dataesr/scientific-paragraphs-categorization huggingface dataset:
Third, statistical analysis of the proteome adaptation between the two bacterial strains was performed on the 2444 filtered proteins. To this effect, we decided to analyse and compare our dataset with (SI approach) and without (AI approach) missing values. Missing values for LFQ intensities were imputed and replaced by random LFQ intensities that were drawn from a normal distribution at the low detection level (Supplementary Fig. S10 ). Yellow indicated imputated values in Supplementary Datasets S2 and S3. In both cases, two-sided T-tests of the log 2 transformed LFQ intensities with a permutation-based FDR calculation at 5%, 1%, 0. 1% and S0 = 1  60  were employed to determine different degrees of statistically significant proteins. This statistical process is the base of the proteomic comparison between the two bacterial strains, which is represented by the two Volcano-Plots, plotting the protein difference values against negative log 10 transformed p-values of the two-sided T-test (Supplementary Figs  S11  and S12 ).
Proteins detected in less than two replicates of one strain and in at least two replicates of the other strain, were designated as "exclusive" to that latter strain. With the SI approach, "exclusive" proteins were considered as significant proteins (Supplementary Dataset S2). The SI approach yielded a list of 299 exclusives proteins (116 in the wild type strain and 183 in the ΔrpoS mutant), and three statistically significant sets of differentially abundant proteins. RpoS was found exclusively in the wild type strain, consistent with the deletion of the rpoS gene in the mutant, and was thus excluded from the final list of σ S -regulated proteins (Fig. 2 ). For further analyses, changes in protein abundance were considered significant only when meeting the threshold of p-value 0. 05 (log 10 > 1.
3, Supplementary Dataset S3). This yielded a final list of 806 significant proteins showing differential abundance in the wild type and ΔrpoS strains, among which 400 proteins were selected only with a 0. 5% FDR, 223 were selected with 0. 5 and 0. 1% FDR, and 183 were selected with 0. 5, 0. 1 and 0. 01% FDR (Fig. 2 , Supplementary Dataset S3). The AI approach, used to evaluate the significance of the 299 exclusive proteins, yielded a final list of 134 statistically significant (p-value < 0. 05) exclusive proteins, including RpoS itself (Fig. 2 , Supplementary Dataset S3). In total, the abundance of 939 proteins (133 exclusives and 806 differentially abundant) was regulated by σ S (Fig. 2 , Supplementary Dataset S3). Other methods. Methods for strains construction, DNA manipulation, immunoblot analysis of proteins, enzymatic assays and sequence analyses are described in Supplementary Methods.
Acknowledgements We are very grateful to  Nara Figueroa-Bossi  for helpful comments about this manuscript and for the gift of strains  MA7224  and  MA7791. We thank all members of the  LSMS Laboratory and BIM Unit  for their kind support. This work was supported by the  French National Research Agency  (grant  ANR-11-BSV3-009  to FN) and by grants from the  Institut Pasteur  and the  Centre National de la Recherche Scientifique.
Gene in ATCC14028 Protein a E. coli K12 homolog b Phylogenetic distribution c Re-annotation and/or features Size aa LC-MS id Name RpoS d STM14_0421 - 33 Yes - Enterobacteriaceae STM14_0460 - 63 Yes yaiA 12 γ-Proteobacteria STM14_1271 YccJ-like protein IPR025600 75 Yes yccJ 11-14 γ-Proteobacteria STM14_2173 Transglycosylase motif IPR007341, 3TM fragments 84 ymgE 11-14 Bacteria and Archaea STM14_2188 - 45 Yes - Enterobacteriaceae STM14_2189 - 32 - Salmonella Start codon re-annotated, STM14_2239 88% identity with E. coli YebV, 78 Yes yebV 13, 14 Enterobacteriaceae DUF1480 IPR009950 STM14_2405 DUF2525 IPR019669 75 Yes yodD 11-14 Enterobacteriaceae STM14_2409 Start codon re-annotated, 83% identity with E. coli YodC, DUF2158 IPR019226 61 Yes yodC 11, 13, 14 γ-, α-, β-Proteobacteria Sm-like protein IPR010920, STM14_3597 pdb 2RA2, SP, Lipo, DUF903 75 Yes ygdI 12-14 Bacteria IPR010305 STM14_4398 Putative transcriptional regulator, DNA-binding domain IPR010982 96 Yes yiaG 7, 11-14 Bacteria 79% identity with E.
coli YibT, STM14_4446 DNA polymerase III-theta 69 Yes yibT 14 Enterobacteriaceae IPR009052 STM14_5097 CsbD like IPR008462, pdb1RYK 70 Yes yjbJ 7, 11-14 Bacteria, Archaea and Eukaryota STM14_5292 DUF1107 IPR009491 68 ytfK 7, 12-14 γ-Proteobacteria 65% identity with E. coli YjjZ, STM14_5469 3TM fragments, DUF1435 78 yjjZ 13, 14 Enterobacteriaceae IPR009885 STM14_5479 Not translated under the conditions used 44 - Salmonella Start codon re-annotated, 98% STM14_5481 identity with E. coli YtjA, 2TM 53 ytjA 13, 14 Bacteria and Archaea fragments, DUF1328 IPR009760 Paralogous genes e STM14_1275 KGG repeat IPR019626 55 Yes ymdF 13, 14 STM14_1829 KGG repeat IPR019626 60 Yes - Bacteria and Eukaryota STM14_2091 KGG repeat IPR019626 60 Yes yciG 12-14.
As we are strongly aware of the feasibility of certain kinds of recommendations, we will aim in the workshop (and have already aimed in our initial discussions) to scope such recommendations to ideas that have a low barrier to implementation and which would not run strongly counter to CHI culture. For example, requiring pre-registration of study designs or requiring open data are recommendations that have been made in some fields that would not be feasible at CHI, at least on a short term; on the other hand, badge systems like the OSF badges  [1]  have been proposed in other fields, have been found to be effective at increasing transparency in published work  [12] , and could in principle be feasible at CHI.
Call for Participation HCI is large and multidisciplinary, drawing on a variety of statistical practices. However, many of these existing practices have drawn increasing criticism within both HCI and related fields, including but not limited to: over-reliance on particular statistical methods, a lack of transparent reporting, a lack of replication and metaanalysis, few studies published with data or study materials, and inadequate education in statistics. These issues have even reached the popular press in coverage of the replication crisis in social science. We are running a working workshop to develop concrete guidelines for improving statistical practice in HCI. Participants will work in groups to flesh out guidelines for helping reviewers fairly assess statistical reports in CHI papers, concrete suggestions for changes to review processes, resources for authors, and other relevant guidelines or proposals the group wishes to advance.
Data analysis The data permitted calculating a score for each activity and a global score. The OIDP scores were expressed by the sum of the different performance scores (severity score × frequency score) divided by the maximum possible global score, then multiplied by 100 to obtain a percentage score. The global score could range from 0 to 72; it was then divided by 72 and then multiplied by 100. Thus the final score of the questionnaire varied from 0 to 100. The highest OIDP scores expressed a lower quality of life. The analysis was performed with the Statistical Package for Social Sciences (SPSS) software, version 18. 0 for Windows. The threshold of statistical significance was set at 0. 05. The face validity and content validity were tested during a pre-test. The reproducibility of the responses to the Malagasy version of the OIDP was evaluated during the test-retest by Intra-class Correlation Coefficients (ICC) where the intra-individual and the inter-individual variations divided by the total variation were expressed as a ratio between 0 and 1.
Expression of Behavioral Fever Occurs at an Advanced Stage of CyHV-3 Disease The data above demonstrate that expression of behavioral fever is beneficial for CyHV-3 infected carp. However, clinical observation of fish in the MCTs revealed that their migration to the warmest compartment occurred only at an advanced stage of the disease. To verify the relatively late onset of behavioral fever with respect to viral replication and cytokine upregulation, fish infected in MCTs were analyzed over time for viral load and carp proinflammatory cytokine gene expression. Data presented in Figure  1D  confirmed that the onset of behavioral fever observed in this experiment at 6 dpi occurred days after systemic replication of the virus (significant at 3 dpi) and upregulation of proinflammatory cytokines (significant for il1b and TNF-a1/a2 at 3 dpi and for all cytokines tested at 5 dpi).
This observation is also illustrated by Movie S3 recorded 6 dpi for the first replicate. Injection of anti-TNF-a neutralizing antibodies did not reduce The number of fish in each compartment was expressed as a mean per day + SD. The two lower graphs represent the global analysis of the data from the three replicates as described in Figure  1B. The statistical significance of the differences between the mean number of fish observed for 12Del and 12Rev groups is presented in the right graph. (C) Carp (n = 15 per tank) were housed in 6 MCTs. On day 0, fish were infected with 12Rev (3 tanks) or 12Del (3 tanks). One randomly selected tank per viral genotype was selected for monitoring the position of the fish (left graph), and the two remaining tanks were used to analyze viral load according to time post-infection.
(B) Silver staining of total proteins found in concentrated supernatants of CCB cells infected with CyHV-3 (WT, 12Del, or 12Rev) or mock-infected (Mock). Arrowheads indicate the band corresponding to the ORF12 protein. (C) ELISA binding assay of carp TNF-a1 and TNF-a2 to CyHV-3 secreted proteins. The data are the mean + SD of duplicate measurements. Results for which a significant difference was observed between WT/12Rev and 12Del/Mock groups are marked by asterisks. See also Figure  S2. (D) Neutralization of carp TNF-a1 and TNF-a2 by CyHV-3 secreted proteins was tested by using a TNF-a bioluminescent reporter assay. The data are expressed as fold change of luminescence relative to the respective controls and represent the mean + SD of quadruplicate measurements. Results for which a significant difference was observed between pTNF-a1 or pTNF-a2 and pEmpty are marked by asterisks.
On day 0, fish were infected with 12Rev (left column, 3 upper graphs) or 12Del (right column, 3 upper graphs). The number of fish in each compartment was expressed as a mean per day + SD. The two lower graphs represent the global analysis of the data from the three replicates as described in Figure1B. The statistical significance of the differences between the mean number of fish observed for 12Del and 12Rev groups is presented in the right graph. (C) Carp (n = 15 per tank) were housed in 6 MCTs. On day 0, fish were infected with 12Rev (3 tanks) or 12Del (3 tanks). One randomly selected tank per viral genotype was selected for monitoring the position of the fish (left graph), and the two remaining tanks were used to analyze viral load according to time post-infection. At the indicated post-infection times, viral load was measured in gills (per time point, a total of 6 fish originating from the duplicate tanks [3 fish/tank], mean + SD).
(C) ELISA binding assay of carp TNF-a1 and TNF-a2 to CyHV-3 secreted proteins. The data are the mean + SD of duplicate measurements. Results for which a significant difference was observed between WT/12Rev and 12Del/Mock groups are marked by asterisks. See also FigureS2. (D) Neutralization of carp TNF-a1 and TNF-a2 by CyHV-3 secreted proteins was tested by using a TNF-a bioluminescent reporter assay. The data are expressed as fold change of luminescence relative to the respective controls and represent the mean + SD of quadruplicate measurements. Results for which a significant difference was observed between pTNF-a1 or pTNF-a2 and pEmpty are marked by asterisks. These data are representative of three independent experiments.
ACKNOWLEDGMENTS We thank  A. Alcami ,  F. Bureau ,  A. Chariot , and  V. Mulero  for discussions,  C. Becco  for his help in the setting of the automated picture recording system,  L. Leinartz  for video editing,  J. Collard  for graphic editing, and  N. Sua  ´rez for generating genome sequence data. This work was supported by the  University of Lie  `ge ( Post-doc IN program ), the  Belgian Science Policy  ( BELVIR IAP7/45 ), the '' Fonds National Belge de la Recherche Scientifique '' ( T. 0153. 13  and  1. 5. 176. 12 ), an Investigator  FCT development grant  ( IF/00641/2013 ), the  European Community 's  Seventh Framework Programme  ( FP7/2007-2013 ) under Grant agreement  PIEF-GA-2011-302444 FISHIL10  (M. C. P. ), the  Netherlands Organization for Scientific Research (NWO)  under  Veni  project number  11200  (M.
ansorgei does not have a sequenced genome or transcriptome. Here we present the first de novo assembled and functionally annotated transcriptome for A. ansorgei. We performed RNA sequencing for A. ansorgei whole retina to a depth of 321 million pairs of reads and assembled 400,584 Trinity transcripts. Transcriptome-wide analyses and annotations suggest that our data set confers nearly full length coverage for the majority of retinal transcripts. Our high quality annotated transcriptome is publicly available, and we hope it will facilitate wider usage of A. ansorgei as a model organism for molecular studies of cone biology and retinal degeneration.
fastq,right. fastq] > out. txt [14]. Cleaned paired reads were combined across both samples and passed to Trinity for de novo transcriptome assembly with in silico normalization  [15]. Trinity was invoked using the command Trinity-seqType fq-max_memory 480G -CPU 48-normalize_reads -left left. fastq-right right. fastq-output out_dir-grid_conf trinity_conf. txt. RSEM, with Bowtie alignment, was used to quantify Trinity assembled transcript abundance in each sample  [16]. The Trinity utility was invoked using the command align_and_estimate_abundance. pl-transcripts Trinity. fasta-seqType fq-left paired_R1. fastq. gz-right paired_R2. fastq. gz-est_method RSEM-aln_method bowtie-trinity_mode.
De novo transcriptome functional annotation TransDecoder was used to search the Trinity assembled transcripts for open reading frames (ORFs) encoding peptides of at least 100 amino acids in length  [15]. Trinity transcripts of any length with ORFs homologous to known proteins or containing protein domains were identified by BlastP (v2. 2. 30)  [17]  queries against the Swiss-Prot database  [18]  and HMMER3  [19]  queries against the Pfam database  [20] , respectively. The final TransDecoder-predicted coding regions include those meeting the minimum length criteria and those of any length with BlastP or Pfam homology. Trinotate was then used for functional annotation  [15]. The TransDecoder-predicted coding regions were searched for Pfam protein domains using HMMER3, signal peptides using SignalP 4.
1  [21] , transmembrane regions using TMHMM  [22] , rRNAs using RNAMMER  [23] , homology to known proteins using BlastP (v2. 2. 30) (E<10 -5 ) against both the Swiss-Prot and the UniRef90  [24]  databases, and annotations from gene ontology (GO)  [25]  and EggNOG  [26]. The Trinity transcripts were also searched for homology by BlastX (v2. 2. 30) (E<10 -5 ) against the Swiss-Prot and UniRef90 database. All annotations were aggregated in a final report.
De novo transcriptome evaluation Trinity transcripts were searched by BlastN and BlastX against the NCBI RefSeq mRNA and protein databases, respectively, for both M. musculus and R. norvegicus. The percent coverage along the target transcript or protein was determined using the Trinity provided utility invoked with the command analyze_blastPlus_topHit_coverage. pl blast_result. outfmt6 Trinity. fasta blast_db  [15]. For each Blast hit in the target database, the best matching Trinity transcript was selected, and the percent of the Blast hit's length covered by the Trinity transcript was determined. Trinity transcripts were filtered for those with BlastX hits against the Swiss-Prot database and ranked by TPM. Gene Set Enrichment Analysis (GSEA) was used to identify Gene Ontology (GO) annotations enriched among these Trinity transcripts with mean TPM>1  [27].
Results Two RNA samples, S1 and S2, with RNA Integrity Numbers (RINs) of 9. 1 ). The Trinity transcripts had a mean length of 801 nt and a N50 length of 1,457 nt, meaning 50% of assembled bases are part of Trinity transcripts of length  Functional annotation for the Trinity transcripts was performed using the Trinotate annotation pipeline. TransDecoder was used to predict coding regions, which were then searched for Pfam protein domains, signal peptides, transmembrane regions, rRNAs, homology to known proteins in both the Swiss-Prot and the UniRef90 databases, and gene ontology (GO) annotations. The Trinity transcripts were also searched for BlastX homology against the Swiss-Prot and UniRef90 database. Alignment of the RNA-Seq reads to the de novo assembled transcriptome was evaluated. Expression levels of Trinity assembled genes and transcripts were estimated in units of TPM (transcripts per million) using RNA-Seq by Expectation Maximization (RSEM) with Bowtie as the alignment algorithm.
The majority of reads aligned to the transcriptome and in proper pairs (Table  2 ). The sequences, full annotations, and expression levels for the Trinity assembled de novo transcripts are available as Supporting Information files (S1 File and S2 File). We next examined the length and level of expression of the identified transcripts. Of the 400,584 assembled Trinity transcripts, 78,915 (19. 7%) were greater than 1kb in length, and of the subset of 63,242 Trinity transcripts with Swiss-Prot BlastX homology, 46,038 (72. 8%) were greater than 1kb in length (Fig  1A ). The subset with Swiss-Prot BlastX homology was also more highly expressed, with 35. 2% of annotated transcripts being expressed at a level greater than 1 TPM, as compared to only 10. 0% of all Trinity transcripts being expressed at this level (Fig  1B ).
musculus were used as the references for estimating the completeness of the A. ansorgei de novo assembled transcriptome. To perform this analysis, Blast was used to query each Trinity transcript against the RefSeq databases of mRNAs and proteins for M. musculus and R. norvegicus, and for each hit in the target database, the length of the hit covered by the best matching Trinity transcript was determined (Fig  3 ). There are 8,551 M. musculus and 8,486 R. norvegicus RefSeq mRNAs that have Trinity transcripts which align with at least 80% coverage, and there are 14,397 M. musculus and 13,095 R. norvegicus RefSeq proteins that have Trinity transcripts which translate to cover at least 80% of their length. We chose 33 canonical retinal cell specific markers and identified their corresponding Trinity transcripts.
The majority show near full length coverage and sequence identity for the coding sequences of the proteins against which they demonstrate BlastX homology (Table  3 ). Proteins expected to be highly conserved, for example 40S ribosomal proteins, 60S ribosomal proteins, beta actin, and cytochrome c, all demonstrate 100% identity and 100% full length coverage. BiNGO was used to identify the GO annotations within the GOSlim subgroup enriched among the Trinity transcripts with Swiss-Prot BlastX homology expressed at greater than 1 TPM using R. norvegicus as the reference (Fig  4A ). The number of genes corresponding to GOSlim annotations with greater than 2% coverage was assessed. Although the absolute number of genes is lower for A. ansorgei than for either the M. musculus reference or the R. norvegicus reference, the relative rank order for the GO annotation coverage is similar between A.
Discussion We performed RNA-Seq on adult retinas from the Nile grass rat A. ansorgei and used Trinity to de novo assemble and functionally annotate the first high quality draft transcriptome of this species. The assembly had an N50 length of 1,457 nt and included 400,584 transcripts, of which 46,038 were greater than 1kb in length and demonstrated Swiss-Prot BlastX homology. As expected, phylogenetic analysis placed A. ansorgei in closer evolutionary proximity to M. musculus and R. norvegicus than to other common model organisms, including C. porcellus (guinea pig). Trinity transcripts conferred full or near full length coverage of 14,397 M. musculus and 13,095 R. norvegicus RefSeq proteins, including highly conserved housekeeping genes and retinal cell specific markers. Pairwise comparison of retinal gene expression for A.
, 2016). ACKNOWLEDGMENTS I thank FAO for the recent capture data and Stan Shea (Bloom/Hong Kong) for the Hong Kong market statistics. Institut Français d'Amérique Centrale and the organizers of 3rd Congreso Latinoamericano de Equinodermos (Costa Rica) are warmly thanked for invitation and financial support. The comments of S. Purcell, I. Eeckhaut and J. J. Alvarado have been very valuable to improve the manuscript. Las pesquerías de pepino de mar se han expandido durante las últimas dos décadas, a un ritmo más rápido que la capacidad de gestión. La explotación ahora se califica como "en serie" y "contagiosa". Aquí presento las tendencias más recientes, según los últimos seis años de los datos de captura de la FAO. Hong Kong sigue siendo el mercado más importante para las importaciones y re-exportaciones de los productos transformados, principalmente el "trepang" seco (o bêche-de-mer), así como otros productos, lo que plantea dificultades para el análisis.
Conclusion 14b] In both trials, nucleic acid/PEI polyplexes were administrated locally. No serious adverse effects were observed indicating that local administration coupled to a surgical procedure may provide benefits. We showed here that Figure  6. In vivo evaluation of the immune response to injected polyplexes. Immunocompetent Balb/c mice were intravenously injected with 1 mg kg -1 siC (hatched blue square) or siC/πPEI (black dots). A-E) Blood samples were collected at various times postinjection and plasma concentrations (in pg mL -1 ) were determined for TNF-α, interferon γ, IL-1β, IL-12, and IL-6. F) The presence of hepatic enzymes in the plasma was measured 24 h after injection. Data are expressed as mean ± SD (n = 8). The basal plasma levels (white bar) of each component were measured in blood samples collected 48 h before injection.
5 nm period W/B4C multilayer monochromator fixed to the energy of 30 keV. The gap of the undulator of the insertion device (U32U) was set to 12. 38 mm. During the scan, 2000 projections were done over 180°with a time of exposure of 0. 3 s. The scanning data were reconstructed using a classical filtered back-projection algorithm (PyHST      software, ESRF) adapted to local tomography  [21]. This was done in edge-detection mode, based on an assumption of chemical homogeneity. Artefacts (e. g. rings and movements) were corrected based on programmed filters. Data for ontogenetic comparisons (figures 2-6) are from scans of two specimens, GIT 760-1 and GIT 760-2, with a voxel size of 0. 696 µm (also obtained with an objective 10×, NA 0. 3, coupled with a 2× eyepiece, a GGG10 scintillator, a FreLoN 2k14 detector and 0.
The draft genome sequence of Geobacillus sp. strain 1017, a thermophilic aerobic oil-oxidizing bacterium isolated from formation water of the Dagang high-temperature oilfield, China, is presented here. The genome comprised 3. 6 Mbp, with the G + C content of 51. 74%. The strain had a number of genes responsible for numerous metabolic and transport systems, exopolysaccharide biosynthesis, and decomposition of sugars and aromatic compounds, as well as the genes related to resistance to metals and metalloids. The genome sequence is available at DDBJ/ EMBL/GenBank under the accession no MQMG00000000. This genome is annotated for elucidation of the genomic and phenotypic diversity of new thermophilic alkane-oxidizing bacteria of the genus Geobacillus.