dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition, the application of revised decay constants for 230 Th and 234 U  (Cheng et al. , 2000 (Cheng et al. , , 2013) )  has introduced systematic offsets among various sets of published U-series dates, further complicating data intercomparisons. We summarize below a proposed set of minimum data and metadata to serve as a community norm that, if provided when a dataset is published in a peer-reviewed journal article, will greatly aid in later reuse. We also encourage researchers to provide suggested additional items of information that would allow subsequent reanalysis. The guidelines in this paper arise out of consultation with end users and producers of U-series data over the course of several community-driven workshops. These discussions helped to define the need for this norm and provided guidance on how current data-reporting practices might be improved to leading practices that would support the needs of the wider community.
To facilitate data inter-comparisons, we advocate the use of SI units when possible for the reporting of all isotope abundances and sample masses, although application-specific modifications to the reported units are sometimes required to have reasonable numbers to present in tables. Units such as ppm (mg/g) and ppb (ng/g) for concentration and Bq/g (decays per second) or dpm (decays per minute) for specific activity are common in the U-series literature. Before the advent of mass spectrometry (primarily the 1960s through 1980s, but continuing even to today), U-series isotopes were measured by alpha, beta, or gamma counting. Decay counting provides direct measurement of isotope activities, which are convenient units for U-series geochronology applications. Mass spectrometric analysis, on the other hand, measures the number of atoms of each isotope of interest present in a specimen.
Uncertainties Uncertainties should be reported for all parameters and should be included in all figures and tables since they are of key importance when making interpretations of the data. Reporting and plotting all uncertainties at the 2s level is the common practice. When the type of uncertainty is clearly stated then useful comparisons among datasets can be made. We note that the term "uncertainty" represents the range of values within which the true value is asserted to lie and is therefore a more appropriate term to use in this context rather than the term "error", which typically refers to the difference between a measurement and its accepted or true value. It is important to state whether uncertainties on reported dates include uncertainties in decay constants. To assess the calculation of dates, we recommend including a brief description of the uncertainty propagation for the results of isotope analyses and the computed ages.
For example, the decay constants for both 230 Th and 234 U were updated in by  Cheng et al. (2000)  and again by  Cheng et al. (2013). This presents a situation where published U-series age data cannot be compared to newer ones without normalizing to the same set of decay constants. To perform this calculation requires the knowledge of how each activity ratio was derived. In the case of 230 Th/ 238 U, activity ratios are typically determined using a Th-U spike (thermal ionization mass spectrometry (TIMS) or multi-collector inductively coupled plasma mass spectrometry (MC-ICPMS)). The spike ratio, in turn, can be calibrated using a gravimetric reference material, or a secular equilibrium reference material, or a combination (average) of these two approaches. If the 230 Th/ 238 U ratio was determined using a spike that has been calibrated to a secular equilibrium reference material, then the activity ratio of that reference material is still 1, even if the decay constant for 230 Th or 238 U gets revised.
For example, alphacounting data were reported as 230 Th/ 234 U and 234 U/ 238 U, whereas mass spectrometry measurements used the convention of reporting 230 Th/ 238 U and 234 U/ 238 U. However, in some laboratories where the 230 Th isotope is measured relative to 234 U rather than 238 U on a mass spectrometer, 230 Th/ 234 U is reported in place of 230 Th/ 238 U. Because analytical protocols still vary between laboratories, this suggests two specific recommendations for reporting the isotope ratios of 238 U, 234 U and 230 Th. First, report the activity or atom ratios for the isotopes measured directly on the mass spectrometer along with their associated 2s analytical uncertainties. Second, give any unreported activity or atom ratios and uncertainties for 230 Th/ 238 U and 234 U/ 238 U if not directly measured.
Data archiving The preferred data archiving path follows the rigorous approaches developed over the last decade for geochemical and other geochronological analyses by major international data repositories such as those operated by the Interdisciplinary Earth Data Alliance (IEDA). The main components of this approach are unique sample identifiers that allow for both locating samples and amalgamating various sorts of data collected on the same sample, the use of standardized data schemas, naming conventions, extensible markup language (XML) and web services to exchange data among data generators, repositories, archives, and data manipulation software. Open access discoverability through various search approaches and interfaces is also crucial. While we do not advocate for a specific repository and associated cyber infrastructure, we will point out that EarthChem, a part of IEDA, is one such group that has developed and uses such cyberinfrastructure for geoscience applications, in close interaction with the IEDA Geochron database, for the preservation and serving of age data of all sorts.
This system (http://geochron. org) allows users to upload data in public or private modes, and users can invite other users to participate in a private group mode to view samples establishing a virtual space in which to share their samples and data. Within these first three modes, the user can update and change data sets as the analysis matures. There is a fourth mode where datasets become read-only and are published with a unique resource identifier (URI). Such datasets are also published to the EarthChem Library (http://www. earthchem. org/library), receive a DOI, and are archived in conjunction with the Columbia University Archives Digital Program.
Concluding remarks The intention of these recommending these practices for data reporting is to encourage researchers and journal editors to collectively improve the utility and longevity of U-series data. These ideals have not been routine practice in the past, and in fact have perhaps rarely been attained, but adopting these practices as a routine part of the workflow in each laboratory will enable enhanced data sharing and interpretation. Ultimately such practices will facilitate online archiving and reprocessing of data. As has been witnessed in the U-Pb community, these capabilities, in turn, allow for larger scale data interlaboratory comparisons and synoptic studies that will be drivers of new theories and research directions (e. g. ,  McKenzie et al. , 2016). While the initial transition to adopting these data reporting norms may require additional effort, the benefits in the long run will include a marked conservation of effort required to compile previously published data in a systematic and comparable way.
To assist in the implementation of these data reporting norms, opensource, platform-independent software is presently under development by a subset of the author team to support seamless data uploading to community database, calculations (date determination, isochrons, etc. ), visualizations (evolution diagrams, etc. ), anddmost relevant to this discussiondgeneration of data tables with templates that include all the required components proposed herein. While the development of this cyberinfrastructure is initially in response to user-based workshops, continued input from the community during the development stage is actively sought and will ultimately be a key factor for community buy-in. The main vehicle for continued conversation between the U-series community as well as those who are users of U-series data is a centralized website: www.
Acknowledgements This work was supported by the  National Science Foundation  (Award # ACI-1443037  to JB, AD, KR, NM) and the  Natural Environment Research Council  (Award #  NE/I013814/1  to NM, GMH, and DAR). We would like to thank the community for their engagement and discussion in a number of workshops, sponsored by  PALSEA  and  PALSEA2  (presently funded by  PAGES and INQUA) ,  NSF  (the EarthCube geochronology end-user workshop),.
aeruginosa PA14. OreR Wol2 (black) and OreR Wolþ (grey) were either (a) pricked with a needle dipped in PA14 culture (OD ¼ 1), or (b) left to feed on a PA14 culture (OD ¼ 25) or on a control solution of 5% sugar for 12 h. Survival was monitored for 24 h (systemic infection) or daily (oral infection). In systemic infections, 100% of control flies survived over the 24 h period. In orally exposed flies, control flies are shown as dotted lines. Each data point shown is the mean of 10 replicate groups of 10 flies; these data were analysed using a Cox proportional hazard model. rspb. royalsocietypublishing. org Proc. R. Soc. B 284: 20170809 rate than control flies exposed only to a sucrose solution (figure  1b ; 'infection status' effect, likelihood ratio x 2 ¼ 64. 27, d. f. ¼ 1, p , 0. 0001). Fly mortality during enteric infection was significantly affected by their Wolbachia status, but the extent of protection depended on fly sex (Wolbachia status Â sex interaction x 2 ¼ 8.
All patients were operated under general anesthesia using remifentanil combined with an ultrasound single-shot interscalenic block with ropivacaine (3 mg/kg). Data included age, sex, duration of hospitalisation, analgesic treatments, adverse events (AE) graded from 1 to 2, VAS (0e10) at rest, morphine consumption and nurse adherence to protocol. Comparison between groups used parametric and non parametric Wilcoxon (p ¼ 0,0129) and Student tests (p ¼ 0,0119). Differences between groups were considered statistically significant if the significance levels were less than 0. 05. The whole patients were hospitalized for an average of 2 days. On awakening, most patients did not complain of pain (VAS ¼ 0 for 85. 7% patients in NP group versus 93. 5% patients in SP group; p value > 0. 05). The primary endpoint aimed to demonstrate an improvement in postoperative pain by comparing maximum pain intensity during the first postoperative 48 h from the PACU.
We also retrieved data in Arachnida, but did not find any suitable Echinoderm data set. Our single sponge (Porifera) data set yielded a ratio of mitochondrial to nuclear mutation rate lower than 1 (l mit /l nuc ¼ 0. 52), which is consistent with  Huang et al. (2008). Porifera were excluded from further analyses due to insufficient sample size (N ¼ 1). The final data sets comprised an average 38. 6 species, 1. 4 mitochondrial genes and 2. 1 nuclear genes.
Discussion High l Mit /l Nuc in Vertebrates Our analysis of 121 data sets encompassing 4,676 species of animals revealed extensive variation in l mit /l nuc among phyla of animals. Although somewhat continuous, this variation was mostly partitioned between vertebrates (with l mit /l nuc typically above 10) and nonvertebrates (with l mit /l nuc typically below 5). Our results confirm early reports, based on very small samples, of a similar order of magnitude for l mit and l nuc in nonvertebrate taxa  (Powell et al. 1986; Vawter and Brown 1986; Brower and DeSalle 1998). We also detected a few non-vertebrate taxa with a high l mit /l nuc , similar to that of vertebrates, but these are exceptions. Analyzing 28 data sets for which fossil calibrations were available, we estimated the per year mutation rate separately for mtDNA and nuDNA.
Despite this large variation, a strong taxonomic effect was detected, confirming that the variation in l mit /l nuc among taxonomic groups is not an artifact of gene sampling. Many of our Arachnida and Mollusca data sets all comprise a single nuclear locus, namely Histone H3. This might have influenced our result if third codon positions were particularly fast-evolving in this gene. However, in the bivalves phylogenomic data set, the l mit /l nuc ratio for histone H3 is 3. 6 which is higher than the mean l mit /l nuc (1. 8). This demonstrates that histone H3 is rather a slow evolving gene (leading an high l mit /l nuc ) compared to other nuclear protein-coding genes and that our results, if anything, underestimate the true effect.
Why Is l Mit /l Nuc Correlated to N e ? There is no obvious theoretical reason to expect a relationship between l mit /l nuc and effective population size. This partly explains why  Bazin et al. (2006)  did not consider mutation rate as a plausible confounding factor, in absence of large-scale data on l mit /l nuc. To gain insight into the causes of l mit /l nuc variation, we estimated absolute mutation rates per year. Our results indicate that both l mit and l nuc are variable among species and higher level taxa. The variation between vertebrates and nonvertebrates seems more pronounced for the nuclear genome than for the mitochondrial genome. Finally, l mit appears correlated to l nuc in vertebrates, suggesting that the per year mitochondrial and nuclear mutation rates are influenced by common determinants.
Multilocus Data sets We extracted all data sets from « Molecular Phylogenetics and Evolution » by systematically scanning the table of content between volume 62 (January 2012) and 97 (April 2016). All selected data sets have at least one mitochondrial gene and one nuclear gene. Any species represented by only nuclear or mitochondrial sequence were excluded. We also selected only one sequence per species, following the taxonomy adopted in the publications. This step aims at excluding polymorphism data from the data sets. The data sets including less than five species were excluded. The data sets were split in 12 taxonomical groups: Amphibia; Arachnida; Aves; Chondrichthyes; Crustacea; Insecta; Mammalia; Molluska; Porifera; Squamata; Teleostei; Testudines. Because the literature review was very time consuming, we limited the research to 20 data sets per taxonomical group.
Molecular Divergence Estimation Coding DNA Sequences (CDS) were extracted using custom made BioPython scripts  (Cock et al. 2009). Sequences were aligned gene by gene using MACSE  (Ranwez et al. 2011). Phylogenetic trees were inferred using RAxML with the substitution model GTRCAT  (Stamatakis 2006). One phylogeny per locus was inferred. This will avoid potential discordance between gene trees that could lead to a spurious excess of inferred substitutions produced by incomplete lineage sorting  (Mendes and Hahn 2016). Next, we extracted third codon positions in order to limit the effect of natural selection. Sites containing more than 20% of missing data were excluded. Molecular divergence was estimated using the BASEML program  (Yang 2007)  and the F84 substitution model without rate variation among sites.
Total third codon positions Divergence (TD) was estimated gene by gene by computing the sum of branch lengths. Assuming that all mutations are neutral at third codon positions, we have: TD ¼ l Â t; where l is mutation rate and t the divergence time. For every data set, the total divergence time is the same for the nuclear and mitochondrial phylogenies because the same set of species was analyzed for both markers. As a result, we are able to estimate the ratio of mitochondrial and nuclear mutation rate l mit /l nuc by computing the ratio of TD. When several mtDNA and/or nuDNA markers were available, we took the mean ratio across all mitochondrial versus nuclear pairs of markers. Besides third codon position analysis, we also calculated branch lengths in unit of per synonymous site synonymous substitutions using CODEML  (Yang 2007 ) and using 4-fold degenerated sites.
Polymorphism Data Mitochondrial and nuclear synonymous polymorphism (p mit and p nuc , respectively) were obtained from  Bazin et al. (2006) (Eric Bazin, pers. commun. ). We defined the mutationcorrected polymorphism, p mit *, as: p Ã mit ¼p mit l nuc =l mit l nuc /l mit being defined as the median l nuc /l mit of each taxonomical group of  Bazin et al. (2006). For 'Pisces' group, we used the median l nuc /l mit of the Teleostei and Chondrichthyes. Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals. doi:10. 1093/molbev/msx197 MBE Assuming neutrality and a balanced sex-ratio, p mit * is expected to be proportional to p nuc. p Ã mit ¼ N e l mit l nuc =l mit ¼ N e l nuc ¼ p nuc =4 Phylogenomic Data sets Four phylogenomic data sets were analyzed: two vertebrates (Birds and Primates) and two nonvertebrates (Drosophila and Bivalvia).
In birds, we used the alignment of  Jarvis et al. (2014). We focused on six species of passerines þ parrots: ((Melopsittacus, Nestor), Acanthisitta (Corvus, Geospiza, Taeniopygia)). In primates, alignments were obtained from the ORTHOMAM database (version 9, http://www. orthomam. univ-montp2. fr/; last accessed April 2016;  Douzery et al. 2014). The data set included 12 species: (((((((Homo, Pan), Gorilla), Pongo), Nomascus), ((Macaca, Papio), Chlorocebus)), Callithrix), Tarsius, (Otolemur, Microcebus)). The Bivalvia data sets were obtained from Gonz alez et al. (2015). We focused on the 11 species of Neoheterodontei: ((Cycladicama, Diplodonta), ((Mercenaria, (Glossus, Arctica)), (Corbicula, Cyrenoida))))))). Finally, the Drosophila data sets were obtained from  Romiguier et al. (2014). The phylogenetic relationship between the 12 species is ((((((D.
melanogaster,(D. Simulans,D. sechellia)),(D. erecta, D. yakuba)), D. ananassae), (D. pseudoobscura, D. persimilis)), D. willistoni), ((D. mojavensis, D. virilis), D. grimshawi)). Nucleotide alignments were available for all the data sets except for the Bivalvia in which only amino-acid alignments were produced. For these data sets, we extracted the nucleotide sequences from assembled transcriptomes  (Vanessa L. Gonzalez, pers. commun. ). Sequences were aligned gene by gene using MACSE  (Ranwez et al. 2011). Full mitochondrial genomes were available for birds, primates and Drosophila. For Bivalvia, we used only the Cytochrome Oxidase 1 gene. Mitochondrial sequences were aligned gene by gene using MACSE  (Ranwez et al. 2011). For all the data sets, alignments were cleaning using Gblocks option: Àt ¼ c Àb4 ¼ 5 Àb5 ¼ h  (Talavera and Castresana 2007)  and sites containing more than 20% of missing data were excluded.
Absolute Mutation Rates and Generation Times When they were available, fossil calibration points were extracted from the publications. We re-estimated a single phylogeny based on mitochondrial and nuclear sequences using RAxML with the substitution model GTRCAT partitioned by gene  (Stamatakis 2006). Molecular dating was performed gene by gene using MCMCTREE  (Yang 2007)  with the HKY85 þ Gamma model. The absolute mutation rate was computed as the average rate across genes. Generation times were approximated using age at sexual maturity or number of generations per year. For vertebrates, we mostly relied on the AnAge database (version 13,  Tacutu et al. 2012). For nonvertebrates, generation times were obtained from the literature and, in rare cases, from websites (see supplementary table S2, Supplementary Material online for details).
Acknowledgments This work is dedicated to the memory of Eric Bazin. We are grateful of  Vanessa L. Gonzalez  for provided the transcriptomes of Bivalvia species. We thank  Sylvain Gle  ´min and the anonymous reviewers for helpful discussion. This work was supported by  Agence Nationale de la Recherche  grants  ANR-15-CE12-0010  "DarkSideOfRecombination" to B. N. and N. G,  ANR-14-CE02-0002-01  " BirdIslandGenomic " to B. N and  ANR-10-BINF-01-01  " Ancestrome " to N. G. This is ISEM publication number ISEM  2017-141.
We present a global carbonyl sulfide (OCS) data set covering the period June 2002 to April 2012, derived from FTIR (Fourier transform infrared) limb emission spectra measured with the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on the ENVISAT satellite. The vertical resolution is 4-5 km in the height region 6-15 km and 15 at 40 km altitude. The total estimated error amounts to 40-50 pptv between 10 and 20 km and to 120 pptv at 40 km altitude. MIPAS OCS data show no systematic bias with respect to balloon observations, with deviations mostly below ±50 pptv. However, they are systematically higher than the OCS volume mixing ratios of the ACE-FTS instrument on SCISAT, with maximum deviations of up to 100 pptv in the altitude region 13-16 km. The data set of MIPAS OCS exhibits only moderate interannual variations and low interhemispheric differences.
Anthropogenic sources of atmospheric sulfur can be quantified rather accurately, but the characteristics of the natural sulfur cycle are still not sufficiently well known. One reason is the lack of widespread measurements of OCS to better constrain our knowledge on its sources and sinks. In this respect the comprehensive data set of MIPAS can give further insight on the global OCS distribution. Various scientific studies have been performed to quantify natural and anthropogenic sulfur emissions and sinks  (Eriksson, 1960; Junge, 1963; Robinson and Robbins, 1968; Kellogg et al. , 1972; Friend, 1973; Adams et al. , 1981; Andreae, 1990; Chin and Davis, 1993; Kuhn et al. , 1999). These authors reported strongly differing values, reflecting large uncertainties in determination of sulfur fluxes.
(2007)  did not find a significant trend in tropospheric OCS. Long time series of OCS are available from a few locations only. Ground-based FTIR measurements at the Jungfraujoch in Switzerland started in the mid-1980s  (Mahieu et al. , 2005). Balloon-borne observations by the MkIV FTIR spectrometer of the Jet Propulsion Laboratory  (Toon, 1991)  have been performed since 1989, with 23 launches mainly from Fort Sumner (New Mexico), Esrange (Sweden), and Fairbanks (Alaska). Since the year 2000, NOAA ESRL has performed flask measurements of OCS on a global network of about a dozen stations  (Montzka et al. , 2007). NOAA ESRL data are available at http://www. esrl. noaa. gov/gmd/hats/gases/OCS. html. A compilation of the latitudinal OCS distribution obtained by different measurement techniques (ground-based in situ and FTIR, balloon-borne FTIR, aircraft and ship measurements) has been presented by  Krysztofiak et al.
The MIPAS OCS data set has already been presented in  Glatthor et al. (2015a) , but focused on the signatures of tropical sources and sinks at the 250 hPa level only. In this paper we will give a more global overview of this data set. We will describe the MIPAS instrument, the OCS retrieval setup and the validation of the MIPAS OCS data. Then we will present time series of the OCS data set at different height levels and discuss latitudinal cross sections as well as seasonal variations. Horizontal distributions at different upper tropospheric pressure levels will indicate source and sink regions of OCS. The contributions of oceanic release and of uptake by tropical vegetation, which have already been presented in  Glatthor et al. (2015a) , will only be briefly discussed. Instead we will investigate the impact of biomass burning and meridional transport patterns visible in the tropopause region.