dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic Analyses VPE protein sequences were obtained from the available databases by BLAST searching  (Altschul et al. , 1997). Multiple alignments were performed using MUSCLE  (Edgar, 2004 ) and well-aligned sites were chosen using G-Blocks  (Castresana, 2000)  with settings to minimize the stringency of selection. Maximum likelihood (ML) phylogenetic reconstructions incorporating 500 bootstrap replicates were performed in PhyML  (Guindon et al. , 2010)  using the LG substitution model  (Le and Gascuel, 2008).
Gene Sequence Annotation To identify genes potentially encoding VPEs in Amborella, Arabidopsis VPE sequences retrieved from the Arabidopsis Information Resource (TAIR)  (Swarbreck, 2008 ; http://www. arabidopsis. org) were blasted against the Amborella EVM 27 Predicted Protein database (http://www. amborella. org/). The annotations of the scaffolds containing the predicted VPE genes (NCBI accession # NW_006499912. 1 and NW_006497648) were then manually checked and eventually re-annotated using the Lasergene Genomics Suite (http://www. dnastar. com/t-productsdnastar-lasergene-genomics. aspx; DNASTAR Inc. , USA). The newly annotated VPE sequences were submitted to NCBI under the accessions n • BK009356 and BK009357. The previous annotated cds # XM_006853855. 2 was not modified.
Gene Sequence Polymorphism Next-generation resequencing data from the Amborella genome (Amborella Genome Project, 2013) were used to characterize SNP polymorphisms corresponding to the VPE sequences characterized in the present work. The genomic information has been generated for 12 individuals (named according to their location: Tonine, Ponandou, Pwicate, Tchamba, Ba, Aoupinié, Boregaou, Amieu, Dogny, Mé Ori, Mé Fomechawa, and Nakada) covering a wide range of Amborella's extant geographical distribution and natural genetic diversity  (Poncet et al. , 2013). All the SNPs identified were defined as informative with a minor allele frequency (MAF) >0. 08 and a missingness rate <0. 42 by SNP. Biallelic exonic SNPs were annotated as synonymous or non-synonymous according to their reference/alternate allele nucleotides and to their position in the updated annotated coding sequences.
For each of the 12 individuals, the average MAF values were first computed across all SNPs for each of the three genes. Then, for each of the four genetic clusters inferred by a previous microsatellite (simple sequence repeats, SSR) analysis  (Poncet et al. , 2013) , namely North (Tonine, Ponandou, Pwicate, Tchamba), Center (Ba, Aoupinié, Boregaou, Amieu, Dogny), Me (Mé Ori, Mé Fomechawa), and Nak (Nakada), we calculated for each gene (i) the mean proportion of polymorphic SNPs and (ii) the mean proportion of private alleles. Computations were performed on intronic and exonic SNP datasets independently by discarding missing data. To assess any impact of natural selective pressures on VPE sequences, we examined the SNP patterns in comparison with 10 neutrally-behaving SSRs. Polymorphisms under neutral evolution co-vary with divergence between populations regardless of the mutation rate  (Hartl and Clark, 2007).
Shotgun Proteomic Analyses A shotgun proteomic analysis revealed 415 proteins from the isolated Amborella embryos (Villegente et al. , unpublished results). In particular, this analysis confirmed the presence of three 11S globulin forms in the Amborella embryos, of which two contained canonical N-G VPE cleavage sites, while the third contained a variant cleavage site (N-V-I) (data not shown). This shotgun proteomic analysis also revealed the presence of two specific peptides (GIIINHPQGEDVYAGVPK and HQADVCHAYQLLLK) (Supplemental Table  S1 ) matching with the amino acid sequences of Amborella VPE proteins encoded by sequences on the scaffold AmTr_v1. 0_scaffold 00002, labeled 27. model. AmTr_v1. 0_scaffold00002. 262 and evm_27. model. AmTr_v1. 0_scaffold00002. 263 (Figure  1 ).
The Amborella VPE Family To identify other genes potentially encoding VPEs in Amborella, we blasted the Arabidopsis VPE sequences retrieved from TAIR  (Swarbreck, 2008 ; http://www. arabidopsis. org) against the Amborella EVM 27 Predicted Protein database (http://www. amborella. org/). Two additional loci were thus revealed, namely evm_27. model. AmTr_v1. 0_scaffold00036. 100 (designated below as AmTr_36. 100) and evm_27. model. AmTr_v1. 0_scaffold 00002. 265 (AmTr_2. 265). To confirm the automatic annotation (http://www. amborella. org/ and http://amborella. uga. edu/) a manual annotation was performed on the retrieved scaffold sequences. The automatic annotation process of the scaffold AmTr_v1. 0_scaffold 00002 was actually wrong leading to truncated genes (Figure  1 ). Two full-length genes duplicated in tandem on the same scaffold (AmTr_v1.
0_scaffold00002) were in fact identified and designated as AmTr_2. 262-1 and AmTr_2. 262-2; (Figure  1 ). They are each composed of nine predicted exons and eight predicted introns like AmTr_36. 100. This structure is shared by almost all VPE genes from the available sequence databases representing green algae, bryophytes, lycophytes, gymnosperms, monocots, and eudicots (data not shown). The two duplicated genes (AmTr_2. 262-1 and AmTr_2. 262-2) show 84. 5% similarity at the nucleotide sequence level and 98. 8% at the protein level (Supplemental Figure  S1 ). The amino acid sequences encoded by all three predicted Amborella VPE genes exhibit the two conserved amino acid residues (H and C), which are also present in the active sites of all known active VPEs  (Chen et al. , 1998 (Chen et al.
, , 2004 ) (Supplemental Figure  S1 ). BLAST searching of the Amborella RNASeq Trinity Assembly using the online Amborella Genome Database (http://www. amborella. org) FIGURE 1 | Gene duplication model for the β-type Amborella VPEs on scaffold 2. The two duplicated genes (AmTr_2. 262-1 and AmTr_2. 262-2) show 84. 5 % similarity at the nucleotide sequence level and 98. 8 % at the protein level. Top: The manual annotation of the two closely related VPE genes, AmTr_2. 262-1 and AmTr_2. 262-2, referred to 262-1 and 262-2, respectively and the gene encoding the pectinesterase/pectinesterase (AmTr_ 2. 264). Bottom: In the framework of the Amborella Genome Project (2013) the EVidenceModeler (EVM) program (http://evidencemodeler. sourceforge. net) automatically annotated VPE genes within the region, leading to wrongly annotated, supernumerary and truncated genes.
identified expressed sequences corresponding to AmTr_2. 262-2 (gnl|Ambo_Trinity|comp32807_c0_seq1 and >gnl| Ambo_Trinity|comp23371_c0_seq1) and AmTr_36. 100 (gnl| Ambo_Trinity|comp847_c0_seq1 and gnl|Ambo_Trinity|comp 777_c0_seq1), though not to AmTr_2. 262-1. We conclude that the Amborella VPE family is composed of three genes: AmTr_2. 262-1, Am_Tr2. 262-2, and AmTr_36. 100 (Figure  1 ; Supplemental Figure  S1 ), of which the former two are very closely related. AmTr_2. 262-2 and AmTr_36. 100 are both transcribed, while the transcription of AmTr_2. 262-1 remains to be demonstrated. It should be noted among others that no seed tissues were used to obtain transcribed sequences in the available Amborella transcriptome databases (see http://ancangio. uga. edu/content/amborella-trichopoda), and so it is possible that AmTr_2.
Phylogenetic Analyses To gain further insight in plant VPEs and benefiting from the present Amborella sequences, the amino acid sequences of VPEs identified by BLAST from a wide range of embryophytes (land plants) taxa were used for phylogenetic reconstruction. These sequences were first blasted at TAIR against the Arabidopsis genome. For all VPEs presently considered, the best hits corresponded to Arabidopsis VPEs, testifying of high amino acid sequence conservation among plant VPEs (data not shown). The phylogenetic reconstruction of embryophyte VPE proteins (Figure  2 ; Supplemental Figure  S3 ) shows two sister clades of VPEs from angiosperms, of which one clade contains the α-, γ-, and δ-VPE proteins from Arabidopsis ("Angiosperm α/γ/δ-VPE clade"), while the other contains the β-VPE protein from Arabidopsis ("Angiosperm β-VPE clade").
, 2013) : "North" (Tonine, Ponandou, Pwicate, Tchamba) in green, "Center" (Ba, Aoupinié, Boregaou, Amieu, Dogny) in blue, "Me" (Mé Ori, Mé Fomechawa) in yellow, and "Nak" (Nakada) in red. of these two genes is expressed in seeds, thus generating the peptide fragments GIIINHPQGEDVYAGVPK and HQADVCHAYQLLLK, which we detected. Transcriptomics data available through both the Amborella Genome Database (http:// www. amborella. org) and Ancestral Angiosperm Genome Project website (http://ancangio. uga. edu) indicate that AmTr_2. 262-2 is expressed in non-seed tissues, though this gene may additionally be expressed in seeds, as no seed tissues were used to obtain these transcriptomics data. We conclude that AmTr_2. 262-1 is either not expressed, or is specifically expressed in seeds. The third VPE gene present in Amborella, AmTr_36.
22,000 years BP) and Holocene (ca. 12,000 years BP) when Amborella experienced a dramatic reduction (about 96%) in suitable area  (Poncet et al. , 2013). The survival and expansion of at least two lineages from putative refugia might have generated major diversity groups. The present data on VPE polymorphisms across the species provides an additional signature of the biogeographical history of Amborella.
16S rDNA V6 Pyrosequencing Total DNA was extracted from the samples using a method modified from the Qiagen stool procedure [QIAamp DNA Stool Mini Kit (Qiagen, Courtaboeuf, France)]  [12]. Primers were designed to produce an amplicon length (576 bp) that was approximately equivalent to the average length of reads produced by the GS FLX Titanium (Roche Applied Science, Meylan, France) as previously described  [12, 13]. The primer pairs commonly used for gut microbiota were assessed in silico for sensitivity to sequences from all phyla of bacteria in the complete Ribosomal Database Project (RDP) database. Based on this assessment, the bacterial primers 917F and 1391R were selected. The V6 region of 16S rRNA V6 was pyrosequenced with unidirectional sequencing from the forward primer with one-half of a GS FLX Titanium PicoTiterPlate Kit 70×75 per patient with the GS Titanium Sequencing Kit XLR70 after clonal amplification with the GS FLX Titanium LV emPCR Kit (Lib-L).
16S rRNA pyrosequencing analysis The 16S raw data for all samples was processed and compared using QIIME pipeline 1. 7. 0  [14] , which contains a suite of Python scripts for data analyses. The raw reads were demultiplexed with split_libraries. py and were trimmed using a minimum read length of 150 bp and an average quality score of 30. One mismatch was allowed along the primer sequences. The number of homopolymers authorized in a sequence was limited to 6. The high quality reads were classified to their corresponding operational taxonomic unit (OTU) at 97% similarity using the open-reference OTU picking strategy in QIIME pipeline. The representative OTU sequences were taxonomically classified using the RDP classifier  [15]  algorithm implemented in QIIME and using the most recent Greengene database gg_12_10 (http://greengenes.
secondgenome. com/ downloads/database/12_10). The NAST multi-aligner implemented in QIIME performed the multiple sequence alignment that is used to build phylogenic trees. Before building the phylogenic tree, the chimera identification sequence was performed by USEARCH  [16]. We also applied a QIIME random subsampling normalization to the OTU table of samples for the sample with the fewest read numbers. Moreover, the OTU table of all samples was filtered, discarding all OTUs that did not contain a minimum of three reads. The QIIME results, including tree, mapping and OTU files, were import into Phyloseq, an R package, for manipulation, alpha indices determination and graph visualizations. The 16S pyrosequencing raw data has been submitted to the SRA archive under the accession number SRP059828.
Metagenomic analysis The metagenomic paired-reads were assessed for quality (minimum average of 25) and assembled using the Panda package  [17]. The prodigal software performed the detection of open reading frames from metagenomic assembled reads (parameter-p = m) data. The KEGG assignment of the ORFs against the genepep KEGG database was provided by BLASTP, with an E-value of 10 -4 , a minimum bit score of 50 and sequence coverage >70. The corresponding tables from geneID to KO numbers, from KO to EC Enzyme or to pathways numbers, as well as the KEGG mapper tool (http://www. genome. jp/kegg/mapper. html) were used to build the different metabolic pathways. The assignment to Cluster of Orthologous Group (COG) was performed using RPS-Blast against the COG position-specific scoring matrix (PSSM) from the NCBI Conserved Domain Database, with a minimum E-value of 10 -4 , a bit score > 50 and sequence coverage > 70.
After the indicated post infection times, macrophages were lysed and live internalized mycobacteria were quantified using the colony counting method (colonyforming unit, CFU). The results showed an increase in Mabs viability and proliferation over the 7-day observation period in DMSO-pretreated cells (Figure  2 ). Interestingly, SFN-pretreated macrophages infected with Mabs yielded a 2-fold decrease in CFU at day 3 post infection and a 3-fold decrease at day 7 post infection compared with DMSO-treated cells. These data suggest that SFN may have an inhibitory effect on mycobacterial proliferation in macrophages.
Inhibitory effect of PD98059, SB203580, and SP600125 was verified by immunoblotting using phosphorylated antibodies to ERK, p38, and JNK (data not shown). Interestingly, immunoblots showed that increased expression of Nrf2 in SFN-pretreated and Mabs-infected macrophages was not inhibited by the specific MAPK inhibitors suggesting that induction of Nrf2 expression is upstream from ERK, p38, and JNK pathways (Figure  7a ). To determine whether Nrf2 is implicated in the activation of ERK, p38, and JNK pathways, macrophages were transfected with siRNA designed to specifically silence Nrf2 expression levels 24 h before SFN and/or Mabs treatment. Western blotting of protein lysates extracted 24 h after infection showed a significant decrease in Nrf2 protein level although the abolition was not complete (Figure  7b ).
Subcellular fractionation and immunoblotting For immunoblot analysis, THP-1-derived macrophages were rinsed with cold PBS then lysed with cold RIPA buffer (150 mM NaCl, 1% Triton X-100, 0. 5% sodium deoxycholate, 0. 1% 50 mM Tris-HCl, pH 7. 5, supplemented with Complete protease inhibitor cocktail mixture). Protein concentrations were determined using DC protein assay kit. Twenty micrograms of total proteins were resolved by SDS-PAGE (4-20% gradient gels) and transferred onto polyvinylidene difluoride membrane. Membrane blocking was performed in 5% BSA/TBST (10 mM Tris-HCl, pH 7. 4, 150 mM NaCl, and 0. 1% Tween-20) for 1 h before incubation with primary antibodies. The corresponding horseradish peroxidase-conjugated secondary antibodies were used at dilution 1/20 000. Immunoreactivity was visualized using the ECL prime detection reagent and detected using the QuantityOne software (ChemiDoc XRS, Bio-Rad, Marne-la-Coquette, France).
Immunoblots shown are representative of three independent experiments. Total RNA isolation, reverse transcription, and quantitative real-time PCR Total RNA was isolated from treated cells using the RNeasy Mini kit (Qiagen). RNA concentration and purity were determined using the GE NanoVue spectrophotometer (GE Healthcare). RNA was reverse transcribed into cDNA using Superscript III First strand synthesis kit (Life Technologies, St Aubin, France) with an oligo(dT) primer, according to the manufacturer's instructions. cDNA was analyzed using real-time qPCR, with each sample done in triplicate. qPCR was performed using the CFX96 thermocycler (Bio-Rad) and EurobioGreen qPCR mix. The specific oligonucleotides for Nrf2, HO-1, and NQO1 were designed using Primer-BLAST (NCBI website), and purchased from Eurogentec (Angers, France; Supplementary Table  1 ).
Gene expression levels were calculated as a ratio to the expression of the reference gene ubiquitin C (UBC). Data were analyzed on the Bio-Rad CFX manager 3. 1 using the ΔΔCt method. Apoptosis and necrosis assays, activated Caspase 3/7 assay, and ROS production assay Apoptosis assay was performed according to the manufacturer's procedure. Briefly, THP-1 cells cultured in 6-well plate at 1 × 10 6 cells/well were pretreated with SFN or DMSO for 3 h before mycobacterial infection. At the indicated times, cells were trypsinized, washed once with PBS, resuspended in Annexin binding buffer 1 × , and stained with Annexin V-FITC for 5 min in the dark and at room temperature. After one PBS wash, the cell pellet was suspended in 100 μl Annexin binding buffer 1 ×. Quantification of necrotic THP-1-derived macrophages was performed by incubating the infected and non-infected cells with 2 μg/ml PI.
Imaging flow cytometry Apoptotic/necrotic/infected cells, H 2 DCFDA-labeled cells, and activated Caspase 3/7 FLICA-labeled cells were quantified using ImageStream Mark II (Amnis, Merck-Millipore) imaging flow cytometer, which allows simultaneous imaging and analysis of cells. Depending on the assay, data from 5000 to 10 000 events were acquired at × 40 magnification and using 488, 658, and 785 nm lasers. Compensation settings were adjusted on singlecolor controls for each fluorochrome and analyses were performed using the IDEAS 5. 0 data analysis software (Amnis). The brightfield images were used to verify cell integrity. A brightfield area versus brightfield aspect ratio scatterplot was used to gate on single cells and eliminate cell aggregates. The single cells were then plotted on an Annexin V bright detail intensity versus brightfield area to gate on the Annexin V + cells.
Cells were rinsed with PBS and fixed with 4% paraformaldehyde at room temperature for 30 min. After one rinse with PBS, coverslips were mounted on slides using Fluoromount-G. Cells were observed using a confocal microscope (Leica TCS SPE, Nanterre, France). Images were treated and analyzed using ImageJ software (National Institutes of Health, Bethesda, MD, USA).
ACKNOWLEDGEMENTS This work was supported by funding from the  « Chancellerie des Universités de Paris (Legs Poix) » (MB) , the  Fonds de Dotation « Recherche en Santé Respiratoire » (MB) , the  « Centre d'Assistance Respiratoire à Domicile d'Ile de France (CARDIF) » (MB), LVL Médical (TBD, MB) , and the « Bonus qualité recherche-émergence » (TBD). We acknowledge the imaging core facility for the use of the imaging flow cytometer and the confocal microscope.
Especially the ethnographic studies of community have much to suggest about the relative range, strength, and forms of community, and how community is mediated, whether by social structure, language, ethnicity, or technology. Not only has ethnography been the preferred research method in CS, from the earliest studies of Middletown  (Lynd & Lynd, 1929)  and Yankee City  (Warner et. al. , 1963)  on through its densest period in the 1950s and 1960s. Ethnography has also been central to the large number of interventions characteristic of Applied Community Studies, many of which grew out of 1906's era urban renewal. These also presented much of the data which informed the creation of community organizing as a practice and profession. In our view, there is a general commitment among people in CI to combining 1) an understanding of specific community' dynamics and 2) interventions aimed at making such communities better.
Let C i n be the mass concentration of any species, referred as i, in the compartment n A f1; …; Ng. Then, the mass conservation equation for this species in the n-th compartment is given in the following equation: ∂C n i ∂t ¼ R i þ T i þ ∑ N m ¼ 1 ðM f m;n C m i ÞÀC n i ∑ N m ¼ 1 ðM f n;m Þ ð 1Þ The term T i is a gas-liquid transfer rate and R i an overall reaction rate, both expressed in g i L À 1 h À 1. The calculation procedure for the bioreaction rates will be detailed in following parts through a population balance model and a metabolic model. The mass balances, for each species and over each compartment, lead to a set of Ordinary Differential Equations. The ODEs sets were solved using a program written with MATLAB s 7. 9 (R2009b) using the ODE solver ode23 with relative and absolute error tolerances set respectively to 10 À 3 and 10 À 6.
Batch culture First, our biological model has been challenged by a set of experimental data coming from a batch culture conducted in a 15 liters stirred tank reactor. This culture and related measurement methods have been described by  Xu et al. (1999). From these data, it can be assumed that mixing and oxygen mass transfer were not limiting, so that the reactor is treated as perfectly mixed. Thus, the associated Compartment Model consisted in a single compartment (M f ¼0). In the experiment, the oxygen concentration was regulated around a value corresponding to 30% of saturation. Accordingly it was decided to discard the conservation equation for oxygen in the liquid phase and to impose a constant value in the simulations. During a 12 h culture, measurements of glucose, biomass and acetate concentrations were carried out each hour.
Conclusions In this study, trends of soil temperature (T s ) over boreal regions from nine process-based models were analyzed for the past 40 years. All models produce a warming of T s , but the trends of T s at 20 cm depth range from 0. 010 ± 0. 003 • C yr -1 (CoLM) to 0. 031 ± 0. 005 • C yr -1 (UVic) during 1960-2000. Most models show a smaller increase of T s with deeper depth. Air temperature (T a ) and LWDR are found to be the predominant drivers of the increase in T s averaged across large spatial scales. The relative contribution of T a and LWDR trends to the increase of T s is, however, different across the models. Note that the relative contribution of LWDR is based on only two models in this study, and this needs further investigation. The total uncertainty of the trend of T s at 20 cm is decomposed into the uncertainty contributed by uncertain climate-forcing data sets (0.
Acknowledgements. This study has been supported by the  PAGE21  project, funded by the  European Commission   FP7-ENV-2011  (grant agreement no. 282700 ), and has been developed as part of the modeling integration team of the  Permafrost Carbon Network  (PCN, www. permafrostcarbon. org),funded by the  National Science Foundation. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the  US Government. B. Decharme  and  C. Delire  were supported by the  French Agence Nationale de la Recherche  under agreement  ANR-10-CEPL-012-03. Edited by:  T. Bolch.
In many real world datasets both the individual and coordinated action of features may be relevant for class identification. In this paper, a computational strategy for relevant feature selection based on the characterization of redundant or complementary features is proposed. The characterization is achieved using fuzzy measures and an interaction index computed from fuzzy measure coefficients. Fuzzy measure identification requires raw data to be turned into confidence degrees. This key step is carried out considering the distributions of feature values across all the classes. Fuzzy measure coefficients are then estimated with an improved version of the Heuristic Least Mean Squares algorithm that includes an efficient management of untouched coefficients. Then, a generalization of the Shapley index for an arbitrary number of features is used.