dataesr/scientific-paragraphs-categorization huggingface dataset:
Here, we develop a well-replicated, exactly dated chronology from the annual growth-increment widths of G. pilosa along the eastern coast of the northern Adriatic Sea (Fig. 1 ). This chronology provides a long time series to test the hypothesis that local forcing (such as rivers, precipitation, heat fluxes) is relatively more important than remote forcing (through advection of remote water masses) to biological processes of shell growth. In doing so, the chronology is related to a number of local and remote physical drivers extracted from a variety of long-term datasets: atmosphere reanalysis, ocean climate models and satellite altimetry. Determining the relative role of these processes will provide baseline information of use for marine resources management and understanding the role of climate variability and change on Adriatic ecosystems.
2 ). Mean segment length was 39. 9 years, and over 10 individual time series were measured over the period spanning 1973 to 2016. Running Expressed Population Signal calculated over a 30-year window with 29-year overlap indicated that the chronology was robust after 1979. Synchronous shell growth was noted also prior to this period with conspicuously narrow growth increments corresponding to years 1976 and 1968. Correlations to environmental drivers. Po River discharge (PO) and surface salinity (SSSN) are not correlated with the shell growth chronology in any month of the year (Fig. 3 ). The chronology correlates with precipitation (TP) for just one month of the year (February), and only at the 90% level (r = 0. 28, p = 0. 093, Fig. 3 ). Poor relationships with precipitation or salinity are typical across most of the Adriatic, as evidenced by a correlation analysis with gridded data (not shown), although there are some small patches of significant correlations at 95% between chronology and SSSN or TP.
1 M HCl for 2 minutes or 0. 3 M HCl for 30 seconds, as has been previously applied to this species  29. An Axio Lab A1 microscope equipped with Zeiss AxioCam ERc 5s camera was used to photograph acetate peels. Due to the size and magnification required, multiple photographs were taken of each sample and then stitched into a single panoramic using Image-Pro Premier software. A total of 66 shells was processed of which 30 were older than 35 years, had clearly delineated growth increments, and were used for chronology construction. The length of these shells ranged from 66. 6 to 89. 6 mm (80. 52 ± 5. 49 mm). According to oxygen isotope geochemistry  49  , G. pilosa in the North Adriatic forms an annual growth line in autumn. Therefore growth increment referred to as "2015" corresponds to shell growth from approximately October 2014 through September 2015.
The list-year method  50  was used for visual crossdating, proceeding backward in time from the increment at the margin formed in the year of collection. Following visual crossdating, growth-increment widths were measured from the margin toward the center using Image-Pro Premier software. Program COFECHA  51, 52  was used for quantitative verification of crossdating. Each measurement time series was fitted with its own cubic smoothing spline of 15-year 50% frequency cutoff. Observed values were divided by those predicted to isolate high-frequency patterns of growth variability. Each detrended time series was then correlated with the mean of all others. Any unusually low correlation (p > 0. 01) was visually re-inspected for possible dating errors. Series intercorrelation, the mean correlation between each individual time series and the average of all others, and mean sensitivity, an index of high frequency (year-to-year) variability between pairs of successive increments  53  , are reported.
The chronology was constructed in the software package ARSTAN 54 using the original measurement time series. Each measurement time series was first power transformed  55  and then detrended using a negative exponential function. Population-level signal strength in the chronology was assessed using the Expressed Population Signal (EPS). Although arbitrary, an EPS ~0. 85 is considered the threshold at which the sample set adequately reflects the theoretical population from which it was drawn  56. Only those portions of the chronology with at least 10 individuals were retained to ensure that this EPS threshold was exceeded. Monthly series of sea surface temperature (SST), downward net heat flux (NHF), total precipitation (TP) and air temperature at 2 m (T2M) were extracted from gridded ERA-Interim reanalysis dataset  57  between 1980 and 2016.
Yet, ERA Interim assimilates satellite products and therefore is the product of much higher reliability than the NEMOMED12 model variables. NEMOMED12 is an eddy-permitting oceanic regional model spanning the entire Mediterranean Sea and a buffer Atlantic zone off Gibraltar, with 50 unevenly spaced z levels in in the vertical dimension and a horizontal resolution of up to 8 km that is irregularly stretched to properly reproduce Gibraltar dynamics  58, 59. The model is run in hindcast mode and covers the ERA Interim period between 1980 and 2012. Annual and semi-annual cycles were removed from all environmental data sets. Absolute dynamic topography multimission gridded data available at Copernicus -Marine Environment Monitoring Service were used for assessment of the Adriatic-Ionian Bimodal Oscillating System (BiOS) regimes.
Annual and semi-annual cycles were removed from the data and then averaged for each month  20. The difference between these values in the northern Ionian Sea and the central Ionian Sea (delineated here as the blue and red squares in Fig. 1 , respectively) is defined as the absolute dynamic topography (ADT) variable. This difference has been used as an indicator of the BiOS  18, 20, 60  , or as an indicator of the cyclonic and anticyclonic circulation regime in the North Ionian. Spearman's rank correlation coefficients were used to relate chronologies with environmental data. Correlations were performed using monthly-averaged environmental variables given that climate conditions during specific months or seasons can strongly influence annual bivalve growth. Correlations were calculated between the chronology and gridded climate variables (T2M, SST, TP, ERA NHF, and NEMOMED12 values of SSTN and SSSN).
Acknowledgements Research has been supported by  Croatian Science Foundation  under the project  SCOOL  ( IP-2014-09-5747 ) and ADIOS ( IP-2016-06-1955 ). The authors are grateful to  Slaven Jozić  and  Dragan Švigir  for help with sample collection, and  Hana Uvanović  for help with acetate peel preparation. We sincerely thank two anonymous reviewers for providing helpful comments.
ACKNOWLEDGMENTS We would like to thank  Charles  and  Perrine Hervé-Gruyer  and  Louise Gehin  for access to their farm and for their openmindedness toward, among other things, this scientific study. We also thank all the people working at  La Ferme du Bec Hellouin  for letting us sample, and for the warm welcome made to  Valentin. Finally , we want to thank  Antoine Marquet  from  Assocation Bio Normandie  for his time and the valuable information he.
Based on the Institut Pierre-Simon Laplace decadal forecast system,  Séférian, Bopp, et al. (2014)  show that marine productivity can be predicted three to five years ahead in the tropical Pacific. The authors attribute this predictability horizon for marine productivity to the persistence of a surface nutrient anomaly generated by the ENSO interannual variability. More recently,  Betts et al. (2016)  proposed a statistical model to predict the yearly seasonal cycle for global mean atmospheric CO 2. This statistical model combines Carbon Dioxide Information Analysis Center anthropogenic CO 2 emissions data and Global Seasonal forecasting system 5 for 1 October 2015 to 31 March 2016. Based on a regression analysis, SÉFÉRIAN ET AL. 2455  Betts et al. (2016)  forecast an annual mean CO 2 growth rate of 3.
Summary and Conclusions The decadal predictability of global land and ocean carbon uptake has been assessed in CNRM-ESM1 using a perfect model framework. This approach assumes that our model reproduces the observed climate and carbon cycle variability, considering that model biases do not affect predictability. An advantage of this framework is that model fields remain consistent between each other, which limits the impact of the model's drift when initialized with data  (Gupta et al. , 2013; Séférian, Gehlen, et al. , 2016) , which otherwise would require complex approaches to reduce initial shock  (Sanchez-Gomez et al. , 2016; Volpi et al. , 2017). With this framework, we have identified key regions where land or ocean carbon uptake are potentially predictable within decades and how far regional carbon uptake can be statistically predicted.
Proteome analyses The soluble intracellular proteome, the enriched membraneassociated proteome, and the soluble extracellular proteome was characterized from exponentially growing cells of Formosa strain B. Details of the protein extraction and subproteome enrichment can be found in Supplementary Information. Peptides were subjected to a reversed phase C18 column chromatography on a nano ACQUITY-UPLC (Waters Corporation, Milford, MA, USA) and separated as described by Otto et al. [25]. Mass spectrometry (MS) and MS/MS data were recorded using an online-coupled LTQ-Orbitrap Classic mass spectrometer (Thermo Fisher Scientific Inc. , Waltham, MA, USA). We searched MS spectra against a target-decoy protein sequence database including sequences of Formosa B (Hel1_33_131) and of common laboratory contaminants.
Protein searches were performed using MaxQuant with the integrated Andromeda engine  [26]  with a peptide level FDR (false discovery rate) set to 0. 01 (1%). Only proteins that could be detected in at least two out of three replicates were counted as identified. The automatically calculated iBAQ values (intensity-based absolute quantification; i. e. , peak area divided by the sum of all theoretical peptides) were used to manually calculate riBAQ values (relative iBAQ; giving the relative protein abundance in % of all proteins in the same sample,  [27] ) for semiquantitative comparisons between samples from different nutrient conditions. Tests for differential expression were performed using Perseus  [28]  v. 1. 6. 1. 1 with Welchs t test (permutation-based FDR 0. 05). The mass spectrometry proteomics data are available through the ProteomeXchange Consortium (http:// proteomecentral.
Protein crystallization and structure solution Crystals of FbGH17A were obtained by hanging drop vapor diffusion of the protein with 12. 3 mg mL -1 mixed 1:1 with a "well solution" (0. 03 M MgCl 2 , 0. 1 M MOPS (pH 7), 9% PEG8K) supplemented with 15% ethylene glycol. The crystals were cryoprotected prior to freezing in the "well solution" supplemented with ethylene glycol to a final concentration of 30%. Crystals were frozen by flash freezing in liquid nitrogen in nylon loops. X-ray diffraction data were collected at the DESY P11 beamline. The structure was solved by molecular replacement using PHASER in the phenix suite  [30, 31]  using the pdb 4wtp  [32]. The model was built using BUCCANEER  [33]  and Coot, refined in REFMAC5  [34] , and validated and deposited with pdb code 6FCG.
Acknowledgements We are grateful to  Jana Matulla  for technical assistance,  Sebastian Grund  for mass spectrometry analyses,  Carol Arnosti  and her laboratory for producing the FLA-labeled laminarin, and  Nicolas Terrapon  for critical comments on the putative function of selected PUL-encoded proteins. We thank the crew of the  Biological Institute Helgoland of the Alfred-Wegener-Institute, especially Antje Wichels , for their excellent logistic support during our sampling campaigns at the Kabeltonne Helgoland from 2009 until 2012. The  Federal Ministry of Education and Research (BMBF)  funded parts of this work within the " Microbial Interactions in Marine Systems " project ( MIMAS  project  03F0480A ). The work was also financially supported by the  DFG  in the framework of the research unit  FOR2406 "Proteogenomics of Marine Polysaccharide Utilization" (POMPU ) by grants of  R.
Besides oxygen level conditions, we also manipulated whether maternal generations received a reliable or an unreliable light cue whenever offspring generations were exposed to anoxia. Populations from both treatments were paired to face the same sequence of oxygen level conditions over the 60 generations (see next section). Here we only use the light cue a nuisance parameter. C. elegans are sensitive to blue light  (Ward et al. , 2008). Petri plate rack holders (Starsted) were fitted with several strips of blue-light LED (Nichia NS6B083T and NSPB300B) in order for individuals inside the plates to have uniform light exposure (Figure  S2 ). 48h after L1 seed blue light was 0. 5 second flashed every 2 seconds during 12h, a period when hermaphrodites were expected to be undergoing oogenesis. A computer with dedicated software (LUCS) controlled light exposure for all plates at the same time, with plates that were not exposed to blue light being kept in a separate incubator.
In our statistical treatment we use the measured growth factor to infer the parameters that determine population viability. The experiments were run in two different "blocks", each defined by the GA250 thawing date  (2012 and 2015)  and by the location where the experiments were done (Lisbon and Paris). A random id was assigned to each population to avoid potential bias during handling. The growth factor was measured by the same experimenter (SD). Data from populations U1-U8 was previously presented in Figure  3B  of  Dey et al. (2016). A total of n=2128 observations were available for analysis (Figure  1 ).
Model validation We performed two types of model validation, both employing posterior predictive fitting, cf. (Gelman et al. , 2013). First, we performed posterior predictive plot analysis using the aggregate statistic of geometric mean population growth over the experimental sequences. We used this method to compare the alternative models of transgenerational inheritance to the data from which the parameters were inferred. This method allows one to identify models that miss key features of the dataset, but does not assess the sensitivity of the fit to the specific data used. We generated distribution plots of the population geometric mean fitness for AME models 1, 2, and 4 as well as for the carryover model. These were compared to the empirically observed geometric mean population growth.
For three days these plates were maintained under our regular lab protocols, except that starting 48h after L1 seeding, and for a period of 12h, maternal hermaphrodites were exposed to a reliable or unreliable blue light cue of offspring anoxia conditions (right panel). Figure  S11 : The environment specific growth rate outcomes of the AME and carryover models. We considered a repeating sequence of N-N-A-A environments and sampled parameters 500 times from the posterior distribution. We calculated the growth factor after one or two generations in Anoxia and Normoxia (A1, A2, N1, N2). Overlaid are the empirically observed distributions of the growth factors, where we have grouped all observations based on whether it is the first generation in that environment. Thus the empirical data have heterogeneity in the history earlier than the maternal generation which is not present in the simulated data.
Acknowledgments We thank  T. Vale  for building the LED plate-racks and writing LUCS,  P. Sandner  for preliminary light sensitivity assays,  I. M. Chelo ,  P. Ibañez ,  H. Gendrot ,  J. Nedli ,  S. Nunes  and  S. Santos  for help with worm handling, and  L. -M. Chevin ,  V. Colot ,  M. -A. Félix ,  L. Frézal ,  G. Lepère  and  L. Noble  for discussion. Data analysis was done at the  Center for Scientific Computing at UC Santa Barbara , an National Science.
This catalytic aspartate corresponds to D610 in Thermus aquaticus Taq DNA polymerase I which interacts with the incoming dNTP through a Mg 2+ ion and stabilizes the transition state that leads to new phosphodiester bond formation  (32). This sequence motif (DYSQLELR) is exceptionally well conserved in Afamily polymerases and within the Pol I family as described in the Supplementary Figure  S1  for Human pol (PDB: 4X0P), Human pol (PDB: 4XVK), Human mitochondrial pol ␥ (PDB: 3IKM), Plasmodium falciparum DNA pol (PDB: 5DKT), Phage T7 DNA pol (PDB: 1T7P), Klenow fragment of E. coli DNA pol I (PDB: 1D8Y), Bacillus stearothermophilus DNA pol I (PDB: 1L3S) and T. aquaticus (Taq) DNA pol I (PDB: 1TAQ). Previous studies in Taq DNA pol I showed that mutation of the catalytic aspartate of Motif A (D610) completely abolished the polymerase activity and was immutable  (33)  while libraries of mutants targeted on the other 13 residues (605 to 617) of motif A showed that some positions tolerated a wide spectrum of substitutions (A608, I614, R617).
2C ). We used energy dispersive spectroscopy (EDS) to investigate the elemental composition of the protrusions. Mapping the elemental distribution in the sample, as well as collecting spectra from designated areas, showed that the protrusions are rich in phosphorus, calcium, and potassium (Fig. 2 D  and E ). This composition is similar to that reported for the Ca-P bodies of E. huxleyi except for the higher potassium content and the absence of magnesium and sodium  (18). However, as the Ca-P bodies of E. huxleyi were characterized in resinembedded cells, their elemental composition may have been subjected to quantitative alterations. The Ca content and the spherical nature of the protrusions suggest that they are the Carich bodies seen in the cryoSXT datasets. The presence of multiple, randomly distributed Ca-P-rich bodies inside a single large compartment of P.
C. reinhardtii is a unicellular, noncalcifying, green alga, which is known to store Ca and P in acidocalcisomes  (6). We used cryoSXT to analyze intracellular Ca pools in C. reinhardtii. The tomography data acquired at 520 eV showed the known organellar components of C. reinhardtii cells in native organization and the presence of bodies containing strongly X-ray absorbing material (Fig. 5  A and B and Movie S2). Spectromicroscopy at the Ca L-edge showed this material to be a calcium-rich phase (Fig. 5C ). This result demonstrates the importance of spectromicroscopy for the interpretation of soft X-ray tomography data, as these strongly X-ray-absorbing bodies were previously interpreted to be lipid bodies  (28). The calcium-rich bodies are located inside larger membrane-bound compartments (Fig.
The visualization and segmentation of the final volumes were carried out using Amira 3D software. For a Ca L 2,3 -edge energy scan, the same field of view was repeatedly imaged under changing X-ray energies starting at 344 eV and going up to 360 eV in 0. 1-eV steps. Calcium localization in the samples was visualized by subtracting the 342-eV image from the 353. 2-eV image. CryoSEM and EDS. Four-hour recalcifying P. carterae cells were pelleted and resuspended in 10% Dextran in seawater. Then 2 μL of cells were sandwiched between two metal discs (3-mm diameter, 0. 1-mm cavities), highpressure frozen (HPM10; Bal-Tec), and freeze-fractured (BAF 60; Leica Microsystems). Samples were imaged at -120 °C in an Ultra 55 SEM (Zeiss) by using a secondary electron in-lens detector and a backscattered electron in-lens detector.
ACKNOWLEDGMENTS. We thank  Prof. Lia Addadi  ( Weizmann Institute of Science ) for her help with the cryoSEM imaging,  Stefanie Seeger  [ Max-Planck Institute of Molecular Plant Physiology (MPI-MP)]  for providing Chlamydomonas, and  Alastair Skeffington  ( MPI-MP ) for comments on the manuscript. X-ray microscopy was conducted at the MISTRAL beamline at  ALBA Synchrotron, Barcelona , and received funding from the  European Community 's  Seventh Framework Program  (FP7/2007-2013) under BioStruct-X (Grant Agreement 283570). This research was supported by the  Max-Planck Society  and  German Research Foundation  Grants  Sche1637/3-1  (to A. Scheffel) and  FA835/9-1  (to D. F. ). A. Scheffel acknowledges support from the  Boehringer Ingelheim Foundation. A. G. was supported by an Alexander von Humboldt postdoctoral fellowship.
In addition, there are several major hurdles in metagenomic analysis of the human gut phageome that need to be resolved. In particular, conflicting data has been reported by different groups on the qualitative and quantitative composition of "healthy" human gut phageomes depending on the protocol used. Published phageome datasets are often compromised by variable levels of bacterial sequence contamination  [31]. Also, many of the reported methods for VLP extraction include protocols (such as CsCl density gradient centrifugation and tangential flow filtration) that are laborious, poorly reproducible, require expensive equipment and are not compatible with a high-throughput. The majority of recently published viral metagenomic studies of the human gut and other body sites have used similar approaches for enrichment of viral particles from biological samples and to remove large amounts of contaminating DNA and RNA of bacterial and eukaryotic origin (Additional file 1: Table  S1 ).
1a ). Nucleic acid yields varied in a wide range from 60. 5 ng to 4. 3 μg (median yield 533 ng) of DNA from the same starting amount of 500 mg of faeces. Obtained samples were then subjected to reverse transcriptase treatment and MDA using φ29 polymerase with the idea to convert any copurified RNA and ssDNA molecules into amplified dsDNA, suitable for use as a starting material in Illumina shotgun library preparation protocols. As a result of various treatment regimens, a total of 81 shotgun libraries were sequenced using Illumina MiSeq platform (2 × 300 nt reads) producing 263,641,845 quality-filtered trimmed reads (minimal Phred score of 30, 119. 27 Gb of quality-filtered sequence data) with a median read count of 3,170,798 per sample. The dataset was filtered to remove sporadic reads aligning to human genomic DNA.
The extent of bacterial and eukaryotic chromosomal DNA contamination in quality-filtered and trimmed reads was estimated by aligning quality-filtered reads to a database of 16S, 23S, 18S, 28S, 5S and 5. 8S rRNA sequences of bacterial, archaeal and eukaryotic origin. The median percentage of reads corresponding to ribosomal RNA genes per sample was 0. 04% (interquartile range 0. 06%), of which an overwhelming majority were   S2 ). We also employed alignment of reads to a database of 549-567 bp segments of a highly conserved bacterial gene cpn60, generally present in a single copy per genome and often employed as an alternative to 16S rRNA taxonomic marker in bacteria  [43]. Median fraction of reads aligned to this gene segment was 0. 00077% (IQR = 0. 00182%; Additional file 3: Figure  S1 ).
Assembly of phage genomic contigs In this study, we employed an assembly-based approach instead of the more often used closed-reference database approach for classifying Illumina reads. Processed reads were assembled into contigs, individually for each sample and across all samples in the study, yielding 88,310 contigs of length greater than 1 kb. Duplicate and highly related (> 90% of identity) contigs were removed across all samples in such a way that the longer contig from each pair of homologues survived. During further processing steps, in order to select viral contigs and remove as much bacterial DNA contamination as possible, contigs were picked which fulfil at least one of the following criteria: (a) predicted as viral by Virsorter package  [44] ; (b) having sufficient similarity (50% identity over 90% of contig length) to known sequences in the viral section of NCBI RefSeq database  [45, 46] ; (c) being circular; and (d) being > 3 kb with coverage of at least 10×, and generating no alignments > 100 nucleotides (with e value < 1e-10) to the NCBI 'nt' database.