dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition, we quantify the modeled and observed trends in these weekend-weekday differences across this period of substantial NOX emissions reductions in the US. The model assessment is carried out using EPA's Air QUAlity TimE Series Project (EQUATES) CMAQ dataset. We identify 3 types of ozone trends occuring across the US: disappearing weekend effect, disappearing weekday effect, and no trend. The disappearing weekend effect occurs in a subset of large urban areas that were NOX -saturated (i. e. , VOC-limited) at the beginning of the analysis period but transitioned to mixed chemical regimes or NOX-limited conditions by the end of the analysis period. Nine areas have disappearing weekend effect trends in both datasets and with both metrics indicating strong agreement that they are shifting to more NOX-limited conditions: Milwaukee, Houston, Phoenix, Denver, Northern Wasatch Front, Southern Wasatch Front, Las Vegas, Los Angeles -San Bernardino County, Los Angeles -South Coast, and San Diego.
Since that time, multiple studies We extract CMAQ modeling data only for days and grid-cells with monitoring data such that both datasets are paired in time and location. Both datasets are subset to ozone monitors located within 51 of the 52 areas that were designated in 2018 as nonattainment for the 2015 O3 NAAQS (a list of areas is available in Tables  S1  and S2 )  (83 FR 25776; 83 FR 35136; 83 FR 52157). Because this analysis focuses on May-September data, we do not include data from the Uintah Basin nonattainment area for which violations of the NAAQS predominantly occur in winter months. Data are analyzed for the 18-year period of the EQUATES modeling dataset. We start by analyzing changes in ozone between weekends and weekdays pooled across all monitoring locations for each nonattainment area for 5-year rolling periods (i.
∆𝑂 3,𝐷𝑂𝑊 ̅̅̅̅̅̅̅̅̅̅ = 𝑂 3,𝑊𝐸 ̅̅̅̅̅̅̅ -𝑂 3,𝑊𝐷 ̅̅̅̅̅̅̅ (1) In this study we mainly focus on differences during the May-Sep ozone season. The Welch's t-test  (Welch, 1947)  is used to denote whether the mean WE-WD difference is statistically different from zero (p < 0. 05). All available ozone monitoring data and model output from all monitoring locations within each nonattainment area are included in the calculation, providing a measure of average behavior across each area. We also examine 24-hour average modeled formaldehyde and NOX concentrations at each of the ozone monitor locations to verify whether the model shows expected patterns of higher NOX on weekdays than on weekends and trends in these ozone precursors. Formaldehyde is used as an indicator of first-generation VOC reaction products for this purpose.
Areas with no trend are characterized by a lack of significance, as determined by the Mann-Kendall test. Trend types for all 51 areas based on observed and modeled datasets are shown in Figure 4 and 5. https://doi. org/10. 5194/egusphere-2023-1974 Preprint. Discussion started: 4 September 2023 c Author(s) 2023. CC BY 4. 0 License.
Study design and participants EU-SolidAct is an investigator-initiated, randomised adaptive platform trial for COVID-19 and emerging infectious diseases. Data capture is modular depending on epidemic waves and available resources. Bari-SolidAct is a double-blind, randomized placebo-controlled phase 3 trial investigating baricitinib for severe or critical COVID-19. The Master protocol (EU-SolidAct) and subprotocol (Bari-SolidAct) are available on euclinicaltrials. eu.
Ethical considerations The trial was conducted in accordance with ICH E6 (R2) Good Clinical Practice and the ethical principles of the Declaration of Helsinki. Informed consent by the study participant or legally authorised representative was given prior to inclusion in the study. This is an international trial conducted in several European countries, with approval from ethics committees and national competent authority in each country. The trial has been transferred to CTIS and is now accepted under the Clinical Trial Regulation (CTR), euclinicaltrials. eu (EU CT number 2022-500385-99-00). EU-SolidAct/Bari-SolidAct is also registered at www. clini caltr ials. gov (NCT04891133).
Statistical analysis Based on mortality rates in the DisCoVeRy  [13]  and NOR-Solidarity  [14]  trials, in addition to publicly available statistics from France, we assumed a 60-day mortality probability of 15% in the placebo group, and 10% in the baricitinib group. To show a difference between the treatment groups with a 5% significance level and a 90% power, we calculated that 924 evaluable participants were needed in each group. We planned to randomise 1900 participants in total to account for expected drop-out of 2. 7%. No formal interim analysis for efficacy was planned. Safety assessment by an independent Data Monitoring Committee (DMC) was planned after prespecified number of enrolled participants. Due to external evidence provided by the RECOVERY trial  [9] , and updated WHO guidelines recommending baricitinib for severe/critical COVID-19  [15] , the trial steering committee decided to stop enrolling immunocompetent participants from 7th March 2022, as the present trial was not expected to alter the overall accumulated evidence.
Kaplan-Meier curves up to day 61 (60 days after inclusion) were plotted. Additional information of analysis of secondary endpoints including safety are available in the Additional file 1: Online Appendix. The statistical analysis plan (Additional file 1: Online Appendix) was finalised and signed prior to database lock and opening of the randomisation list. All p values are 2-sided, with a significance level of 0. 05. The analyses were performed using SAS version 9. 4 (SAS Institute), and Stata SE version 13 (StataCorp).
Acknowledgements We thank site staff for recruitment and follow-up of participants, and the patients for participating in the trial. We thank  Morten Tandberg Eriksen  as representative of the sponsor (OUH). We also thank  Stefano Vella  (chair),  Stuart Pocock ,  Guanhua Du ,  Donata Medaglini ,  Mike Jacobs ,  Sylvie van der Werf ,  Phaik Yeong Cheah ,  Karen Barnes ,  Patrick Yeni ,  Tim Collier ,  Catia Marzolini  and.
Exposure experiments and sampling The UVB irradiances and daily doses applied in this study were based on the data collected in situ (egg-laying area; 48°43 0 40. 1 00 N, 03°58'28. 2 00 W, Coast of Roscoff, France) and the data available in different coastal areas  [27]  (electronic supplementary material, table  S1 ). Sepia officinalis eggs were exposed to the following experimental radiation conditions: PAR (400-700 nm, No-UVB) and PAR + UVA + UVB (280-700 nm). The former was used as the control, while the latter was subdivided into three different UVB doses: (1) low UVB (PAR + UVA + UVBL = UVB-L, 18. 6 µW cm -2 ), (2) moderate UVB (PAR + UVA + UVBM = UVB-M, 33. 4 µW cm -2 ), and (3) high UVB [PAR + UVA + UVBH = UVB-H, 57. 6 µW cm -2 )] (electronic supplementary material, table  S2 ). The spectral irradiance was determined with a Spectrometer STS-UV (Ocean Insight Co, Orlando, FL, USA).
Primers design and selection We designed eight primers sets (electronic supplementary material, table  S3 ) from EST's database (www. ncbi. nlm. nih. gov/dbEST/) and sequences previously reported for Sepia officinalis and Sepia maindroni from the NCBI GenBank database. The primers were designed using Primer 3 software  [28]  and tested using cDNA from cuttlefish eyes, skin and CNS (CNS = brain and optic lobes). The PCR mix includes REDTaq, PCR Reaction Mix (Eurogentec, Seraing, Belgium) and 10 µM of each primer in a final volume of 50 µl. The thermocycler program was: 5 min at 95°C, 40 cycles of 30 s to 95°C, 1 min to 58°C, 30 s at 72°C and the final extension of 2 min at 72°C. For the visualization of PCR products, 2% agarose gel was used.
Three dPCR replicates were analysed for each sample. The initial copy value was automatically calculated by the QIAcuity Suite Software V1. 1. 3 193 (Qiagen, Germany), and quantities were exported as Copies/μl of the reaction. The dPCR assays were performed using automatic settings for threshold and baseline. dMIQE checklists are provided in electronic supplementary material, tables S4-S6 and figures S4 and S5.
Statistical analysis The results of mortality and malformation rates were presented as mean ± s. e. m. Gene expression data were analysed and visualized using Statsmodels (Python module) O. L. S. [29]  to detect significant differences between the treatments (UVB-L and UVB-M) and between groups (BC and WC). Statistical difference was determined using Student's t-test, and the significance level was set at p < 0. 05.
Juveniles Similarly, the effects of UVB treatments on the phenotype were quantified in juveniles (n = 32) from each treatment, using a categorization as 'normal' or abnormal at the J1, J2 or J3 level using morphological criteria (figure  3a ). During the juvenile phase, we did not observe any morphological differences between NUVB and UVB-L treatments after hatching. In WC and BC groups, juveniles exhibited a regular shape with a healthy appearance. The abnormalities were observed only under UVB-M and UVB-H treatments. No royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 10: 230602 data could be collected in the WC group due to high mortality in the UVBM and UVBH treatments during the embryonic phase. In the BC group, which showed no abnormalities before hatching, morphological abnormalities began to appear 9 days after hatching (45 days of UVB exposure), with only abnormalities type J1 observed (19 and 33% in UVB-M and UVB-H treatment, respectively) (figure  3b ).
Discussion The present study is the first to show the effects of continuous controlled UVB radiation exposure during the embryonic and juvenile phases on the cephalopod Sepia officinalis. It offers experimental data emphasizing the role of the black capsule as a protection against UVB radiation. In addition, we examined the relationship between the abnormalities observed and the induction of specific responses at molecular levels after UVB exposure. The daily UVB doses (8. 0-24. 8 kJ m -2 ) tested in this study were based on the data collected in situ and were representative of natural underwater daily UVB levels, where the high daily UVB doses detected underwater (0. 1-0. 3 m depth) were 40 kJ m -2 during July and 31 kJ m -2 during September 2021 in the mid-day light regimes. The daily UVB levels detected on the coast of Roscoff are similar to those reported underwater in other waters, such as the Atlantic Ocean, reaching daily UVB doses up to 44.
Acknowledgements. We are very grateful to the  CRB (Roscoff)  staff and  EMBRC-France. In addition, we thank  Marie-Morgane CORRE , a bachelor student, for her help in setting up the experimental structures and zootechny,  Zoé RAPHALEN , an MSc student, and  Sebastian LEE  for their help in the experimentation phase. royalsocietypublishing. org/journal/rsos R. Soc. Open Sci. 10:  230602.
Bifurcation analysis The bifurcation analysis of the mean Ad Ex has been done using MatCont (version 7. 7)  [Dhooge et al. , 2003] , a numerical continuation library of MATLAB  [Inc. , 2022]. From the equilibrium point of a silence network (0. 0, 0. 0, 0. 0, 0. 0, 0. 0, 0. 0), we compute the change of stability depending on the external excitatory firing rate. The result of the numerical continuation is a stability diagram of the mean-field with a bifurcation point. The steps of numerical continuation are variable and adjusted depending on the sensitivity of the stability of the fixed-points.
Acknowledgments We thank  Mallory Carlu ,  Matteo di Volo , and  Jennifer Goldman  for stimulating discussions. This research has received funding from  CNRS  and the  European Union 's  Horizon 2020 Framework Programme for Research and Innovation  under the Specific Grant Agreement No. 945539  ( Human Brain Project SGA3 ) and Specific Grant Agreement No. 785907  ( Human Brain Project SGA2 ).
ORCHIDEE-MICT ORCHIDEE-MICT (Organising Carbon and Hydrology in Dynamic Ecosystems-aMeliorated Interactions between Carbon and Temperature) has been developed from ORCHIDEE, a land surface component of the French Institut Pierre Simon Laplace (IPSL) Earth system model (ESM) that simulates water, energy, and carbon processes  (Krinner et al. , 2005). The ORCHIDEE-MICT incorporates a new vertical soil parameterization scheme, snow processes, and a fire module, improving the representation of high-latitude processes such as permafrost physics and hydrology  (Guimberteau et al. , 2018). A spin-up simulation following  Guimberteau et al. (2018)  was performed to reach the equilibria for soil conditions and carbon pools. The model discretizes the vegetation into 13 PFTs (eight for trees, two for natural C3 and C4 grasses, two for crops, and one for bare-soil type).
4°C in annual mean temperature and -2. 3% in annual mean precipitation compared to observations at this location. The plot on the top left shows the cooling degree days (CDD) against the mean standardized precipitation index (SPI) as indica tors for heat stress and drought intensity, respectively, for the different scenarios. CDD, here used as a  The correlation for each model based on six data points was transformed using Fisher z transformation, then the values were averaged over all models and transformed back  (Corey et al. , 1998). In white are the areas where the correlation is not significant at the 5% level (calculated based on 36 data points). proxy for heat stress, is calculated as the sum of all temperature exceedances over a high threshold, in this case the 90th percentile of the Control scenario at each pixel.
Data Availability Statement The climate forcing data used to run the vegetation models can be found here: https://zenodo. org/record/4385445#. Y48zvC1oSCM  (Tschumi et al. , 2020). All variables from the model runs relevant for this analysis can be found here: https://zenodo. org/record/7602286#. Y90VLC9XbT8  (Tschumi et al. , 2023).
Twelve genetic samples collected outside of the management area were assigned to area 2 as they were close to area 2 longitudinally. The map was created with the R package "maps" v. 3. 4. 0. The use of tissue samples collected in the breeding grounds is ideal for clarifying the genetic structure of baleen whales because it is assumed that populations are isolated, both spatially and temporally, from other populations when they are in their breeding grounds. However, in terms of management, the genetic structure on feeding grounds is also important as the whales are harvested in these areas and also along migratory corridors where different populations could spatially overlap. Several previous population genetic studies on Bryde's whales in their central and western North Pacific feeding grounds did not observe any genetic population structure in these areas.
This study utilized a large number of additional samples collected in areas 1 and 2 in recent years by different research programs. Notably, genetic samples collected under the International Whaling Commission -Pacific Ocean Whale and Ecosystem Research (IWC-POWER) program are now available for longitudinal sectors not covered by the previous genetic analyses. Furthermore, as this study utilizes genetic samples collected over a period of 30 years, we were able to conduct time-series genetic analyses, which may enhance the resolution allowing better inference of spatial genetic structure. Note: Sample sizes were generated by combining genetic data used in a previous study  (Kanda et al. 2007)  with those obtained in this study.
Negative and positive control samples, one of each, were run in parallel with all PCR amplifications. The amplified PCR products were co-loaded in four combinations (Table  2 ) on different platforms depending on the sample source and (or) the sampling year. The PCR products from the JARPNII and bycatch samples collected until 2013 were run on a 6% polyacrylamide denaturing Long Ranger™ gel (FMC BioProducts, Maine, USA) with an internal size standard (GENESCAN400HD, Applied Biosystems Inc. , Massachusetts, USA) using a BaseStation100 DNA fragment analyzer (Bio-Rad, California, USA). Alleles were visualized using Cartographer software specifically designed for the BaseStation, and the fragment sizes were determined manually in relation to the internal size standard and a positive control sample of known size that were run on each gel.
Sex ratios The sex ratios in the data set containing either or both of the available msDNA genotype and the mtDNA sequence data were tested for deviation from 1:1 using binomial tests. However, commercial whaling samples were excluded from the test, due to the possible contribution of bias resulting from the regulations prohibiting the catch of whales smaller than 12. 2 and 10. 7 m in pelagic and coastal whaling, respectively  (Ohsumi 1995) , which could have resulted in a greater number of females in the catches.
Genetic analyses msDNA variation and differentiation Genetic variations represented by the number of alleles (A), inbreeding coefficient (F IS ), and expected heterozygosity (H E ) were estimated per locus and across loci using the FSTAT program v. 2. 9. 3. 2  (Goudet 1995). The departure from Hardy-Weinberg equilibrium (HWE) was also tested for each locus and across loci using GENEPOP. The analysis of molecular variance (AMOVA) implemented in the ARLEQUIN program v. 3. 5. 1. 2 (Excoffier and Lischer 2010) was used to examine the genetic structure of this species. In this analysis, each area was considered as a population and assigned to two groups: Group 1, which consisted of specimens from areas 1W and 1E, and Group 2, which consisted of specimens from area 2. The genetic difference between areas was examined by Fisher's exact test to test for differences in allele frequencies between areas, as well as by pairwise F ST estimates  (Weir and Cockerham 1984) , which were performed in GENEPOP.
Power analysis The statistical power of the msDNA and mtDNA data sets employed in this study was evaluated using POWSIM v. 4. 1  (Ryman and Palm 2006). Simulations were run to yield different F ST values corresponding to the empirical estimates (i. e. , 0. 0003, 0. 0030, and 0. 0045 for msDNA and 0. 030, 0. 0065 and 0. 0227 for mtDNA: see Results) by fixing the effective population size at 7000 for msDNA and at 3500 for mtDNA and varying the number of generations (t), with empirical sample sizes, numbers of loci, and global allele/haplotype frequencies. The probability of committing type I errors was also evaluated for both markers by drawing the alleles/haplotypes directly from the base population and omitting the drift steps (F ST = 0). Power is expressed as the proportion of significant outcomes rejecting the null hypothesis of no difference in allele/haplotype frequencies or F ST = 0, by Fisher's exact test at p < 0.
Quality control The mean mismatch rate in repeated genotyping of the same individuals differed among loci (Table  3 ), with the highest and second-highest mismatch rates estimated to be 0. 039 at EV94Mn and 0. 026 at GATA417, respectively. All spatial analyses of genetic differentiation, i. e. , pairwise F ST estimates and heterogeneity testing, were performed twice using both data sets with and without EV94Mn and GATA417. Furthermore, the MICRO-CHECKER program detected a signal of null alleles at locus GATA53 (Table  3 ). The influence of this locus on estimates of population structure was therefore tested in the same manner as EV94Mn and GATA417. These analyses showed that there were no differences between the results with and without the three more error-prone loci (results not shown), which suggests that they are sufficiently low to not have a significant influence on our biological conclusions.
Power analysis POWSIM analysis indicated that the mtDNA data employed in this study had sufficient power for detecting genetic differences between areas 1W and 2 (F ST = 0. 0227: 100%) as well as between areas 1E and 2 (F ST = 0. 0065: 93. 9%), which was reduced to 60. 0% at F ST = 0. 0030 observed between areas 1W and 1E. The power analysis showed that msDNA data also had sufficient power to detect genetic differences between areas 1W and 2 (F ST = 0. 0045: 100%) and between areas 1E and 2 (F ST = 0. 0030: 93. 6%), but not between areas 1E and 1W (F ST = 0. 0003: 35. 1%). The type I error rate remained low for all simulation scenarios based on the empirical data sets for both markers (msDNA = 3. 8%-5. 8%; mtDNA = 5. 0%-5. 3%).
e. , areas 1W or 2; both populations mix geographically around area 1E. Future studies should be undertaken to clarify which of the two scenarios proposed in this study is most likely and efforts should focus on obtaining additional information from breeding grounds. grateful to Hiroyuki Oikawa and Tomonari Iida for their laboratory work at the Institute of Cetacean Research. We also thank Naohisa Kanda, who organized most of the msDNA data used in this study. Biopsy samples obtained by the IWC-POWER survey within the US EZZ were permitted under US National Marine Fisheries Service (NMFS) Permit No. 20465. Biopsy samples obtained in the high seas of international waters during the JARPNII and Japanese dedicated sighting surveys were authorized by annual SUIKAN permits issued by the Fisheries Agency, Government of Japan.
Our estimates are consistent with previous reef structural complexity estimates at this location  27. Hydrodynamic and topographic measurements. Mo' orea (French Polynesia) is encircled by coral reefs, 500-700 m wide with a dominant swell direction coming from the southwest. In this study, we focus on Ha'apiti, a site with a southwest orientation that is considered as a high-energy site  28. We extract 30-year offshore wave data (1980-2010) from a wave hindcast  8, 29  (Fig. 2a ). We also collect high-frequency, in situ wave data using INW PT2X Aquistar and DHI SensorONE pressure transducers (PTs), which are logged at 4 Hz 30. The sensors are installed at four locations along a cross-shelf gradient (Fig. 2b, c ) covering a 250 m long stretch, including sections through the fore reef, reef crest, and reef flat.
Funding This research was supported by the  BNP Foundation  ( Reef Services  Project), the  French Polynesian government (RisqueRecif Project) , the  Fondation de France  ( Acid Reefs  project) the  Fondation pour la Recherche et Biodiversité and Ministère de la Transition Ecologique et Solidaire  (Acid Reefs 2 Project). AR is funded by the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (grant agreement No. 802414 ). Moorea Coral Reef Long-Term Ecological Program (LTER) , funded by the  U. S. National Science Foundation.
Two hundred forty-six MSM aged 18 years or older will be invited to participate. Discussion: The ICECREAM study is a trial aimed at establishing interventions that could effectively decrease the incidence of HCV re-infection in MSM with a previous HCV infection. By offering an online behavioural risk-reduction intervention and HCV-RNA self-sampling, both of which are aimed to in uence risk behaviour, we are able to provide products to at-risk MSM that could further reduce population-level HCV incidence and ultimately help reach HCV micro-elimination. Trial registration: This study has been registered at clinicaltrials. gov identi er NCT04156945.
Additional consent provisions for collection and use of participant data and biological specimens {26b} All participants are asked to give consent to link HCV test data results from routine care and to test stored blood samples. These stored samples are collected during regular clinical visits at the HIV treatment centre or CSH/CeGIDD during participation in the ICECREAM study and are stored at the laboratory in accordance with legal regulations. Retrospective testing of stored samples takes place at the end of the study only if the participant has not been tested for HCV during routine care in the 6 months prior to study completion.