dataesr/scientific-paragraphs-categorization huggingface dataset:
Skn7 binds to the promoter of genes involved in oxidative stress adaptation and morphogenesis To test if the genes that emerged from the transcript profiling analysis were directly regulated by Skn7, a chromatin immunoprecipitation coupled with hybridization to genome-wide tiling array (ChIP-chip) was performed. We compared binding of the HA3-tagged Skn7 to untagged control following 2 h of ATc induction (see Experimental Procedures). We used the CisGenome peak finding algorithm to identify Skn7 binding sites  (Ji et al. , 2008). In total, 74 binding peaks were found at the promoters for individual ORFs, and 38 peaks were found in regions shared between two ORFs in opposite orientations (Table  1  and Table S4 ). Additional bona fide binding peaks associate with 16 target genes were not detected by the peak-finding algorithm and were added to our target list (Table  S2 ).
5B ). We also conducted motif-enrichment analyses of the DNA sequences encompassing 250 bp around peak summits in Skn7 binding data, using three motif discovery algorithms: the RSAtools (RSAT) peak-motifs (http:// rsat. ulb. ac. be/rsat/, Thomas-Chollier et al. , 2011; 2012) , the MEME suite  (Bailey et al. , 2009)  and SCOPE (genie. dartmouth. edu/scope/; Carlson et al. , 2007;  see Experimental Procedures for details). The three algorithms identified the same three motifs, CACAAA (Ndt80 binding site), TATGCA (Efg1 binding site), and TCTAGA (Fig. 5C ), highlighting the high frequency of co-binding of regulators at the same promoter regions. The latter sequence, similar to the S. cerevisiae transcription factor Abf2 binding motif (involved in mitochondrial function; JASPAR database, http://jaspar.
Chromatin Immunoprecipitation (ChIP) and ChIP-on-chip Two independent cultures of CEC4228 (PTET-SKN7-HA3) and CEC4848 (PTET-SKN7, untagged control strain were grown overnight at 30°C in 2 mL of YPD. Strains were diluted at OD600 = 0. 2 and incubated in YPD for 1 h at 30°C, then 3 µg. mL -  ATc was added followed by growth during 2 additional hours. The ChIP procedure was performed as described in  Znaidi et al. (2013)  Data normalization (Quantile) and peak finding were conducted using CisGenome  (Ji and Wong, 2005; Ji et al. , 2008). The Integrated Genomics Viewer (IGV) software was used for visualization of the ChIP-chip results  (Robinson et al. , 2011; Thorvaldsdóttir et al. , 2013)  (Fig. 5A ). The complete Skn7 binding datasets are available in Table  S4. ChIP-on-chip raw data were deposited at GEO under accession number GSE85275, and transcriptomics data under the accession number GSE85276.
Data were analyzed using the Realplex software version 2. 2 (Eppendorf). For each experiment, threshold cycle (CT) values were determined using the realplex software. Skn7 binding enrichment was calculated using relative quantification according to the 2 -ΔΔCT method, as follows: ΔCT = CT(target) -CT(TEF3 reference) calculated in both tagged (Skn7-HA3) and untagged samples, and ΔΔCT = ΔCT(tagged) -ΔCT(untagged), where CT(TEF3 reference) is the CT for the TEF3 amplicon (primers TEF3-F/R, Table  S7 ). The qPCR assays were performed three times independently using two or three biological replicates each time. A two-tailed Student's t-test was applied by comparing, for a given ChIP target, the n-fold enrichment values of the selected target gene to those of the corresponding ACT1 control, followed by false discovery rate according to  Benjamini and Hochberg (1995).
Gene expression microarray data analyses The microarrays were scanned using the Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). The images were analyzed with GenePix Pro 6. 1. 0. 2 software (Molecular Devices, Downington, PA). The GenePix Results (GPR) files were imported into the Arraypipe 2. 0 software  (Hokamp et al. , 2004). Following spot filtering and bad spot flagging, global signal intensities were normalized using Loess normalization and replicates slides (n=3) were combined and P-values calculated using standard Student's t-test. Microarray data were deposited at GEO under accession number GSE85276.
100 µL of o/n cultures were plated on solid media covered with a sterile cellophane sheet and incubated at 30°C for 3 (YPD) or 8 (Spider) days. Cellophane sheets were transferred in 50 mL tubes, washed with 10 mL of RNase-free H2O and cells resuspended through vigorous vortexing. Cells were harvested and stored at -80°C until the RNA extraction (hot-phenol method). Three independent biological replicates were used. Five µg of RNA were used to synthetize the cDNA using SuperScript III (Invitrogen); alternatively, 500 ng of RNA were used with SuperScript IV (Invitrogen). Reactions were done according to the supplier's instructions. Primers were designed using Primer3 and the sequences are listed in Table  S7. Quantitative PCR was performed using 1 µL of a 1/100 dilution of cDNA, mixed with 7.
Microscopy and Image analyses Colony morphology was imaged with a Leica M80 Stereomicroscope at a x25 magnification. Images were captured with a DMC 2900 camera, using the Leica Application Suite (LAS) imaging software. Cells phenotypes were observed with a Leica DM RXA microscope (Leica Microsystems). Images were captured with a Hamamatsu ORCA II-ER cooled CCD camera, using Openlab software version 3. 5. 1 (Improvision Inc. ). Images were then processed with Adobe Photoshop CS6. (C) Phenotypic analysis of skn7 deletion mutant upon exposure to cell wall or osmotic stress. Serial dilutions of C. albicans SC5314, ΔΔskn7 and ΔΔskn7+SKN7 strains were spotted on YPD supplemented or not with different stress agents: 200 µg. mL -  and 300 µg. mL -1 Congo Red, 20 µg. mL -1 and 30 µg. mL -1 CalcoFluor White (cell-wall stress) or 1.
Acknowledgements We are grateful to all members of the  Fungal Biology and Pathogenicity Unit  for constant support throughout this project. We are also grateful to members of the  Transcriptome and Epigenome Core Facility (Biomics Pole, Institut Pasteur)  for the availability of the microarray scanner. We are grateful to  Dr. Carol Kumamoto  and  Dr. Bernard Hube  for providing strains. Work in the d'Enfert laboratory was supported by grants from the  Agence Nationale de la Recherche  ( CANDIHUB ,  ANR-14-CE14-0018 ), the  European Commission (FINSysB ,  PITN-GA-2008-214004 ) and the  French Government 's  Investissements d'Avenir program  ( Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases ,  ANR-10-LABX-62-IBEID ). Work in the LeibundGut laboratory was supported by the  Swiss National Science Foundation  (grant number  PP00P3_150758 ) and the program " Rare Diseases -New Approaches " from  Gebert Rüf Foundation  (grant number  GRS-044/11 ).
V. B. was supported by a stipend from the  Pasteur -Paris University (PPU)   International PhD program  and the " Fondation Daniel et Nina Carasso ". S. Z. was supported by grants from the  Agence Nationale de la Recherche  ( CANDIHUB ,  ANR-14-CE14-0018 ) and the  French Government 's  Investissements d'Avenir program  ( Institut de Recherche Technologique BIOASTER ,  ANR-10-AIRT-03 ). V. C. was the recipient of a PhD fellowship of the  European Commission (FINSysB ,  PITN-GA-2008-214004 ).
nirs Measurement and analysis Near infrared spectroscopy measurements were performed using a continuous wave system (INVOS 5100C, Somanetics, Troy, MI, USA), used the two-channel mode, with channel 1 for cerebral monitoring and channel 2 for somatic/renal monitoring. One Cerebral/Somatic oximetry Infant-Neonatal sensor (Somanetics, Troy, MI, USA), made of an emitting diode and two detectors, was used on channel 1 and one on channel 2 during this study. The continuous wave NIRS system uses the properties of luminous absorption of photons going through the tissues by two different wavelengths (730 and 810 nm), both used in this study. Light travels from the sensor's light emitting diode to either a proximal or distal detector, permitting separate data processing of shallow and deep optical signals.
epidemiologic and complications Data collection We collected epidemiologic and complications data for each patient: term birth (in weeks of amenorrhea), gender, birth weight (BW), APGAR at 1/5/10 min, main diagnosis, associated malformations, age at the time of surgery (in days), number of surgeries, duration of the surgery (min), resuming of urine output <6 h post-surgery, complications in the first 24 h post-surgery, duration of NICU stay (in days), total hospitalization duration (in days), and neonatal death or not.
statistical analysis Statistical analyses were performed using SAS 9. 4 software. Qualitative variables were described as sample and percentages and quantitative variables as means and SD or median and Interquartile Range (IQR). Comparative analysis to compare the average cerebral and renal ΔrSO2, pre and post FM were performed with a Student t-test for paired samples. Comparative analyses to compare H0-H1 with H1-H2 period during surgery and H0-H6 with H6-H24 period after surgery for the cerebral and renal pathological rSO2 were performed with a Chi-square test. A generalized estimation equation model with a correlation matrix for structured residues was used first to analyze independently the correlation between: (1) C and R rSO2 during the first day (from m0 of surgery to H24 after surgery), (2) C rSO2 with R rSO, (3) C and RrSO2 with MAP, (4) C and R rSO2 and pre-ductal SpO2, and (5) evolution of C and R rSO2 between operative and postoperative period.
Population Near infrared spectroscopy monitoring was performed on twenty-one patients. Two patients were excluded: reasons were death before surgery (n = 1) and no available perioperative data (n = 1). Among the 19 patients included, three patients with abdominal wall defect (two gastroschisis and one omphalocele) benefited from a silo pouch stoma allowing the progressive reintegration of the herniated viscera, as it was not feasible to perform the reintegration in one surgical step (complete closure occurred, respectively, 6, 8, and 11 days after the initial surgery). There were thirteen boys (68%) and six girls (32%). Population characteristics are listed in Table  1. After the initial surgery, 16 patients urinated before H6 (84%). No death or postoperative complications were reported in this patients' cohort.
Neither of the Phase III studies showed any difference on primary or secondary outcomes between the high doses and 4 mg twice a day in the as-randomized comparisons. In the first study, treatment status with cholinesterase inhibitors and/or memantine was found to be a significant covariate in the primary analysis model  [16]. Exploratory analyses showed that this was due to significantly lower rates of progression on clinical and brain atrophy end-points in patients receiving any of the LMTM doses as monotherapy, including 4 mg twice a day, which did not appear to be explicable by cohort differences in severity at baseline. The results of study TRx-237-015, which became available prior to database lock and unblinding of the present study, suggested the hypothesis that LMTM might be effective only as monotherapy and that the minimum effective dose might be substantially lower for LMTM than that previously identified using MTC  [13, 15].
As the originally intended analysis was unlikely to achieve its intended purpose, we modified the primary analyses and treatment comparisons in the TRx-237-005 Statistical Analysis Plan prior to database lock and unblinding to investigate whether the monotherapy differences could be confirmed as observational cohort comparisons defined as primary outcomes with strong control of family-wise type I error in the second independent study. The monotherapy cohort comparisons which were of particular interest in light of the earlier study were: (A) 100 mg twice a day a monotherapy compared with 4 mg twice a day as originally randomized, and (B) 4 mg twice a day as monotherapy compared with 4 mg twice a day as add-on to standard AD treatments. Each of these comparisons was required to reach a statistical threshold of 0.
Other outcomes included the Alzheimer's Disease Cooperative Study-Clinical Global Impression of Change scale (ADCS-CGIC), administered by an independent rater at the same visits as ADAS-cog and ADCS-ADL, and MMSE, Neuropsychiatric Inventory (NPI), and Montgomery-Åsberg Rating Scale (MADRS, administered at screening and weeks 26, 52, and 78 with MMSE again at week 82). MRI scans were undertaken at baseline or screening and at weeks 13, 26, 39, 52, 65, and 78 (or at early termination) using a standardized protocol at all sites and volumetric analyses were performed by a central imaging core laboratory (BioClinica). Volumetric data were used to measure changes in lateral ventricular vol-ume, whole brain volume, and estimated mean of left and right for temporoparietal and hippocampal volumes. 18 F-fluorodeoxyglucose PET ( 18 F-FDG-PET) imaging was done at screening and weeks 39 and 78.
Statistical analysis Post-hoc analyses of the earlier trial in mild to moderate AD trial (TRx-237-015  [16] ) suggested the hypothesis that LMTM might be effective only as monotherapy. We therefore revised the originally intended primary analysis prior to database lock and data unblinding to examine whether differences in favor of monotherapy could be confirmed as primary outcomes in non-randomized observational cohort comparisons based on the use of a two-sided test with an ␣ of 0. 025 to control family-wise Type I error. The final Statistical Analysis Plan is provided in Supplementary Materials. The primary statistical tests were (Comparison A) comparison of patients receiving 100 mg twice a day as monotherapy with the control arm as randomized (all patients receiving 4 mg twice a day regardless of AD comedication status with cholinesterase inhibitors and/or memantine), and (Comparison B) comparison of patients receiving 4 mg twice a day as monotherapy with those receiving 4 mg twice a day as add-on to approved ADlabelled treatments.
Inferior temporal gyrus 18 F-FDG-PET SUVR normalized with respect to pons was determined at baseline and compared with the values reported for mild AD, MCI, and normal elderly controls using the same methodology  [24]. Frontal, parietal, and temporal lobe 18 F-FDG-PET SUVR data normalized with respect to pons and cerebellum were also analyzed. Coordinates permitting determination of nucleus basalis volume were kindly provided by Ingo Kilimann  [25]. Safety analyses were based on the safety population comprising all patients who received at least one dose of study drug, with summaries presented according to dose and AD co-medication status. Data analyses specified in the Statistical Analysis Plan were undertaken independently of the funder by SynteractHCR (Carlsbad, CA, USA) using SAS 9. 4 (Enterprise Guide v7.
1). The results were verified and additional exploratory analyses were provided by one of the co-authors (BOS) using R version 3. 3. 0 (2016-05-03). Additional voxel-based morphometric analyses were provided by VV, TA, and RTS using the Statistical Parametric Mapping (SPM12) software package (http://www. fil. ion. ucl. ac. uk/spm/). This trial is registered at http://www. clinicaltrials. gov (NCT01689233) and the European Union Clinical Trials Registry (21012-002847-28).
Clinical efficacy outcomes The treatment comparisons for the co-primary outcomes as defined in the Statistical Analysis Plan finalized prior to database lock were significant at the ␣ threshold of 0. 025 for 100 mg twice a day as monotherapy compared with all patients receiving 4 mg twice a day as randomly assigned (ADAS-cog effect size -3. 14, 95% CI -5. 32 to -0. 97, p = 0. 0047; ADCS-ADL effect size 3•49, 95% CI 0. 66 to 6. 30, p = 0. 0157 [comparison A, Table  2a , Fig. 2] ). The treatment comparisons for the co-primary outcomes were also significant at the ␣ threshold of 0. 025 for 4 mg twice a day as monotherapy compared with 4 mg twice a day as add-on to approved AD treatments (ADAS-cog effect size -4•22, 95% CI -6. 19 to -2. 24, p < 0. 0001; ADCS-ADL effect size 4. 85, 95% CI 2. 31 to 7.
DISCUSSION There was no evidence of any difference on any of the primary or secondary endpoints in the as-randomized analyses defined in the protocol comparing all patients receiving LMTM at a dose of 100 mg twice a day and those receiving 4 mg twice a day. In the non-randomized cohort comparisons defined as the primary outcomes in the revised Statistical Analysis Plan finalized prior to database lock and unblinding, both primary Comparisons A and B met the required statistical threshold of p < 0. 025 for both co-primary clinical outcomes (ADAS-cog and ADCS-ADL), as well as for volumetric MRI and glucose uptake biomarker outcomes. Patients receiving LMTM as monotherapy at either of the two doses tested had consistently better outcomes than patients receiving the same doses as add-on to cholinesterase inhibitors and/or memantine, and patients receiving 100 mg twice as day as monotherapy had better outcomes than patients receiving 4 mg twice a day as randomized.
Statistical relationships reported in the main text are for the overall significance of the term covariate x visit in explaining cognitive decline. terms in the analysis model. If differences in baseline characteristics explain the differences in rate of progression over 18 months, then the significant differences in favor of LMTM as monotherapy would be expected to disappear when rate was corrected for baseline effects. In a similar analysis for patients with MMSE 20-26 in the currently available ADNI data set, this correction for baseline severity eliminated the apparent differences in rate of progression (publication in preparation). Rate-correction for differences in clinical severity at baseline, APOE 4 frequency, vascular pathology load, hippocampal atrophy, temporoparietal atrophy, glucose uptake in the temporal lobe, and basal forebrain atrophy did not eliminate the significant differences in favor of LMTM monotherapy for ADAS-cog, ADCS-ADL, or lateral ventricular volume.
Every experiment was performed at least two times with each genotoxic agent, and in several different cell lines. For each situation, at least ten images (40x magnification) were taken. Experimental conditions for immunofluorescence were described previously  17, 19. Immunofluorescence and digital interference contrast images were captured (microscope Leica CTR6000, objective Leica 40X HCX PL APO 1. 25-0. 75 oil, camera Coolsnap HQ2) and a composite generated using Adobe Photoshop (Adobe Systems Inc, San Jose, CA, USA) and Microsoft PowerPoint (Microsoft Corp, Redmond, WA, USA) softwares. For the results presented in Fig. 4d ,f immunofluorescence signal was quantified using ImageJ software. The DAPI images were used to identify the individual nuclei using a background correction, a mask creation based on threshold, a watershed segmentation and the analyse particles function in ImageJ.
The total intensity of individual nuclei in p21 or Ki-67 and CycE1 images were quantified. 3 classes of object were created based on an arbitrary threshold: low, medium and high intensity. The % of cells per class was calculated for the each condition with the Excel Microsoft software. The population with high CycE1 intensity corresponded to 3-7% of cells. Beta-galactosidase experiments. HCT-116 cells were seeded on coverslips in 12-well plate, in a density of 100. 000 cells per well. Cells were treated after 24 h with bleomycin (10 μg/ml). The drug was washed away from the cells after 48 h of incubation, followed by staining after 3 weeks using Senescence detection kit, according to the protocol (Abcam, ab655351). Photos were taken using an upright microscope magnification 20x. siRNA transfections.
Acknowledgements This work was originally supported by grants of  ARC  ( N°3793  to V. D. ) and the  Cancéropole Grand Sud Ouest. The team (G. L. , K. B. , V. D. and D. F. ) was funded by the  Ligue Nationale Contre le Cancer  ( EL2013. LNCC/DF ). K. B. and G. L. received a PhD fellowship from LNCC. T. N. A. was funded by  Inserm. We are grateful to  KUDOS Pharmaceuticals  for gift of KU-55933. We thank  Dr Annick Péléraux  for helping with statistical analysis and  Drs Marion Peter ,  Jacques Piette  and  Etienne Schwob  for critically reading the manuscript. We acknowledge the Montpellier RIO imaging facility for their help.
affinity Measurements Binding of Nanobodies™ to TNF was characterized by surface plasmon resonance in a Biacore 3000 instrument (Biacore International AB, Uppsala, Sweden). In brief, TNF was covalently bound to a CM5 sensor chip surface via amine coupling until an increase of 250 response units was reached. Remaining reactive groups were inactivated. Nanobody™ binding was assessed, and KD values were calculated using the instruments software.
X-ray structures Determination The complex between TNF and VHH#1 was crystallized by mixing 100-300 nl of purified complex (8 mg/ml in HEPES 10 mM pH 7. 0) with 100 nl of precipitant solution (20% PEG3000, 0. 2 M NaCl, and 0. 1 M HEPES at pH 7. 5) and equilibrating 100 µl of precipitant solution. A crystal was exposed at beamline ID14-1 (ESRF, Grenoble, France), and a complete dataset was collected at 2. 15 Å resolution (Table  1 ). Data were integrated with XDS and scaled using Xscale (20) (Table  1 ). The structure was solved by molecular replacement with Molrep (21) using the TNF trimer from Protein Data Bank (PDB) entry 1TNF and the framework region (FR) of the VHH domain from PDB entry 1HCG as search models. Refinement was carried out with cycles of autoBUSTER  (22)  alternated with manual rebuilding with Coot  (23).
Crystals of the complex between TNF and VHH#2 were obtained by mixing 100-300 nl of purified complex (11 mg/ml in HEPES 10 mM pH 7. 0) with 100 nl of precipitant solution (12% PEG4000, 130 mM NaCl, 366 mM CaCl2, 70 mM CAPS pH 9. 0, and 30 mM MES pH 8. 0) and equilibrating against 100 µl of precipitant solution. Data to 1. 9 Å resolution were collected from a single crystal at beamline ID14-1 (ESRF, Grenoble, France) (Table  1 ). Data were integrated with XDS and scaled using XSCALE (20) (Table  1 ). The structure was determined by molecular replacement with Molrep (21) using a single TNF monomer and a single VHH domain stripped from its complementarity determining region (CDR) loops and taken from the TNF-VHH#1 complex as search models. Refinement was performed as described above. Crystallization of the complex between TNF and VHH#3 was achieved by mixing 100-300 nl of protein (8-10 mg/ml in HEPES 10 mM pH 7.
0) with 100 nl of precipitant solution (9% PEG3350, 8% PEG-MME550, 130 mM NaSO4, 70 mM BTP, 30 mM MES, and 3 mM ZnSO4, 7. 0 < pH < 8. 0) and equilibrating against 100 µl of precipitant solution. A crystal was exposed at beamline ID14-3 (ESRF, Grenoble, France), and a complete dataset was collected at 2. 3 Å resolution (Table  1 ). Data were integrated with XDS and scaled using XSCALE  (20). The structure was determined by molecular replacement using the coordinates of the TNF trimer and VHH#1 stripped from its CDR loops as search models. Refinement was performed as described above for the other two TNF complexes. Protein contacts were analyzed using PISA  (24). Figures were prepared with Pymol (Pymol, Schrödinger). Coordinates and structure factors have been deposited at the PDB as entries 5m2i,.
TnF receptor neutralization The 3D structure of TNF in complex with TNFR is not known. However, given that TNF and LTα bind equally well to TNFR1 (p55) and TNFR2 (p75) and considering the high structural identity between TNF and LTα, a plausible model for the TNF/TNFR1 complex can be obtained by superimposing TNF onto LTα in its complex with the ectodomain of the TNFR1 p55 receptor (PDB entry 1TNR)  (5). In this model, each TNFR1 p55 monomer covers about 1,200 Å 2 of one of the three TNF monomers without significant steric clashes. The structures of the TNF/VHH complexes reported here were superimposed onto that of the TNF/TNFR complex. The binding areas of VHH#1, VHH#2, and VHH#3 overlap in part with that of TNFR (Figure  4 ). VHH#1 and VHH#2 occupy the central area of the receptor binding site, while VHH#3 occupies the "bottom" of the receptor binding area (Figure  4 ).