dataesr/scientific-paragraphs-categorization huggingface dataset:
In summary, our analysis of the B. duncani nuclear genome and transcriptome has shed light into the biology, evolution, and drug susceptibility of this important human pathogen. It is anticipated that this knowledge will help advance new strategies to develop reliable, sensitive, and specific diagnostic tools as well as therapeutic strategies for a better management of the disease. The close relationship between B. duncani and other hemoparasites including malaria parasites will help future efforts to better understand the evolution of virulence in Apicomplexa. of the most highly expressed genes. GO was calculated using the R package TopGO with the weight01 algorithm and the biological process tree. REVIGO was used to visualize the GO results of the most highly expressed genes (500TPM or higher).
WR99210, JPC2067 and JPC2056 with ≥ 95% pure by reversed-phase highperformance liquid chromatography (HPLC) were purchased form Jacob's pharmaceuticals company. DNA prep for PacBio sequencing. Genomic DNA was isolated from 100 ml in vitro culture of B. duncani (15% parasitemia and 5% hematocrit) using DNasy Blood and Tissue kit (Qiagen; Cat. No. 69506), and quality control along with concentration determination was performed using nanodrop and qubit. DNA integrity was evaluated using Blue Pippin pulse gel and the DNA was then used for library preparation using Pacific Biosciences SMRTbell Express template Prep Kit 2. 0 (Cat. No. PN: 100-938-900) according to the manufacturer's instructions. The Pacific Biosciences Smart Link software was used to determine loading concentration and proper stoichiometric measurements.
The gDNA library was then annealed to the Pacific Biosciences V5 primer for 1h at 20°C. The annealed library was then bound to polymerase using Pacific Biosciences Polymerase 2. 2 for 1-4h at 30°C and was loaded on to the Sequel II Instrument as an adaptive sequencing run. At least one smart cell was sequenced for each genomic DNA library with a movie time of 30h and a pre-extension of 2h. After the DNA library sequencing was complete, the loading metrics were evaluated by mean read length, polymerase read length, data yield and P1 values to ensure the sample ran as expected and data had met Yale's gold standards. DNA preparation for Bionano optical map. Exactly 3 ml packed frozen pellets of B. duncani WA1 in human RBCs were used to isolate ultra-high molecular weight (uHMW) genomic DNA for use in genomic optical mapping by Histogenetics (Ossining, NY) using the Bionano Prep™ Blood and Cell Culture DNA Isolation Kit (Bionano Genomics, cat No.
80004). Following this, DNA was quantified using Qubit™ dsDNA BR Assay Kit. A total of 0. 75 ug of HMW DNA was then labeled using the Bionano Prep direct label and stain (DLS) method (Bionano Genomics, cat No. 80005) and loaded onto a flow cell to run on the Saphyr optical mapping system (Bionano Genomics). Approximately 1,177 Gb of data was generated per run. Raw optical mapping molecules in the form of BNX files were run through a preliminary bioinformatic pipeline that filtered out molecules less than 150 kb in size with and less than 9 motifs per molecule to generate a de novo assembly of the genome maps. Genome sequencing and assembly. 100 mL in vitro culture of B. duncani in hRBCs was propagated to a parasitemia of 10% at 5% HC. DNA was isolated from infected hRBCs and sequenced at the Yale Center for Genome Analysis using Illumina HiSeq 2500 and PacBio HiFi (CCS) sequencing.
A total of 177,189 PacBio HiFi reads were obtained; the average HiFi read length was 8,814 bp; the longest read was 29,067 bp. The HiFi reads totaled 1. 56B bases which translated to an expected ~156x coverage of the B. duncani genome (assuming a ~13Mb genome). HiFi reads were mapped using Minimap2  (42)  to the B. duncani mitochondrion and apicoplast. Only 0. 41% of the reads mapped to these organelles, which were then discarded to enrich the data for nuclear DNA. HiFi reads were also mapped to the human genome to determine possible host contaminations, but only 1. 48% of them were flagged. Cleaned reads were assembled using HiCANU v2. 2 (18) using default parameters. HiFiASM v0. 16  (43)  and Wengan  (44)  were also tested on the HiFi reads, but they generated slightly inferior assemblies (based on assembly statistics, comparison with the optical map and transcript isoform annotations).
Briefly, interaction data were first manually fitted to a threecolumn interaction count matrix, where the first two columns indicate the two separate bins within the genome and the third being the number of interactions between those two bins. Then the threedimensional coordinate matrices were generated using PASTIS and converted to. PDB format, with each line being one of the coordinates output by Pastis. The data was visualized using ChimeraX  (49). PacBio IsoSeq processing. PacBio IsoSeq reads were mapped to the B. duncani genome using Minimap2 (42) with options "splice:hq -uf --secondary=no -C5". The resulting SAM files sorted using "sort -k 3,3 -k 4,4n" then fed into the PacBio cDNA_Cupcake ToFU pipeline (https://github. com/Magdoll/cDNA_Cupcake) using the Python code "collapse_isoforms_by_sam.
py" to collapse redundant isoforms (more details about this pipeline can be found at https://github. com/Magdoll/cDNA_Cupcake/wiki). The resulting isoform sequences were used in the gene finding pipeline below. database to determine degrees of evolutionary conservation) and a file of leftover proteins that did not map to any OrthoMCL groups but did cluster with at least one other B. duncani protein (these were considered species specific gene duplications or families). between loci i and j as a decreasing function of d !"  (11) , λ !" = β d !" (X) # with parameters β > 0 and α < 0. Here d !" (11) (or simply d !" ) is the Euclidean distance between loci i and j in structure X. Therefore, the likelihood of observing c !" 's can be formulated as: L(X, α, β) = 7 Poisson<λ !" = = 7 <βd !" # = $ !" c !" ! e (&'( !" # ) !," !," By maximizing the log-likelihood function, PASTIS optimizes the 3D structure X as well as the distance decay parameters α and β.
Since the 3D model predicted by PASTIS contained a set of discrete points, cubic Bezier curve smoothing was applied for visualization purpose. Cubic Bezier curves guarantees the interpolated curve passes through all points in the original structure and the first-order geometric continuity at all points are maintained. GPI-associated proteins (GPI-AP) identification. GAPI-AP were selected based on a two transmembrane domain model, SignalP 5. 0 and PredGPI online predictions. TMPred software was used to validate the presence of hydrophobic regions associated with the N-terminal signal peptide (ER-targeting) and C-terminal GPI-anchor signal (recognized by the transamidase). The maximum distance between the N-terminal TM with the start of the sequence was set to 10 with a minimal score of 500.
Fluorescence from the background (uninfected RBCs in complete HL-1medium) was subtracted from each concentration and determined the 50% inhibitory concentration (IC50) of the drug by plotting sigmoidal dose-response curve fitting with drug concentration and per cent parasite growth in the Graph Pad prism 9. 2. 1 from two independent experiments with biological triplicates. Data are shown as mean ± SD. Assessment of drug cytotoxicity on human cell lines. We obtained HeLa, HepG2, HEK and HCT116 cell lines from the American Type Culture Collection and maintained them in Dulbecco's modified Eagle's medium (DMEM) (Invitrogen 11995-065) containing 25 mM glucose, 1 mM sodium pyruvate and supplemented with 5 mM HEPES, 10% FBS and penicillin-streptomycin (50 U/mL penicillin, 50 µg/mL streptomycin).
Study Subjects, Blood Samples, and Phenotypes Malaria patients were recruited from two major Senegalese sites, the principal hospital of Dakar and the regional hospital of Tambacounda, including 90 cerebral malaria cases and 27 severe noncerebral cases, as described  [46]. The control samples (n = 79) were obtained from healthy volunteers living in Dakar. Written informed consent was obtained for each patient and their accompanying family members. The study was approved by the institutional research ethics committee of the Université Cheikh Anta Diop. Venous blood samples and biological data including parasite density, hematology, and other characteristics were collected on the day of admission. The presence of Plasmodium falciparum was determined by at least two trained biologists by microscope examination of thin and thick smears before antimalarial treatment.
Reverse Transcription-Quantitative PCR Total RNA was extracted for each selected clone and wild-type K562 cell using the RNeasy mini kit (Qiagen, Hilden, Germany). One µg of RNA per clone was converted into cDNA using Superscript VILO Master Mix (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). Three independent RNA/cDNA preparations were performed for each clone. Real-time quantitative PCR (RT-qPCR) was subsequently performed using SYBR Select Master Mix (Thermo Fisher Scientific, Waltham, MA, USA) on a QuantStudio 6 Flex instrument. Primers were designed using Primer 3 software to span exon 1 of ATP2B4 (F3 and R3) to specifically quantify the long transcripts (ENST00000357681, ENST00000367218) or to span exon 19 and exon 20 (F4 and R4) to quantify all the ATP2B4 transcripts (ENST00000357681, ENST00000367218, ENST00000341360, ENST00000458092, and ENST00000356729) (Supplementary Table  S9 ).
Statistical Analysis A Chi-squared test was used to determine whether the genotype distribution in healthy Senegalese subjects conformed to the Hardy-Weinberg equilibrium. Chi-squared tests and logistic regression analyses were carried out with SPSS (statistical software version 20) to assess the association between the SNPs and SM in Senegalese subjects. Differences were considered significant if the P-value obtained in a two-tailed test was <0. 05. The odds ratio (OR), 95% confidence intervals (CIs), and the influence of covariates on the phenotype were evaluated by logistic regression analysis. A meta-analysis of the genetic association was performed using MetaGenyo  [47]. Statistical differences between luciferase constructs or between clones were performed using Student's t-tests. Mixed models were also used to consider the triplicates performed for each independent experiment.
Acknowledgments: We thank all the individuals who participated in the study, especially the patients from the regional hospital in Tambacounda and the Hospital Principal in Dakar. We thank  Iris Manosalva  and  Charbel Souaid  for helpful discussions, and  Richard Redon  for critical reading of the manuscript. We also thank  Sabrina Baaklini  and  Mai Le Phuong Nguyen  for the technical assistance. We thank  Mouhamedou Mansour Fall  for his technical assistance and follow-up of patients. We thank  Laurence Borge  for assistance and the use of the cell culture platform facility ( CRCM U1068 ,  Marseille ).
1, 13 However, rapid infusion of United States of America (USA)-sourced rituximab, Rituxan® (Genentech) and US-licensed Truxima® (Celltrion) is permitted in patients with previously untreated FL and diffuse large B-cell lymphoma (DLBCL). 1, 16, 17 [20] [21]  With the exception of an abstract from a single UK center,  22  no data are available on the safety of rapid infusion of CT-P10. Hence, more information is needed to inform evidence-based decisions for the prescription of CT-P10 by HCPs. The aim of this study was to address this evidence gap by collecting real-world data on the safety and effectiveness of rapid infusion of CT-P10 in patients with NHL and CLL in Europe. In addition, the IRR rate obtained (primary endpoint) was compared to the IRR rates of rituximab published previously.
| Study design and study setting This study was a multi-center, retrospective, non-interventional, post-authorization safety study conducted in 10 European specialist treatment centers or hospitals (UK, 4; Spain, 2; France, 1 and Italy, 3) which routinely use CT-P10 for the treatment of NHL and CLL. In the pre-index observation period, patient-level data for patients with NHL or CLL from hospital medical records (including infusion records) were collected from the date of diagnosis until the index date (date of first rapid infusion of CT-P10 [for the second or a subsequent treatment cycle]), to acquire demographic and clinical characteristics data. Safety and clinical outcome data were collected in the 6-month post-index observation period.
| Patient consent and local authorization Approval was sought from institutional review boards and/or independent ethics committees and local hospitals, as appropriate for BISHTON ET AL. each country. In accordance with French regulations, where patient consent is not required for some non-interventional investigations, a 'non-opposition' model was used. Patients, or their next of kin were sent information about the study by post and data collection proceeded if no objections were raised within 10 working days; consent was obtained for all living patients from the UK, Spain and Italy and deceased patients' data were collected by the direct care team to preserve confidentiality.
For overall survival (OS) and progression-free survival (PFS), the proportion of patients surviving and free from disease progression at 6 months following the index date were calculated; the Kaplan-Meier method for OS and PFS was used, calculated from index with surviving patients being censored at 6 months or the date of the last known contact. Demographic, clinical and disease characteristics data were described using summary statistics, as appropriate to the data distribution. Treatment patterns for NHL or CLL in patients who received rapid infusion of CT-P10 were described for the entire study period. Summary statistics were calculated for the treatment dose and treatment duration, and a distribution for the treatment discontinuation reason. Treatment duration was analyzed using the Kaplan-Meier method, calculated from the index event date until the date of discontinuation, with the patients that remained on treatment censored at 6 months post-index date or the date of last infusion (if the patient was lost to follow-up).
18, 23 The first, a Phase III safety study of rituximab administered as a 90-min infusion in patients with previously untreated DLBCL, reported an IRR rate of 38. 3% following the first rapid infusion  18   (2017). 23 The meta-analysis described an audit standard for the rapid infusion of rituximab biosimilar using data from 20 rapid rituximab infusion studies relating to hematological malignancies. An estimated IRR rate of 8. 8% (95% CI 7. 2%-10. 8%) was reported with a suggested recommendation that the IRR rate with rituximab biosimilar should be less than 10. 8% for all grades and 0. 7% for grade 3 or more. [20] [21]  The results of the present study support this, where 22% of patients experienced an IRR during the 6-month observation period (Table S1), most IRRs recorded were mild or moderate and 17% (n = 14/ 83) of IRRs were considered 'possibly related' to CT-P10.
ACKNOWLEDGEMENTS The authors thank  OPEN Health , a healthcare consultancy company specializing in real-world evidence, who were commissioned by  Celltrion Healthcare Co. Ltd  to provide support for study design and implementation, data analysis and interpretation, and medical writing support. Editorial support for development of this manuscript was provided by  Edward Ottley  from  OPEN Health  in accordance with Good Publication Practice 3 guidance, funded by  Celltrion Healthcare Co. Ltd. Mark Bishton: Research funding = Takeda ,  Gilead ,  Roche , Abbvie; Travel/acc/expenses  = Roche ,  Takeda ,  Gilead ,  Celltrion ,  Honararia Tevapharma ,  Roche ,  Celltrion ;  Advisory board = Beigene. Pier Luigi Zinzani: Has  received personal fees for consulting from Verastem,  EUSA Pharma ,  MSD  and  Novartis ; personal fees for participating in a speaker's bureau from Verastem,  Celltrion ,  Gilead ,  Janssen-Cilag ,  BMS ,  Servier ,  MSG ,  TG Therapeutics, Takeda ,  Roche ,  EUSA Pharma ,  Kyowa Kirin ,  Novartis ,  Incyte  and Beigene; and personal fees for participating in advisory boards from  Verastem ,  Celltrion ,  Gilead ,  Janssen-Cilag ,  BMS ,  Servier ,  Sandoz ,  MSG ,  TG Therapeutics, Takeda ,  Roche ,  EUSA Pharma ,  Kyowa Kirin ,  Novartis ,  ADC Therapeutics, Incyte and Beigene.
5 μl + 2 μl protein to well solution. Crystals were cryo-protected with additional 20% glycerol and 1. 8 mM CTD peptide in mother liquor and flash-frozen in liquid nitrogen. Data were collected on ESRF beamline ID29 and integrated with an ellipsoidal mask using AUTOPROC/STARANISO to an anisotropic resolution of 2. 42-2. 95 Å. The structure was solved using molecular replacement with PHASER  [34]  using PDB:5FMZ as model  [35]. The model was iteratively corrected and refined using COOT  [36]  and REFMAC5 [37] and quality-controlled using MOLPROBITY  [38]. See Table  1  for data collection and refinement statistics. For crystals enabling simultaneous visualisation of CTD binding in sites 2A and 2B, wild type FluPol B at 11. 7 mg ml -1 (45 μM) was mixed with 52 μM of nucleotides 1-14 (5 0 -pAGUA GUAACAAGAG-3 0 ) and 1-18 (5 0 -UAUACCUCUGCUUCUGCU-3 0 ) of respectively the vRNA 5' and 3' ends, 104 μM of capped 13-mer (5'-m 7 GpppAAUCUAUAAUAGC-3'), and 380 μM CTD 28-mer Ser5P peptide, in buffer containing 50 mM HEPES pH 7.
PLOS PATHOGENS with a drop ratio of 1 μl + 2 μl protein to well solution. The drops were soaked with 840 μM CTD peptide for 17 days. Crystals were cryo-protected with an additional 30% glycerol and 885 μM peptide in mother liquor and flash-frozen in liquid nitrogen. Data were collected on ESRF beamline ID30A1 (MASSIF) and processed and refined as described above, using PDB:5MSG as model for molecular replacement. See Table  1.
CTD sequences and alignment The RPB1 CTD domain amino acid sequences of Homo sapiens (NP_000928. 1), Sus scrofa (XP_020923484. 1), Equus caballus (XP_014584045. 2), Canis lupus (XP_038521325. 1), and Mus musculus (NP_001277997. 1) host species were obtained from the RefSeq database  [49]. As the predicted RefSeq sequences available for the Gallus gallus (XP_040551262) and Anas platyrhyncos (XM_038172734) RPB1 subunits were only partial, we designed a targeted protein sequence assembly strategy data based on RNA-seq and/or WGS SRA public data available for these two species. To obtain the Gallus gallus RPB1 complete sequence (1969 aa), we first aligned Illumina RNA-seq short reads (ERR2664216) on the human RefSeq curated protein sequence (NP_000928) using DIAMOND algorithm  [50] , and then used the aligned reads for subsequent Trinity transcript assembly ("-longreads XP_040551262" option to use the partial sequence as a guide) followed by Transdecoder for the ORF prediction  [51].
The Anas platyrhyncos RPB1 complete sequence (1970 aa) was obtained by aligning Illumina RNA-seq short reads (SRR10176883) and PACBIO long reads (SRR8718129, SRR8718130) on the JACEUL010000271. 1 genomic scaffold by using respectively HISAT2  [52]  and minimap2  [53]  followed by Stringtie2  [54]  with the "-mix" option to allow hybrid de novo gene assembly. The RPB1 coding sequences from Gallus gallus and Anas platyrhyncos are held on the Zenodo repository: https://doi. org/10. 5281/zenodo. 6467097. The CTD sequences were aligned with SnapGene 6. 0 and visualised by Espript 3. 0  [55].
We observed clear electron density, not only for the 5' hook, but also for the CTD peptide bound in site 2A (S1B and S2C Figs), essentially identically bound as previously seen for bat influenza A/H17N10 polymerase (S2D Fig). However, there was no CTD peptide bound in site 1AB. The most likely explanation for this is that in the symmetrical dimeric form of influenza A (core only, or full trimer), both polymerases are in the so-called 'dislocated' conformation  [18]  with an open active site. In particular, PA regions 425-452 and 586-618 are rotated by ~20˚, compared to the active, monomeric promoter bound state (e. g. A/H3N2 polymerase structure,  [58] , PDB:6RR7). This particularly affects the position of key site 1AB binding site residues Y445, E449 and F612 (S2D.
Luciferase activities were measured in cell lysates at 24 hpt. Normalised luciferase ratios (NLRs) were calculated as described in the Materials and Methods section. The data shown are the mean ± SD of at least three independent experiments performed in technical triplicates. �� p � 0. 002; ��� p � 0. 001 (two-way ANOVA; Dunnett's multiple comparisons test). C-D. The CTD binding of FluPol A mutants PA K289A and R638A was investigated. HEK-293T cells were transfected as described in (A) and (B), respectively. Relative Light Units (RLUs) are expressed as percentages relative to the FluPol A PA wt. The data shown are the mean ± SD of three independent experiments performed in technical triplicates. �� p � 0. 002; ��� p � 0. 001 (one-way ANOVA; Dunnett's multiple comparisons test). The dotted line labelled "Ctrl" indicates the background signal i.
e. the sum of the luminescence activities measured in control samples co-transfected with either the FluPol-G1 and G2 plasmids, or the G1 and G2-CTD plasmids. E. Schematic representation of the CTD constructs used in (F) and (G): the wild-type G2-CTD (wt, top) and the G2-CTD in which all serine 5 residues were replaced with an alanine (S5A, bottom). F-G. The interaction of the wt or the S5A mutated CTD to FluPol B (F) or FluPol A (G) was investigated by transient transfection in HEK-293T cells as described in (A-B). The data shown are the mean ± SD of four independent experiments performed in technical triplicates. � p � 0. 033; ��� p � 0. 001 (two-way ANOVA; Sidak's multiple comparisons test). In parallel, cell lysates were analysed by western blot using antibodies specific for the pS5 or pS2 CTD, G.
F-G. The interaction of the wt or the S5A mutated CTD to FluPol B (F) or FluPol A (G) was investigated by transient transfection in HEK-293T cells as described in (A-B). The data shown are the mean ± SD of four independent experiments performed in technical triplicates. � p � 0. 033; ��� p � 0. 001 (two-way ANOVA; Sidak's multiple comparisons test). In parallel, cell lysates were analysed by western blot using antibodies specific for the pS5 or pS2 CTD, G. princeps luciferase (Gluc) and tubulin. The slow-and fast-migrating bands detected with the pS2 CTD antibody, which likely correspond to the hyperphosphorylated and hypophosphorylated forms of the CTD, respectively, are indicated by a star and a triangle, respectively. The smeared signal in the G2-S5A-CTD samples likely corresponds to the detection of phosphorylation intermediates.
Data collection regarding food intake and milk production of cows that continued to produce milk for commercial purpose Data on sold milk and the composition of this milk was collected from reports of the dairy company (Arla Foods) in both 2016 and 2020. In addition, the daily milk production and daily roughage and non-roughage intake of 272, 163 and 272 cows, respectively, was collected for December 1, 2015 to January 31, 2016. These animals were fed roughage in weighted feed troughs and non-roughage in automatic feeders and the milk was weighed in the milking systems. Cows with the most severe clinical signs were placed in the sick ward, where neither milk nor food intake was recorded. Data from cows at these time points were thus missing and, consequently, the estimation of food intake and milk production during the outbreak was valid only for cows without severe clinical signs of disease.