dataesr/scientific-paragraphs-categorization huggingface dataset:
Notably, surface modification with steric molecules, such as poly (ethylene glycol) (PEG) or poly(2-ethyl-2-oxazoline) (PEtO), applied in academia and industry to reduce overall protein binding (Supplementary Fig. S3a ), efficiently reduced NP attachment to bacteria (Table  1 ; Fig. 2a ; Supplementary Fig. S3a ). This data suggests their use as chemical tools to rationally modulate NP-microbe complex formation. Of note, even exposure to high doses of those NPs that are typically used in the food industry did not affect the vitality and growth of commensal microbes or enteric pathogens when examined in liquid culture assays (Fig. 2b ). Moreover, we did not observe that Si NPs were able to directly penetrate the rigid bacterial cell wall (Fig. 2c ). Often, NP-bacteria interactions have been analyzed by electron microscopy only.
ACKNOWLEDGMENTS Noan Henri Knauer  for critically reading the manuscript. Grant support:  Impulsfonds RLP, BioMAS ,  DFGDO/SR10902/SFB1066/1093 , UMM S-I:D. W. (retrospectively revoked by UMM),  NanoTransMed , which is cofounded by the  European Regional Development Fund (ERDF)  in the framework of the  INTERREG V Upper Rhine program , the  Swiss Confederation and the swiss cantons of Aargau, Basel-Landschaft and Basel-Stadt.
High-performance liquid chromatography separation of amino acids The AccQ-Fluor amino acid derivates were separated on ELITE LaChrom HPLC system (VWR™ Hitachi, Tokyo, Japan). Sample of 20 μL was injected into an HPLC reversed phase AccQ-Tag™ silica-bonded amino acid column C18, 3. 9 mm×150 mm (Waters). The elution of the amino acids was performed by gradient system with mobile phase, eluent A, buffer WAT052890 (Waters) and mobile phase, eluent B, 60 % acetonitrile (Sigma-Aldrich, Merck), in a separation gradient with a flow rate of 1. 0 mL/min (Table  1 ). The amino acids were detected using a diode array detector (DAD) at 254 nm with the column condition set at 37 °C for 40 min. The amino acid peaks were acquired using EZChrom Elite™ software  (15)  and were calculated based on amino acid calibration standard (amino acid standard H, Thermo Fisher Scientific).
Acknowledgements The authors are thankful to JSPS Core-to- Core Program ,  A. Advanced Research Networks  for `International research core on smart layered materials and structures for energy saving' supporting this research. The  Institute of Fluid Science from Tohoku University  is also gratefully acknowledged for providing support through the  General Collaborative Program Figure 1: Experimental set-up schematic Figure 2: Initial  results project #  J17I065. The authors also acknowledge the support of LGEF at  INSA Lyon  for providing the facility to conduct these experiments.
For background initialization, Laugraud et al. [6]  present a method based on semantic segmentation in background generation. Experiments conducted on the Scene Background Initialization (SBI) and SceneBackgroundModeling. NET (SBMnet) datasets show that LaBGen-P-Semantic has better robustness against intermittent motions, background motions and very short video sequences than previous LaBGen versions. For the evaluation of background generation methods, Shrotre and Karam  [7]  first discuss shortcomings in existing metrics and then propose a full reference Reconstructed Background image Quality Index (RBQI) that combines color and structural information at multiple scales. Furthermore, two different datasets consisting of reconstructed background images and corresponding subjective scores are provided for the evaluation.
Participants All participants were included in the Imagerie Multimodale de la maladie d'Alzheimer a un stade Pr ecoce (IMAP1) study (Caen, France), and the inclusion and exclusion criteria are detailed in the Supplementary Materials and the previous publication  [23] [24] [25] [26]. For the sake of the present study, 68 right-handed native French-speaking participants were included, comprising 44 patients with aMCI (20 Abneg aMCI and 24 Abpos aMCI; see section 2. 4. Neuroimaging procedure) and 24 Ab neg healthy controls (HCs) (all amyloid negative; see section 2. 4. Neuroimaging procedure). Participants were selected from the IMAP1 study database, if they were older than 55 years (inclusive), and had magnetic resonance imaging (MRI), FDG-PET, and florbetapir-PET imaging. We included in the present study all aMCI patients from the IMAP database meeting these criteria, but only the HCs who met these criteria and whose florbetapir PET scan was classified as amyloid negative (see section 2.
4. Neuroimaging procedure). The two groups of participants were matched for age, gender, and education (Table  1 ). Within a few days from recruitment, each participant underwent (1) a detailed neuropsychological battery detailed below, (2) a structural MRI scan, (3) a PET scan using 18F-fluorodeoxyglucose, and (4) a PET scan using [18F] florbetapir (AV45). All participants were scanned on the same MRI and PET cameras. The IMAP study was approved by regional ethics committee (Comit e de Protection des Personnes Nord-Ouest III) and registered with ClinicalTrial. gov (number NCT01638949). All participants gave written informed consent to the study before the investigation.
Demographic, clinical, and neuropsychological data Continuous demographic and clinical data (age, education level, Mini-Mental State Examination) were compared between groups (Abneg HC, Abneg aMCI, and Abpos aMCI) with single-factor (group) analyses of variance and post hoc comparisons when the effect of group was significant. Categorical variables (gender and apolipoprotein E (APOE) genotype) were compared using proportional c 2 tests (Pearson). All results were considered significant at P ,. 05. Neuropsychological W-scores were compared between Abneg aMCI and Abpos aMCI using two-sample t-tests, except for language (categorical variable) where proportional c 2 tests were performed. Bonferroni correction was applied to control for multiple comparisons so that a threshold of P ,. 00625 (. 05/8) was required for results to be considered as significant.
Neuroimaging data analyses 2. 5. 2. 1. Voxelwise analyses The smoothed normalized gray matter segments issued from the DARTEL toolbox and the smoothed preprocessed FDG-PET images were entered in voxelwise full-factorial analyses with three groups (Abneg HC, Ab pos aMCI, and Abneg aMCI) and including age and education (and total intracranial volume for MRI data) as nuisance variables. The total intracranial volume was obtained by summing the volumes of the gray matter, white matter, and cerebrospinal fluid obtained from the T1-weighted images using the VBM12 toolbox implemented in SPM12. To address the issue of multiple comparisons, a voxel-level P (uncorrected) ,. 001 threshold was combined with a cluster size allowing to.
Acknowledgments The authors thank  J. Gonneaud ,  B. Desgranges ,  B. Landeau , F. M ezenge,  J. Mutlu A. Perrotin ,  G. Poisnel ,  M. Leblond ,  T. Anquetil ,  K. Mevel ,  N. Villain ,  M. Fouquet ,  A. Quillard ,  C. Schupp ,  J. Dayan ,  A. Chocat ,  L. Barre ,  A. Manrique , and the  Cyceron MRI-PET  staff members for their help with data acquisition. The authors are grateful to  C. Andre ,  R. La Joie , and  A. Bejanin  for their insightful comments and to the participants of the IMAP1 study. The study was supported by  Fondation Plan Alzheimer  (Alzheimer Plan  2008-2012 );  Programme Hospitalier de Recherche Clinique  ( PHRCN 2011-A01493-38  and  PHRCN 2012 12-006-0347 );  Agence Nationale de la Recherche  ( LONGVIE 2007 );  R egion Basse-Normandie ;  Association France Alzheimer  et maladies apparent ees AAP 2013.
The bubblers used constantly renew the air in the closed plastic chambers and create a slight overpressure (Figure  2 ). In order to demonstrate the performance of this system, the air temperature and relative humidity were recorded every 15 min with a HOBO data logger (U12-011, Onset Computer Corporation, Bourne, MA, United States). A comparison of the temperature and RH variations between the growth chamber and the closed plastic vessels showed that the setup allowed shoots to be maintained at 100% RH atmosphere during the course of the experiments (Supplementary Figure  S2 ). Hence, RH values were sufficiently contrasted to compare the effects of KNO 3 and KCl concentrations under high (HT) and low (LT) transpiration conditions in the gravimetric device (see below). Extinction of light intensity induced by plastic chambers was less than 8%.
The structure of the studied molecules is shown in Scheme 1 with CQAs IUPAC numbering. Eight coffee species were studied. They were grown in tropical greenhouses located in Brussels (Belgium) and the studied leaves were collected during two different periods: January and July 2016. The LC-EC data on CQAs content in the water extracts were confirmed by LC-HRMS. Antioxidants 2018, 7, x FOR PEER REVIEW 3 of 14 the electro-oxidation of the three CQAs and the three diCQAs occurred at approximately the same potential. Oxidation of the feruloylquinic acids (FQAs) occurred at more positive potentials. It was possible, by this method, to determine the total amount of CGAs in aqueous solution of different brands of coffees. The CQAs and diCQAs represented ca. 90-95% of all CGAs found and 5-CQA prevailed in all investigated coffee samples.
51. 00. t REPORT 2. 51. 0425 software (BASi, West Lafayette, IN, USA) was used for peak detection and integration. All data analysis was performed by using Matlab version 2016b (The Mathworks, Natick, MA, USA). The algorithms for de-trending and Principal Component Analysis (PCA) were part of the ChemoAC toolbox (Freeware, ChemoAC Consortium, Brussels, Belgium, version 4. 1)  [34]. Peak alignment was realized using the algorithm for Correlation Optimized Warping (COW)  [35] [36] [37] [38]. Microsoft, Excell 2011 (Brussels, Belgium) was used for regression analyses. A pH-meter with a combined glass-Ag/AgCl (KCl 3 M) electrode from Metrohm (Antwerpen, Belgium) was used for pH measurements. Sample agitation was performed with a vortex-mixer (Vell, Brussels, Belgium). Dried leaves were ground into a fine powder using a mill.
LC-HRMS analyses were performed using a 1200 series rapid resolution LC (RRLC) system coupled to a G6520A series electrospray ionization (ESI)-quadrupole time-of-flight (QTOF) high-resolution mass spectrometer from Agilent Technologies (Waldbronn, Germany). Data acquisition for LC-QTOF-MS analysis was carried out by MassHunter Acquisition ® software for QTOF (Version B. 04 SP3), MassHunter Qualitative Analysis ® (Version B. 06) software, and MassHunter Quantitative Analysis ® (Version B. 04) software (Agilent Technologies, Waldbronn, Germany).
Chemometric Data Analysis Extracts of the coffee leaves, harvested in January and July, were analyzed by both LC-EC and LC-QTOF-MS for each of the eight coffee species studied. Interestingly, LC-EC only detected readily oxidized compounds and each chromatogram provided a unique "antioxidant profile". PCA was applied to the data matrix with the baseline corrected and peak aligned fingerprints to test whether the chromatogram resulted in a clustering of the extracts. The score plots obtained after PCA are shown in Figure  3 , as well as Figures  S2  and S3.
Chemometric Data Analysis Extracts of the coffee leaves, harvested in January and July, were analyzed by both LC-EC and LC-QTOF-MS for each of the eight coffee species studied. Interestingly, LC-EC only detected readily oxidized compounds and each chromatogram provided a unique "antioxidant profile". PCA was applied to the data matrix with the baseline corrected and peak aligned fingerprints to test whether the chromatogram resulted in a clustering of the extracts. The score plots obtained after PCA are shown in Figure  3 , as well as Figures  S2  and S3. Principal Component 1 (PC1) versus PC2; PC1 = 90. 8% and PC2 = 6. 8%. Label (1) indicates January and label  (7)  indicates July. Some species share the same symbol (C. arabica, canephora, mannii, charrieriana, humilis, anthonyi) and correspond to samples with a very low response and were thus not distinguished for better clarity of the figure.
Application to Extracted Leaves The LC-EC method was applied to determine the concentration of the three major chlorogenic acid isomers in water extracts. Eight coffee species were studied, namely: Coffea arabica, Coffea canephora, Coffea liberica, Coffea humilis, Coffea mannii, Coffea charrieriana, Coffea anthonyi, and Coffea liberica var. liberica. The LC-EC data were compared with respect to quantitative data obtained by LC-QTOF-MS (Tables  2  and 3 ). The results obtained by both methods were comparable within the same order of magnitude. When CQAs are present, the 5-CQA appears to be the major isomer, in agreement with literature data for homemade brewed coffee samples  [28] , green coffee beans  [14] , and coffee leaves  [31]. Its content was in the concentration range reported for coffee leaves  [2, 31]  in which 5-CQA was found to represent about 90% of the total CGA amount  [31].
Supplementary Materials: The following are available online at http://www. mdpi. com/2076-3921/7/10/143/s1, Figure  S1 : Typical LC-EC chromatogram of Coffea liberica var. liberica and LC-EC chromatogram of standard solution of catechin. Blue chromatogram corresponds to Coffea liberica var. liberica and green chromatogram corresponds to standard solution of catechin (1 × 10 -4 M), Figure  S2 : Score plot obtained after PCA of the data matrix with all fingerprints due to species, and harvest period. PCA results after centering of dataset. PC1 versus PC3; PC1 = 90. 3% and PC3 = 0. 7%. Label  (1)  indicates January and label  (7)  indicates July, Figure  S3 : Score plot obtained after PCA of the data matrix with all fingerprints due to species, and harvest period. PCA results after centering of dataset.
Dehbaoui at al. [8]  shows that electromagnetic pulses allow to recover a cryptographic secret key. Then Moro et al. [12]  describes the faulting mechanism and how it translates in a software model. Hardware fault attacks can be generated by software. The recent CLKSCREW work by Tang et al. [14] , where the authors modify a phone's energy and clock controller to inject faults, demonstrates such an attack. Another illustration is given by the RowHammer attack  [16]. These attacks are relevant and must be mitigated: HAPEI must ensure CFI even in the presence of HFAoI. CFI ensures that jumps, routine calls and returns are legitimate, but it does not prevent an attacker to alter any other instruction. New mitigation techniques should be used for that: II and DI must be ensured. Most system integrity techniques rely on the encryption of memories, preferably with dedicated hardware.
The p coefficients of P are stored as program metadata with the corresponding instruction i n. At packing, HAPEI encrypts with i n = C(r) ⊕ i n. To decrypt instruction i n , we use acc n = P (acc n-1 ). Note that the polynomial evaluation replaces the HMAC call. p-predecessors, solution B F 2 b can be decomposed in different subgroups µ p where ∀x ∈ µ p , x p = 1 (subgroup of pth-root of unity). Such subgroups exist for all p such that p | 2 b -1. For all valid p (depending on b), we can define a scheme that allows p predecessors. For example, b = 16 allows a scheme with 5 predecessors (p = 5 divides 65535 = 2 16 -1). Let acc i n , i ∈ [[1, p]] be the allowed previous accumulator values for current instruction i n. Let r be a random value in F 2 b. Let m ∈ µ p be a generator value for the subgroup.
Experimental set-up and flow conditions 2. 1. Flume and velocity measurements The study is based on one-point and two-point Acoustic Doppler Velocimetry measurements. We have used two 3D Nortek Vectrino+ Acoustic Doppler Velocimeters (ADVs), with a side looking probe (sampling volume 5 cm away from the probe). The sampling volume of an ADV can be approximated as a cylinder 6 mm in diameter and 7 mm long. At each measuring point, the three velocity components (u, v, w) were recorded at 100 Hz for 300 s. The ADV data were despiked using the phase-space thresholding technique of  [4].
In parallel, cells were transfected with the empty vector to obtain the control parental cells (pEmpty). (A) Following RNA extraction, the mRNA level of HS3ST3B was quantified by real-time RT-PCR in each clone. Relative abundance of the transcripts was normalized to endogenous HPRT mRNA. Data are means ± SD of triplicates. (B) HS3ST3B expression in the clones C and D was analyzed by confocal microscopy. To this end, cells were seeded on glass coverslips, permeabilized and then incubated in the presence of anti-HS3ST3B antibodies. After wash, they were immunostained with secondary antibodies conjugated to Alexa-568, in order to highlight the enzyme in red fluorescence. For the detection of 3-O-sulfated motifs, recombinant HSV-1 gD (10 µg/mL) was incubated with primary anti-gD antibody for 30 min at 4 °C, and the immune complex was added to cells for an additional 30 min-incubation.
In parallel, cells were transfected with the empty vector to obtain the control parental cells (pEmpty). (A) Following RNA extraction, the mRNA level of HS3ST3B was quantified by real-time RT-PCR in each clone. Relative abundance of the transcripts was normalized to endogenous HPRT mRNA. Data are means ± SD of triplicates. (B) HS3ST3B expression in the clones C and D was analyzed by confocal microscopy. To this end, cells were seeded on glass coverslips, permeabilized and then incubated in the presence of anti-HS3ST3B antibodies. After wash, they were immunostained with secondary antibodies conjugated to Alexa-568, in order to highlight the enzyme in red fluorescence. For the detection of 3-O-sulfated motifs, recombinant HSV-1 gD (10 µg/mL) was incubated with primary anti-gD antibody for 30 min at 4 • C, and the immune complex was added to cells for an additional 30 min-incubation.
Results are expressed as fold changes by comparison with the parental cells that have been transfected with siCtrl and cultured in the absence of pro-apoptotic stimulus. Data correspond to means ± S. D. from three independent experiments (*** p < 0. 001, significantly different when compared with the parental cells; # p < 0. 05, ### p < 0. 001, significantly different when compared with the siCtrl-treated cells; n. s. , not significant). We used these reagents in order to mimic the delivery of extracellular death signals mediated by a TNF receptor and the Fas antigen  [31]. In the first experiment, cell viability was analyzed without the pro-apoptotic treatment. As expected, we confirmed that HS3ST3B-mediated increase in cell viability was not altered by treatment with the siRNA control. We found indeed that the stable expression of HS3ST3B resulted in a 2-fold increase in cell viability of the clones C and D, compared with the parental cells.
Data correspond to means ± S. D. from three independent experiments (*** p < 0. 001, significantly different when compared with the parental cells; # p < 0. 05, ### p < 0. 001, significantly different when compared with the siCtrl-treated cells; n. s. , not significant). We used these reagents in order to mimic the delivery of extracellular death signals mediated by a TNF receptor and the Fas antigen  [31]. In the first experiment, cell viability was analyzed without the pro-apoptotic treatment. As expected, we confirmed that HS3ST3B-mediated increase in cell viability was not altered by treatment with the siRNA control. We found indeed that the stable expression of HS3ST3B resulted in a 2-fold increase in cell viability of the clones C and D, compared with the parental cells. In contrast, silencing the expression of Nrp1 strongly reduced the enhancing effect induced by HS3ST3B, while it had only a minor effect on the viability of the parental cells.
After washing, cells were fixed and incubated with Alexa 488-conjugated secondary antibody, as above. In all experiments, cells were stained with 500 ng/mL DAPI (Sigma-Aldrich) for 10 min, in order to visualize cell nuclei. Immunofluorescence was analyzed with an inverted Zeiss LSM 780 microscope (Oberkochen, Germany) equipped with a 63 × oil immersion lens. Data were collected using the Zeiss Zen Pro 2. 1 software and processed with Image J software (Bethesda, MD, USA).
Figure5. Effect of Nrp1 silencing on HS3ST3B-mediated protection against apoptosis. Parental (pEmpty) and HS3ST3B expressing (clones C and D) cells were transfected with siNrp1 or siCtrl and then cultured for 24 h in complete medium. After wash, cells were collected and cultured in medium containing 1% FCS in the absence (control) or presence of a mixture of anti-Fas antibody (100 ng/mL) and TNF-α (100 ng/mL) for 24 h. Thereafter, the number of viable cells was estimated by using MTS assay. Results are expressed as fold changes by comparison with the parental cells that have been transfected with siCtrl and cultured in the absence of pro-apoptotic stimulus. Data correspond to means ± S. D. from three independent experiments (*** p < 0. 001, significantly different when compared with the parental cells; # p < 0.
Soil characterisation Soil samples were taken with a 5-cm diameter auger to 20 cm depth. In each of the plots, two composite samples were produced from fertilised and unfertilised locations. The fertilised composite consisted of 18 well-mixed samples taken within planted rows/holes or around coffee plants. The procedure was repeated for the unfertilised composite, but with sampling undertaken between planted rows/holes or coffee plants. For the incubation experiment, a composite was produced from nine coffee plots in the region. Soil textures were determined by Laser Diffraction Particle Size Analysis (LDPSA, Horiba LA-960) at the ICRAF's Soil and Plant Diagnositic laboratory in Nairobi, Kenya. Soils samples were analysed using mid-infrared spectroscopy (MIRS, Tensor 27 HTS-XT). Calibration spectral models from ICRAF's database of N 100 samples were used with the resultant spectra of the soil samples predicting soil attributes.
Data analysis There is no consensus on the best method to calculate GHG fluxes from static chambers  (Venterea et al. , 2009). Though linear models can underestimate GHG fluxes if the underlying empirical data is nonlinear, nonlinear models can also be very sensitive to sampling errors and outliers  (Hutchinson and Mosier, 1981; Venterea et al. , 2009). Given our aim of finding differences at temporal (e. g. wet and dry seasons) and spatial scales (e. g. fertilised vs unfertilised), we selected a linear scheme with an appropriate deployment times and chamber heights to reduce non linearity. Fluxes were thus calculated using linear regression of gas sample concentrations versus closure time of the chambers. Auxiliary measurements of headspace volume, internal temperature and ambient pressure were used according to the ideal gas law to convert concentrations into mass per volume.
Calculations were automated using KNIME workflow (KNIME 2. 9. 2 software GmbH, Germany). The flux equation programmed in KNIME can be found below (Eq. 1). Flux μg m -2 h -1 ¼ m•M w •V ch •60•10 6 A ch •V M •10 9 ð1Þ where "m" is the slope, as the increase or decrease in concentration (ppb or ppm min -1 ), "M w " is the molecular weight of the component (g mol -1 ), "V ch " is the volume of the chamber (m 3 ), "A ch " is the area of the chamber (m 2 ) and "V M " is the corrected standard gaseous molar volume (m 3 mol -1 ). Cumulative GHG fluxes were calculated with the R package flux, which includes several functions for the estimation of GHG fluxes rates from closed-chamber concentration measurements (FLUX package, R 3. 3. 1). The function auc() integrates the curve formed by the fluxes of N 2 O, CH 4 and CO 2 versus time, following the trapezoid rule.