dataesr/scientific-paragraphs-categorization huggingface dataset:
We acknowledge the use of B21 beamline at the Diamond Light Source (DSL, U. K. ) facility. We thank T. W. Muir and M. R. Pratt for the ubiquitin-intein clone and guidance on the disulfide formation reaction. ORCID Javier Murciano-Calles: 0000-0002-8667-1651 Francisco J. Blanco: 0000-0003-2545-4319 Notes The authors declare no competing financial interest. ■ ACKNOWLEDGMENTS Spanish Ministerio de Economi ́a y Competitividad and the Fondo Europeo de Desarrollo Regional (MINECO/FEDER) [CTQ2017-83810-R to F. J. B. ]; Labex EpiGenMed, an "Investissements d"avenir' program [ANR-10-LABX-12-01 to PB]. MOSTMicro [LISBOA-01-0145-FEDER-007660 to T. N. C. and H. M. ]. A. G. M. acknowledges Spanish MINECO for predoctoral contract BE-2015-075847, and the CIC bioGUNE acknowledges MINECO for the Severo Ochoa accreditation Sev-2016-0644.
The CBS-Montpellier is a member of France-BioImaging (FBI) and the French Infra- structure for Integrated Structural Biology (FRISBI), two national infrastructures supported by the French National Research Agency (ANR-10-INSB-04-01 and ANR-10-INSB- 05, respectively). 10. 1021/acschem- bio. 9b00679. SDS-PAGE analysis, chemical shifts deviations, trans- verse 15 N relaxation R 2 values, comparative SAXS data of p15CCSS and dmUbp15 to the monomeric globular ubiquitin, comparative experimental and calculated SAXS data before and after conformational ensemble optimization, overlay of 1 H-15 N HSQC spectra, calori- metric titrations of PCNA with dmUbp15 or p15 mutant C54S, NMR signal intensities measured in the 2D 1 H, 15 N HSQC spectra of dmUbp15 in the absence or presence of PCNA, overlay of 1 H, 15 N TROSY spectra of perdeuterated PCNA [U-2 H, 15 N] in the absence or presence of unlabeled dmUbp15, NMR analysis of p15CCSS, overlay of 1 H-15 N HSQC spectra, calori- metric titrations, thermodynamic parameters of the binding of p15 molecules to PCNA, thermodynamic parameters of the binding of RFTS to different p15 molecules, and supporting references (PDF) ■ AUTHOR INFORMATION Corresponding Author *E-mail: fblanco@cicbiogune.
As a basis for our investigation, we used vital rates estimated from modeling of capture-recapture-recovery data from several study sites. We then used the reported cause of death associated with an extensive number of recoveries to estimate proportions of birds dying due to hunting and other causes. By allowing for adjustments in survival rates depending on hunting intensity, we explored the flyway population consequences of past and present harvest management using a stochastic demographic model. We hypothesize that the efficacy of using hunting regulations to increase flyway population size largely depends on current levels of natural mortality.
| Step 1-Flyway vital rates Grouped by site, 46 years  of ten colony-specific markrecapture-recovery datasets of breeding females were arranged in one encounter history file. We used the Burnham model  (Burnham, 1993)  for mixtures of live-and-dead encounter data implemented in Program MARK  (White & Burnham, 1999). The Burnham model estimates survival (S) unbiased by permanent emigration, recapture probability (p), recovery probability (r), and site fidelity (F)  (Burnham, 1993). We specified models with time-dependent and site-specific survival and recapture probabilities, while using Akaike's information criterion adjusted for small sample sizes (AIC c ) to select between candidate models varying with respect to recovery and site fidelity  (Burnham & Anderson, 2002). Annual survival of prebreeders and adult males was estimated for colonies with suitable data.
| Step 2-Hunting mortality of adult females For this step, we used only dead recoveries and pooled data from all colonies. Following  Schaub and Pradel (2004)  and  Souchay and Schaub (2016) , we used the known cause of death reported by the public to tease apart mortality due to hunting ( h ) versus other ( o ) causes. We used program E-SURGE  (Choquet, Rouan, & Pradel, 2009)  to develop a multi-event ring-recovery model that simultaneously estimated survival (S), proportions of birds dying due to either cause (α h, α o ), cause-specific recovery probabilities (r h, r o ), and probabilities that dead individuals were assigned to the correct cause (δ h , δ o ). We specified a model with four biological states: alive, newly dead due to hunting, newly dead due to other causes, and old dead. The newly dead states ensured that encounters of dead birds were assigned to only one recovery period, whereas the old dead state was absorbing and unobservable  (Gauthier & Lebreton, 2008).
| Goodness-of-fit testing Prior to model fitting, we assessed the degree of overdispersion. Because the currently available goodness-of-fit test for multistate models  (Pradel, Wintrebert, & Gimenez, 2003)  does not allow for unobservable states, this method was considered inappropriate. We therefore computed the median c-hat in Program MARK for an analogous capture-recovery model which did not consider separate causes of death. The resulting median c-hat value can thus be considered conservative in relation to both step 1 and step 2 because these models decrease heterogeneity by splitting data by colony (step 1) or mortality into two components (step 2). Not all demographic quantities necessary to model the population were directly available, and some parameters had to be approximated while making assumptions and by including other data sources.
46%. An estimate of first-year survival was only available for the initial period of population increase, up to 1981. To approximate survival from the subsequent period, we used data from The Danish Hunting Bag Record and The Danish Wing Survey, which annually since 1982 has assigned age and sex of 1. 3%-4. 0% of all eiders shot in Danish waters. Assuming that first-year birds constituted c. 28% of the total population at the start of the open season in the early 1990s  (Noer et al. , 1995)  and that the relative hunting risk of first-year individuals was the same before and after the decline (but prior to the first sex-differentiated hunting regulation), we calculated the proportion of first-year (1Y) birds for the phase of decline: where Relrisk is the estimated relative hunting risk of first-winter birds and logit(p) = ln(p/(1 -p)).
| Harvest management Harvest rates assessed from independent data sources, that is, ring recoveries and hunting statistics, both indicated a major reduction over time in the contribution of harvest to the mortality of adult females. This is partly due to fewer active, Danish seaduck hunters  (Asferg, Bregnballe, Christensen, Clausager, & Clausen, 2003; Christensen, 2005) , but also to a set of restrictions on the length of the hunting season on females  (Christensen & Hounisen, 2014). The effectiveness of shortening the hunting season depends on both the spatiotemporal distribution of the hunted population and the motivation for hunters to maintain their annual harvest  (Sunde & Asferg, 2014). In this case, hunters did not compensate for the shorter season by intensifying their kill of females, in contrast to males  (Christensen & Hounisen, 2014).
The changing world of scholarly communication and the emerging new wave of 'Open Science' or 'Open Research' has brought to light a number of controversial and hotly debated topics. Evidence-based rational debate is regularly drowned out by misinformed or exaggerated rhetoric, which does not benefit the evolving system of scholarly communication. This article aims to provide a baseline evidence framework for ten of the most contested topics, in order to help frame and move forward discussions, practices, and policies. We address issues around preprints and scooping, the practice of copyright transfer, the function of peer review, predatory publishers, and the legitimacy of 'global' databases. These arguments and data will be a powerful tool against misinformation across wider academic research, policy and practice, and will inform changes within the rapidly evolving scholarly publishing system.
For example, climate change skeptics have published studies in the Energy and Environment journal, attempting to undermine the body of research that shows how human activity impacts the Earth's climate. Politicians in the United States downplaying the science of climate change have then cited this journal on several occasions in speeches and reports 9. At times, peer review has been exposed as a process that was orchestrated for a preconceived outcome. The New York Times gained access to confidential peer review documents for studies sponsored by the National Football Leagues (NFL) that were cited as scientific evidence that brain injuries do not cause long-term harm to its players 10. During the peer review process, the authors of the study stated that all NFL players were part of a study, a claim that the reporters found to be false by examining the database used for the research.
Topic 5: Is Open Access responsible for creating predatory publishers? Predatory publishing does not refer to a homogenous category of practices. The name itself coined by American librarian Jeffrey Beall who created a list of "deceptive and fraudulent" Open Access (OA) publishers which was used as reference until withdrawn in 2017. The term has been reused since for a new for-profit database by Cabell's International  [73]. On the one hand, Beall's list as well as Cabell's International database do include truly fraudulent and deceptive OA publishers, that pretend to provide services (in particular quality peer review) which they do not implement, show fictive editorial boards and/or ISSN numbers, use dubious marketing and spamming techniques or even hijacking known titles  [74]. On the other hand, they also list journals with subpar standards of peer review and linguistic correction  [75].
Where publishers have already implemented such policies, such as the Royal Society, Sage, and Emerald 40 , there has been no documented impact on their finances so far. In a reaction to Plan S, Highwire suggested that three of their society publishers make all author manuscripts freely available upon submission and state that they do not believe this practice has contributed to subscription decline 41. Therefore, there is little evidence or justification supporting the need for embargo periods. 2. 9. Topic 9: Are Web of Science and Scopus global platforms of knowledge? Clarivate Analytics' Web of Science (WoS) and Elsevier's Scopus platforms are synonymous with data on international research, and considered as the two most trusted or authoritative sources of bibliometric data for peer-reviewed global research knowledge across disciplines  [22, [131] [132] [133] [134] [135] [136].
They are both also used widely for the purposes of researcher evaluation and promotion, institutional impact (for example the role of WoS in the UK Research Excellence Framework 2021 42 ), and international league tables (Bibliographic data from Scopus represents more than 36% of assessment criteria in the THE rankings 43 ). But while these databases are generally agreed to contain rigorously assessed, high quality research, they do not represent the sum of current global research knowledge. It is often mentioned in popular science articles that the research outputs of researchers in South America, Asia, and Africa is disappointingly low. Sub-Saharan Africa is often singled out and 36 Open Access, Fifth Report of Session 2013-14, House of Commons Business, Innovation and Skills Committee, September 2013.
37 Journal Usage Half-Life, Phil Davis, 2013. 38 Half-life is half the story, Danny Kingsley, 2015. 39 Global scientific community commits to sharing data on Zika, Wellcome Trust. 40 Zero embargo publishers, database maintained by Stuart Taylor. 41 Plan S: The options publishers are considering, Highwire Press. 42 Clarivate Analytics will provide citation data during REF2021. 43 World University Rankings 2019: Methodology, Times Higher Education. chastised for having "13. 5% of the global population but less than 1% of global research output" 44. This oft-quoted factoid is based on data from a World Bank/Elsevier report from 2012 which relies on data exclusively from Scopus 45. Similarly, many others have analyzed 'global' or international collaborations and mobility using the even more selective WoS database  [137] [138] [139].
Research outputs in these contexts refers specifically to papers published in peer-reviewed journals that are indexed either in Scopus or WoS. Both WoS and Scopus are highly selective. Both are commercial enterprises, whose standards and assessment criteria are mostly controlled by panels of gatekeepers in North America and Western Europe. The same is true for more comprehensive databases such as Ulrich's Web which lists as many as 70,000 journals  [140] , but crucially Scopus has fewer than 50% of these, while WoS has fewer than 25%  [131]. While Scopus is larger and geographically broader than WoS, it still only covers a fraction of journal publishing outside North America and Europe. For example, it reports a coverage of over 2000 journals in Asia ("230% more than the nearest competitor") 46 , which may seem impressive until you consider that in Indonesia alone there are more than 7000 journals listed on the government's Garuda portal 47 (of which more than 1300 are currently listed on DOAJ) 48 ; while at least 2500 Japanese journals listed on the J-Stage platform 49.
Similarly, Scopus claims to have about 700 journals listed from Latin America, in comparison with SciELO's 1285 active journal count 50 ; but that is just the tip of the iceberg judging by the 1300+ DOAJ-listed journals in Brazil alone 51. Furthermore, the editorial boards of the journals contained in WoS and Scopus databases are dominated by researchers from western Europe and North America. For example, in the journal Human Geography, 41% of editorial board members are from the United States, and 37. 8% from the UK  [141]. Similarly, Wooliscroft and Rosenstreich  [142]  studied ten leading marketing journals in WoS and Scopus databases, and concluded that 85. 3% of their editorial board members are based in the United States. It comes as no surprise that the research that gets published in these journals is the one that fits the editorial boards' world view  [142].
Comparison with subject-specific indexes has further revealed the geographical and 'topic bias-for example Ciarli, Rafols, and Llopis  [143]  found that by comparing the coverage of rice research in CAB Abstracts (an agriculture and global health database) with WoS and Scopus, the latter "may strongly under-represent the scientific production by developing countries, and over-represent that by industrialized countries", and this is likely to apply to other fields of agriculture. Crucially, this under-representation of applied research in Africa, Asia, and South America may have an additional negative effect on framing research strategies and policy development in these countries  [135]. The overpromotion of these databases diminishes the important role of 'locally-focused' and 'regional' journals for researchers who want to publish and read locally relevant content.
One way to bridge this gap is with discipline-and region-specific preprint repositories such as AfricArXiv and InarXiv. In the meantime, we need to remain critical of those 'global' research databases that have been built in Europe or Northern America and be wary of those who sell these products as a representation of the global sum of human scholarly knowledge. Finally, let us also be aware of the geopolitical impact that such systematic discrimination has on knowledge production, and the inclusion and representation of marginalized research demographics within the global research landscape. This is particularly important when platforms such as Web of Science and Scopus are used for international assessments of research quality 57.
Many items on the list could be argued to be of value primarily to the publishers themselves, e. g. , "Make money and remain a constant in the system of scholarly output". However, others provide direct value to researchers and research in steering the academic literature. This includes arbitrating disputes (e. g. , over ethics, authorship), stewarding the scholarly record, copy-editing, proofreading, type-setting, styling of materials, linking the articles to open and accessible datasets, and (perhaps most importantly) arranging and managing scholarly peer review. The latter is a task which should not be underestimated as it effectively entails coercing busy people into giving their time to improve someone else's work and maintain the quality of the literature. Not to mention the standard management processes for large enterprises, including infrastructure, people, security, and marketing.
Acknowledgments: For contributions to the preprint version of this manuscript, all authors would like to thank  Janne-Tuomas Seppänen ,  Lambert Heller ,  Dasapta Erwin Irawan ,  Danny Garside ,  Valérie Gabelica ,  Andrés Pavas ,  Peter Suber ,  Sami Niinimäki ,  Mikael Laakso ,  Neal Haddaway ,  Dario Taraborelli ,  Fabio Ciotti ,  Andre Rathemaccher ,  Sharon Bloom ,  Lars Juhl Jensen ,  Giannis Tsakonas ,  Lars Öhrström ,  John A. Stevenson ,  Kyle Siler ,  Rich Abdill ,  Philippe Bocquier ,  Andy Nobes ,  Lisa Matthias , and  Karen Shashok. Three anonymous reviewers also provided useful feedback.
Publications 2019, 7 , 25 Figure 3. 7253 Figure 3. Proportion of journals indexed in the DOAJ (Directory of Open Access Journals) that charge or do not charge APCs (article-processing charges). For a small portion, the information is not available. All code and data needed to reproduce these figures are on Zenodo: http://doi. org/10. 5281/zenodo. 2647404.
03, unpaired t-test) reduced from 131 ± 4 (n = 44 DiI + -neurons) in control mice injected with saline solution to 118 ± 5 (n = 50 DiI + -neurons) in mice treated with sumatriptan (data not shown). Changes in PKA expression in TGs from sumatriptan-treated mice (n = 8) were also evaluated by quantifying band intensities on phospho T197 PKA blots and comparing to blot band intensities in saline-treated mice (n = 8) as controls. Densitometry analysis of background-subtracted blots from 20 µg of total lysate showed a 22% decrease in phospho T197 PKA expression in sumatriptan-treated mice versus control mice (Supplementary Fig. 8C ). This decrease however did not reach significant level due to sample variability (Supplementary Fig. 8D ). Collectively, these data suggest that nitrergic activation of Nav1.
Many of these phenomena are similar to mechanisms seen in dependence processes  33, 34. Our approach to modeling MOH symptoms was the quantification of increased sensory sensitivity in response to one of the most common reported trigger for headache and migraine  8, 9, 35, 36. NO donors reliably trigger headache in normal subjects, but trigger migraine and severe pain in migraineurs  36  , and this condition is accompanied by an increase in blood levels of CGRP, which is directly linked to the severity of headache pain  [37] [38] [39]. In our study, MOH following NO infusion was evaluated using multiple headache-like responses in each individual animal, including cutaneous facial and extracephalic allodynia as well as aversion to light and noise. Our data show that chronic sumatriptan treatment of mice induces a state of dormant sensitization characterized by sharp, exacerbated sensory responses to NO  8, 9, 40.
The head withdrawal tactile sensory threshold was the lowest force to elicit withdrawal in 2 of 3 trials. Data points were normalized to the control sensory threshold values determined just before minipump implantation (i. e. at day 0) or before SNP injection (i. e. at day 21, H0). Light aversive test. To evaluate the light-aversive behavior after SNP injection, we used a light-dark test. The light-aversion chamber consisted of two equally sized compartments (10 cm width, 13 cm length, and 13 cm height), one painted white and lacking a top, the other painted black and fully enclosed. A corridor (7. 2 cm width, 7. 2 cm length, and 13 cm height) connects the two compartments. Mice were acclimatized at least 1 h in their cages in the testing room and were allowed to explore the light-aversion chamber 10 min before testing.
Images were acquired using a LSM 780 laser-scanning confocal microscope (Zeiss), initially processed using ZEN software (Zeiss) and later exported into Adobe Photoshop (Adobe Systems, San Jose, CA) for final processing. Staining for beta-galactosidase enzyme activity. Evaluation of β-gal enzymatic activity was performed on transgenic mice that express β-gal at the Scn11a loci. Once dissected out, the TGs were slightly fixed 15 min in PBS containing 2% PFA, 0. 2% glutaraldehyde, and 2 mM MgCl 2. The tissues were washed with two changes of PBS containing 2 mM MgCl 2 for 5 and 8 min. The staining is achieved with an overnight incubation of TGs in PBS added with 4 mM Ferrocyanide, 4 mM Ferricyanide, 2 mM MgCl 2 , 1% Tween-20, and 0. 2 mg/ml X-gal at 37 °C. The TGs were finally post-fixed for 15 min in PBS containing 2% PFA, 0.
05% saponin. PKA antibodies (rabbit polyclonal #ab75991, AbCam) were diluted at 1/200 in blocking buffer and applied to tissues to be incubated overnight at 4 °C in sealed humidified chambers. Tissues were washed three times for 10 min in PBS and incubated for 3 h at RT in PBS containing 3% fish gelatin added with secondary antibodies Alexa Fluor 488-conjugated donkey anti-rabbit (1/200, Life Technologies). After four 5 min washes in PBS, sections were stained with DAPI, washed once in PBS and mounted in Mowiol (Sigma-Aldrich). In order to compare the fluorescence intensities of PKA immunostaining between NaCl-treated and sumatriptan-treated DiI-positive TG neurons, images were acquired using a LSM 780 laser-scanning confocal microscope (Zeiss) using constant acquisition settings. ImageJ software was used to measure intensities of fluorescence on planar projections of confocal raw images spanning 6 µm.
Acknowledgements This work is supported by grants from the  CNRS  and the  Fondation pour la Recherche Médicale  ( FRM 2013 DEQ20130326482  to P. D. ). We thank  M. Mekaouche ,  A. Fernandez  and  Dr J. Wang  ( INSERM U1051 ) for technical assistance, and  F. Maingret  for supervising C. B. during her Master. We thank  M. Masse  for the gift of the CD31 antibody. C. B. was supported by the  French ministry and Fondation pour la Recherche Médicale.
Considering the mutations may lead to difficulty in modeling, we should remove these near-zero values. A thresholding process is designed to eliminate these coefficients in the magnitude and the relative phase. The purpose of setting the threshold is to remove the near-zero coefficients and keep the image information as much as possible. For the magnitude, we studied the coefficients of all the images in the LIVE 2 database and found that the threshold will increase with the decomposition scales. For example, for the 1-scale, 2-scale and 3-scale decom-position, the thresholds are respectively around 10 -6 , 10 -4 and 10 -2. The process to set the threshold is as follows: 1. Dividing the images into two parts: images with uniform areas and the one without. 2. Performing the DT-CWT coefficients and sorting all the elements of the coefficient.
The comparison between the MRD and the IGD models was performed by an experimental method. The KLD value between the original distribution and the model serves as the criterion. The model with less KLD value will be selected. We took all the images in the LIVE 2 database as a test. The experimental results show that the average KLD value of the MRD model is around 0. 04 and the one of the IGD model is around 0. 01. Thus, we chose the IGD model as the model of the magnitude. Fig. 5  shows the fitting performance of the two candidate models, taking the image "Bikes" as an example.