dataesr/scientific-paragraphs-categorization huggingface dataset:
All gels were scanned with photomultiplier tube voltages to maximize the signal without saturating fingerprint bands. Band patterns were analyzed using GELCOMPARE 6. 5 software package (Applied Maths, Kortrijk, Belgium). In band assignment, a 1% band position tolerance (relative to the total length of the gel) was applied, which indicates the maximal shift allowed for two bands in different TTGE patterns to be considered as identical. Richness (number of TTGE bands in a profile) and diversity (Shannon-Wiener index) were computed as previously described  (Smith and Wilson, 1996).
Have Microbial Ecologists Caught Almost All the Diversity of Marine AAP Bacteria? Investigations on the diversity of AAP bacteria are relatively recent, and although the number of sequences in public databases has greatly increased over the past 10 years, one might expect to find populations exhibiting new puf M OTUs in newly explored ecosystems. It could be considered that a hidden part of the AAP diversity is not accessible through classical cloning-sequencing approaches and that high-throughput sequencing methods could reveal a "rare biosphere of AAP bacteria" as most of the prokaryotic diversity is in the less abundant taxa  (Sogin et al. , 2006). The recent work of  Ferrera et al. (2014)  addressed this issue by generating about hundreds of thousands reads through pyrosequencing of puf M genes from seasonal water samples at a coastal oligotrophic environment of the northwestern Mediterranean Sea.
Acknowledgments We wish to thank the F/F Johan Hjort crew as well as the  Norwegian Marine Research Institute  for providing ship time. This work was supported by the program  LEFE-CYBER (CNRS-INSU ) and the  Micro B3  project funded from the  European Union 's  Seventh Framework Programme  (Joint Call OCEAN. 2011-2: Marine microbial diversity-new insights into marine ecosystems functioning and its biotechnological potential)  under the grant agreement no  287589. We are grateful to  M. Perennou  (Biogenouest sequencing platform at the  Station Biologique de Roscoff ) for help with sequencing. ACL was supported by a postdoctoral fellowship from the  CNRS.
K. ). 45, 46 The neutrons entered and exited the environmental chamber via fused quartz windows. For experiments performed above room temperature, the windows were heated to prevent the condensation of water vapor. The reflection of visible laser light at the interface was used to check regularly the height alignment of the interface with respect to the neutron beam. The incident neutron beam with a range of wavelengths, λ (2. 2-25 Å for FIGARO and 0. 5-6. 5 Å for SURF), was collimated and inclined so that it fell at a grazing angle of incidence, θ, of either 0. 624°and 3. 78°(FIGARO) or 1. 5°(SURF) to the horizontal plane of the air-liquid interface. This provided neutron reflectivity data as a function of momentum transfer normal to the interface, q, where q = (4π/λ) sin θ. The measured reflectivity of a sample of pure D 2 O contained in the Langmuir trough was used to obtain a scale factor with which to normalize the intensity spectrum of the incident beam.
Both X-ray and neutron reflection measurements were taken to examine the amount and thickness of peptide monolayers at the air-water interface following exposure to gas-phase ozone of monolayers of SP-B (1-25) and SMB on a buffered aqueous subphase. The surface pressure was recorded during these X-ray and neutron reflectometry experiments. Figure  7  shows reflectivity data obtained for SP-B (1-25) on buffer before and after exposure to ozone. Three scattering contrasts are shown: that from X-rays and those from neutrons involving two isotopic contrasts of the subphase (NRW and D 2 O). In the case of X-rays, the presence of the peptide at the air-water interface significantly changes the reflectivity profile from that recorded for just the buffer alone. In the case of neutrons, the weak reflectivity comes from the presence of the peptide at the interface when spread on a NRW buffer, and the strong reflectivity of the subphase is modified by the presence of the peptide at the interface when spread on a D 2 O buffer.
As can be seen from Figure  8 , the reaction of monolayers of SMB at the air-water interface does not lead to any significant change in the neutron or X-ray reflectivity profiles, whether the reaction was performed at 21 °C or the more physiologically relevant temperature of 37 °C. Fitting the data recorded after exposure of SMB to ozone reveals no changes, outside the uncertainty, in the amount of material at the interface or the positioning of the peptide at the interface. This is a surprising result as the fluorescence data clearly show that the tryptophan residue of SMB is quickly oxidized by ozone under these conditions and the reaction leads to a significant change in the surface pressure. The nature of the reaction products that remain at the interface was investigated by performing SDS-PAGE and HPLC analysis of the reaction mixture extracted from the interface with chloroform, as described above.
A decrease in total b n to ∼73% of the initial value would be expected for the mixed monolayer if just material from d 31 -POPG were lost from the interface (no loss of SMB) and the loss of material from POPG were not influenced by the presence of the SMB. It is not possible to determine, from the data recorded, whether the additional loss of material is due to the loss of more POPG from the interface when SMB is present or whether the presence of POPG causes some SMB to be lost from the interface upon oxidation. Further experiments in the future, with a deuterated version of SMB, would be required to answer this question. To examine selectively changes upon oxidation of SMB to interactions with the anionic headgroup of POPG, we also performed neutron reflectivity studies in which mixtures of SMB and the saturated anionic lipid d 62 -DPPG, 1:12 by molecule, on NRW buffer were exposed to ozone.
A rapid drop in surface pressure occurs when both SMB and SP-B (1-25) in monolayers of the lipid DPPC are exposed to ozone. The lipid DPPC does not react with ozone. When SMB is present in monolayers with the unsaturated anionic lipid POPG, a rapid reaction of the lipid is clearly observed, and more material is lost from the interface than if just the lipid POPG were present. However, it is not possible to determine if the additional material lost is of lipid or peptide origin. The role of protein SP-B is thought to be to interact with unsaturated anionic lipids such as POPG, possibly by binding to the lipids and bringing them back to the interface as the lungs expand. The interaction is thought to be facilitated by presence of several positively charged residues in SP-B. Looking at the experimentally determined structure of Mini-B, SP-B(8-25,63-78), PDB entry 1SSZ, shown in Figure  14 , it can be seen that the positively charged arginine residue (residue 8 of Mini-B) is very close to the tryptophan, residue 2 of Mini-B.
■ ASSOCIATED CONTENT * S Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI: 10. 1021/acs. biochem. 5b00308. As an example is shown the fit obtained to the X-ray data for SMB when a single-layer model is used, rather than a two-layer module for the peptide. An image of a polyacryalmide gel for a sample of SP-B (1-25) and a sample of SP-B (1-25) after heating with DTT is shown, confirming the band at ∼16 kDa is from an oligomer of SP-B (1-25). The X-ray and neutron reflectivity curves for monolayers of SMB and DPPG before and after ozone exposure are included (PDF) ■ AUTHOR INFORMATION Corresponding Author *E-mail: k. thompson@bbk. ac. uk.
Acknowledgments We thank  Dr JP Jacob  from "la coordination hospitalière des prélèvements d'organes et de tissus" ( CHU, Angers, France ). We also thank  P Legras  and  J Roux  ( Service commun d'animalerie Hospitalo-Universitaire, Angers, France ),  Prof P Schiller  ( University of Miami School of Medicine, USA ),  Dr L Lemaire  and  L Sindji  ( INSERM U1066, Angers, France ) for providing facilities, and  Alex Edelman and Associates  for correcting the English language of the manuscript.
S3. Database survey A search in the Cambridge Structural Database, version 5. 36 reveals 9 hits with related structure having two fused 6 and 7 membered rings  (Chiaroni et al. , 1992 (Chiaroni et al. , , 1995;; Chiaroni et al. , 1996a,b,c; Sbai et al. , 2002; Benharref et al. , 2010; Oukhrib et al. , 2013; Bimoussa et al. , 2014 ).
+ )À(I À )]/[(I + )+(I À )] (Parsons et al. , 2013) Absolute structure parameter: À0. 02 (2) Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR97 (Altomare et al. , 1999); program(s)Supporting information for this paper is available from the IUCr electronic archives (Reference: XU5855).
Background: Induction of labor is a major issue in pregnancy management. Finding strategies to increase rate and decrease time to vaginal delivery is an important goal, but maternal or neonatal safety must remain the primary objective. Misoprostol is a synthetic analogue of prostaglandin used off label to ripen the cervix and induce labor. The misoprostol vaginal insert (MVI) was designed to allow a controlled-release delivery of misoprostol (from 50 to 200 µg) with a removal tape. The objective of this review was to make a critical appraisal of this device referring to the literature. Methods: A literature search was performed in the PubMed and Cochrane databases using the keywords "vaginal misoprostol insert". Results: Several studies compared different doses of MVI (50, 100, 150, and 200 µg) with the 10 mg dinoprostone insert.
Methods We performed a literature search, limited to English language, in the PubMed ® and Cochrane library databases using the keywords "misoprostol vaginal insert". We considered pharmacological studies, retrospective studies, randomized clinical trials, secondary analyses, and review of use of the MVI. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were followed. We mainly focused on the biodisponibility of misoprostol administered by MVI and also on efficacy and safety for maternal and fetal outcomes related to induction of labor. Even if randomized, clinical trials that compared misoprostol tablets introduced orally, sublingually, or vaginally with other cervical ripening methods were not included in our analysis but were used to discuss the current evidence available about the use of misoprostol as a labor induction drug.
g. Phi11  Xia et al. , 2011) , Lactobacillus phages  (Casey et al. , 2014) , etc. In a recent paper, Bielmann et al. identified the RBPs from siphophages A118 and P35, infecting the Gram-positive bacterium Listeria monocytogenes, as well as their receptor specificity  (Bielmann et al. , 2015). These authors also performed a topological study of the A118 baseplate using EM-immuno labeling, making it possible to identify and localize the baseplate proteins. Using the program HHpred  (Hildebrand et al. , 2009; Soding et al. , 2005)  they identified similarities between the A118 structural proteins and the baseplate components of other phages  (Bielmann et al. , 2015). Here, following full exploitation of the information from HHpred and from the Bielmann et al. paper  (Bielmann et al. , 2015) , a molecular model of the A118 phage baseplate was generated from the individual building blocks.
2g ). The main topological differences between TP901-1 and A118 baseplate are (i) the fused BppU/BppL configuration of gp20 results into to a single RBP trimer instead of three, (ii) a shortening of the horizontal arm of the BppU, as can be deduced from the HHPRED figure and the width of the baseplate as seen by EM (200 Å for A118 vs. 280 Å for TP901-1) and (iii) a longer span of the vertical helix bundle (Figs. 3  and 4 ). A topological model of the full gp20 was constructed using the molecular graphics program Coot  (Emsley et al. , 2010)  by deleting the final part of TP901-1 BppU, before the β-stranded C-terminal domain, and grafting the helical bundle of TP901-1 BppL, the RBP, after deleting the extended 17 amino-acids long N-terminal stretch. Because the baseplate looked less large on the EM view, the length of the helical bundle between BppU N-terminal domain and the kink was shortened (24 residues shorter).
The EM immuno labeling of gp19 is consistent with two positions: one at the upper end of the   (Hildebrand et al. , 2009)  outputs display (i) a bar graph summarizing the positions of the database matches with more than 95% probability and the PDB identifier inside the bar and (ii) a tabular hit list with probabilities, E-values, scores, and match regions in query and templates (for more details see http://toolkit. tuebingen. mpg. de/hhpred/help_results). (A) Results of the gp17 analysis. The two hits are the Dit proteins of phages SPP1 and TP901-1, respectively. (B) Results of the gp18 analysis. The first hit is the structure of a gp18 variant obtained by a structural genomics consortium (no publication). (C) Results of the gp20 analysis. All the HHpred hits returned are from the TP901-1 phage proteins BppU and BppL  (Veesler et al.
Methods Molecular modelling of phage A118 baseplate was performed using as a starting model the crystal structure of the TP901-1 baseplate (  (Veesler et al. , 2012) ; PDB identifier 4D96, previously 4DIV, 4DIW). Model building was performed with Coot  (Emsley et al. , 2010). Phage A118 gp17 structure was represented directly from the structures of the TP901-1 Dit (extracted from 4D96). Phage A118 gp18 sequence is 95. 5% identical to that of 3GS9. Hence the 3GS9 structure was used to represent gp18 (Tal) structure. The 3GS9 trimer was docked "manually" (by rotationtranslation of the whole molecule) against the gp17. Phage A118 gp20 structure was built by fusing parts of TP901-1 BppU and BppL. More precisely, the C-terminal domain of BppU was removed (after residue 190) and the horizontal arm was shortened by 28 residues (deletion, Δ146-163).
The horizontal helix of BppU was then extended by 15 helical residues. The BppL N-terminus non-helical stretch wad deleted (Δ2-15) and BppL helix 16-30 was placed manually in continuation of the BppU extended vertical helix. During this process, attention was paid to obtain a gp20 model with the proper length and a baseplate model fitting the dimensions of the EM views. Fig. 1  is composed from the HHpred program outputs. Figs. 2 and 3 are made with Pymol. Fig. 4  uses as background an EM view of phage A118 presented in Figure  5  of  Bielmann et al. (2015) ; the EM tail representation (taken from the structure of phage TP901-1 tail  (Bebeacua et al. , 2013) ) and the A118 baseplate view were produced with Chimera  (Pettersen et al. , 2004).
Background Adolescent idiopathic scoliosis (AIS) is a four dimensional deformity of the spine arising in otherwise healthy children during puberty. The fourth dimension is time. This dimension is the characteristic of our database created in 1998 with systematic reconvening of our patients at regular intervals which increases the level of scientific evidence  [1]. The use of a brace in the conservative treatment for AIS plays an important role and has the aim to stop the evolution of the deformity in immature adolescents in order to prevent problems during adulthood  [2, 3]. Long-term follow-ups indicate that patients with scoliosis may have a higher prevalence of back pain and of worsening pulmonary function if the curve becomes extremely severe  [4]. A randomized control trial BRAIST study conducted by Weinstein showed that bracing is significantly effective in reducing the progression of AIS  [5].
Many previous studies support the positive results associated with the casting and Lyon braces  [14, 16, 17]  but the difficulty and cost of making the plaster cast, administrative economical questions and low compliance, can also explain the reasons which ultimately have prompted the development of new design concepts with immediate in-brace correction. It was only in 2013 that advances in computer technology with the latest generation software (OrtenShape) allowed the superposition of different CAD/CAM moulds and a segmental 3D reconstruction  [18, 19]. The aim was to use this new software to replace the plaster cast with a new Lyon brace: the ARTbrace. Segmental moulding is one of the fundamental innovations of the ART brace. The overcorrection is performed in the frontal plane and the sagittal plane precisely and individually for each child at three levels: pelvis, lumbar spine and thoracic spine.
All the data are recorded immediately into a database and a serial number is automatically assigned at T1 about 3 days after bracing. All other statistical tests are done with the package SPSS v20. The first step is to confirm the normality of distribution (Kolmogorov-Smirnov & Shapiro-Wilk) and then use an independentsamples T test to compare Cobb angles T0 (before brace), T1 (in-brace),T2 (at 6 months) and T3 (at 1 year). A p value of less than 0. 05 was considered to be significant. A copy of the Excel database can be downloaded to allow any comparisons (Additional file 1).
5 ). With SPSS we can confirm with two tests: Shapiro-Wilk, and Kolmogorov-Smirnov, that the data comes from a normal distribution (Additional file 2). We also use SPSS comparison of means tests to compare the two independent groups and answer the following questions (Additional file 3). There was not a significant difference in the score of Thoracic Cobb angles before brace for control group with the old Lyon brace (M = 31. 14, SD = 9. 62) and the ARTbrace group (M = 30. 03, SD = 8. 30, t(182) = 0. 834, p = 0. 405. There was not also a significant difference in the score of Lumbar Cobb before brace for control group with the old Lyon brace (M = 26. 69, SD = 7. 72) and the ARTbrace group (M = 27. 82, SD = 7. 51, t(144) = -0. 884, p = 0. 378. There was a significant difference in the scores for thoracic and lumbar curves: in brace, at 6 months and after 1 year.
Indeed, locus-specific functional interactions in these TADs necessarily occur from this underlying dynamics of the chromatin. Therefore, any constraints favouring intrinsically the probability of contact between two genomic regions will also favour the probability of interaction between the regulatory elements that they contain. Long-range interactions should thus tend to occur at preferred relative separation distances where the probability of contact is the highest. We previously showed that, in loci containing co-expressed genes, conserved elements (UCSC database) are overrepresented at a distance of ~100 kb from the surrounding Transcriptional Start Sites (TSS)  [4]. In the same line, ChIP-seq experiments at 885 loci containing genes overexpressed in the mouse forebrain showed that p300 peaks linked to enhancer activities are more significantly enriched for separation distances of about 70 to 80 kb from the nearest TSS  [34].
Standards curves for qPCR have been generated from BACs (RP serie from Invitrogen) as previously described  [4] : RP23 55I2 for the Usp22 locus; RP23 117C15 for the Dlk1 locus; RP23 463 J10 and RP23 331E7 for the Lnp locus; RP23 117 N21 for the Mtx2 locus; RP23 131E7 for the Emb locus; RP23 30H4 and RP23 247C7 for the 3qH2 and 19qC2 gene-poor regions respectively; and a sub-clone derived from RP23 3D5 for the 11qA5 genedesert region (also see Additional file 1a). Quantitative 3C primers sequences are given in Additional file 6. Data obtained from these experiments are included in Additional file 7 (WT mESC) and Additional file 8 (H1 TKO mESC). The number of sites analysed in each experiment were as follows (Additional file 1b). For WT mESC: Usp22 locus, for anchor sites F1 and F7, 33 and 35 sites were analysed respectively; Dlk1 locus, for anchor sites F3/F5/F14 and F16, 9/16/21 and 26 sites were analysed respectively; Emb locus, for anchor sites R4 and R7, 30 sites were analysed for each anchor; Lnp locus, for anchor site R35, 49 sites were analysed; Mtx2 locus, for anchor sites R2 and R56, 52 and 50 sites were analysed respectively; 3qH2 gene-poor locus, for anchor sites R6 and R27, 25 sites were analysed for each anchor; 19qC2 gene-poor locus, for anchor sites R41 and R59, 33 sites were analysed for each anchor, and for the 11qA5 genedesert locus, for anchor sites F5/F25/F35 and F48, 21/ 20/21 and 20 sites were analysed respectively.
Datasets have been submitted to Gene Expression Omnibus (GEO) under accession no [GSE61471] (http://www. ncbi. nlm. nih. gov/ geo/query/acc. cgi?acc=GSE61471). The relative contact frequencies used to construct the "virtual 3C" profiles were obtained by assembling these 5 kb bins into larger 25 kb (5*5 kb) bins that were analyzed with a step of 5 kb along the chromosomes. For each 25 kb bins, the relative contact frequencies were calculated each 5 kb within a region surrounding 400 kb (80*5 kb bins) from the start of the 25 kb bin. For each "virtual 3C", the unconstrained chromatin model [eqs. 1 and 2]  was fitted to the first 70 kb (14*5 kb bins) using the "nls2 object" under the R software (R Development Core Team 2008, http://www. R-project. org), and the best-fit parameters were extracted.
Acknowledgements We thank  Hidemasa Kato  for stimulating discussions,  Françoise Carbonell ,  Cosette Rebouissou  and the staff from the IGMM animal unit for technical assistance. This work was supported by grants from the  Institut National du Cancer  [ PLBIO 2012-129 ,  INCa_5960  to T. F. ], the  Association pour la Recherche contre le Cancer  [ SFI20101201555  to T. F. ], the  Ligue contre le cancer (comité Hérault ) and the  Centre National de la Recherche Scientifique. Y. F. & Y. Z. are supported in part by a  Georgia Research Alliance   Distinguished Cancer Scholar Award  (to Y. F. ) and by a  US National Institutes of Health  grant  GM085261  (to Y. F. ).
A mean of 56 Ϯ 27 million passing illumina quality filter reads was obtained for each of the three samples. The whole RNA-Seq data analysis was performed using the Eoulsan software version 1. 1. 6 (Jourdren et al. , 2012)  with the following parameters. Before mapping, poly N read tails were trimmed, reads Յ11 bases were removed, and reads with quality mean Յ12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from the University of California, Santa Cruz) using the Bowtie mapper (version 0. 12. 7; Langmead et al. , 2009)  using the -best and -k 2 parameters. Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, M. musculus GFF3 genome annotation from UCSC (mm10) was used. All overlapping regions between alignments and referenced exons were counted.
Data normalization and differential analysis were performed using the DESeq package version 1. 6. 10 (Anders and Huber, 2010). We selected transcriptional changes observed in Cx43KO brain vessels compared with WT libraries, considering only transcripts read Ͼ50 times with a fold change Ͼ2. Selected events were further validated by qPCR on purified brain vessel RNAs. RNA sequencing data are available at http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?tokenϭ mfqjqmscvxqbtoh&accϭGSE54458. Quantitative RT-PCR. Reverse transcription was performed from RNA extracted from purified brain vessels, dissected cortex and hippocampus, or sorted cells using the RNeasy kit (Qiagen). The primer list is provided in Table  2. QuantiTect primer assays (Qiagen) were used for Ighg1, Igkc, Igkv4-50, Igkv6-15, P-Selectin, E-Selectin, VCAM-1, and Flow cytometry.