dataesr/scientific-paragraphs-categorization huggingface dataset:
This is true, but the measured drifts appear sufficiently evident to reflect a real refinement of the skew correction. Observational evidence for RR07 is therefore compatible with our suggested explanation of missing samples. For RR35, the OBS lacking a skew value, we would expect identical clock drift rates before and after the jump, irrespective of its cause. This is not strictly the case in Fig. 8(b ), but again the different clock drift rates (see Table  1 ) may well be due to the short remaining recording duration (25 d) after the jump, which prevents a proper estimate of a long-term trend. A priori it is unlikely that the physical clock changed its drift rate in the presumed absence of sudden, significant seafloor temperature variations (only) around the time of the jump. An undetected data gap manifests as an apparent clock jump and can only be distinguished from a true, physical clock jump when a measured skew value is available (Fig.
13a versus b ). This is the case for RR07 and RR11, and their drift curves in Fig. 8 (a) clearly support a data gap. In absence of a skew measurement, we cannot totally reject the possibility that a true clock jump occurred at RR35 (red curve in Fig. 8b ) but the nearly identical jump magnitude of 1 s at all three OBSs reinforces our inference that the jump has the same technical cause in all three OBSs: a batch of 50 samples (probably corresponding to one data buffer worth of recordings) must not have been written to disk in each instance, given the sampling rate of 50 Hz. The good news is that clock timing corrections using our CCF method succeed regardless of the nature and cause of these apparent clock jumps, whereas the problem would go undetected and uncorrected in the standard practice of simple, linear skew interpolation.
A P P E N D I X C : C O M PA R I S O N W I T H L A B O R AT O RY E X P E R I M E N T S For OBSs without skew measurements,  Stähler et al. (2016)  attempted to obtain clock drift estimates by re-running their data loggers in the laboratory. Short of specialized equipment, these tests were run under ambient pressure and temperature conditions. They ran two tests of 7 and 33 d duration, on the seven afflicted stations that had not already been re-deployed at the time (RR06, RR11, RR41, RR43, RR44, RR45 and RR55). The measured skew values were linearly extrapolated to derive a hypothetical skew value for a 365 d long experiment. For direct comparison, we also calculated hypothetical cumulative clock errors after 365 d of deployment from our estimated drift rates (Table  1 ) for these seven OBSs.
Wishkerman et al. [20]  used the machine vision system to extract and classify the albinism based on skin colour and texture features in fish. Wallat et al. [21]  also employed a machine vision system that was designed by Luzuriaga et al. [22]  to measure skin colour of gold fish (Carassius auratus) for optimizing diets to achieve the most desirable skin colour. The most essential component of machine vision system is machine learning (ML) algorithms. It provides a mechanism in which the human thinking process is simulated artificially and can assist in human decision making more accurately, quickly and consistently  [23]. ML algorithms are usually employed to either trivial or nontrivial relationships in a set of training data automatically, which produces the generalization of these relationships that can be used to interpret new datasets.
Image Acquisition Before measurement, each fish was mildly anesthetized with Benzocaine to reduce the movement and minimize stress. The surface of each rainbow trout was wiped with a piece of tissue paper to remove extra water from the skin before data acquisition. Each live fish was photographed with a 12-megapixel Nikon D3300 digital camera (Nikon Corp. , Tokyo, Japan) under a lighting system consisting of four halogen lamps (200 W bulb) at an angle of 45 degrees and 35 cm above the sample to not only provide constant intensity output but also to give the uniform light intensity over the fish sample. Images were collected in a dark room with only light source, coming through halogen lamps cast on fish skin. Digital camera was located vertically at 56 cm from the sample. All setting on the camera were on manual.
Acknowledgments: This work was funded by projects  CENAKVA [CZ. 1. 05/2. 1. 00/01. 0024 ]and  CENAKVA II  (the results of the project  LO1205  were obtained with a financial support from the  MEYS  of the CR under the  NPU I program ); The  CENAKVA Centre Development  [No. CZ. 1. 05/2. 1. 00/19. 0380 ];and the  European Union 's  Horizon 2020 research and innovation program  under grant agreement "No. 652831 " (Aquauexcel2020).
(b) Data analysis We measure the two-dimensional velocity field v(x, y, t) (Fig. 1B  and Fig. S1A, C ) using Particle image velocimetry  [45]. We use the open source toolbox MATPIV matpiv. m [46]  of Matlab (The MathWorks, Inc. , Natick, Massachusetts, United States), with the "singlepass" option, square box of side 32 pixels (20 µm) for 200 µm wide strips and 128 pixels (80 µm) for 1 mm wide strips, and box overlap is 50 % or 75 % for both widths. The Particle image velocimetry method, option "single", interrogation box size of 128 pixels, yields qualitatively identical results, and is quantitatively around 10% larger, when compared either with "multin" option, windowsize-vector [128 128 ;  64 64]  or with Kanade-Lucas-Tomasi (KLT) feature matching algorithm, pyramid parameter 2, successive interrogation box sizes of 128 and 64 pixels.
We entirely exclude the first box, where statistics are noisy due to the front. In Figs. 5C, S3B, the average near the front is taken on the three boxes (3 × 176 = 528 µm) next to the front one. To perform quantitative analyses of the kymographs, we use wavelets as measurement tools (rather than as filtering tools). They extract from a signal its wavelengths and time frequencies, like Fourier Transform does, but in addition wavelets can determine the space and time variations of these quantities. We use a custom-made software for wavelet transform profilometry (WTP), a method inspired by 3D-fringe projection profilometry  [47, 48]. It involves a one-dimensional continuous wavelet transform with a phase estimation approach. It is reliable, easy to implement, and robust to noise. We choose a Morlet wavelet and the wavelet transform is computed using a FFT algorithm (which is equivalent to an analytic Morlet Wavelet) with a Matlab script  [49].
Library sequencing Libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 51bp Single Read sequences were generated on the Hiseq2000 sequencer according to manufacturer's instructions (Illumina). The multiplexing level was 6 or 8 samples per lane. Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1. 7) giving FASTQ formatted reads. The FASTQ formatted reads were cleaned from adapter sequences and sequences of low quality using an in-house program (https://github. com/baj12/clean_ngs). Only sequences with a minimum length of 25 nucleotides were considered for further analysis. Bowtie (  [20] , version 0. 12. 7, --chunkmbs 400, -m 50, -e50, -a --best, -q) was used to align to the N16961 reference genome (accession numbers AE003852 and AE003853) with modified gene and new ncRNAs positions (this work).
Statistical analysis of SOS RNA-Seq Count data were analyzed using R version 3. 2. 0 [22]  and the Bioconductor package DESeq2 version 1. 8. 1  [23]. Data were normalized with DESeq2 and the "shorth" parameter. The dispersion estimation and statistical test for differential expression were performed with default parameters (including outlier detection and independent filtering). The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition (SOS vs. noSOS). Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH,  [24] ) procedure and genes with an adjusted p-value lower than 0. 001 were considered differentially expressed.
TAP treatment allowed for the detection of native 5'ends of RNAs. While primary transcripts with 5′-triphosphate ends, which survive TEX treatment, were enriched in the TEX+ libraries. We combined two independent sequencing approachesdirectional whole-transcript cDNA sequencing (RNA-seq) and differential 5'end sequencing. To ensure TSS annotation accuracy, manual curation of the V. cholerae N16961 genome was performed using the MAGE platform of the Genoscope  [28, 29]  (www. genoscope. cns. fr/agc/microscope/home/index. php; Genome Browser Vibrio cholerae N16961). All TSSs were manually validated when a corresponding peak was found with TEX and/or TAP treatment fewer than 50 bases from the beginning of the reads obtained through RNA-Seq. The TSS also had to show at least 3 bases identical to the 6 bases of the -10 promoter consensus of its sigma-70 element (TATAAT), located around 10 bases upstream TSS candidates.
We identified ncRNAs belonging to known functional classes using blastn against the Rfam database (http://rfam. xfam. org). This allowed for identification of the ubiquitous tmRNAs (ncRNA154 and 155), those involved in the SRP ribonucleoprotein complex (ncRNA183, 184, 185), RNaseP class A (ncRNA383), the 6S/SsrS RNA (ncRNA392), the amino acid transport regulator gcvB (ncRNA161), the leucine operon leader (ncRNA394) and the thiamine pyrophosphate (TPP) (ncRNA215), lysine (ncRNA68) and glycine (ncRNA235) riboswitches (Additional file 4). Determination of the TSS and ncRNAs content of the V. cholerae N16961 genome enabled us to fully characterize the SOS response from a transcriptional standpoint.
Funding This study was funded by the  Institut Pasteur , the  Centre National de la Recherche Scientifique  ( CNRS-UMR3525 ), the  French National Research Agency  ( ANR-2012-Blanc SVSE3-DynamINT ), the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (grant n°ANR-10-LABX-62-IBEID), the  Spanish.
5, 2 mM MgCl 2 , 0. 1% Triton and 10 mM EGTA to stop the digestion reaction. DNA was extracted, analyzed by electrophoresis in a 1% agarose gel with Sybr Safe dye (Invitrogen) and photographed under ultraviolet light using a ChemiDoc Gel Imaging System (Bio Rad). Images were analyzed with Fiji software to extract density profiles. STORM imaging. We acquired 3D STORM images on a custom setup based on a Nikon iSPT-PALM inverted microscope. We excited Alexa 647-used to label EdU -with a 640 nm laser with a power of 10. 8 mW at the sample. We excited TMRused to label histones-with a 560 nm laser with a power of 41. 3 mW at the sample. In addition, both for Alexa 647 and TMR, we used a 405 nm Coherent laser with a power of 18. 5 μW at the sample. We imaged the fluorescence from the activated Alexa 647 and TMR molecules with an EM-CCD camera (Ixon Ultra 897 Andor) using a 100×/1.
45NA (Nikon) objective. Using this objective, the image pixel size was 160 nm. We used a cylindrical lens (Melles Griot) for 3D  72. We controlled the microscope with NIS software (Nikon). The number of acquisitions for each experiment is indicated in the figure legends. We detected the localizations in STORM movies with a custom algorithm as in Sergé et al. 73. For data visualization, detections were rendered using the ViSP software as an isotropic Gaussian whose full-width half-maximum was 40 nm  74. We performed z stacks on fluorescent beads (TetraSpeck Microspheres, ThermoFisher) for z calibration. We also used fluorescent beads monitored during STORM image acquisition to correct for sample drift  75  and to align the two signals. When two localizations were detected in consecutive frames within a 50 nm radius, we considered them as one.
STORM data analysis. We identified conglomerates of H3. 3 and H3. 1 or replication foci using the density-based clustering algorithm DBSCAN  76. DBSCAN uses two input parameters-Eps and MinPts-and determines that a point is in a cluster if at least MinPts points are within a distance of Eps. We used an Eps value of 75 nm and a Minpts of 10 for DBSCAN analysis. For replication foci, we only used clusters with a detection number above a threshold value (100) for further analysis. To measure the volume of the conglomerates, we used the convex hull function in Matlab. For the density, we calculated the number of detections-normalized by the total number of detections in the nucleus-divided by the volume. We visualized the volume and density as distribution plots using the ksdensity function in Matlab.
In the plotted graph, when the function is above 1, it indicates attraction, while below 1 indicates repulsion. Immunofluorescence and epifluorescence microscopy. For standard epifluorescence imaging of histone post-translational modifications, after blocking with BSA and Click reaction for EdU labeling, coverslips were incubated with primary and secondary antibodies and stained with DAPI. Coverslips were mounted in Vectashield medium. We used an AxioImager Zeiss Z1 microscope with a 63× objective. For confocal images, we used a Confocal Zeiss LSM780, and images were acquired using 63×/1. 4NA under Zen blue software (Zeiss Germany). Antibodies were used at the following dilutions: H3K9me3 1:1000 (39765, ActiveMotif), H3K27me3 1:500 (07-449, Millipore), H3K4me3 1:500 (07-473, Millipore), H3K36me3 1:500 (ab9050, Abcam) and γH2AX 1:1000 (05-636, Euromedex).
DNA was then purified with Agencourt AMPure XP Beads (Beckman Coulter) according to the manufacturer's recommendations in 20 μL water. Sequencing libraries (TruSeq ChIP) were prepared with 15 ng of DNA and paired-end sequenced on Illumina HiSeq 2500 at the Institut Curie Next Generation Sequencing (NGS) platform. Reads were aligned to the human genome version hg19/GRCh37 with Bowtie2 78 (version 2. 2. 9), run in paired-end mode using the very-sensitive parameter. Genome-wide coverage in bedGraph format was obtained for each alignment using bedtools  79  (version 2. 17. 0) after sorting and indexing the corresponding BAM file with samtools 80 (version 1. 1). Custom Python scripts were used to compute the mean per-base coverage at consecutive 10 kb bins along each chromosome, after normalizing the read counts to the total sequencing depth for each sample.
Acknowledgements This work is dedicated to the memory of our friend and colleague  Maxime Dahan. We thank  Antoine Coulon  and the members of the  PIC3i  " UNDERSTAND DYNAMIC ARC " for helpful discussions,  Shauna Katz  and  Dominique Ray-Gallet  for critical reading of the manuscript,  Chloé Guedj ,  Patricia Le Baccon  and the  PICT-IBiSA  platform for help with the iSPT-PALM microscope. This work was supported by  la Ligue Nationale contre le Cancer  ( Equipe labellisée Ligue ),  ANR-11-LABX-0044_DEEP  and  ANR-10-IDEX-0001-02   PSL ,  ANR-12-BSV5-0022-02  " CHAPINHIB ",  ANR-14-CE16-0009  " Epicure ",  ANR-14-CE10-0013  " CELLECTCHIP ",  EU  project  678563 "EPOCH28", ERC-2015-ADG-694694  " ChromADICT ",  ANR-16-CE15-0018  " CHRODYT ",  ANR-16-CE12-0024  " CHIFT ",  ANR-16-CE11-0028 "REPLICAF"  and  "Parisian Alliance of Cancer Research Institutes.
"High-throughput sequencing and Library preparation has been performed by the  ICGex NGS platform of the Institut Curie  supported by the grants  ANR-10-EQPX-03  ( Equipex ) and  ANR-10-INBS-09-08  ( France Génomique Consortium ) from the  Agence Nationale de la Recherche  (" Investissements d'Avenir" program ), by the  Canceropole Ile-de-France  and by the  SiRIC-Curie program-SiRIC Grant  " INCa-DGOS-4654 ".
Purpose: To review the recent literature on opioid rotation (ie, switching from one opioid drug to another or changing an opioid's administration route) in cancer patients experiencing severe pain and to develop a novel equianalgesia table for use in routine clinical practice. Methods: The MEDLINE database was searched with terms "cancer pain," "opioid rotation," "opioid switching," "opioid ratio," "opioid conversion ratio," and "opioid equianalgesia" for the major opioids (morphine, oxycodone, fentanyl, and hydromorphone) and the intravenous, subcutaneous, oral, and transdermal administration routes. Selected articles were assessed for the calculated or cited opioid dose ratio, bidirectionality, and use of the oral morphine equivalent daily dose or a direct drug-to-drug ratio. Results: Twenty publications met our selection criteria and were analyzed in detail.
Methods The MEDLINE (via PubMed) database was searched up until April 30, 2018. Given the lack of MESH terms for opioid rotation, opioid switching, or the opioid ratio, we used the search terms "cancer pain," "opioid rotation," "opioid switching," "opioid ratio," "opioid conversion ratio," and "opioid equianalgesia. " The search was limited to studies of human subjects: published systematic reviews of RCTs, RCTs, other clinical trials, meta-analyses, and case reports. There were no restrictions on year, language, minimum number of study participants, or length of follow-up. We selected articles for further analysis if at least one of the keywords was mentioned in the title or abstract. We also searched the reference lists of articles identified using this search strategy and selected those judged to be relevant.
Given that our ultimate objective is to make an inventory of ratios, which could serve as a basis for devising proposals for routine clinical practice, we focused on the major opioids Studies were eligible for inclusion if they involved adult patients with chronic cancer pain and contained clear data on opioid conversion ratios and equianalgesia. Evaluation of articles was performed by two pain specialists (ET and YH). Both reviewers agreed on inclusion of the specific articles. In case of disagreement, a third reviewer (SL) decided regarding the inclusion. After reading the full text of each selected article, we noted i) the calculated opioid ratio (when this was a trial end point) or the cited ratio (when used in the study design), ii) whether dose dependency (ie, whether the ratio differed according to the dose of the first opioid) or directionality (ie, whether the ratio differed according to the direction of the switch) had been investigated, and iii) whether the ratios were based on the oral morphine equivalent daily dose (MEDD) or on direct (drug-to-drug) ratios.
68), reporting a daily oral morphine dose/daily fentanyl patch delivered dose ratio of 78:1. Donner et al performed a multicenter study with 98 patients (38 patients were treated according to protocol and their data were analyzed) with controlled cancer pain with the aim of studying the most convenient conversion ratio when switching from morphine to transdermal fentanyl. 51 Initial doses were calculated with the Mpo:Ftd ratio of 100:1. The regression analysis comparing fentanyl dosages at the end of the study (day 15) with the morphine dosages at day 1 demonstrated a mean Mpo:Ftd ratio of 70:1 (R 2 =0. 82). This result implicates that a calculation table with a ratio 100:1 is by 30% subequianalgesic but may be appropriate with allowance of a safety margin. Watanabe et al reviewed the charts of 22 patients with cancer-related pain who were switched from a variety of opioids to subcutaneous fentanyl by continuous infusion.
Hydromorphone Hydromorphone is a hydrogenated ketone analogue of morphine. As with morphine, there is great interindividual variation in oral bioavailability (10%-65%). Some metabolites may have greater analgesic activity than hydromorphone itself but are unlikely to contribute to the pharmacological activity of hydromorphone. 63 According to the summary of product characteristics (hydromorphone hydrochloride 1. 3 mg and 2. 6 mg capsules), 1. 3 mg of hydromorphone has an efficacy approximately equivalent to 10 mg of morphine given orally. We identified one double-blind crossover study, three prospective studies, and three retrospective studies with   relevant data regarding equianalgesic conversion ratios to and from hydromorphone (po, sc) in cancer pain (Table  4 ). In a study by Wallace et al, patients with chronic cancer pain were enrolled in an open-label conversion trial, from various opioids to HMpo, using an oral M:HM ratio of 5:1 for a MEDD conversion.
37 Based on their results, the calculated ratio for HMpo:OXpo is 1:4. 13 and is bidirectional. Gagnon et al prospectively collected the data of cancer patients who were rotated from another strong opioid to OXsc to establish conversion ratios. 32 For the 11 patients who were switched from HMsc to OXsc, the authors reported an equianalgesic ratio of 0. 5 (±0. 4):1. Inoue et al investigated the efficacy and safety of switching from oral morphine to hydromorphone immediate-release tablets at the HM to M conversion ratio of 1:5 or 1:8 in cancer patients with adequate pain control with oral morphine (60 or 90 mg/d). 54 This multicenter, active-controlled, randomized, double-blind, parallel-group, comparative study enrolled 30 adults patients in conversion ratio 1:5 group and 40 patients in conversion ratio 1:8 group.
Acknowledgments The authors acknowledge the assistance of  Pascal Fangio  ( Poissy Hospital, Poissy, France ) and  Anna Patrikidou  ( Institut Gustave Roussy, Villejuif, France ) in the development of the present review's search strategy. The authors thank  Philippe Mayran  of  PM Sante (Garches, France ) for providing medical writing support, which was funded by  Mundipharma, Paris, France.
• WHO hosts one of the largest databases of ambient air pollution measurements in cities. Currently, the publicly available WHO Global Urban Ambient Air Pollution Database contains air quality measurements from 3000 cities, representing 103 countries. In the past 2 years alone, the database has nearly doubled in size, with more cities now measuring air pollution concentrations and recognising the associated health effects than ever before. This database also provides inputs to the integrated models that use satellite remote-sensing and chemical transport models to estimate ambient air pollution exposure globally, including estimates for regions without any ground-level monitoring (eg, smaller cities and rural areas). The Global Urban Ambient Air Pollution Database also supports monitoring of urban air quality for SDG 11 indicator 11•6: "to reduce the adverse per capita environmental impact of cities, including by paying special attention to air quality and municipal and other waste management".
These struggles have forced contemporary legal systems, including legal systems in the high-income home countries of mining conglomerates, to accommodate indigenous world views and to correct, rather than perpetuate the unjust effects of economic growth upon the poor. 313, 317 ith the worldwide spread of toxic chemicals and modern-day pollution, interest has grown in investigating, documenting, and mapping environmental injustice. Information produced through these efforts, especially information documenting patterns of pollution at the local level, can provide powerful leverage to disproportionately exposed communities who are struggling to reduce their exposure and their inequitable burden of pollutionrelated disease. In Europe, the Environmental Justice Atlas, a global online database, now lists information on about 2000 sites around the world where pollution and environmental injustice are documented or suspected.