French vaccination strategies against B IMD, serogroup B isolates corresponding to clusters are also investigated for coverage by the Bex-sero® vaccine. In general, an isolate is covered if the sequence of PorA P1. 4 antigen is detected and/or if the expression level of at least one of NHBA, fHbp or NadA antigens is higher than the protective bactericidal threshold, as determined by the Meningococcal Antigen Typing System (MATS)  [10]. MATS can be applied when culture isolates are available. In this study, the diagnosis was confirmed by PCR only and no cultured isolates were available.
Vaccination coverage estimates In the middle school (11 to 15 years pupils) and in the high school (15 to 19 years old students), vaccination sessions were organized directly on site for each dose. The vaccination coverage was calculated in real-time after each vaccination session as the ratio of the number of vaccinated children to the number of children in the school. In the community (11 to 19 years old individuals living or studying in the area), two sources of data were used to assess vaccination coverage during the campaign. The total number of vaccine doses distributed to pharmacies was obtained from wholesale distributors. These distribution data were exhaustive and were transmitted regularly by wholesale distributors to the RHA during the campaign. To estimate the proportions of dose 1 and dose 2 that were distributed, we used delivery data from a sample of 18 pharmacies in the area which received 62% of the total vaccines distributed by wholesale distributors during the campaign.
And lastly, the younger the children are, the greater the probable influence of parents in the decision making process concerning vaccination. Other sociodemographic factors might have influenced vaccine uptake  [20]  such as gender, socio-economic group, education level of parents. However, we had no individual data on the vaccinated population to address this question. The two sources of data used for estimating vaccination coverage in the community were complementary and the method could be used in future campaigns. Distribution data from wholesale distributors were exhaustive and transmitted regularly during the campaign. However, those data did not contain information about the proportions of each dose. Delivery data obtained from a sample of 18 pharmacies allowed us to estimate the proportions of first and second dose.
A limit of the method is that we hypothesized that the proportions of doses 1 and 2 in this sample of pharmacies were the same than in the other pharmacies of the area. The best way to assess vaccination coverage would have been to use the French healthcare reimbursement databases. However, the delay necessary to obtain these data ranges from 6 to 12 months which was not compatible with our objective of real-time monitoring of the vaccination coverage. Although less accurate, our method allowed the health authorities to assess in real time the dynamic of vaccination in the target population. High variation in the notification rates of adverse effects was observed between the first (31. 2%) and the second vaccination campaign (3. 7%). This can be explained by the modalities of data collection.
Contagious caprine pleuropneumonia is an infectious and contagious disease affecting goats and wildlife ruminants, mostly in Africa and Asia. It is caused by a mycoplasma, Mycoplasma capricolum susbp. capripneumoniae, which is very fastidious. This may be the reason why there are few reports of its isolation and characterization. This study describes the development of a whole genome typing strategy based on sequencing reads assemblies on a reference genome (Abomsa, GenBank accession LM995445) and extraction of informative single nucleotide polymorphism. FASTA sequences inferred from the variant calling files were used to establish a comprehensive phylogenetic tree based on 2880 SNPs. This tree included a total of 34 strains originating from all the regions where CCPP has been detected, as well as strains isolated from wildlife.
Ten ml of cultures were centrifuged at 12000g for 25min, the pellet was resuspended in 200μl of PBS, and DNA was extracted using the Qiagen blood and tissue kit and sent to Macrogen (Seoul, Republic of Korea) for DNA sequencing. Genomic libraries (Illumina TruSeq DNA PCR Free) were constructed and then analysed by Illumina HiSeq 2500 (rapid run mode 2X250bp sequencing lane). Genome assemblies were performed with Seqman NGen (V14) using the genome of Mccp strain Abomsa (GenBank accession LM995445) as a reference. The assemblies were first performed with a single genome representative of each of the six clusters formerly identified by a large-scale genomic analysis/a sample of 57 genes  (Dupuy et al. , 2015). Inconsistencies were resolved by analysing individual flanking reads, which were used to evaluate if the inconsistency was due to a deletion or an insertion.
Core genome analysis Snippy pipeline (https://github. com/tseemann/snippy) was used to analyse complete genome sequences present in the NCBI database and raw sequence data generated from the CIRAD-ASTRE biobank. For FASTA sequences previously published ((Dupuy and Thiaucourt, 2014)  (Falquet et al. , 2014)   (Yu et al. , 2013)   (Li et al. , 2020) ), pseudo reads were generated to keep a homogeneous methodology. For each sample, reads were mapped on the genome sequence of strain Abomsa with "bwa-mem"  (Li and Durbin, 2009) , keeping only reads uniquely mapped with a quality above 60 (Phred score). Duplicates were filtered with samtools  (Li et al. , 2009)  and soft clipped positions removed with samclip (https://github. com/tseemann/samclip). Variants were called using freebayes  (Garrison and Marth, 2012) , filtering variants with less than 10X coverage and a calling quality of 100.
Additional filtering steps were taken to remove variants called from read extremities. FASTA sequences were inferred from the variant calling files and core genome alignments were produced with snp-sites  (Page et al. , 2016). Maximum-likelihood phylogenetic trees were inferred from core genome alignments using FastTree  (Price et al. , 2010)  with a GTR þ gamma model. Shimodaira-Hasegawa tests (SHT) were used to assess the local support values of the nodes. Tree visualization was done using iTOL  (Letunic and Bork, 2019)  or Figtree (http://tree. bio. ed. ac. uk/software/figtree/).
This technique is particularly well suited for Mccp whose genome is not prone to recombination events. The WGS analysis pipeline described here will easily accommodate additional samples to the core genome alignment, and become a useful international portable surveillance procedure in the near future. Its primary use will be the analysis of transmission pathways and spatiotemporal analysis of CCPP. However, additional laboratory efforts to obtain complete whole genomes and metabolomics results for the whole set of strains, could provide valuable information when integrated into more comprehensive epidemiological databases. Information on strain virulence would be particularly helpful for genome data mining and deciphering the basis for virulence traits that are still elusive for Mccp.
Thioridazine Induces Autosis in OS CSC-Enriched Populations Next, we analyzed the cytotoxicity of TZ in UMR and MN CSC-enriched populations. Based on literature and previous experiments (data not shown), TZ treatment for 24 h at 10 µM kills the majority of cells in both CSC-enriched populations. To test whether some cells could recover after this treatment, we analyzed sphere development during the five days after seeding in the absence or in the presence of TZ 10 µM (or 20 µM, data not shown). As shown in Figure  6A ,B, we observed that TZ inhibited large sphere formation in both CSC-enriched populations (Figure  6C, D ). To further investigate cell behavior during TZ-induced cell death, we performed TEM experiments after treatment with different TZ concentrations for various periods (Figure  7A, B ).
Effect of Thioridazine on CSC Formation After sphere dissociation, the cells were seeded in a 24-well microplate (1000 cells/cm 2 ) in the presence or the absence of thioridazine (TZ; Bio-techne, Lille, France) at 10 µM. On day 5, the spheres were counted and their diameter was measured using the AxioVision software (Zeiss).
Results For years now, E-cadherin is often considered as a tumour/invasion suppressor. However, recent studies demonstrated the involvement of E-cadherin in tumour invasion pro-cess19,24,31. To clinically confirm E-cadherin's profile in pancreatic cancer, we first accessed PaCaOmics data constituted by a series of patient-derived xenografts (PDX) from a multi-centric clinical trial  (25). PDAC tumours included in this PaCaOmics program are considered as localised, locally advanced and metastatic  (25). From these PDX samples, RNA-seq analysis were performed and E-cadherin protein expression was determined by immunodetection and scored as described in material and methods. First, we tried to correlate E-cadherin expression at RNA or protein levels respectively with various criteria: (1) the survival rate of patients (Figure  1A  and 1B); (2) the stages of the pathology (localised, locally advanced and metastatic) (Figure  1C  and 1D); (3) the pancreatic adenocarcinoma molecular gradient (PAMG) ; a transcriptomic signature that predicts clinical outcome (25) (Figure  1E  and 1F ) and (  4 ) the subtypes of PDAC-Classical vs Basal-like subtypes (26) (Figure  1G  and 1H ).
Materials and Methods E-cadherin RNA-seq and protein analysis on tumours samples. Data from PaCaOmics program (Clinical-Trials. gov: NCT01692873) were used for E-cadherin expression analysis. RNAseq was performed as previously described on PDAC samples from 90 xenograft tumours  (25). E-cadherin was also immunodetected on a tissue array containing PDAC samples from 83 xenograft tumours. E-cadherin staining was scored as previously described  (24). Different correlations were performed: E-cadherin transcript and E-cadherin protein level were correlated with the patient's survival or with the pancreatic adenocarcinoma molecular gradient (PAMG) signature  (25).
After washing, the sections were incubated with Alexa conjugated antibodies, washed and mounted in aqueous mounting medium. Images were captured with LSM 880 Zeiss confocal microscope equipped with ZEN Software. Human pancreatic cancer samples were obtained as previously described  (51). Indirect immunofluorescence microscopy. Cells were fixed in 4% formaldehyde for 30 min then permeabilized and blocked in PBS/BSA 4%/Saponin 0. 1% for 1h. Cells were successively incubated with indicated primary antibodies in PBS/BSA 1%/Saponin 0. 1% for 2h at RT and with Alexa-Fluor-594 and -647 conjugated secondary antibodies (PBS/BSA 1%/Saponin 0. 1%, 1h at RT) raised against mouse and rabbit Igs. Samples were then washed and mounted in ProLong Gold antifade reagent (Thermofisher). Images were acquired with Sp5 Leica or LSM 880 Zeiss confocal microscopes equipped respectively with LAS AF Lite or ZEN Software.
Z-Stack acquisitions (Range: 0. 5µm) were performed using a 63X objective magnification and analysed through orthogonal projections using ImageJ software (rsb. info. nih. gov/ij/). Invadopodia assay. Coverslips were coated with FITC-conjugated gelatin (Sigma), fixed with Glutaraldehyde 0,5% and incubated for 3 min at RT with Sodium Borohydride (5mg/ml). After several washes, 10 000 isolated cells were seeded on top of the coverslip. BxPC-3 cells were incubated 16h at 37°C, fixed in 4% formaldehyde and stained for proteins of interest as described previously. The areas of degraded matrix were observed using a LSM880 Zeiss confocal microscope (25X objective). 15 microscopic fields per coverslips were acquired with all fluorescent channels. Immunoprecipitation. BxPC-3 cells were plated in 10 cm2 culture dishes.
Data Processing Protocol. Relative intensity-based label-free quantification (LFQ) was processed using the MaxLFQ algorithm from the freely available MaxQuant computational proteomics platform, version 1. 6. 3. 4. Spectra were searched against the Human database extracted from UniProt on the 1th of September 2020 and containing 20375 entries (reviewed). The false discovery rate (FDR) at the peptide and protein levels were set to 1% and determined by searching a reverse database. For protein grouping, all proteins that cannot be distinguished based on their identified peptides were assembled into a single entry according to the MaxQuant rules. The statistical analysis was done with Perseus program (version 1. 6. 14. 0) from the MaxQuant environment (www. maxquant. org). Quantifiable proteins were defined as those detected in above 70% of samples in one condition or more.