dataesr/scientific-paragraphs-categorization huggingface dataset:
2 ). We compared genes specific to zebrafish iridophores  (Higdon et al. , 2013)  with genes differentially expressed in clownfish white skin and showed that overlap between datasets was significantly greater than would be expected by chance, showing that white skin in clownfish had a transcriptomic signature of iridophores. In particular, 12 genes were common to both datasets and could thus constitute conserved iridophore markers within actinopterygians. Although significant, this overlap was relatively small compared to the size of respective clownfish (86) and zebrafish sets of genes (237). This presumably reflects differences in sample origins: zebrafish RNA-Seq data were obtained from purified iridophores whereas clownfish data were derived from whole skin in which many other cell types are present  (Higdon et al.
, 2013). Thus, clownfish data represented a more diverse set of cells compared to the zebrafish dataset, though biological species differences in iridophore transcriptomes may also explain some of the differences between both datasets. These and other possibilities will be resolvable with transcriptomic profiling of purified populations of clownfish iridophores. Third, we retrieved previously identified iridophore markers in the list of the most DEGs in white skin (Fig. 3 ). Among the 12 genes found in common between the clownfish white bar and zebrafish iridophores, 4 (pnp4a, prtfdc1, tfec and fhl2a) were already demonstrated or inferred to be important for the development or function of iridophores in teleost fishes  (Lister et al. , 2011; McMenamin et al. , 2014; Kimura et al. , 2017; Petratou et al.
, 2013). Gpnmb was also expressed in iridophores of zebrafish  (Higdon et al. , 2013)  and cichlids  (Santos et al. , 2014). Among the 10 most DEGs in white skin, we identified two other genes (gja5 and trpm1a) associated with pigmentation although not necessarily in iridophores. Mutations in gja5 result in the zebrafish leopard mutant phenotype, characterized by a spotted pattern  (Irion et al. , 2014; Watanabe et al. , 2006). In addition, we identified several genes that, to our knowledge, have not been previously assigned roles in pigmentation. Three of those (ada2, prtfdc1, slc2a9) are involved in purine metabolism  (Welin et al. , 2010; Pei et al. , 2016) , consistent with a function in platelet formation. Ranked second within the most DEGs in white skin was saiyan also identified in the comparison between both zebrafish and iridophore datasets.
ACKNOWLEDGEMENTS TL hold a grant from the  French MENRT. We thank  Bruno Frédérich  for critical reading. We thanks the OOB's  Bio2Mar and Biopic platforms  for technical help. Clownfish husbandry supported by the  CNRS interdisciplinarity actions and EMBRC-France  ( ANR-10-INBS-02 ). Additional support provided by  NIH   R35 GM122471  to D. M. P.
In a linear dose-response relationship, every 100 g increase in exposure to EL was associated with an increased milk yield from 0. 11 to 0. 14 kg/day, decreased milk fat from 0. 06 to 0. 13 g/kg and decreased milk protein from 0 to 0. 02 g/kg, according to the cow parity. This study provides information on the associations between estimated intakes of EL and milk production and composition using a large database obtained from commercial dairy herds. Milk and dairy products constitute an important part of human diet 1. Concerning human health, there is an opportunity to improve the fatty acid (FA) intake of humans 2 by increasing polyunsaturated fatty acids (PUFA) at the expense of saturated fatty acids (SFA) or by rebalancing the ratio n-6/n-3 3,4 as milk and dairy products represent a major part of FA supply and especially SFA 5.
Methods General study design and available data. A retrospective observational study was conducted on data from French dairy herds enrolled in the official Milk Recording Scheme and wherein dairy cows were supplemented with EL between January 2008 and December 2015. Milk performance of cows at each test day (cow-TD, over 24 h) during periods of EL supplementation was compared to cow-TDs during periods of EL non-supplementation within the same herd. The EL exposure data were obtained from commercial companies delivering products containing EL during the study period. The TD information obtained from the official Milk Recording Scheme Lactation includes the date of TD, MY, MFC and milk protein content (MPC), calving date, parity and animal movement data. Estimation of exposure to extruded linseed and determination of exposure status.
A cow daily exposure to EL for each delivery in each herd was calculated from the time-line of product delivery distribution, the quantity delivered, the products' EL content, and the average number of lactating cows in the herd during the period of delivery distribution. The beginning of EL supplementation to dairy cows in each herd was considered to occur immediately the day after the date of feed arrival on the farm. The number of cows by herd and day was calculated based on movement data and test-day records. Doing that, we considered that all cows (i. e. , whatever their lactation stage and MY) were supplemented with the same EL quantity within a herd. When a farmer received supplies of several feeds containing EL at the same time (i. e. , on the same day), herd daily exposures from each delivery were added.
In the end, a mean EL intake by cow by herd for each day of the study period was calculated. For every cow-TD, an exposure status was determined according to the exposure of the herd at the moment of the TD. A cow-TD was considered exposed only if the cow was supplemented with EL continuously since the previous TD (or since its calving in the case of the first TD within a lactation). For each cow-TD, an average daily EL exposure during the interval between TD and previous TD (or TD and calving) was calculated by adding each daily exposure (from each day of this interval), estimated as described above, divided by the number of days of this interval. Based on the findings of a recent meta-analysis and on recommendations for EL use in practice, daily intakes higher than 1500 g/cow/day (0. 13% of cow-TD) were considered plausible and related lactations were removed from the dataset  6.
The precision on the temporal sequence of exposure events was enhanced by excluding from the dataset all cow-TD records comprising the first TD after beginning EL supplementation and the first TD after stopping EL supplementation. In summary, the exposure variable accounted for both the dose and minimal time of exposure. For each herd, all cow-TDs recorded in the Milk Recording Scheme during the study period were considered for the study. All the cow-TDs that were defined as not exposed constituted the reference population (unexposed category).
Data selection. The initial study population consisted of 4979 French dairy herds having deliveries of EL during the study period. However, only 2250 herds were included due to a lack of herd identification number, and the lack of enrolment in the official Milk Recording Scheme. Furthermore, in order to ensure the heterogeneity of the EL exposure within and between herds, only herds receiving a minimum of four deliveries of feeds with EL during the study period were included in the dataset reducing the sample to 1836 herds. Likewise, the absence of fit between the delivery and the Milk Recording Scheme records, as well as missing data in deliveries reduced the sample to 1415 herds. Then, herds with unusual management (i. e. , <10 calvings per year and with <15 or >65 percent of primiparous cows) were excluded reducing the sample to 1294 herds.
Additionally, within herds, only data from Holstein cows were included because of the strong effect of breed on MY and milk contents. Only lactations that lasted at least 180 days, beginning after 1 January 2008 and before 6 July 2015 were included. In addition, cows and/or lactations with missing, implausible or unusual data were excluded: age at first calving <22 months or >40 months, calving to first TD <7 days, interval between TD <22 days or >73 days, milk contents equal to zero at TD. Finally, TDs occurring after 500 days in milk were excluded.
Discussion This study based on a large dataset composed of 404161 lactations recorded on 1294 herds and was to our knowledge the first large field-based epidemiological study exploring the association between nutrition (i. e. , exposure to a feed) and dairy cow milk performance. The high statistical power resulting from our large sample size allowed us to demonstrate that supplementing EL in commercial farms could represent an economically viable strategy for enhancing dairy cow performance. Indeed, exposure to EL was associated linearly with an increase in MY, a decrease in MFC and, to a lesser extent in MPC. In France, private milk traders fix the price of raw milk adjusting for imbalances in the content of fat (38 g/L) and protein (32 g/L). Therefore, farmers supplementing EL may be expected to compensate for the decrease of MFC by the benefits of an increased MY.
The cost of EL, as well as well-known negative effects of feeding high-fat diets, may restrict the quantity of EL supplemented in a commercial dairy herd diet. To our knowledge, very few experimental trials investigated the effects of such a low intake of EL on milk performance. The average estimated daily intake in our study represent 25% of experimental trials doses (1180 g/cow/day)  6. High quantities of EL were supplemented in these experimental trials because they were mainly designed to study the evolution of milk FA profile after EL supplementation. The effect of EL on milk performance was seldom discussed in these trials. Finally, the present study was carried out on a large dataset designed to detect even small effects of a practical range of EL supplementation on milk performance if they exist.
Indeed, we detected significant effects on milk performance of EL supplementation in low levels to dairy cows. In conclusion, under field conditions, supplementing EL to dairy cows was associated with a linear increase in MY and a decrease in milk fat content. We clearly demonstrated that large scale epidemiological studies in commercial herds are complementary to experimental trials in order to quantify the associations between cow nutrition and cow performance, despite the lack of precise data on cow diets. To our knowledge, this is the first time an association between cow nutrition and milk performance was assessed in this way. Further studies under field conditions exploring the association between EL exposure and cow health and performance are needed to evaluate how dairy farmers willing to improve human health may benefit from this feeding practice.
Acknowledgements The authors gratefully acknowledge  Chambres d'Agriculture, organismes de contrôle de performances et d'insémination artificielle, and organismes de sélection aux Systèmes Nationaux d'Information Génétique  for providing the milk performance data. Support for this research was provided by the  Association Nationale de la Recherche et de la Technologie (ANRT) ,  BIOEPAR ,  INRA , Oniris (post-doctoral fellowship, to J. M. A. ). T. M. was the recipient of a  CIFRE doctoral fellowship  from  ANRT  and  Valorex (Combourtillé, France). The authors also acknowledge  P. Gontier  ( BIOEPAR, INRA, Oniris, France ) for aggregating data.
Secretory capacity and [Ca 2+ ] i dynamics of delta cell filopodia. We next asked whether delta cell filopodia have a secretory/regulatory role. From our in vivo TPM imaging dataset (Fig. 1 ), we identified a total of five delta cells with discernable filopodia in four different SST-GCaMP3 islets (n = 1 islet/mouse, total of four different mice). Under resting conditions, delta cell somata and filopodia displayed low amplitude [Ca 2+ ] i spikes that were not synchronized, with the filopodia displaying generally lower amplitudes (Fig. 3a ). Analyses of the first 80 s after glucose injection revealed a marked increase in [Ca 2+ ] i spiking frequency and spike amplitude in both cell compartments (Fig. 3a-f ). In some cases, filopodia exhibited [Ca 2+ ] i spikes that were not synchronized with somatic [Ca 2+ ] i spikes (Fig.
Glucose tolerance tests (GTT) were performed as described in  30. Briefly, animals were fasted for 4-6 h after which the fasting blood glucose levels were measured at two time points 5 min apart. Next, mice were injected with 2 g glucose/kg body weight and blood glucose levels were measured every 15-30 min. For I. V. GTT in Sst-GCaMP3 transplanted mice, animals were anesthetized according to the imaging protocol (i. e. , i. p. injection of a mixture of fluanisone (25 mg/kg), fentanyl (0. 788 mg/kg) and ) of the mean. For e, f source data are provided as a Source Data file midazolam (12. 5 mg/kg)), glucose was injected in the tail vein (0. 4 g/kg) and blood glucose was measured every 2 min (Accu-Check, Roche, Switzerland). For dietary treatments, animals were assigned for 6-7 weeks to either a control diet, CD (CD88137, 11% of energy from fat, 66% from carbohydrates, and 23% from proteins) or to a HFD (TD88137, 43% of energy from fat, 42% from carbohydrates, and 15% from proteins).
Diets were acquired from Ssniff Spezialdiäten GmbH, Soest, Germany. Transplantation of islets into the anterior chamber of the eye (ACE) and in vivo microscopy. Transplantation and in vivo imaging of ACE islets were performed as previously described  20. In brief, islets from SST-ChR2-YFP or SST-GCaMP3 mice were isolated 24-48 h prior to transplantation using the collagenase method and recovered in vitro with fresh CMRL-1066 or RPMI 1640 medium supplemented with 10% fetal bovine serum. Delta cell GCaMP3 imaging was performed under the following anesthesia conditions: mixture of fluanisone (25 mg/kg), fentanyl (0. 788 mg/kg), and midazolam (12. 5 mg/kg). To image delta cell GCaMP3 in vivo (data shown in Fig. 1 ), animals were injected with insulin (0. 25U/kg) 2 min prior to the injection of glucose.
Confocal imaging was performed on a Leica up-right or inverted SP5 or SP8 microscope fitted with a white light laser and gated Hybrid detectors. FM-4-64 stained islets were imaged using the following excitation and emission configuration: YFP, Ex510nm and Em520-570nm, FM-4-64, Ex510nm and Em630-680nm. Islet viability was checked prior to imaging with backscatter analyses  20. For colocalization studies, isolated islets or sections were mounted on 80% glycerol/PBS (with 0. 2% n-propyl gallate (NPG, Sigma) as anti-fade agent) and acquired with a glycerol 63×/1. 3NA objective with a correction collar adjusted to the focal plane prior to imaging. Images were acquired using Nyquist acquisition parameters for the X,Y, and Z axis and de-convolved using Huygens software (Scientific Volume Imaging).
For deconvolution, the signal-to-noise ratio was determined for each channel and the deconvolution parameters set for 40 iterations and a quality threshold of 0. 05. Co-localization was determined with IMARIS software (Bitplane) co-localization module and automatic thresholding for each channel. Imaging of mouse pancreatic sections from animals fed with a CD or HFD was performed in samples mounted in Prolong ® antifade solution with DAPI (ThermoFisher) and acquired with a glycerol 100× objective. Imaging of isolated islets treated in vitro, was performed in PBS with a water-immersion 25 × /0. 95NA objective. Somatostatin was imaged with Alexa488 secondary antibodies and TPM with an excitation line of 800 nm. For simulations determining the reach and contact density of delta cells in mouse and human islets, we utilized a 3D tissue analysis ImageJ algorithm as previously described  29.
In vivo Ca 2+ trace imaging data extraction and analysis. Extraction of in vivo delta cell Ca 2+ traces (i. e. , raw GcAMP3 signal) was done in MATLAB using the CaImAn plugin as previously described  48. In brief, we used the "demo script" within the CaImAn package to extract the Ca 2+ data from movement-corrected and background-subtracted GCaMP3 image stacks. We used the script to identify cells (i. e. , regions of interest, ROIs) automatically (CaImAn parameters: K = 50, tau = 10, and p = 1) and normalized the GCaMP3 signal to the highest intensity peak in each cell. As a second step, the software-detected ROIs were manually curated to make sure that only ROIs representing cells were selected for analysis. Next, we ran a peak-finding function and considered all peaks that met the arbitrary threshold of 1× higher than the standard deviation of the whole in vivo recording for each cell.
This threshold was chosen because it could detect peaks in all control and HFD-fed animals imaged in vivo, where the latter have overall lower peak amplitudes that could not be detected with higher thresholds. Next, the peak location and amplitude for each cell was plotted and analyzed using excel software. In addition, the modified demo script contains a classic MATLAB function that integrates the normalized GCaMP3 signal from each detected cell in a given islet to generate a hierarchical clustering analysis (HCA) (details in https://www. mathworks. com/help/stats/hierarchical-clustering. html). Analysis of beta cell Ca 2+ traces acquired via GCaMP6s imaging was done as follows: First, we calculated the GCaMP6s/dtTomato signal intensity ratio for each identified beta cell for the entire imaging session.
Next, the files containing the GCaMP6s/dtTomato ratio were analyzed with a custom MATLAB script that identified [Ca 2+ ] i peaks that passed the arbitrary threshold of 1. 5× above the standard deviation for the entire imaging experiment and for each cell. Next, the location and amplitude for all [Ca 2+ ] i peaks in control and SST-ChR2 islets were quantified and normalized to the highest amplitude peak in the entire run. Electron microscopy of mouse and human pancreas. Small volumes of a mouse and a human pancreas were fixed and prepared for electron microscopy as described in reference  49. Islet sections were imaged with scanning and transmission electron microscopy and delta cells identified using established guidelines for islet electron micrographs. 3D electron tomograms of mouse delta cell filopodia were acquired as described in reference  49  and their structure was reconstructed using IMOD software (University of Colorado).
Acknowledgements This work was supported by the  Lee Kong Chian School of Medicine, Nanyang Technological University  start-up grant to  Per-Olof Berggren , the  Lee Foundation  grant, the  Swedish Research Council , the  Family Erling-Persson Foundation , the  Novo Nordisk Foundation , the  Stichting af Jochnick Foundation , the  Swedish Diabetes Association , the  Scandia Insurance Company Ltd. ,  Diabetes Research and Wellness Foundation ,  Berth von Kantzow's Foundation , the  Strategic Research Program in Diabetes at Karolinska Institutet , the ERC-2013-AdG 338936-Betalmage, and the  Knut and Alice Wallenberg Foundation. Rafael Arrojo  e Drigo was supported by a research fellowship from the  Nanyang Structural Biology Institute (NISB)  and by an  AXA Research Fund postdoctoral fellowship.
Flavia Letícia Martins Peçanha  was supported by a grant from the  National Council for Scientific and Technological Development-Brazil (CNPq). The authors would like to thank  Javier Chow  from  The Salk Institute  for assistance with implementing MATLAB scrips for delta cell activity analysis. P-OB is co-founder and  CEO of Biocrine , an unlisted biotech company that is using the ACE technique as a research tool, S. J. was employed by  Biocrine AB  and I. L. is a consultant for Biocrine AB. Open access funding provided by  Karolinska Institute.
Construction of SH gene deletion mutant cDNA and HMPV ΔSH recovery The strategy for the construction of the plasmid encoding the full-length genomic cDNA of HMPV A1/C-85473 strain (GenBank accession number KM408076. 1) and the subsequent production of recombinant viruses is described in details in  [64]. Briefly, the full-length genomic cDNA of HMPV A1/C-85473 strain was generated by RT-PCR using the Superscript II reverse transcriptase (Thermo Fisher Scientific) and amplified by Phusion DNA polymerase (New England Biolabs, Whitby, ON, Canada). A Gibson Assembly (Cloning Kit, New England Biolabs) was performed to integrate the genomic viral cDNA into a pSP72 plasmid (Promega, Madison, WI, USA) containing a T7 terminator, the hepatitis delta virus (HDV) ribozyme and a T7 promoter. To generate HMPV ΔSH virus, the mentioned plasmid was amplified using specific primers, designed to match before the SH gene start sequence (5'-GGGACAAGTA GTTATGGA-3') and after the intergenic SH-G region (5'-ACTCTGATGTGTTTTTACTAA C-3'), in order to extract completely the SH gene sequence.
Red blood cells were lysed with BD Pharm Lyse (RBC Lysis Buffer 10X -BioLegend, San Diego, CA, USA) and the recovered leukocytes were washed and resuspended in D-PBS. After the washing step, cells were incubated on ice for 40 min with a pool of antibodies (anti-CD45, anti-CD11b, anti-CD170 (Siglec-F), anti-Ly6C, anti-Ly6G, anti-CD11c, anti-CD115, anti-B220, anti-CD3ε, anti-CD4 and anti-CD8a /BD Bioscience, CA, USA). Number of cells was determined with Precision Count Beads (BioLegend, San Diego, CA, USA). Labeled cells were then washed and resuspended in DPBS. Flow cytometry analyses and data acquisition were performed by using a BD SORP LSR II and the BD FACSDiva software, respectively.
Histological analysis On day 5 post-infection, mice were euthanized and their lungs were removed. Tissue was fixed in 4% paraformaldehyde, embedded in paraffin, sectioned in slices of 5 μm, and stained with hematoxylin and eosin. Slides were digitalized at 40X magnification using a Nanozoomer slide scanner (Hamamatsu, Japan) and scored using NDP viewer 2. 0 software (Hamamatsu, Japan). The histopathological scores were determined by a pathologist and a medical biologist who were blinded to the experimental data. A semi-quantitative scale was used to score bronchial/ endobronchial, peribronchial, perivascular, interstitial, pleural and intra-alveolar inflammation  [73]. Scores represent consensus between the two observers. The results were expressed as lung total inflammatory scores.
Statistical analysis All statistical tests were conducted using the GraphPad Prism version 6. 0 (GraphPad Software, La Jolla, CA, USA). The results were expressed as the mean ± S. E. M for each group and 'n' referred to the sample size. Survival data were analyzed by comparing Kaplan-Meier curves using the log-rank test. Viral titers, cytokines and total protein levels, immune cell recruitment, cell differentiation as well as lung histopathological scores were analyzed using unpaired Student t-test, Mann-Whitney U-test, one-way analysis of variance (ANOVA) followed by Tukey post hoc or Kruskal-Wallis test followed by Dunn's post hoc for multiple comparisons. Differences were considered statistically significant when P < 0. 05.
Acknowledgments The authors are grateful to  Dr Steve Lacroix  ( Infectious Disease Research Centre, Quebec City, QC, Canada ) for providing IL-1β -/-mice. We are thankful to  Audrey-Ann Dupont  ( Animal Research Facility of the Quebec University Health Centre, Quebec City, QC, Canada ) for help in the reproduction of IL-1β -/-mice. We thank  Dr Francesca Cicchetti  ( Quebec University Health Centre, Quebec City, QC, Canada ),  Dr Sachiko Sato  ( Infectious Disease Research Centre, Quebec City, QC, Canada ) and  Dr Benedicte Py  ( Centre International de Recherche en Infectiologie CIRI, Universitede Lyon, Lyon, France ) for providing human monocyte-like THP-1, J774. 2 cells and BMDM (WT and  NLRP3  KO) cells, respectively. We thank  Thomas Julien  ( VirPath, Universitede Lyon, Lyon, France ) for technical assistance.