dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments  C. Rubiano-Labrador  was supported by a fellowship from  COLCIENCIAS  ( Departamento Administrativo de Ciencia, Tecnología e Innovación ) and the  Colombian Center for Genomics and Bioinformatics of Extreme Environments-GeBiX (Colombia). C. Bland was supported by a fellowship from the  Commissariat à l'Energie Atomique et aux Energies Alternatives (France)  and the  Région Languedoc-Roussillon (France). We thank the  Commissariat à l'Energie Atomique et aux Energies Alternatives (France), Pontificia Universidad Javeriana (Colombia) , and the  ECOS-NORD bilateral program  for financial support. This work was carried out under MAVDT Research Permit Resolution No. 0168 , 2009 and  MAVDT  Contract No. 56 , 2013 for Access to Genetic Resources.
atDDBJ/EMBL/ GenBank under the accession numbers  CBKU010000001-CBKU010002377  and is available at the  European Nucleotide Archive  (http://www. ebi. ac. uk/ena/ data/view/ CBKU010000001-CBKU010002377 ). The authors thank the  Commissariat àl'Energie Atomique et aux Energies Alternatives (C. E. A. Lab Biochim SystemPerturb, France), (Colombia) ,  Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS, Colombia), Colombian Center for Genomics and Bioinformatics of Extreme Environments (GeBiX, Colombia) , and the  ECOS-NORD  bilateralprogram for financial support. This work was carried out under MAVDT Research Permit Resolution No. 0168 , 2009 and  MAVDT  Contract No. 56 , 2013 for Access to Genetic Resources.
Genomic DNA extraction and sequencing of T. consotensis cells was performed as described by Rubiano-Labrador et al. (2014). Briefly, the DNA was fragmented and a 454-library with an average 8-kb insert size was constructed and sequenced on the Roche 454 GS FLX+ System (Titanium XL+ sequencing chemistry) by the GATC company. A total of 171,055 sequencing reads were recorded which resulted in 59,754,518 bases read. De novo assembling with the 454 Newbler assembler tool resulted in 2377 contigs (5,701,113 nt, 161,098 reads used) for the T. consotensis genome (10. 4× coverage). This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers CBKU010000001-CBKU010002377.
ACKNOWLEDGMENTS We thank  Cogentech facility  for hybridization of Affymetrix chips and production of raw data files;  C. Lucca  for assistance with robot-assisted screens;  M. Foiani ,  I. Psakhye ,  M. Giannattasio , and  T. Abe  for critical reading of the manuscript;  F. Castellucci  for demonstrating ChIP-on-chip experiments;  W. Carotenuto  for help with microarray data analysis; and  B. Szakal  for reagents and help with the artistic work. This work was supported by the  ERC  (Starting Grant  242928 ),  AIRC  ( IG 14171 ) and  Fondazione Telethon  ( GGP12160 ) grants (to D. B. ), and  Ligue contre le Cancer  and  ANR  (to P. P. ). A. L. thanks the  Region Languedoc-Roussillon  ( Programme Chercheur d'Avenir)  and  ARC  for support. A. D. was supported by fellowships from the  French Ministry of Research and Fondation Recherche Medicale.
SAXS data were collected at a synchrotron (Diamond Light Source, station I22, Didcot, UK). A 2D SAXS detector (hybrid photon counting Dectris Pilatus 2M) was used for all experiments. SAXS patterns were recorded over a scattering vector (q) range from 0. 025 to 1. 65 nm -1 using monochromatic X-ray radiation (wavelength λ = 0. 1001 nm), where the length of the scattering vector is given by q = (4π sin θ)/λ and θ is half of the scattering angle. A 2 mm diameter flow-through glass capillary cell was used as a sample holder for all measurements. Scattering data were reduced using Nika SAS data processing macros for Igor Pro (integration, normalization, and background subtraction) and further analyzed using Irena SAS macros within Igor Pro. 86 The structural model used for the SAXS data analysis is given in the Supporting Information.
This model is based on the analytical expression for a spherical micelle form factor  87  and has been reported previously for other PISA formulations. 88 ultiangle laser light scattering (MALLS) was used to determine the molecular weight of the PDMA 94 -PBzMA x diblock copolymer spherical nanoparticles. Measurements were performed at 15°-160°u sing a DAWN HELIOS II 18 angle laser light scattering instrument (Wyatt Technologies Corp. USA) equipped with a 130 mW linearly polarized GaAs laser operating at 658 nm. Dispersions were diluted with ethanol to afford a copolymer concentration of approximately 0. 01% w/v (0. 1 mg mL -1 ) and measured in batch mode. Data were analyzed using ASTRA V software for Windows and extrapolating using the Zimm, Debye and Berry formalisms. Typical plots obtained for PDMA 94 -PBzMA 392 nanoparticles analyzed using each of the three formalisms can be found in the Supporting Information (see Figures  S4  and S5 ).
Multiangle laser light scattering (MALLS) was used to determine the weight-average molecular weight, M w , of the diblock copolymer nanoparticles. 8] [99]  However, this  a These structural parameters are the micelle core radius (R s ), solvophobic block volume (V mc ), overall particle diameter (D total = R s + 2R g ), mean aggregation number of copolymer chains per spherical micelle (N agg ), and the number of copolymer chains normalized with respect to the surface area of the spherical nanoparticles [S agg = N agg /(4πR s 2 )]. Further details regarding these SAXS spherical micelle model parameters can be found in the Supporting Information. technique requires the differential refractive index (dn/dc) as an input parameter. This was calculated for each diblock composition using a commercial differential refractometer (see Figure  S2  for representative raw data and Figure  S3  for the corresponding dn/dc values).
The Zimm,  100  Debye,  101  and Berry 102 methods are the most common analytical techniques for determining molecular weights via MALLS. Light scattering data obtained for PDMA 94 -PBzMA x diblock copolymer nanoparticles were analyzed by each of these three methods; the associated equations can be found in the Supporting Information. It was found that each method gave very similar results for the micelle molecular weight (see Table  S1 ). Taking into consideration the various experimental errors associated with each method,  103  it was decided to use the M w values calculated using the Debye method to determine the corresponding micelle aggregation numbers. The Debye method uses eq 1 to construct a graphical plot of the type shown in Figure  7. Andersson et al. also concluded that this approach was superior to either the Berry or Zimm methods for spheres with mean diameters greater than 50 nm.
A power law plot of core diameter against the DP of the PBzMA block indicated an α exponent of 0. 62, which is consistent with the relatively low solvent volume fraction indicated by  1  H NMR spectroscopy studies. MALLS was also used to determine N agg values for selected dispersions, and these data were generally in good agreement with those values calculated from SAXS analysis. For both techniques, N agg increased linearly with the target DP of the core-forming PBzMA block. This suggests that the particle growth mechanism during PISA involves exchange of individual copolymer chains between monomer-swollen nanoparticles and/or isotropic sphere-sphere fusion events. There is reasonable indirect experimental evidence in the PISA literature to support both mechanisms.
Gene silencing assays RNAi-mediated gene-silencing assays were performed to evaluate the effect of AGAP007752 gene knockdown on P. berghei-infected An. coluzzii mosquitoes. Specific primers containing T7 promoter sequences at the 5′-end were synthesized (Additional file 3: Table  S3 ) and dsRNA produced using the MEGAscript T7 kit (Ambion, Austin, TX, USA), according to manufacturer's instructions. An exogenous gene, mouse beta-2microglobulin (β2M) (GenBank: NM_009735) was used as control for the silencing experiments. The dsRNA was purified, diluted in sterile water to a concentration of 4 μg/ml and quality was assessed by spectrometry and agarose gel. For gene knockdown, we perform three experiments of 300 P. berghei infected female mosquitoes (three to five-days-old) for each gene. Fourteen days PBM, cold anesthetized mosquitoes were injected intrathoraxically with 69 nl (4 μg/ml) of dsRNA using a nano-injector (Nanoject, Drummond Scientific, Broomall, PA, USA).
The relative abundance of transcripts was analyzed. Of the total predicted transcriptome (15322 genes of An. coluzzii, according to version 72, ENSEMBL (http:// www. ensembl. org/index. html), 12690 genes and 13611 transcripts were found in the SG transcriptome. Of them, 2588 genes were differentially expressed in response to P. berghei infection (Additional file 4: Table  S4 ), being 1578 (61 %) upregulated and 1010 (39 %) downregulated (Fig. 1a-c ). RNA-seq data are available in the ArrayExpress database (www. ebi. ac. uk/arrayexpress) under accession number E-MTAB-3415. These results indicates that RNA-seq is a high-throughput technique enabling to detect a high number of transcripts when compared with other approaches  [59, 60] , as microarrays that was recently used by Waisberg and co-workers  [61] , finding 43 genes differentially expressed.
coluzzii  [67]. Previous results highlighted the fact that the Imd pathway in An. coluzzii is part of an effort to limit the malaria transmission cycle, associating the Imd-directed immune response against P. falciparum  [68]  and showing that these genes are upregulated in response to Plasmodium infection  [15]. Equivalent data were obtained in the present study, where all Imd-pathway genes (AGAP010815, AGAP007035, AGAP007036, AGAP006348, AGAP007033 and AGAP005693) were found to be upregulated. These findings support the evidence that Imd pathway and PRR genes play a part in mosquito response to Plasmodium infection. The gene AGAP006421 was also found upregulated. It is considered a member of the antigen AG5 family of the SG mosquito transcripts  [19] , categorized as an immunity gene, but related with a family of secreted proteins with different functions  [69].
An. coluzzii protein putative function Classifying the putative function of the An. coluzzii protein coded by the AGAP007752 gene as a sugar transporter was done by performing five PSI-BLAST  [93]  interactions using the default settings-a pfam database search  [94]  confirmed this classification. The top hits were from insect trehalose and glucose transporters (E value 3e-38). It was previously shown that insects glucose transporters cluster with several organisms, including mammalian glucose transporters and not with insecta trehalose transporters. suggesting a function related to phylogenetic clustering  [95]. Maximum likelihood and Bayesian phylogenetic analyses with threalose and glucose transporters from members of metazoa (Mammalia, Insecta and Trematoda) show that An. coluzzii AGAP007752 protein (named as EAA12343) (Fig.
Acknowledgements We are grateful to  Dr. Dinora Lopes  for technical support and valuable suggestions for the sporozoite quantification. We thank  Ana Catarina Alves  for assistance with mosquito rearing and  Mário da Costa  for his support on mosquito dissection. This work was partially supported by the  GHTM-UID/Multi/04413/2013  project and by the  PhD course on Biomedical Sciences, IHMT-UNL.
Low levels of atrazine do not affect testicular morphology and cell viability After treatment, the mice were euthanized, and reproductive organs were dissected. We measured the organs and body weights of treated and control animals. We found that the body weight and reproductive organs (testes, epididymis and seminal vesicles) were not affected at this dose (data not shown). To evaluate morphological changes in seminiferous tubules caused by ATZ, we analyzed paraffin-embedded sections stained with hematoxylin and eosin and compared matching stages from treated and control animals. The morphological analysis did not reveal any significant changes in either the seminiferous tubules or the epididymis (Additional file 1: Figure  S1 (A-D )). However, we could not exclude small changes in the proportion of cells, which are difficult to distinguish by this method.
Decreased sperm count and serum testosterone levels in ATZ-treated mice One essential metric of reproductive state is the number of spermatozoa per epididymis. To evaluate the effect of ATZ, we counted spermatozoa in the epididymis of treated and control mice. We found that ATZ-treated mice had a significantly lower sperm count (68 %) than untreated animals (*p < 0. 05; n = 10, Fig. 1a ). To assess endocrine function after treatment, we measured serum levels of testosterone and follicle-stimulating hormone (FSH). We found that serum testosterone was 3. 4 times lower in treated animals (*p < 0. 05, n = 10), while the level of FSH was not significantly affected (p = 0. 06, n = 10, Fig. 1b ). Our data show that a relatively low dose of atrazine decreases sperm counts and serum testosterone levels.
3b ). ATR acts stage-specifically to regulate multiple aspects of mammalian meiotic silencing  [75]. If asynapsis persists at the pachytene stage, ATR leads to the induction of repressive post-translational modifications and irreversible gene silencing over many megabases  [75]. To analyze the role of ATR in ATZ-treated mice, we counted the number of cells that showed staining of ATR at the sex body only or that showed simultaneous ATR staining of both XY bivalents and autosomes. In ATZ-treated mice, there was 1. 8 times more ATR staining of autosomes (Fig. 3c ). Consistent with previous data on the role of ATR in chromatin silencing  [75] , our experiments showed that ATZ treatment increases the number of chromosomes with incomplete synapsing.
7a ); expression of the latter gene was downregulated. We found increased H3K4me3 marks in Cyp19a1, also known as aromatase (Fig. 7b ). The number of H3K4m3 marks was also decreased within the Star gene (Fig. 7c ), a finding in agreement with the microarray data (Additional file 1: Figure  S5 ). Because STAR activity is essential for steroid-hormone biosynthesis, decreased H3K4me3 marks and Star transcription suggest that the function of STAR in steroid-hormone metabolism is modified in ATZ-treated animals. Subsequently, we asked whether differential H3K4me3 regions were located near genes that share common biological functions. We chose the subset of differential peaks within +/-1 kb genes and performed functional annotation using DAVID software (details and parameters of analysis in Material and Methods section).
The analysis confirms that ATZ damage spermatogenesis function most likely due to metabolism of ATZ. Our data show that ATZ changes the number of H3K4me3 marks in genes with a wide range of important cellular functions. Comparison of ChIP-Seq and Gene-Chip data reveal common genes related to GTPase regulation, mitochondrial function and steroid-hormone levels ChIP-seq and Gene-Chip have different sensitivities. The ChIP-Seq method is very sensitive; it involves integrating a large number of short sequencing reads. Compared to RNA sequencing, the Gene-ChiP assay is less sensitive in detecting genes with very low expression and is less accurate in detecting highly expressed genes  [107]. To compare the two datasets, we calculated the averaged signal values of ChIP-Seq peaks at the TSS of differentially expressed genes.
We found that 31 genes were present (Table  2 ) in both datasets, while six differential genes identified by Gene-Chip had no H3K4me3 peaks either because they were encoded by mitochondrial DNA or because no peaks were identified near the TSS. All differentially expressed GTPase-regulating genes had altered H3K4me3 marks, suggesting that the transcription of genes was mediated via epigenetic modifications of histones. However, 13 differential genes had no changes in H3K4me3 marks at their TSS; the expression of mRNA from these genes could be modulated by other mechanisms, such as distally located enhancers, epigenetic mechanisms and ncRNA. Thus, atrazine induces epigenetic modifications at the TSS of the majority of differentially expressed genes.
The Y-axis presents the plotted values of tags at each position after normalizing to all reads in the same dataset (intensity range shown on the left side of the plot); the X-axis shows the schema of the gene; rectangles are exons, and lines are introns. Note that the differential regions are located within genes. The H3K4me3 profiles from control biological replicates are shown in red, and those from ATZ-treated mice are in blue. For illustration, the "Integrative Genomic Viewer" (IGV) software version 2. 3. 36 was used. d qPCR analysis of the Ncoa2, Cyp19a1, and Star genes. qPCR analysis of RNA samples was performed in three independent experiments. Primer sequences for each gene are shown in the Materials and Methods section. The data are presented as fold change in treated samples compared to controls, *p < 0.
Exposure to pesticides results in increased susceptibility of fragile sites to breakage in workers exposed to pesticides  [57, 79]. It is possible that we failed to detect a set of DSBs not associated with recombination because a set of DSBs induced by ATZ is absent from published datasets. Future work will address this possibility. Fig. 8  The motif discovered by MEME-ChIP. The top image is a statistically over-represented sequence within the differential peaks discovered by MEME-ChIP  [49]. The bottom image is the consensus sequence within the motif discovered by MEME-ChIP. This consensus sequence significantly resembles an Nr5a2-binding site In summary, our data elucidates the molecular mechanisms underlying ATZ's negative effect on meiosis. Importantly, we found a number of effects at the molecular level at a stage in which no morphological changes are detectable.
Animals and atrazine exposure All animal procedures were performed according to the guidelines for animal models in research defined by the Ethics Committee and approved by the Ministry of France (reference project number is 01861. 02). All experiments were performed by A. G. P. or F. S, who Fig. 9  Differential peaks are associated with DSB regions. a The association of differential H3K4me3 peaks with the hottest DSB hotspots. The DMC1 tags associated with differential H3K4me3 peaks were extracted from published datasets  [12, 86] , and intensity values were calculated and presented as log(#tags) on the left plot. The right plot is the intensity of all DSB hotspots signal from the whole dataset  [86]. The median signal of DSB peaks associated with differential H3K4me3 peaks was higher than the median signal of all DSBs hotspots, suggesting that differential trimethylation peaks in ATZ-treated mice are associated with the strongest hotspots.
Testosterone and FSH quantification Serum was collected from ketamine/xylazine-anaesthetized adult animals by terminal cardiac exsanguination and aliquots were stored at -20 °C. Testosterone levels in the serum were assayed in duplicate using a commercial radioimmunoassay (RIA) based on competitive binding with I125-labeled testosterone (Immunotech, Beckman Coulter, Villepinte, France), according to the manufacturer's recommendations. FSH measurements were conducted according a standard protocol provided by a FSH measurement kit (KA2330, Abnova, Walnut CA, USA). In each hormone measurement, the data from at least 10 treated and control animals were averaged and plotted, and the results were expressed in nanograms per milliliter.
Cells sorting by flow cytometry Germ cells were isolated from control and ATZ-treated testis tissue. The testis cells were subjected to collagenase and DNAse treatment and purified by FACS, as described previously  [73]. The dispersed cells were fixed in 1 % (wt/ vol) buffered PFA for 20 min at 4 °C and permeabilized in a solution of 0. 2 % (wt/vol) saponin containing propidium iodide to label the DNA. The cells were sorted at concentration of 1×10 6 cells/ml on FACSCalibur cell-sorting machine. The data were analyzed by CellQuestPro software, which was provided with the machine.
Spermatozoa count Spermatozoa counts were conducted according to an established protocol  [98]. Briefly, the mice were euthanized, and the epididymis was dissected, rapidly frozen in liquid nitrogen and stored at -80 °C until the sperm heads were counted as follows. The organ was first cut with a scalpel into several fragments and homogenized in 50 ml 0. 15 M NaCl containing 0. 005 % (vol/vol) Triton X-100 (Sigma). After homogenization with three rounds of sonication (12 kHz), an aliquot of the cell suspension was loaded onto a Malassez hemocytometer, and spermatozoa heads were counted. The data from at least ten controls or ATZ-treated animals were averaged and plotted; a t-test was then conducted using Excel software.
Quantitative PCR and microarray experiments Total RNA was prepared using TRIzol reagent (Life Technologies). Reverse transcription of total RNA was performed using QuantiTect Reverse Transcription (Qiagen) according to the manufacturer's instructions. Quantitative PCR was performed using the ABI 7500 real-time PCR system. Relative expression values were calculated with ABI SDS software version V2. 0. 5. The primer sequences used in this research are indicated below. Duplicates of at least three independent experiments were used. Statistical significance was assessed by Student's t test. For Affymetrix microarray experiments, RNA samples were converted to single-stranded biotin-labeled DNA, according to the GeneChip whole-transcript terminal labeling user's manual, and hybridized to an Affymetrix Gene-Chip mouse gene 2.
0 st array. The RNA amplification, biotin labeling and hybridization, washing and scanning were carried out according to Affymetrix protocols. Differentially expressed genes were detected using AMEN software  [15]  with a fold-change cutoff value of 1. 5 and a p-value <0. 05. The qPCRquantification Chip-Seq experiments were carried out as previously described  [87]. Equal amounts of ChIP and input DNA were taken for PCR. Quantitative PCR was performed using the ABI 7500 real-time PCR system. The copy number for each locus was calculated with ABI SDS software version V2. 0. 5 using a standard curve. Enrichments were estimated as a ratio of copy number in ChIP samples to the copy number in the input sample. The averaged values of enrichment of at least three treated samples were compared, plotted and expressed as fold change.
Immunofluorescence The slides were incubated with blocking solution (1 % (vol/vol) donkey serum, 0. 3 % (wt/vol) BSA, and 0. 005 % (vol/vol) Triton X-100 in PBS) for 20 min at 37 °C in a humidity chamber. The primary antibodies were diluted in blocking buffer and incubated under the same conditions for 1 h. After two 5-min washes in 0. 4 % (vol/vol) Photo-Flo/PBS solution, the slides were blocked for an additional 5 min and incubated with secondary antibodies for 20 min at room temperature. The slides were washed twice with 0. 4 % (vol/vol) Photo-Flo in PBS, rinsed twice with 0. 4 % (vol/vol) Photo-Flo, and allowed to air dry. The images were taken using an AxioImager microscope equipped with an AxioCam MRc5 camera and AxioVision software version 4. 8. 2 (Zeiss, Le Pecq, France) with a 63X objective lens.
Peak calling and differential-peak finding Between 71 and 97 millions tags were derived from anti-H3K4me3 ChIP and input. The resulting sequences were quality filtered with the Sickle program  [40]  with -q33 and mapped back to the mouse mm9/ NCBI37 genome using Bowtie 1. 0. 0 with seed length 20. The results were visualized in the Integrative genomics viewer IGV version 2. 3. 36  [95]. Only tags that passed the quality filter and mapped uniquely to the genome were used. ChIP enrichment was further verified using CHANCE  [21]. The H3K4me3 mark peaks were identified using MACS 2. 0. 1  [24]  with two biological replicate samples, including corresponding input, shift-size window 73 bp, no model, with p-value threshold <10 -5. Two biological replicates for each condition were analyzed independently.