dataesr/scientific-paragraphs-categorization huggingface dataset:
HOXA1-FL mRNA expression is upregulated in human MDS To determine if HOXA1 was dysregulated in MDS patients, HOXA1 mRNA expression was evaluated by in silico analysis of a microarray database of human MDS CD34 + cells (17 healthy controls, 183 MDS patients)  (31). HOXA1 mRNA expression was significantly increased in approximately 50% of MDS samples in comparison to healthy controls, with a mean fold increase of 1. 87, although some patients showed up to 12-fold increased expression (Fig. 7A ). Amongst the 11 HOXA cluster genes, HOXA1 displayed the highest fold-change in expression in MDS patient cells (Table  S4 ). Furthermore, HOXA1 was significantly upregulated in patients with MDS independent of chromosomal abnormalities (Fig. 7B ). HOXA1 expression was significantly increased in two MDS subtypes assessed on the microarray, classified according to the French-American-British (FAB) system: RA with ringed sideroblasts (RARS) and RA with excess blasts 1 (RAEB-1) (Fig.
S5A ). Somatic mutation data were available from the published RNA-seq series  (32)  and the RAEB-1 and RAEB-2 patients shown in Fig. 7D  (33) therefore the mutation patterns were assessed together with HOXA1-FL and HOXA1-T expression (Fig. S5B-C ). The majority of patients in both datasets had one or more somatic mutation, irrespective of HOXA1 expression. There were no differences in the distribution of somatic mutations within the different functional categories based on HOXA1-FL expression (Fig. S5B-C ). The 3D atomic structure of HOXA1 has not yet been determined, however, it shares 78% homology with HOXB1, for which the structure has been determined  (34). To understand how HOXA1-T might regulate HOXA1-FL we threaded amino acids 202-290 of the HOXA1 sequence onto the solved structure of HOXB1 in complex with DNA and its co-factor PBX1, then minimized the complex utilizing molecular dynamics.
Gene Expression Analysis Gene expression data for 183 MDS CD34 + cells and 17 controls  (31)  were obtained from Gene Expression Omnibus microarray database (GEO accession number GSE19429). RNA-seq data for 44 MDS and 23 controls  (32)  were likewise obtained (GEO accession number GSE111085). For murine gene profiling studies, BM GFP + CMPs and MEPs were sorted from primary recipient mice at 16 weeks post-transplant (n= 4 independent transduction groups/vector, with 4 mice per group). Total RNA was extracted using the RNeasy Micro kit (Qiagen). RNA was hybridized to the Affymetrix Mouse 1. 1 ST genechip at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Australia in accordance with the manufacturer's instructions.
Statistical analyses Unless otherwise indicated all data are expressed as the mean ± the standard error of the mean (SEM) for n= number of samples. One-way analysis of variance (ANOVA) or twoway ANOVA followed by post-hoc testing were used for multiple comparisons. The paired or unpaired two-tailed Student's t-test were used for other statistical comparisons where indicated. Statistical analysis was performed using Prism 8 software (GraphPad), with p<0. 05 considered significant. Kaplan-Meier survival plots were prepared using Prism 8 software (GraphPad). roles in B lymphopoiesis. Blood 2021;138:304-17 doi 10. 1182/blood. 2020005865. Figure Legends G F P + W T -H o x a 1 G F P - M U T -H o x a 1 G F P + M U T -H o x a 1 G F P - H o x a 1 -T G F P + H o x a 1 -T G F P - M X I E G F P + M X I E G F P - W T -H o x a 1 G F P + W T -H o x a 1 G F P - M U T -H o x a 1 G F P + M U T -H o x a 1 G F P - H o x a 1 -T G F P + H o x a 1 -T G F P - p=0.
Acknowledgements We thank  Tanja Jovic  and  Mannu Walia  for excellent technical assistance,  Jörg Heierhorst  for excellent discussions, the  SVH Bioresources Centre  for care of experimental animals and  SVI FACS Facility  for FACS sorting. This work was supported in part by grants from the  Leukaemia Foundation  (to LEP, MW, EKB and MWP), the  Cancer Council Victoria (to LEP), Cancer Australia  (to LEP and JKH), the  Zig Inge Foundation  (to LEP), the  Leukaemia Foundation  (to MW) and the  Victorian State Government Operational Infrastructure Support Program  (to St. Vincent's Institute). ST was the recipient of a  Leukaemia Foundation   Clinical  PhD Scholarship supported by  Andrew Cadigan  in honour of  Chris Simpson. CSG was the recipient of an  Australian Government Research Training Program   PhD Scholarship.
abscessus GD01 transposon insertion mutant strains. Plaque assays were performed at least twice with similar results. The locations of amino acid substitutions in Muddy gp24 that confer the ability to infect TPP-deficient strains (bottom panel) are indicated. Extended Data Fig. 2 ). Complementation fully restores liquid infection of GD180_RM2 and partially restores infection of GD22_RM4 (Fig. 4d ), as well as fluorescence with the reporter phage (Fig. 4e, f ). These data are consistent with an early defect in phage infection in these mutants, consistent with loss of adsorption to the cell surface. We note that disruption of TPP synthesis does not interfere with Ziehl-Neelsen staining of the bacteria or alter antibiotic sensitivities (Extended Data Fig. 3 ).
6c ). It is plausible that the BPs resistant phenotype results from overexpression of this gene. Analysis of the cell wall lipids shows that all of the mutants retain TPPs, except for GD01Tn_phKSW1_RM10 (Fig. 6d ), which has a Tn insertion in papA3 in addition to a secondary insertion in MAB_1686 (Extended Data Table  1 ). Two additional mutants (GD01Tn_phKSW1_ RM1 and RM4) have an insertion in the nearby MAB_1690 gene and have normal TPPs (Fig. 6d ); MAB_1686 and MAB_1690 are within a large Fig. 3  | Phage infection profiles of M. abscessus phage-resistant mutants. a, Tenfold serial dilutions of phage lysates (as indicated on the left) were spotted onto solid media with M. smegmatis mc 2 155, the parent M. abscessus strains or spontaneously isolated phage-resistant mutant (RM) derivatives.
Phylogenetic analysis of TPP pathway amino acid sequences in M. abscessus A phylogenetic tree was constructed for a concatenated alignment of amino acid sequences of the five TPP synthesis pathway members for 143 clinical isolates of M. abscessus and M. abscessus ATCC19977. Homologues were identified using MMSeqs2 (v. 13. 45111) and phammseqs (v. 1. 0. 4)  50  and subsequently aligned using ClustalO (v. 1. 2. 4) and Trimal (v. 1. 4. 1)  51. A concatenated alignment was generated with a custom Python script and the maximum-likelihood phylogeny was generated using RAxML (v. 8. 2. 12)  52.
Reporting summary Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article. Extended Data Fig. 2  | Gating strategy for flow cytometry analysis of fluorophage-infected bacteria. Bacteria untreated or infected with nonfluorescent phages were used as controls. The first gate was plotted on SSC-A / FSC-A to exclude cellular debris. SSC-H / SSC-A was analysed to eliminate multiple cells. The gate for fluorescence was drawn thanks to controls to exclude non-fluorescent bacteria. The analysis was performed on approximately 300,000 bacteria using NovoExpress software. Here is shown an example of analysis for GD22 strain performed at least twice.
Results and discussion Vitamin D supplementation elevates type I interferon, chemokine and PRR gene expression and decreases IL-1 and inflammasome gene expression in unstimulated samples. Whole blood from control calves and calves that had been supplemented with vitamin D 3 from birth was stimulated for 24 h with PAMPs LPS, Pam3CSK4 and R848 at 3, 5 and 7 months of age, as well as a 24h unstimulated condition (Fig. 1a ). The vitamin D supplemented calves had significantly increased 25(OH)D concentrations at 5 and 7 months of age (Fig. 1b ). Firstly, expression of 96 genes were measured in the unstimulated samples at 7 months of age. Sixteen genes exhibited no or low expression, and therefore the other 77 genes (excluding the normaliser genes) were used for subsequent analysis. Principal component analysis (PCA) of unstimulated (baseline) gene expression data from the 77 genes revealed that vitamin D supplemented calves clustered separately to controls, indicative of a distinct expression profile (Fig.
1. Unpaired t tests were used to calculate differences between groups for gene expression scores. Two-way ANOVA was used to calculate differences between groups in protein levels over 3 time points using weight difference between timepoints as a covariate. All box and dot plots were made with ggplot2 package, PCA plots in Factoextra package, heatmaps with ComplexHeatmaps package and radar plots with fmsb package. ComplexHeatmaps package carries out hierarchical clustering using the k-means clustering method.
l. (4. 8%), of Haemaphysalis leachi group (4. 6%), Hyalomma truncatum (2. 6%), Hyalomma rufipes (1. 7%), Rhipicephalus muhsamae (1. 1%), Rhipicephalus (Boophilus) annulatus (0. 6%), Rhipicephalus (Boophilus) decoloratus (0. 3%), Ixodes rasus (0. 1%), Ixodes spp. (0. 2%) and Rhipicephalus spp. (3. 3%). Tick legs were subjected to MALDI-TOF MS analyzes, and the spectra of 929 (98. 4%) specimens were of good quality. Analysis of these spectra provided intra-species reproducibility and interspecies specificity of MS profiles obtained from the different species. Our in-house MALDI-TOF MS arthropod database was upgraded with spectra from 44 specimens of 10 different tick species. Blind testing of good quality spectra revealed that 99% agreed with the morphological identification. Of these, 96. 9% had log score values (LSVs) between 1.
, 2016). To overcome this issue, molecular biological approaches (PCR, sequencing) have been developed over several decades to identify these arthropods by amplifying different target genes fragment  (Mangold et al. , 1998; Lv et al. , 2014). However, these methods require expertise and a molecular biology technical platform, which is expensive and time-consuming, preventing their use in large scale studies. In addition, the lack of referenced sequences in GenBank for uncommon tick species may increase the limitation of this tool  (Yssouf et al. , 2016). Recently, innovative technologies have been developed for the identification of arthropods in general, with the development of a multiplex technique using mass spectrometry coupled with a matrixassisted laser desorption/ionization time-of-flight analyzer: MALDI-TOF MS.
MALDI-TOF MS parameters The leg proteins mass profiles of each tick sample were generated using a Microflex LT MALDI-TOF Mass Spectrometer (Bruker Daltonics, Germany). Measurement was performed with detection in the linear positive-ion mode at a laser frequency of 50 Hz within a mass range of 2-20 kDa. The acceleration voltage was 20 kV, and the extraction delay time was 200 ns. Each spectrum corresponded a succession of 240 laser shots taken in six regions of the same spot and acquired automatically by AutoXecute method with the defaults settings of the flexControl v2. 4 software (Bruker Daltonics)  (Boyer et al. , 2019; Kumsa et al. , 2016).
Spectra analysis and reference database upgrading The spectral profiles obtained from the tick legs were first visually controlled using the Flex Analysis v3. 3 software to evaluate spectral quality (peak intensities, reproducibility, homogeneity), then processed in ClinPro Tools v2. 2 software and MALDI-Biotyper v3. 0. software (Bruker Daltonics, Germany). The assessment of the reproducibility and specificity of the MS spectra from ticks was performed by principal component analysis (PCA) and dendrogram analysis (cluster analysis). The dendrogram was performed using MALDI-Biotyper v3. 0. software, as previously described  (Boyer et al. , 2019). Based on the consistency of the morphological identification of tick and molecular confirmation, one to twelve specimens per species (a total of 44 spectra) were used to upgrade our in-house arthropod MALDI-TOF spectra database, which already contained spectra of nine tick species (Amblyomma variegatum, Haemaphysalis leachi, Hyalomma rufipes, Hyalomma truncatum, Rhipicephalus (Boophilus) annulatus, R.
(B. ) microplus, Rhipicephalus (Boophilus) decoloratus, Rhipicephalus muhsamae, R. sanguineus temperate lineage from Algeria and R. sanguineus tropical lineage from Mali and Vietnam). These spectra had been obtained from tick specimens that were fresh, frozen or preserved in alcohol for a long time. (Diarra et al. , 2017; Ahamada M'madi et al. , 2022). Those from Ixodes rasus, Rhipicephalus lunulatus, Haemaphysalis muhsamae and Haemaphyslis paraleachi were not previously present in our database. To upgrade the database, reference spectra were created by combining the results of spectra from specimens of each species using the automated function of the MALDI-Biotyper v3. 0 software (Bruker Daltonics). Main spectrum profile (MSP) were created based on an unbiased algorithm using peak position, intensity and frequency data using the default parameter  (Boyer et al.
Blind test for identification A blind test against the upgraded database was performed with the spectra of the remaining tick specimens from Cameroon. The reliability of tick species identifications was estimated using the log score values (LSVs) obtained from the MALDI-Biotyper software, which range from 0 to 3. These log score values, obtained from each spectrum of the samples tested, correspond to the degree of similarity between the MS reference spectra in the database and those submitted by blind tests.
DNA extraction and molecular identification of ticks Each half-tick without legs was placed in a 1. 5 mL tube containing 180 µL of G2 lysis buffer and 20 µL of proteinase K (Qiagen, Hilden, Germany) and incubated at 56 • C overnight. Genomic DNA extraction was then performed individually from each specimen with an EZ1 DNA Tissue Kit Qiagen according to the manufacturer's instructions. DNA from each sample was eluted with 100 µL of Tris-EDTA (TE) buffer (Qiagen) and stored at -20 • C under sterile conditions to avoid crosscontamination until further analysis. Molecular analyzes were performed with DNA extracted from the ticks used to update the in-house MALDI-TOF MS arthropod database; some engorged females not identified to the species level, all specimens that had LSV< 1. 7 and all specimens with a discrepancy between morphological identification and MALDI-TOF identification.
Phylogenetic analysis of tick species from Cameroon To build the phylogenetic tree, 3 sequences were randomly selected for species with ≥3 sequences and for the other species, all the sequences obtained were used. Sequences from tick species were aligned with BioEdit v 7. 2. 5. 0 software. The aligned sequences were imported into MEGA X v 10. 2. 6 software and phylogenetic trees were made using MEGA X v 10. 2. 6. The maximum likelihood (ML) phylogenetic tree model proposed by default by the software was used to construct the phylogenetic tree. Node numbers are percentages of bootstrap values obtained by repeating 100 interactions of the analysis to generate a majority consensus tree (only those with values equal to or greater than 80 were retained).
MALDI-TOF MS identification of ticks A total of 944 (543 males and 401 females) ticks were subjected to MALDI-TOF MS analysis. Of 944 specimens, 929 (98. 4%) had good spectra visualised by FlexAnalysis v. 3. 3 software. Good quality spectra obtained from the legs of 44 ticks morphologically and molecularly identified (as mentioned below) were added to our MALDI-TOF MS reference database (Table  2 ). The spectra of the ticks introduced in the MALDI-TOF MS database are accessible at the following link; DOI:10. 35081/p7f4-q871. Visualisation of the MS spectra of two specimens per species showed intra-species reproducibility and inter-species specificity (Fig. 2 ). The dendrogram made with the MS spectra of two specimens per tick species identified morphologically showed that specimens of the same species grouped together, confirming once more the intra-species reproducibility and inter-species specificity (Fig.
3 ). In addition, the spectra of R. sanguineus s. l. specimens from Cameroon (known as tropical lineage) cluster with those of the tropical lineage in our database (from Mali and Vietnam) and not with those of the temperate lineage in our database (Supplementary data 1). Of the remaining 885 good-quality tick spectra, 852 spectra of the specimens morphologically identified to species level, 2 Ixodes spp. and 31 engorged Rhipicephalus spp. were blind queried in our updated database. The result of the blind test of specimens identified to species revealed that 845/852 (99. 1%) presented a concordance with the morphological identification. From 845 specimens with concordance, a total of 821 were identified with LSVs between 1. 73   2 ). The identification of these 24 specimens were also confirmed by molecular biology (see below).
The seven tick specimens that showed discordances between morphology and MALDI-TOF MS included ticks morphologically identified as R. (B. ) annulatus (4), R. muhsamae (2), and Hy. truncatum (1) and identified by MALDI-TOF MS as R. (B. ) microplus (4), R. lunulatus (2), Hy. rufipes (1) respectively. However molecular identification confirmed MALDI-TOF identification. The spectrum of one specimen of the 2 Ixodes spp. matched with the spectrum of Ixodes rasus that had been introduced in the database (LSV:1. 78). The other spectrum matched with reference spectrum of R (B. ) microplus but with a low score (1. 21). Of the 31 engorged Rhipicephalus spp. that could not be morphologically identified to the species level, 26 were identified by blind test as R. lunulatus and 2 as R. muhsamae with LSVs between 1.
52 and 2. 07. Molecular identification confirmed MALDI-TOF MS identification of these 28 engorged specimens. The remaining 3 engorged Rhipicephalus sp. specimens matched with the spectra of various species with LSVs between 1. 53 and 1. 65. These 3 specimens could not be identified by molecular biology. The spectrum of one of these 3 Rhipicephalus sp. was temporarily added to the database as a potential reference of spectrum for the remaining Rhipicephalus sp. The blind test showed that the two other unidentified Rhipicephalus sp. indeed matched with the spectrum of the Rhipicephalus sp. introduced in the database with LSVs of 2. 23 and 2. 25.
Molecular identification of ticks A total of 118 morphologically identified ticks were subjected to standard PCR and sequencing. These ticks specimens included 44 whose MS spectra was used to update the in-house MALDI-TOF MS database, 31 engorged females Rhipicephalus spp. not identified to the species level morphologically, 24 specimens whose spectra had a LSVs< 1. 7 when blind tested against the database, 7 ticks with a discrepancy between morphological and MALDI-TOF MS identification, 6 ticks with a low number of collected specimens per species (2 R. (B. ) decoloratus, 2 Ixodes spp. and 2 R. (B. ) annulatus), and 7 to identify species within the Ha. leachi group. The success rate of the sequencing based on the 16S rRNA gene (the main one used in this study) was 88. 1% (104/118), with at least one sequence for each species.
Twelve sequences of the 14 remaining were obtained when targeting 12S rRNA, and 9/11 sequences were obtained when targeting COI gene. The comparison of the sequences obtained from ticks of the same species showed that these sequences presented intra-species identities varying from 97 to 100% (Table  3 ). From 44 specimens used to update the in-house MALDI-TOF MS database, 43 sequences of the 16S rRNA gene fragment were successfully obtained. Blast results indicated that sequences obtained from 5 A. variegatum ticks, 12 R. (B. ) microplus, 9 R. lunulatus, 4 R. sanguineus s. l. , 2 R. muhsamae, 4 Ha. leachi, 3 Hy. truncatum, 2 Hy. rufipes and 1 R. (B. ) decoloratus were from 98. 49% to 100% identity to the corresponding sequences in the GenBank, apart from Ha. leachi which 3 sequences had 99.
64% identity with Ha. muhsamae, and one had 96. 57% identity with Ha. elliptica (HM068961), with no sequence of Ha. paraleachi available in GenBank. The only 16S rRNA sequence obtained from one I. rasus tick In brackets, number of females had 91. 53% identity with the sequence of Ixodes cumulatimpunctatus (MN959774), in the context of limited and partial 16S rRNA sequences of I. rasus in GenBank. The spectrum of this specimen was the one that was including in the database. We also obtained a 644 bp fragment of COI sequence (OP718636) of this specimen. Our 16S and COI sequences of I. rasus were deposited in GenBank (OP698035 and OP718636). For the 31 engorged females of Rhipicephalus spp. , 30 sequences of the 16S rRNA gene were obtained. Twenty-six were 98. 47 to 98. 51% identical to the sequences of R.
lunulatus (98. 47% with LC634585) and 1 Hy. rufipes (99. 75% with ON532092) (Table  3 ). Concerning the remaining 6 tick with low numbers collected specimens, sequences from R. (B. ) decoloratus had 99. 49% and 99. 50% identity with those of GenBank (MN266914). Those from R. (B. ) annulatus were 100% identical to his GenBank counterpart (MT229191). The COI sequence of one Ixodes sp. appeared to be 99. 53% to the sequence of I. rasus obtained from the specimen whose spectra had been introduced in the MALDI-TOF database. The obtained sequence from our 3rd Ixodes sp. with the COI gene was 83. 71% identical to those of Ixodes hirsti (KM821524), in the context of absence of I. rasus COI sequence in GenBank. The 16S and 12S rRNA gene sequencing failed for these 2 Ixodes spp. For the 7 specimens of the Ha.
leachi group, 7 sequences of the 12S rRNA gene were obtained. Four sequences had 99. 70% identity with those from Ha. muhsamae (MT586105), and the other 3 sequences were 97. 05% identical to the sequence of Ha. elliptica (HM068953). Both are members of the Ha. leachi group Table  3. Our 12S and 16S rRNA sequences of Ha. paraleachi (OP698031, OP698032, OP698033 and OP698036) were deposited in GenBank. Phylogenetic analysis revealed that all Cameroon tick individuals belonging to the same species cluster together with their respective homology sequences in GenBank (Fig. 4 ).
Discussion Most studies conducted in Africa on the inventory of tick species are based on morphological identification, and very few have combined MALDI-TOF MS and molecular tools  (Silatsa, et al. , 2019b). In Cameroon, no study has focused on the use of MALDI-TOF for arthropod identification. View of the inherent complexity and relativism in biological taxonomy, accurate identification of species requires an approach that highlights multiple sources of evidence. This framework is emerging in the wider biological community as the "integrative taxonomy"  (Padial et al. , 2010). In this study, we use identifications based on nucleotide data, as well as identifications based on morphology, to test the validity of determinations based on MS profile values by compared to the in-house MALDI-TOF database.
, 2021a). The principle here is based on the ionisation of proteins extracted from the arthropod by a laser beam and the creation of characteristic peaks called spectrum. From a database of spectra, associated software searches for a match to the arthropod species according to a reliability index between the four spectra of a single sample  (Yssouf et al. , 2016). In this study, MALDI-TOF MS was used to identify alcohol-preserved ticks collected from cattle in Cameroon. In general, the part of the arthropod used for MALDI-TOF MS analysis is one of the parameters to be developed. For tick specimens, the legs are the part providing the best results in most published studies  (Boyer et al. , 2019; Yssouf et al. , 2013). Among the specimens of tick legs that were subjected to MS analysis, 98. 3% had a good spectrum.