dataesr/scientific-paragraphs-categorization huggingface dataset:
After enumeration of the infected (blue) cells, all cells were lysed and subjected to the protein assay (Bio-Rad) to establish total protein sample concentration, and all data were normalized by total protein concentration. The values for inhibition of HIV-1 replication were calculated based on the formula [(R 1 -R 0 )x100/ Z]-100, where R 1 is the value obtained from cells infected by HIV-1 and treated with a specific dilution of DING protein and R 0 is the basal value obtained from the uninfected, untreated cells; Z is the absolute HIV-1 replication value calculated as Z = R max -R 0, where R max is the value representing 100% of HIV-1 replication in the untreated cells. The IC 50 values were calculated from titration curves using two adjoining dilutions for each DING protein that showed inhibition close to 50% inhibition of LTR (RSA) or HIV-1 replication (MAGI).
4B  and Table  1 ). The control C3 Peptide P16 had only a minor effect on HIV-1 replication, with 11% inhibition at the highest dose of 1 mg/ml. The RSA and MAGI data reflected the direct effect of DING proteins on HIV-1 LTR transcription and the replication of virus in a single-cycle infection. To study DING-mediated restriction of virus in the normal course of infection, we subjected HIV-1infected PBLs to DING treatments and measured replication of virus five and seven days later, assessing the intracellular levels of p24 core protein. As shown in Fig. 5  (bars -right axis), all DING homologues blocked replication of HIV-1. Five days after infection, the intracellular p24 core protein was lower by 6 to 10-fold in DING-treated samples as compared to the untreated control. Seven days after infection, the X-DING-CD4 and pDING treatments reduced replication of HIV-1 by 11-fold, HPBP by 6-fold and PfluDING by 1.
Acknowledgments We appreciate the past and present members of the  Department of Neuroscience/Center for Neurovirology  and the basic Science Core I of the  NIMH-funded Comprehensive NeuroAIDS Center (CNAC)  for preparation of highly purified cultures of primary human brain cultures and HIV-1 viral stocks as a service to the  NeuroAIDS community. The CNAC offers its unique expertise to study the pathogenesis of HIV neurological diseases from both the basic science and clinical perspectives. We thank to  Galina Bentsman  for technical support in performing the p24 Elisa.
This work was supported by funds:  RO1NS062649  ( NIH)  awarded to MS;  12264  ( ANRS)  awarded to EC;  Research Grant  ( Auckland Medical Research Foundation)  awarded to KS,  Pennsylvania Department of Health   Research Grant  awarded to ND;  PO1NS43980  and  RO1MH074392  ( NIH)  awarded to SA;  RO1MH086358  and  RO1MH092371  ( NIH)  awarded to KK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Aevol digital evolution system In this study we use the Aevol platform, an individual-based model of evolution, especially well suited for the study of selection pressures on genomic architecture  [21, 22, 25, 33]. It is free and open-source software and is downloadable from http://www. aevol. fr/download. The specific version of the platform we used in this study, including analysis routines, parameter files, other minor modifications, is available on request. Aevol has already been used in several peer-reviewed publications including some that studied cooperation, so we invite the reader to refer to  [34]  for more information on how cooperation has been implemented and for characterization of the related parameters, and to  [22, 35]  for more general details about the original version of Aevol that did not incorporate cooperation.
Acknowledgments We thank  Tatiana Dimitriu ,  Julien Benard-Capelle  and  Ariel B. Lindner  for useful discussions and comments on this study and  David Parsons ,  Carole Knibbe  and  Guillaume Beslon  for their help with the Aevol platform. We are grateful to the  Center for the Study of Evolution in Action  ( BEACON, Michigan State University ) and the  CC-IN2P3  ( Computation Center of the French National Institute for Nuclear and Particle Physics ) for providing the computational resources needed by this study.
The effective success of these movements has been variable both in space and time. This paper draws on two original case studies, researched through interview data and online material. In France, protest groups have actively contested the DADVSI and HADOPI laws on digital copyright and unauthorized online file-sharing during their chaotic route through the French Parliament between 2005 and 2009. At the European level, the reform of the 'Telecoms Package' (a set of five directives regulating the European telecommunications market) 1  completed in November 2009 gave rise to an intense Internet-based lobbying effort, carried out by an ad hoc coalition of European activists. In both cases, online mobilization was an essential element of political contention for opponents of these legislative projects.
Data collection The main data for this project were collected between January 2008 and April 2010, consisting of over a thousand documents for each case (including the relevant legislation and legal documents, parliamentary debates, official reports, press releases, speeches, etc. ), of which approximately two thirds are of news reports from general and specialized media outlets, as well as blogs, radio shows, and selected video coverage. Our documentary analysis draws on specialized media sources, which generally expressed a pro-activist, anti-legislation and anti-industry bias, but which also provided the best in-depth coverage of the conflict; these media actively supported activist groups by spreading their material and calling upon their readership to rally to the cause, including through financial donations.
Among the various issues debated in the Telecom Package Reform, QdN activists focused their attention on the safeguarding of network neutrality and on the fight against the 'graduated response' procedure. Network neutrality, that is, the preservation of indiscriminate routing of data packets over the Internet, was threatened by several aspects of the Telecom Package Reform, which considered Internet filtering for traffic management purposes. Although QdN activists were very active on the network neutrality debate, the most prominent element of their campaign, which attracted relatively widespread media coverage, had to do with their fight against the 'graduated response', which rapidly crystallized around Amendment 138 (initially Art. 8. 4. g of the Framework directive). In its original version, the Amendment stated that "no restriction may be imposed on the fundamental rights and freedoms of end-users, without a prior ruling by the judicial authorities.
1998; Lyon 2001 ). In the same perspective, CCTV also often parallels the negative dystopias depicted by certain SF universes, in particular George Orwell's Big Brother. Henceforth, CCTV is presented as a technologically advanced expression of the 'surveillance society', which qualifies a situation in which 'precise details of our personal lives are collected, stored, retrieved and processed everyday within huge computer databases belonging to big corporations and government departments'  (Lyon 1994: 3). These analyses have been criticized as highly abstract and lacking empirical background  (Marx 2007; Manning 2008). De facto, the very limited empirical elements upon which such studies are based often lead their authors to overestimate the rationality of power and its practice: they tend to overvalue the effectiveness of authority regimes.
13 They also attribute a political goal to the tools without examining 12 Between 1960 and 1969, there were only 6 articles associated with the keyword 'surveillance' in the database for Sociological Abstracts. There were 563 between 1990 and 1999! (Marx 2007). This research trend is becoming more and more institutionalized thanks to the publication of readers  (Norris and Wilson 2006; Hier and Greenberg 2007; Lyon 2007 ) and handbooks  (Ball, Haggerty and Lyon 2012)  but also the creation of an online journal, Surveillance & Society. However, what 'Surveillance Studies' is still generates controversies, as illustrated by the debate between David Murakami Wood and Sean P. Hier and Josh Greenberg (Murakami Wood 2009; Hier and Greenberg 2009). 13 A British study of local policy networks in the field of security  (Fussey 2004 ) came to this conclusion.
Systematic review of outcomes Search and selection of trials. Eligible studies were RCTs comparing different pulp treatments with each other (direct pulp capping, pulpotomy or pulpectomy) in children with extensive decay in primary molar teeth. To identify trials, we searched bibliographical databases (Cochrane Oral Health Group's Trials Register CENTRAL; MEDLINE; EMBASE; Science Citation Index Expanded; Social Science Citation Index; Index to Scientific and Technical Proceedings; System for Information on Grey Literature in Europe). Search equations for each database were built by the Trial Search Coordinator of the Cochrane Oral Health Group. The equations combined free text words and controlled vocabulary pertaining to the condition and interventions (see Supporting Information, Text S1  [10] ).
The last search for articles was conducted in February 2012, with no restriction on date or language. We also screened the reference lists of included reports and searched ClinicalTrials. gov for the protocols of included studies and to identify ongoing trials. Two authors (V. S. and H. F. ) independently and in duplicate screened the titles and abstracts of records retrieved by the search, then screened the selected full-text reports. Any disagreements were resolved by discussion. These 2 reviewers independently collected data on publication year, number of arms in the trial, treatments compared, duration of follow-up, number of patients enrolled and number of treated teeth. Finally, the risk of bias within each RCT was assessed by the Cochrane Collaboration Risk of Bias tool, which includes the following items: methods for sequence generation and maintaining allocation concealment, blinding, incomplete outcome data, and selective outcome reporting  [11, 12].
An outcome designates individual components of the success or failure composite outcome or other individual outcomes. We abstracted the precise definitions of clinical, radiological and overall success or failure (ie, which component outcomes were part of the composite success or failure outcomes). Each individual outcome or component outcome was detailed in terms of its specific name or label, the time(s) when it was assessed and whether it was the ''primary outcome'' of the study (explicitly described as such or used in a power calculation to determine study design). For each report of RCT, we also assessed whether each outcome was defined in the Methods section and whether numerical data for each outcome (ie, number of patients with the outcome in experimental and control arms) were reported in the Results section.
Systematic review of outcomes Description of trials. The search yielded 1,736 potentially eligible articles. We included 47 reports of RCTs in the review. The flow chart of article selection is in Figure  1. Included and excluded reports of studies are in Supporting Information, Text S2. We did not find the protocol for any included trial at ClinicalTrials. gov. We identified 1 ongoing trial, but the outcomes definitions were not detailed  [19]. The characteristics of included studies are in Table  1. Details for each included RCT are in Supplementary Information, Table  S2  reports (57%), the risk of bias was unclear, frequently due to lack of information about allocation concealment and blinding of participants and staff. In total, 18 reports (38%) described attrition bias, due to amount, nature or handling of incomplete outcome data.
Acknowledgments We thank  Anne-Marie Glenny  and  Anne Littlewood  ( Cochrane Oral Health Group ) for help with the preparation and conduct of this study. We thank  Sybille Vital  and  Charles Pilipili  for help with the small-group consensus process. We thank all responders to the Delphi survey (authors of primary trials and members of the COLEP). We thank  Laura Smales  ( BioMedEditing, Toronto, Canada ) for editing the manuscript.
g. hypoplasia of premolars)*/Succedaneous tooth structural anomaly (e. g. hypoplasia) 21. Unerupted succedaneous tooth anomaly 2 Damage to succedaneous follicle/Deviated eruption of succedaneous teeth -position (radiographically) and eruption pathway of the permanent successor tooth 22. Erupting succedaneous tooth mobility 1 23. Signs/symptoms of erupting succedaneous 1 tooth 24. Succedaneous tooth position anomaly* 1 Problems in the developing occlusion (e. g. loss of space, mesial drift of first permanent molars, etc. ) ''…''-''…'': identical outcomes; ''…'' / ''…'': different but close outcomes. *outcomes retained in the Cochrane review by Nadin et al. [Nadin G, Goel BR, Yeung CA, Glenny AM (2003) Pulp treatment for extensive decay in primary teeth. Cochrane Database Syst Rev: CD003220.
Methods The analysis is based on a representative sample of the French population (the Echantillon Démographique Permanent) created by the French National Institute of Statistics (INSEE) containing about 1% of the population  [15]. The sample includes all persons born on any one of four specific calendar dates in any year and is regularly updated to include new subjects with any of these birthdays. Data are updated at each successive census. We excluded people born outside of mainland France because their vital status was not adequately recorded. Causes of death were obtained by linkage with the French national death registry (CépiDc, INSERM). The causes of death were identified for over 99% of the deceased included in this analysis. The underlying causes of death were classified according to the International Classification of Disease, Ninth Revision (ICD-9) for the years until 1999 and the International Classification of Diseases, Tenth Revision (ICD-10) for the years 2000-2007.
However, the educational differences observed in uterine cancer mortality are mostly driven by cervical cancer  [43]. Misclassification of some secondary cancers as primary liver cancers is also likely to have occurred. The percentage of missing values on education was extremely low in 1990 due to some internal procedures performed by Insee on the 1990 census dataset. This could have slightly altered the results; however we expect the influence, if any, to be small. Conversely, 5. 8% of our population had missing education in 1999. Additional analyses showed that this group displayed mortality similar to that found among men and women with primary education.
Moreover, these individuals made distinct identity appraisals, depending on whether they faced discrimination, and these appraisals were specifically linked to outcomes such as personal and collective self-esteem, and identity management strategies. When applied in an organizational context, this model can help researchers to explore the impact of identity appraisal on adjustment. For example,  Lesage, Berjot, Altintas, and Paty (2013)  measured, in a sample of 1,440 occupational physicians, symptoms of burnout, perceived stress, and identity appraisals. Results showed that stress and burnout were significantly and positively linked to threat to personal and professional identity. Moreover, results showed that threat to personal identity (TPI) explained twice as much feelings of low personal accomplishment than perceived stress and as much depersonalization than stress.
Threat Appraisals as Mediators Between Sources of Difficulties and Perceived Stress To test for multiple mediations, we followed the procedure described by Preacher and Hayes, using their macro for SPSS 18. This statistical analysis is based on the  Baron and Kenny procedure (1986)  for testing for mediators, but makes it possible to test for more than one at a time. Given that the correlational analyses only showed significant relations for threat appraisals, we excluded challenge appraisals from these fresh analyses (expect for the patient relations category, which was linked to CPI). We ran a multiple regression analysis for all the independent variables (IVs), with the two types of threat as simultaneous mediators and perceived stress as a dependent variable (DV). Total number of sources.
Chronology The sediment chronology was based on five radiocarbon accelerator mass spectrometry (AMS) dates. All samples have been analyzed at the Laboratoire de Mesure du Carbone 14 (LMC14) -UMS 2572 (CEA/DSM -CNRS -IRD -IRSN -Ministère de la culture et de la communication) (Table  1 ). All the radiocarbon ages were calibrated to calendar years Before Present (cal. yr BP) using the calibration curve for the Southern Hemisphere SHCal04  (McCormac et al. , 2004)  and with the Southern Hemisphere postbomb curves from  Hua and Barbetti (2004). Construction of the age-depth model was performed by running the 'CLAM' program  (Blaauw, 2010)  under the mathematical software 'R' version 2. 12. 2, and age-depth relationship was estimated using a smooth spline approximation (Figure  2 ).
Acknowledgements This research is part of the  UR GREAT ICE program  at  IRD  and  ANR 2010 BLANC 608-01  ELPASO. All radiocarbon dates were measured at the  Laboratoire de Mesure du Carbone 14  ( LMC14) -UMS 2572 (CEA/DSM CNRS IRD IRSN ). The authors thank the Bolivian authorities for facilitating our fieldwork in the Zongo Valley and  Jaime Argollo  for his help during fieldwork. The authors thank  Vera Markgraf ,  Francisco Valdez , and  Hugo Yaccobaccio  for their comments on an earlier draft of the manuscript.
This analysis uses data collected in the Ouagadougou Health and Demographic Surveillance System (Ouaga HDSS), a research platform for studies and health interventions set up by the Institut Supérieur des Sciences de la Population, University of Ouagadougou in five Ouagadougou neighborhoods  (Rossier et al. , 2012). Two of these neighborhoods (Kilwin and Tanghin) are official districts, with full access to municipal services. The remaining three neighborhoods (Nonghin, Polesgo and Nioko 2) are unplanned, unofficial peri-urban settlements that lack public services such as electricity and running water. After an initial survey conducted between October 2008 and March 2009, the population of the Ouaga HDSS has been regularly interviewed to register vital events (births, deaths, marriages and migration).
As of May 2012, the population tracked by the Ouaga HDSS totaled approximately 83,000 individuals. Over the course of the fourth round of interviews, between July 2011 and May 2012, fieldworkers recorded information on vaccines received by all children less than 5 years of age, allowing for evaluation of EPI coverage in the HDSS areas. Ethical approval was granted by the Comité d'Ethique pour la Recherche en Santé, Ministry of Health, Burkina Faso (approval number 2010-10, Ethical review board for health research in Burkina Faso). The dependent variables in this paper (as explained below) require us to limit our analysis to children between 12 and 59 months of age. Two sources were used to obtain this data for 4,985 young children eligible for inclusion. Fieldworkers asked to see children's vaccination booklets, which were produced in 74% of cases.
Children who died were probably those who were not immunized. A lack of information on religious beliefs and participation in religious activities requires us to limit our measures to religious affiliation as the proxy for religion in this study. A measure of religiosity would probably better capture the impact of religion on health behavior. Moreover, given the nature of the data used, the study could not test all the theoretical hypotheses that explain the relationship between religion and health. Only the selectivity hypothesis was tested and the results showed that it cannot alone explain the religious differences in children's vaccination rates in Ouagadougou. Finally, birth order was not included in this analysis due to a lack of data on the subject. Care given by parents to a child can often depend on birth order; the lack of inclusion of this information presents a limitation.
Acknowledgements The authors are grateful to the  Wellcome Trust , which provided the financial support to create and maintain the Ouagadougou HDSS, on which this study is based (grant number  WT0 81993MA ). The authors also wish to acknowledge the contributions of the field staff of the Ouagadougou HDSS and their important role in maintaining a good rapport with the study population. Central du  Recensement. Becher ,  H, Muller, O, Jahn, A, Gbangou, A, Kynast-Wolf , G, and Kouyaté, B 2004. "Risk factors of infant and child mortality in rural  Burkina Faso" Bulletin  of the World Health Organization 82:  265-273. BURKINA FASO,  MINISTERE DE LA SANTE 2003. Revue approfondie du Programme Elargi de Vaccination. Ouagadougou :  Ministère de la santé. Caldwell ,  J. C 1979. "Education as a factor in mortality decline: an examination of Nigeria data" Population Studies 33, (3):  395-415.
Data collection The instantaneous scan sampling method  [41]  was used to record the position of each visible individual inside the enclosure every 15 minutes. We collected 479 scans from the enclosure during the observation period. We then constructed a matrix considering the number of scans each time a dyad was seen to be in contact (contact matrix). We calculated a half-weight association index (HWI) for each pair of individuals: HWI~x xzy AB z0:5(y A zy B ) where x is the number of scans where A and B were observed associated, y AB the number of scans where A and B were not associated, y A the number of scans with A only, and y B the number of scans with B only  [42]. As we did not observe the entire group at each scan, the individuals were not all observed at the same frequency (chi-square test: x 2 = 456.
98, df = 17, P,0. 01). The half-weight association index therefore allowed us to control for absences. We then visualized the contact network with Gephi 0. 8. 1 (Gephi Consortium 2008,  [43] ). In order to investigate the stability of the network over time, the whole dataset was split into two equal periods: from April to mid-June and from mid-June to August. The comparison of association matrices for the two periods using the Dietz'R matrix correlation test implemented in Socprog 2. 4  [44]  revealed the two matrices to be significantly correlated (Dietz'R matrix correlation: R = 0. 249, P,0. 01), meaning that the social relationships observed during the two periods were similar. We also found that the number of associations observed per day corrected by the number of scans recorded per day was homogeneous over time (Fig.
1371/journal. pone. 0083015. t002 statistically not different from 0, linear regression, t = 21. 462, P. 0. 05). In conclusion, the network was stable over the entire observation period (April to August) and this allowed us to consider the whole dataset for the subsequent analyses. We established the dominance/subordination hierarchy of the group by recording spontaneous agonistic events (all-occurrences sampling,  [41] ). Socprog 2. 4 was used to determine individual rank. This hierarchy was significantly linear (1000 permutations, P,0. 001, h9 = 0. 632,  [45] ), and also significantly unidirectional (Dietz'R matrix correlation, r = 20. 531, P. 0. 05). We then constructed a hierarchy matrix, representing the rank difference within each dyad. Finally, we constructed matrices of sex, age and kinship.