dataesr/scientific-paragraphs-categorization huggingface dataset:
Thus, GRA can be used as a sea-level proxy. To use GRA as a proxy, noise was first removed from the composite onboard GRA data  (Tada et al. 2015b (Tada et al. , 2015c)). GRA values below the specific gravity of seawater (1. 02 g cm -3 ) were discarded, as were data corresponding to tephra and cracked intervals. The filtered GRA profiles for sites U1425 and U1430 are presented in Additional file 2. We next performed a spectral analysis of the filtered GRA data to assess their fit to our tuned biostratigraphic age model using REDFIT software  (Schulz and Mudelsee 2002). We generated Gaussian-filtered GRA time-series for both sites and assessed their correlation with temporal variations of Earth's orbital parameters, including long-eccentricity cycles (405 kyr) and short-eccentricity cycles (100 kyr) calculated by  Laskar et al.
(2004). For the Gaussian band-pass filtering, we used AnalySeries 2. 0. 8 software  (Paillard et al. 1996)  to sample evenly spaced data points from unevenly spaced original data. Band-pass filters were centered at 0. 0025 kyr -1 (0. 0005 kyr -1 bandwidth) and at 0. 01 kyr -1 (0. 003 kyr -1 bandwidth) to extract 405-and 100-kyr cycles, respectively. Tuning assumed no phase lag between GRA variability and orbital parameters, because the response time of an ice sheet is not known in this time interval  (Holbourn et al. 2007). To further improve our orbitally tuned age model, we tuned the GRA data from site U1425 to the oxygen isotope record, which is sensitive to sea-level fluctuation. The site U1425 record was chosen for its continuity and for its wide range of variability, which aided the tuning process.
Comparison of physical properties with sea-level change After adjusting our GRA records on the basis of our short-eccentricity-tuned age model, we compared them to a previously published sea-level record. Miller et al. (2005)  compiled two high-resolution benthic oxygen isotope records covering the last 9 Myr from ODP site 846 in the equatorial Pacific  (Shackleton et al. 1995)  and ODP site 982 in the northern North Atlantic  (Hodell et al. 2001)  and converted them to a record of eustatic sea level, using a calibration ratio of 0. 1‰/10 m. In this record, sea-level fluctuations over glacial-interglacial cycles were roughly 40 m before ~6 Ma, gradually increased to about 100 m by 1. 5 Ma, then remained at that amplitude until the present  (Miller et al. 2005). For this comparison, we compiled the GRA dataset from both sites, then resampled it and the sea-level record of  Miller et al.
(2005)  at 100-kyr intervals between 9 and 1. 45 Ma. The result (Fig. 7 ) shows a fair correlation (r = 0. 63) between the two datasets for this period. Between 6. 6 and 3. 6 Ma, the GRA amplitudes were small and the estimated sea levels were mostly restricted between 10 and -20 m. These lower values of estimated sea-level changes may be reflected in the low amplitude of the GRA dataset, and the correlation between GRA and estimated sea-level amplitude was slightly stronger when we excluded the data from 6. 6 to 3. 6 Ma (r = 0. 65). DeVleeschouwer et al. (  2017 ) compiled a high-resolution benthic oxygen isotope record for the entire Neogene and Quaternary from multiple drill sites in the Atlantic, eastern equatorial Pacific, and South China Sea. We used this record to compare the variabilities of NGR and GRA at sites U1425 and U1430 with the oxygen isotope record of benthic foraminifers since 12 Ma.
The GRA and NGR data were well correlated with the benthic oxygen isotope record before 8 Ma and after 3. 3 Ma (Fig. 8 ), including the last 1. 45 Ma  (Tada et al. 2018) ; however, the correlation was unclear between 8 and 3. 3 Ma, when both datasets had orbital-scale variations of small amplitude. In the benthic oxygen isotope record of  Miller et al. (1991) , excursions Mi-5 to Mi-7 occurred during the time interval covered by the Japan Sea sediments examined in this study. In their orbitally tuned age model based on Fe signals in South Atlantic shallow marine sediments,  Westerhold et al. (2005)  recognized the Mi-5 and Mi-6 events at 11. 7 and 10. 7-10. 4 Ma, respectively. At site U1430, we recognized GRA and NGR maxima corresponding to these two events at 11. 7 and 10. 6 Ma, respectively (Fig.
2015a Tada et al. , 2015c)) , which range in age from 9. 3 to 7. 6 Ma. The hiatus at site U1430 coincides in depth with a major regional unconformity on seismic profiles (MB3 unconformity in  Horozal et al. 2017 ) that extends over much of the eastern South Korea plateau where site U1430 was drilled. The origin of this unconformity is unclear. Watanabe (1994)  and  Horozal et al. (2017)  attributed it to erosion by bottom currents or a brief episode of tectonic uplift. Whatever its origin, this hiatus must reflect a local, basin-scale event because there are no drastic changes in LSRs in this time interval in other Japan Sea cores. 7  Relationship between GRA and estimated sea level. GRA data are from sites U1425 and U1430 and resampled every 100 kyr. Sea level is converted from oxygen isotope values using a calibration ratio of 0.
1‰/10 m  (Miller et al. 2005). Estimated sea level is also evenly sampled every 100 kyr. Regression line is applied to the all data during the last 9 Myr. Red circles are the data from 6. 6 to 3. 6 Ma Fig. 8  Comparison of NGR, GRA, and LSR with composite benthic isotope curve from DeVleeschouwer et al. (2017) (purple). Vertical green lines indicate good correlation between physical properties and oxygen isotope, while yellow lines are indicated that correlation is unclear. Marine isotope stage number from  Lisiecki and Raymo (2005)  and  Miller et al. (1991)  is also shown in the top panel. Variations at site U1425 are shown as blue and U1430 as red. Lithological unit  (Tada et al. 2015b (Tada et al. , 2015c) )  and paleoceanographic condition stage number  (Tada 1994)   Tada et al. (2015b Tada et al.
( , 2015c)) , and 61. 14 m at site U1430, the same depth specified in the original definition. The age of this boundary is 2. 61 Ma according to our revised age model (Fig. 8 ). During deposition of unit IB, NGR and GRA fluctuated strongly, as they did in unit IA, but at a lower frequency than in unit IA. In unit II, the boundary between subunits IIA and IIB is defined by a downward increase in diatom content, which is recorded as a downward decrease in NGR or GRA at 137. 34 m at site U1425 (4. 14 Ma in our age model) and 74. 42 m at site U1430 (4. 04 Ma in our age model). NGR data do not show a clear downward decrease at 74. 42 m at site U1430, but this probably reflects the proximity of an NGR peak from a glauconite layer (e. g. ,  Tada et al. 2015c ) at ~78. 8-79. 7 m. The age of the boundary differs slightly between the two sites; however, the age of the upper hiatus at site U1430 is based on a biodatum, which has an error of about ± 0.
Methods The samples have been prepared and analyzed using photographs, polished sections, thin sections, and computed tomography (CT) scans. The usual qualitative observations on polished surfaces and thin sections have been supplemented by morphometric measurements. Nine characters were measured on photographs by the lead author using the measurement software Canvas 9 (see Table  2 ); these characters are: great calicular diameter (Gd): the longest linear length passing across the center of the calice; small calicular diameter (Sd): the shortest linear length passing across the center of the calice; number of calicular septa (Ns): septa counted along the corallite periphery; homogeneous septal density (hsd): in order to compare all samples with a homogeneous parameter, the septal density of only S1 and S2 (first and second septal size orders) has been measured over a 5 mm distance at the periphery of the calice; length of S1 (lS1): measurement of the longest and the shortest septa of the first size order S1; length of S2 (lS2): measurement of the longest and the shortest S2; length of S3 (lS3): measurement of the longest and the shortest S3; greater pseudocolumella diameter (dp): the longest linear length passing across the center of the calice from the edges of the pseudocolumella in transverse section; number of pseudocolumellar septa (nps): septa counted along the pseudocolumella periphery.
Middle of variation range value for length of S3 (mlS3). Finally, two other pieces of information have been added to the database. Sampling outcrop (Os)-some numbers have been allocated to different sampling zones for each sample: 1, Amellagou plain; 2, MNHN; 3, Dades Valley; 4, Jebel Taabest; 5, Beni Tadjit (Menchikoff collection); 6, Jebel Serdrar; 7, Koudiat Ech Chehem; 8, Taililout. Pseudocolumella shape (ps): the two main shapes of pseudocolumella observed have been labelled with associated numbers and each sample has been associated with an apparent pseudocolumella shape. Examples of pseudocolumella observed in transverse section among the samples are presented in Appendix 1. Measurements have been used to perform univariate and multivariate statistical analysis, in order to distinguish characters and identify poten-TABLE 2.
ACKNOWLEDGMENTS We would like to thank  S. Charbonnier  and  J. Pacaud  for their help in the collections of MNHN. Our field campaign in Middle Atlas has been successfully leaded by  A. Charrière  and  H. El Arabi , we express our profound appreciation for that. We are equally grateful to  M. Ousri  and his family for the hospitality and help in the field in Morocco. We express gratitude to our friend and colleague  R. Martini  for her collaboration in this work and also to  P. Neige  and  C. Meister  for their precious help with the ammonite identifications. J. Sterpenich  and  C. Morlot  are thanked for carrying out CT-Scan analysis. R. Vasseur would like to acknowledge  A. Flammang  and  J. Moine  from the laboratory of lithopreparation of Georessources, as well as  C. Delangle  and the association  Terrae Genesis  for their help in the production of thin sections.
ACKNOWLEDGMENTS Authors would like to thank  M. Misiak ,  G. Paz  and  M. Endo  for fruitful discussions. A. I. is supported by the  Japan Society for the Promotion of Science (JSPS)  Grant No. 16H03968. We thank the  KEKB group  for the excellent operation of the accelerator; the  KEK cryogenics group  for the efficient operation of the solenoid; and the  KEK computer group , the  National Institute of Informatics , and the  Pacific Northwest National Laboratory (PNNL) Environmental Molecular Sciences Laboratory (EMSL) computing group  for valuable computing and  Science Information NETwork 5  ( SINET5 ) network support. We acknowledge support from the  Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan , the  Japan Society for the Promotion of Science (JSPS) , and the  Tau-Lepton Physics Research Center of Nagoya University ; the  Australian Research Council ;  Austrian Science Fund  under Grant No.
| Study population and data collection A. Predictive model development: Medical records of cats were retrospectively reviewed between 2008 and 2016 at the University of Illinois Veterinary Teaching Hospital. Cats were included if they had a measurement of ionized calcium concentration, a serum biochemistry panel (creatinine, blood urea nitrogen [BUN], total protein, albumin, globulin, tCa, phosphorus, sodium, potassium, chloride, glucose, alkaline phosphatase [ALP], alanine transferase, gamma-glutamyltransferase [GGT], total bilirubin, cholesterol, triglycerides, and bicarbonate), and a T4 level, all performed within 24 hours of each other. Cats were excluded if any laboratory values were missing. Ionized calcium concentration was measured by sampling 0. 4 mL of whole blood that was placed directly into a lithium heparin-coated plastic tube containing <15 USP units of heparin/mL of blood.
Eligibility criteria were the use of a different biochemistry analyzer than the ones used for model development, and availability of miCa and of the predictors required for piCa calculation. If only one predictor was not available, eligibility would still be considered if the missing predictor had low contribution to the prediction (defined by a generalized crossvalidation statistics [GCV] < 10 in Table  3  and a small range of miCa variation on the corresponding graph on Figure  1 ). As the institution fulfilled eligibility criteria, cats were retrospectively selected from the Royal Veterinary College database from 2008 to 2018. Ionized calcium concentration was measured on nonheparinized whole blood immediately after venipuncture by a point-of-care analyzer (i-STAT 1, Abbott, Princeton, New Jersey).
| DISCUSSION In this study, a MARS model was created to predict serum ionized calcium in cats and was tested in two different datasets, from two different countries. The purpose of the study was to calculate piCa by measurements universally available; the variables included in the study were all easily obtained and readily available. Similar to the analogous dog model, the variables that had a major impact on miCa variations in cats included tCa, albumin, and chloride; however, there was also variation associated with age, creatinine, and potassium levels. Unlike in dogs, cholesterol, BUN, BCS, and GGT were also associated with miCa changes. For tCa, chloride, and albumin, the relationship with miCa was relatively similar to what was described in dogs. 4 A previous study found a weaker relationship between tCa and albumin in cats compared to dogs,  11  which might explain why miCa was affected only with increased albumin levels.
7%) versus 191 cats in the test set (prevalence: 29. 3%). The small number of hypocalcemic cats in the external set likely impacted the diagnostic performance assessment, as reflected by the large difference in terms of diagnostic discordance between the test set (diagnostic discordance between piCa or tCa and miCa around 25-27%) and the external set (diagnostic discordance around 3-4%). In our study, the training set and the test set were not randomly extracted from the same population of cats. The cats of both sets are different in several ways, as those included in the training set all had T4 measurement performed and were therefore older than the cats of the test set. Testing a predictive model from a dataset that comes from a population that is different from the data used to build the model is called extrapolation, as opposed to interpolation.
Methods This prospective, multicentric, observational study was conducted in two tertiary care retina practices. The Institutional Review Board (IRB)/Ethics Committee of Saint Louis Hospital (Paris) approval was obtained, and digital data management was declared and approved by a French national committee (Commission Nationale de l'Informatique et des Libertés), as required by the French law. The study was also registered in the database of the National Institutes of Health (NIH) on clinicaltrials. gov (identifier no. NCT01080898). All patients signed a consent form for the use of their data.
Data Collection Only data obtained at the first examination were used, including CFP, SD-OCT, and FA. The study did not interfere with patient management, which was at the investigator's discretion, regardless of the subsequent interpretation of imaging data by the readers. In practice, imaging data of each patient were duplicated, anonymized, and recorded in a secured computer for further analysis. Color fundus photography. The Topcon TRC 50 DX was used in the two inclusion centers to obtain CFP centered on the macula after pupil dilation. Spectral domain optical coherence tomography. The Cirrus 4000 OCT (Carl Zeiss Meditec, Dublin, CA) was used to acquire a macular cube (128 lines • 512 pixels) and horizontal and vertical 5-line raster scans spaced 75 mm apart centered on the fovea, corresponding to our routine practice.
This study has some limitations. Each reader had access to CFP as a surrogate to biomicroscopic fundus examination to be close to the current clinical practice. However, it was not stereophotography, which would have allowed clinicians to view retinal thickness and macular edema. The diagnosis was simply based on a consensus opinion because no follow-up data were included in this study. The reference was purely qualitative because we did not try to quantify any CNV feature. We did not follow the procedures of a reading center,  29  but rather remained as close as possible to the current practice: the reading was made by retina specialists involved in the management of exudative AMD and relied on their clinical expertise. The study was performed using the Cirrus 4000 spectral domain OCT. Results could have been different with a device including eye tracking and averaging.
Analysis All interviews were audio-recorded and transcribed verbatim, and notes were taken in the interview setting. Nvivo, a software package that is used to organize, analyze and find insights in qualitative data, was used to facilitate data management. 21 The five steps in framework analysis were followed for analysis: familiarization, identifying a thematic framework, indexing, charting, mapping, and interpretation. 22 Each audio recording was listened to at least twice while checking for the accuracy of the transcripts to assess their validity. Line by line coding was used to generate initial ideas that were later built into a framework. Two of the researchers (HO-K and KP) independently coded a sample of the transcripts to ascertain the level of agreement in the coding matrices after which the rest of the transcripts were coded by HO-K and shared between all researchers (authors) and discussed.
Whole HPV16 genome sequencing All HPV16-positive DNA samples from the above described studies were processed according to the same protocol in the Cancer Genomics laboratory, Leidos Biomedical Research, Inc. , Frederick, MD. A custom Thermo Fisher Ion Torrent AmpliSeq HPV16 panel approach was used to amplify the entire 7906 bp HPV16 genome, as previously reported in detail  [16]. The next-generation sequencing assay used the Ion Torrent Proton and a custom HPV16 Ion Ampliseq panel of 47 multiplexed primer sets. Custom overlapping degenerate primers were designed to cover the entire viral genomes for all HPV16 variant lineages. Raw sequencing reads were quality and adaptor trimmed using the Torrent Suite Software and aligned to the HPV16 reference sequence (7906 bp) from GenBank (NC_001526.
A large proportion of ICO samples failed sequencing due to the older FFPE-derived DNA being too degraded for amplification. We used these stringent quality control thresholds to minimize sequencing errors in the dataset for analysis. ADC, adenocarcinoma/adenosquamous cell carcinoma; CIN, cervical intraepithelial neoplasia; HPV, human papillomavirus; HSIL, high-grade squamous intraepithelial lesion; SCC, squamous cell carcinoma. a Not included in case: control analysis (Table  2 ). b Not included in analysis by histological type of cancer (Table  3 ).
Acknowledgements The members of the  IARC HPV Variant Study Group include current/previous IARC  staff ( N. Munoz ,  R. Herrero ,  X. Bosch ,  S. Franceschi ,  M. Tommasino ,  T. Gheit ) and local study coordinators in the following countries: Algeria ( D. Hammouda ),  Argentina (D. Loria, E. Matos), Benin (E. Alihonou) ,  Bolivia  ( J. L. Rios-Dalenz ),  Brazil  ( J. Eluf-Neto ),  Canada (P. Ghadirian), China (Qiao YL) ,  Chile  ( C. Ferreccio ,  A. Luzoro ,  J. M. Ojeda ,  R. Prado ),  Colombia  ( N. Aristizabal ,  L. A. Tafur ,  M. Molano , H. Posso),  Cuba  ( M. Torroella ),  Georgia  ( T. Alibegashvili ,  D. Kordzaia ),  Guinea  ( N. Keita ,  M. Koulibaly ),  India  ( T. Rajkumar ,  R. Rajkumar ),  South Korea  ( D. -H. Lee ,  H. R. Shin ),  Mali (S. Bayo), Morocco (N. Chaouki) ,  Nigeria  ( J.
We recorded the demographic data (age and gender) and the cardiovascular risk factors (active or discontinued smoking, insulin dependent or not diabetes mellitus, arterial hypertension (HBP), dyslipidemia), coronary artery disease (previous myocardial revascularization with stent or bypass), impaired renal function (clearance < 60 mL/min according to the method of Cockroft and Gault), the need for dialysis or not, heart failure, chronic obstructive bronchopneumopathy (COBP) scored higher than 1 according to the Gold classification,  10  and the presence of peripheral arterial disease (PAD) treated by surgery or not. We collected the symptoms of mesenteric ischemia: abdominal pain, postprandial pain and weight loss, and we recorded the use of perioperative parenteral nutrition. We also collected the type of bypass carried out (anterograde or retrograde) for open surgery, and the number of revascularized arteries as well as the use of stents in case of endovascular treatment.
Statistical analysis The statistical analysis was carried out with the SAS software (version 9. 4; SAS Institute, Cary, NC, USA). The data are presented as mean (standard deviation) and number (percentage). The Fisher exact and the Chi² tests were applied to compare qualitative variables. The Student's t test was used for quantitative variables. The survival analysis was carried out using the Kaplan Meier method with a log-rank test. p < 0. 05 was considered statistically significant.
Several publications reported a lower immediate morbi-mortality with endovascular treatment compared with open surgery. 14 As such, a retrospective study conducted from the "National Inpatient Sample" database included 15. 475 patients treated for chronic mesenteric ischemia between 2000 and 2014. Seventy percent of the patients had been treated by endovascular route and 29. 4% by open surgery. 15 In-hospital mortality after endovascular treatment was 2. 4% vs. 8. 7% for open surgery. However the long term results appear better with open surgery. 16 In our experience the proportions of patients treated by endovascular and open surgery were similar in the two groups, with 52. 6% and 56. 3% of the patients treated by endovascular route in the malnourished the non-malnourished groups, respectively (p=0.
However, clinicians usually have access to only minimal, if any, information on the vascular properties of their patients. Our study presents experimental data of continuous invasive arterial pressure recorded during AA repair surgery, before and after clamping the abdominal aorta. In order to enhance the data acquired from routine monitoring studies, we introduced a parameter estimation strategy, based on the experimental measurements, to identify valuable information on vascular mechanics that is otherwise difficult to obtain. Parameter estimation can also allow following the evolution of a disease in a minimally invasive way. A common parameter estimation technique is the Kalman filter (  [44] ,  [45] ) developed to estimate the elastic properties of arterial vessels and the values of terminal boundary condition coefficients  [46].
| Experimental data acquisition As stated above, we recorded arterial pressure signals of a patient undergoing an abdominal aneurysm (AA) repair intervention that required aortic cross-clamping at the Hôpital Universitaire Pitié-Salpétrière in Paris, France. We obtained the continuous and invasive pressure data with a fluid-filled catheter from the right radial artery of the patient during the surgery. The use of invasive arterial pressure measurements during this type of surgery is part of the surgical protocol and, therefore, routine clinical practice. The recording of these pressure data does not modify the signal used for clinical monitoring nor presents additional risks for the patient during the surgery. To carry out the measurements, we used a disposable pressure transducer (TruWave, Edwards Lifescience R ).