dataesr/scientific-paragraphs-categorization huggingface dataset:
This lack of intermediate data prevented us from describing the complete diagnostic and treatment cascade and may have contributed to the unfavourable outcomes. This issue was illustrated by a large scale ACF study from India, where only 54% of referred patients underwent sputum smear examination and 8% were found to be smear positive  [14]. There are some strengths to this study. Data from all 84 CBTC project townships, which were launched in Fig. 1  The location and coverage of CBTBC project 84 townships which were launched in 2011 2011, were used and therefore there was no selection bias. The volunteers were all trained by local NGOs under the guidance of the NTP and following NTPdeveloped guidelines for this kind of work. All reported data was recorded and analysed centrally by the NTP.
Acknowledgement This research was conducted through the  Structured Operational Research and Training Initiative (SORT IT ), a global partnership led by the  Special Programme for Research and Training in Tropical Diseases at the World Health Organization (WHO/TDR ). SORT IT Programmes include a teaching component developed jointly by the  International Union Against Tuberculosis and Lung Disease ( The Union ) and Medécins sans Frontières. The specific SORT IT programme which resulted in this publication was implemented by: WHO/TDR; The  Department of Medical Research (DMR) ,  Ministry of Health and Sports, Myanmar , The National Malaria Control Program and The National TB Program,  Department of Public Health, Ministry of Health and Sports, Myanmar ; the  WHO Country Office for Myanmar , the  Operational Research Unit (LuxOR) ,  Médecins Sans Frontières, Brussels Operational Centre, Luxembourg ; the  Centre for Operational Research , The Union, France; The  Institute of Tropical Medicine, Antwerp, Belgium ; the  Academic Model Providing Access to Healthcare(AMPATH) ,  Kenya  and; the  National Institute of parasitic diseases, China CDC.
Anti-GLUT-1 antibody staining (Figure  2f ) enabled localizing GFP-LC3 puncta within endothelial cells. These data were then uploaded into Imaris for threedimensional (3D) reconstitution and analyzed with the Imaris MeasurementPro module. This 3D reconstitution indicates that autophagic vacuoles were abundant and located within the microvessel endothelial cells (Figure  2g ). This finding is also illustrated by the animation provided in Supplementary Material. These data suggest that ethanol exposure impairs autophagy in brain cortical microvascular endothelial cells. Therefore, cultured MPMVEC were used to further investigate if the LC3 puncta increase was related to excessive autophagosome production (the generated vacuole number exceeds that of the degraded vacuoles) or the inhibition of autophagic process final steps.
Secondary antibodies in blocking solution were then incubated with the preparations for 1 h at room temperature (Alexa Fluor 594-conjugated donkey anti-goat; 1/400 (A11058, Life Technologies), Alexa Fluor 488-conjugated donkey anti-rabbit; 1/400 (A21206 Life Technologies)). Laser scanning confocal microscopy and reconstitution 3D images. The confocal images were collected with a TCS SP2 AOBS laser scanning confocal imaging system (Leica Microsystems) equipped with × 40 and × 63 high numerical-aperture oil immersion objective lenses. Image size was set to 1024 × 1024 pixels. Multitrack sequential acquisition settings were used to prevent interference between channels. A 561 nm diode solid-state laser and the 488 nm line of an argon ion laser were used for excitation. Emission detection bandwidths were optimized with Leica software.
The confocal pinhole was set to 1 Airy unit. Z-stack acquisition intervals were selected so as to satisfy Nyquist sampling criteria. As described in the Imaris version 7. 6 reference manual (Bitplane, South Windsor, CT, USA), Imaris software provides eight different viewing functions for the generation and visualization of high-quality confocal images. In this project, confocal Z-stacks comprising up to 40 images were reconstructed into 3D animations with the aid of Imaris software in the Slice and Easy 3D modes. The Spot function of Imaris automatically locates autophagosomes on the basis of size and intensity thresholds. Each autophagosome is represented by a sphere of arbitrary size determined by the user. The sphere is displayed at the center of mass of the identified autophagosome. Subfractionization of cellular proteins.
Membranes were then incubated with the corresponding secondary antibody, either goat anti-rabbit IgG-HRP (1/5000, sc-2030, Santa Cruz Biotechnology) or goat anti-mouse IgG-HRP (1/5000, sc-2031, Santa Cruz Biotechnology), for 1 h at room temperature. Secondary antibody binding was then detected by electrochemiluminescence. We checked for equal protein loading, by stripping the membranes and reprobing them with β-actin antibody (1/5000, A-5441, Sigma-Aldrich). The intensity of the immunoreactive bands was quantified by densitometry with Quantity one software from Bio-Rad (Hercules, CA, USA), and the results were expressed as a ratio with respect to β-actin immunoreactivity intensity. RNA extraction and reverse transcription-quantitative PCR. Total RNA was extracted from endothelial cells with the Nucleopsin RNA/protein kit (740933, Macherey-Nagel, Hoerdt, France), according to the manufacturer's recommendations.
We generated cDNA by the reverse transcription of 0. 5 μg of total RNA in a final volume of 20 μl with the A3500 reverse transcription system (Promega, Charbonnieres Les Bains, France). Quantitative PCR was then performed in duplicate with the CFX96 real-time PCR detection system (Bio-Rad) and the IQ SYBR Green supermix (170-8882, Bio-Rad), according to the manufacturer's protocol. The amplification of specific transcripts was confirmed by melting curve profiles generated at the end of the PCR program. The primers were designed with Primer Express software from Life Technologies (Supplementary Table  3 ). The values for each target gene were normalized with respect to the Ct value for rRNA β2M (ΔCt = Ct target gene -Ctβ2M). The relative amount of target mRNA is given by 2 -ΔΔCt , where ΔΔCt = (ΔCt of target) -(ΔCt of control).
Living cells were identified as displaying green fluorescence due to calcein AM only. Any cell displaying red fluorescence due to EthD-1 staining was considered to be dead or dying. The number of ethidium-labeled cells was determined from photomicrographs by image segmentation with ImageJ analysis software (Bethesda, MD, USA). Real-time videomicroscopy. Pups were killed by decapitation, and their brains were rapidly dissected for isolation of the cerebral hemispheres. The meninges covering the brains were carefully removed and the brains were immediately placed in aCSF. Transverse slices (250 μm) were cut at 4 °C with a VT1000S vibratome (Leica Microsystems, Wetzlar, Germany). They were transferred to 24-well Costar plates containing aCSF and incubated for 30 min at 37 °C, in a humidified incubator, under an atmosphere containing 5% CO 2 and 95% air.
The slices were washed with fresh aCSF and incubated for 6 h at a constant temperature (37 °C), under a controlled atmosphere containing 5% CO 2 , on an inverted microscope (Leica microsystems) equipped with an incubation chamber (PeCon GmbH, Erbach, Germany), computercontrolled illumination shutters and filter wheels (Roper Scientific, Lisses, France). Slices were continuously perfused with aCSF with or without 50 mM ethanol and 200 nM rapamycin. Images were acquired with a × 10 objective at 30 min intervals over a 6 h period. Microvessel length was then determined from the acquired images with MetaMorph software (Sunnyvale, CA, USA). Mitochondrial membrane potential analysis. JC-1 stain from (Life Technologies) was used for labeling brain MPMVEC at 2 μM concentration followed by incubation for 20 min at 37 °C.
Labeled cells were imaged using a Leica DMI-600B fluorescence microscope (Leica Microsystems). Each group of cells (cells incubated with control, ethanol or acetaldehyde medium) were imaged using 488 nm excitation wavelength, and the emission signals were obtained through 525 and 590 emission channels at the same parameters of pinhole aperture and detector voltage. Statistical analyses. Data obtained from human brains were expressed as median interquartile range, and range of values and Mann-Whitney test was used to compare the number of immune-positive dots per cell and between pFAS/FAS and control groups. Data obtained in vitro and ex vivo were expressed as mean ± S. E. M. The overall significance of the results obtained was examined using Student's paired t-test. Statistically significant differences between multiple comparisons were determined by a two-way analysis of variance with the appropriate Bonferroni correction for multiple comparisons test.
At 54 dag, chlorosis covering 2-3 leaves per plant (score 2) was observed. At 12 mag, all storage roots were non-necrotic. The storage roots from mock-inoculated plants were also non-necrotic at 12 mag. Detection of UCBSV in UCBSV-inoculated cassava using RT-PCR and RNAseq. In the early phase, all samples (UCBSV-and mock-inoculated) were negative (non-detectable) for UCBSV except at 6 dag, when one of the ten UCBSV-inoculated plants of both the Albert and Namikonga varieties were positive for UCBSV using the RT-PCR assay (data not shown). Seven out of ten UCBSV-inoculated Albert plants were consistently positive at the late time phase (data not shown). For the Namikonga variety, seven out of ten UCBSV-inoculated plants tested positive for at least one sampling point during the late time phase (data not shown).
However, this was not as consistent as the results from the Albert variety. To confirm the presence of UCBSV in UCBSV-inoculated plants, leaves were sampled at 3 mag, after sampling for RNAseq at early and late time phases. End-point RT-PCR with the UCBSV-specific primers CBSDDF2/CBSDDR was performed on these 3 mag samples of Albert and Namikonga and 7 of the 10 plants of each variety tested were positive for UCBSV, having a 440-bp RT-PCR fragment when resolved on a 2% agarose gel (Fig. 2 ). Mock-inoculated plants had no visible RT-PCR fragment on the same gel, confirming the absence of UCBSV. An RT-PCR fragment putatively diagnostic for UCBSV (approximately 440 nt) was gel purified and Sanger sequenced before being aligned to the full UCBSV genome sequences from GenBank. The best alignment (98% identity, 100% query cover, E value = 3e179) was obtained with accession KF878103.
1 (annotated as UCBSV). The same RT-PCR fragment size was amplified from the UCBSV inoculum source (variety NDL06/132), which indicates that the same virus species was present in the inoculum and UCBSV-inoculated plants (Fig. 2 ). Ten plants of each variety and each treatment were confirmed to be negative for UCBSV by RT-PCR prior to grafting. At 3 mag, after samples for RNAseq had been taken and frozen from all 40 plants at all time points, RT-PCR was conducted to determine whether they were UCBSV positive or not. Sanger sequencing of the RT-PCR products was performed to confirm the identity of UCBSV. Three of the UCBS-positive plants of each variety were randomly selected along with three mock-inoculated plants of each variety and used as biological replicates for the RNAseq study. The number of UCBSV reads detected in each RNAseq sample at each time point is given in Supplementary Data S1.
In Namikonga, very few UCBSV reads were detected in UCBSV-inoculated samples. The highest count (117 UCBSV sequences) was recorded in one biological replicate at 54 dag (Supplementary Data S1). This is 14 times lower than the highest count recorded in Albert at the same time point. The rest of the UCBSV-inoculated Namikonga samples had ≤10 UCBSV reads detected at any time point. For Namikonga, at 45 dag, one replicate from a mock-inoculated plant had one UCBSV sequence; the other two samples from mock-inoculated Namikonga plants had no detectable UCBSV sequence. The same was true for Namikonga at 54 dag.
Read depth and mapping to the cassava reference genome (v4. 1). A total of approximately 1. 92 billion raw reads were sequenced from 96 cDNA Namikonga and Albert libraries at eight time points with a coverage of approximately 20 million reads per library (Supplementary Table  S1 ; Supplementary Data S2). All sequences have been deposited in NCBI's Sequence Read Archive (SRA) SRP with BioProject ID PRJNA360340. After sequence quality control (QC), including filtering based on Phred score and trimming, reads from each library were mapped to the cassava reference genome using Tophat2  41. The cassava reference genome (version 4. 1) is derived from a partial inbred line, AM560-2, a third generation self of the Latin American variety MCOL-1505  42. Albert had 29,755,234,095 mapped reads and 8,231,859,633 unmapped reads, while Namikonga had 32,490,332,800 mapped and 8,477,326,725 unmapped reads (Supplementary Data S3).
Clustering of samples using data from RNAseq reads mapped to the cassava genome. Using Pearson's correlation, the normalized reads of samples from both Albert and Namikonga clustered by variety (Supplementary Figure  S1 ). Respective biological replicates clustered together by time point, variety and treatment (UCBSV inoculated and mock inoculated), irrespective of the laboratory where samples had been sequenced. This was expected, as RNAseq samples sequenced from different laboratories are comparable provided that recommended laboratory procedures are followed and sequence reads are filtered appropriately  44. However, ten of 96 samples were outliers, and these were removed from further analyses (Supplementary Table  S3 ). Seven of these removed outlier samples were from Albert (1dag_Alb_Inf_2, 5dag_Alb_Inf_1, 1dag_Alb_Ctl_3, 2dag_Alb_Ctl_3, 5dag_Alb_Ctl_2, 8dag_Alb_Ctl_1 and 45_dag_Alb_Ctl_1) (Supplementary Figure  S1a ), and three were from Namikonga (2dag_Nam_Ctl_2, 54dag_Nam_Ctl_3 and 6hag_Nam_Ctl_2) (Supplementary Figure  S1b ).
Translation initiation in the ribosomal subunit. The role of eIF4E genes in Potyvirus resistance has been demonstrated in many plants  28. We identified two eIF4E genes (Cassava4. 1_016620 m. g and Cassava4. 1_013223 m. g) for which reads were mapped in our dataset. Neither gene was significantly differentially expressed in our experiment, except for Cassava4. 1_016620 m. g in Namikonga at a single time point (5 dag) (log2FC = 0. 72; adj. p-value = 0. 02) (Supplementary Table  S5 ). The eIF4E gene Cassava4. 1_013223 m. g 20 had a log2FC of -0. 17 and 0. 63 at 2 dag and 5 dag in Namikonga. This gene was up-regulated by a log2FC of 0. 1 and 0. 4 in Albert at 2 dag and 5 dag, which was not statistically significant. Although the data did not show transcriptional differences in eIF4E, there were three main enriched GO terms (GO:0006414, GO:0008135 and GO:0044391) associated with translation in Namikonga at the early time points.
This observation suggests that defense mechanism in Namikonga controls virus multiplication without necessarily eliminating the virus. Our data support earlier studies in which Namikonga was declared 'resistant' to CBSD  20. Read mapping to the cassava reference genome. Over 75% of the raw reads mapped to genic regions of the cassava reference genome. Of the unmapped reads, 2% mapped to multiple gene models, irrespective of length. Other possible explanations for the unmapped reads could include sequence variation from SNPs between the cassava reference genome version and Namikonga and Albert. The cassava reference genome is from a partial inbred line (accession number AM560-2) derived by three generations of selfing from variety MCOL-1505 of Latin American origin  42  , while Namikonga is a local variety derived from early cassava breeding work at Amani, Tanzania  56  , and is known to contain approximately 14% M.
Ten plants of each variety were grafted as controls with virus negative NDL06/132 scions. Samples were taken as described below from all grafted plants, and frozen until selection of biological replicates was made based on RT-PCR diagnostic results. An RT-PCR test at 3 mag (data not shown) confirmed that only one out of 15 grafted Namikonga plants was positive for CBSV, while seven of 10 plants each grafted with UCBSV or CBSV + UCBSV infected scions were positive for the respective virus. In Albert seven of the 15 plants grafted with CBSV infected scions were positive, and seven of 10 plants each infected with UCBSV or CBSV + UCBSV were positive. It is on the basis of successful graft transmission of UCBSV that this species was chosen for downstream studies. Three biological replicates for each of the two treatments (UCBSV-inoculated and mock-inoculated plants) of Albert and Namikonga were selected for RNAseq.
Detection of UCBSV in RNAseq reads. The availability of RNAseq data from this experiment was exploited as an additional method to detect UCBSV RNA virus molecules in the cassava samples. To confirm successful graft inoculation with UCBSV and that control samples were UCBSV-negative, RNAseq reads from all 96 samples were mined for UCBSV sequences. To retrieve virus sequences from RNAseq reads, all five fully sequenced UCBSV genomes from NCBI were used as a reference to map the RNAseq reads of UCBSV-infected and mock-inoculated samples. The five UCBSV genomes were isolates HG965222. 1, FN434109. 1, FJ185044. 1, HM181930. 1 and NC_014791. 1 and were combined to form one UCBSV reference file. RNAseq reads that failed to map to the cassava reference genome (unmapped reads) were each aligned to the UCBSV reference genome using Bowtie2  41.
Data analysis. Read quality analysis and mapping to the cassava reference genome. Individual files received as batches of ≤four million reads (later combined to make one large file of 20 million reads) were analyzed for sequence quality using FastQC (FastQC)  109. All reads had a Phred score above 20, meaning that 99% of the bases were accurately called. The first low-quality 10-13 bp of each read, which is typical for Illumina sequencing, were trimmed to 37 bp (for 50-bp reads sequenced at UC Berkeley) and 88 bp (for 101-bp reads sequenced at Dow AgroSciences) using FASTX_toolkit (fastx_trimmer)  110. The trimmed files were mapped to the cassava reference genome v4. 1 (plant accession number AM560-2) 42 using Tophat2  41  , which runs Bowtie2 in the background. The default settings were used, allowing up to two mismatches per read.
Allowing two mismatches for both 37 bp and 88 bp reads did not affect mapping, as reads that map to the same gene model are only counted once, irrespective of their length, taking into account the two allowed mismatches. This was tested and confirmed using randomly selected samples of 37 bp or 88 bp (data not shown). The mapped reads were de-duplicated using Picard's dedup function, correcting for any amplification bias caused during the PCR used in constructing the sequencing libraries. Mapped reads with gene models on the cassava genome were counted with HTseq_count 43 , a python script widely used to count RNAseq reads  43. Genes without gene models (counted altogether as no_feature) or matching more than one gene model (ambiguous) were removed before clustering and identification of DEGs.
The fourth and last filtering was based on how close the biological replicates clustered by respective treatments, variety and time point. Outlier biological replicates were removed from the downstream analysis, although at least two samples per treatment were retained. As was done for differential gene expression analysis, data for clustering were normalized using the estimateSizeFactors function of the DESeq package  45. Data normalization was performed with combined gene counts from both Albert and Namikonga. To do this, only good-quality genes (genes that passed the four filtering stages described above) were used for the normalization analysis in both varieties. Clustering was performed using Pearson's algorithm. The algorithm clusters samples based on their covariance, providing a robust method of grouping samples as opposed to the distance-based Euclidean method.
The filtering, clustering, selection of DEGs and plotting of data were performed using the R statistical package  111. Identification of DEGs and cluster analysis. Compared to distribution-based methods and cuffdiff  112  , negative binomial algorithms implemented by DESeq (edgeR and bayseq) provide a higher statistical power for identifying DEGs  43, 113. Using filtered reads, DESeq was applied to identify DEGs between control and treated samples of each variety and at each time point. In DESeq, each variety had a dataset for respective sampling time points (example: Albert_6hag). Each dataset contained filtered biological replicates for one time point and two treatments (UCBSV inoculated and mock inoculated). The function newCountDataSet, which imports gene counts with pre-defined conditions, was used to import samples under "infected" or "control", where "infected" identifies gene counts of UCBSV-inoculated samples and "control" identifies gene counts from mock-inoculated samples.
Therefore genes for a treatment comparison with log2FC > 0 and FDR < 0. 1 were classified as up-regulated, whereas those with log2FC < 0 and FDR < 0. 1 were down-regulated. This was done to capture the maximum number of genes with differential expression across the time points. Functional annotation, GO enrichment and network analysis of DEGs. The lists of DEGs were queried against the cassava genome database at VirtualPlant (http://www. virtualplant. org)  114 to determine functional annotations and GO enrichment. VirtualPlant is annotated using cassavaCyc data (functional categories) from Phytozome's version 4. 1 of the cassava reference genome (plant accession number AM560-2) (26). VirtualPlant contains 30,666 cassava genes, 28,610 of which have predicted Arabidopsis orthologues that have protein-coding annotations.
Acknowledgements The authors would like to thank  Illumina Inc. , which provided a grant through the ' Greater Good Initiative ' for the cDNA library preparation and sequencing of 48 samples (101 bp), conducted in collaboration with  S. Rounsley  (formerly with the  University of Arizona and Dow AgroSciences , currently with Genus PLC) at  Dow AgroSciences, BecA  and  IITA. The first set of cDNA libraries (48 samples, 50 bp) was sequenced at  UC Berkeley , in  D. Rokhsar 's laboratory. We thank  S. Prochnik  and  T. Mansfield  for performing quality checks on the raw data for  UC Berkeley  and  Dow AgroSciences , respectively. J. Bredeson  provided two weeks of Unix training to TA. The experiment was designed in consultation with  K. Denby  from the  University of Warwick. J. Harvey  (formerly with Bioscience east and central Africa, currently working with  Kansas State University ) provided technical support on the identification of virus inoculum and isolation of RNA.
Multineutron and multiproton transfer channels, populated in the inverse kinematics reaction 197 Au+ 130 Te at E lab =1. 07 GeV, were measured at Laboratori Nazionali di Legnaro using the presently heaviest ion beam delivered by the PIAVE-ALPI accelerator complex and detecting both projectile-like and targetlike ions. To this end the large solid angle magnetic spectrometer PRISMA was coupled to a second arm for the detection of the heavy fragments in kinematic coincidence with the light ones selected and identified with the spectrometer. The data analysis is still in progress and will allow to compare the yields of both light and heavy partner with theoretical predictions performed with the GRAZING code to get quantitative information on transfer channels and the effect of evaporation and fission on the production rate of primary fragments.