dataesr/scientific-paragraphs-categorization huggingface dataset:
Then, in a second techno-legal part (part 3), we explore the concrete implications of the decision on web archiving. The RTBF is not the only problem facing web archiving, other challenges and regulations exist to remove content. After a presentation of the existing techno-legal arsenal to delete, we will explain that web crawlers do not archive everything and point to the more pressing issues facing web archiving. Finally, we explore the impact of the newest version of the RTBF, which will be implemented during 2016 in the European General Data Protection Regulation and actually mentions web archiving. We look at the detail of the new 'right to erase' contained in the Regulation, and we comment on a proposed exception for archiving in the public interest. We conclude with the broader challenges raised by privacy-by-design and the technical enforcement of 'digital forgetting'.
The socio-legal context Privacy, Data Protection and Freedom of Expression: legal concepts as cultural constructs In a video about surveillance and privacy, French activists La Parisienne Libérée and Jérémie Zimmermann remark that "everyone has something to hide" (Zimmermann & la Parisienne Libérée, 2014). It can be something innocuous, like a mild Farmville addiction, a guilty musical pleasure, or an embarrassing viral video. Some things can be more serious, such as a sexting session that has been made public, an incriminating picture that may seriously hinder future employment efforts, information about one's sexual orientation while living or working in a community that has low thresholds of tolerance; affiliation to a political entity or union. What if a link to that sensible personal information was made available online for the world to see? Could you have a legal recourse to remove it?.
8 As a response, Europe has a robust system to ensure the protection of personal data. Article 8 of the European Convention of Human Rights (ECHR) clearly specifies that "everyone has the right to respect for his private and family life, his home and his correspondence. " The main embodiment of this principle can be found in the application of the 1995 European Data Protection Directive (DPD), which enables the information selfdetermination 3 of European citizens  (Bygrave, 2002). The Data Protection Directive has the main objective of safeguarding the rights of an identified or identifiable natural person (known as a data subject), by setting a number principles and situations in which any information relating to the data subject (known as personal data) can be processed lawfully. Any legal entity that can determine the purpose and means of controlling a subject's personal data is known as a data controller.
9 The existing Data Protection Directive regime received in 2016 an update in the shape of the General Data Protection Regulation (GDPR). This text updates most of the existing provisions contained in the Data Protection Directive in order to better accommodate data protection to the digital era. Specifically, the GDPR contains specific provisions regarding the right to be forgotten, which we will be covered in more detail in the next section. 10 The right to privacy and the data protection regime do not exist in a vacuum: a person's right to enjoy a private life can often clash with other rights, particularly the right to freedom of expression present in Article 10 of the European Convention on Human Rights. Over the years, this conflict between privacy and freedom of expression has been the source of countless legal battles in the courts  (Bignami, 2008).
Indeed, the U. S. has been following an almost opposed view of privacy to that present in Europe, what Werro calls the 'right to inform'  (Werro, 2009) , and others have gone as far as labeling the 'right to remember'  (Balkam, 2014). This right does not exist in any legal sense, but the name neatly encapsulates the different approaches to privacy. While Europe has protected privacy to the point of creating a new right to be forgotten, the U. S. protects freedom of expression to the extent that it almost constitutes a right to remember. The European Data Protection Directive includes a principle stating that personal data from European citizens can only be transferred to a third country if the recipient territory provides an adequate level of protection for that data. The level of adequateness is assessed according to several circumstances, including "the nature of the data, the purpose and duration of the proposed processing operation or operations, the country of origin and country of final destination, the rules of law, both general and sectoral, in force in the third country in question and the professional rules and security measures which are complied with in that country.
This case seems to pit privacy against freedom of speech. Indeed, if a result cannot be found -even if it can technically be accessed to when performing another search query, based on other words than the name of the person (e. g. the facts or the date) -the practical effect will be obscurity. While the court does mention freedom of speech, and makes a few considerations about the ongoing balancing act between both, the main thrust of the legal opinion seems directed at the privacy issue. The Court comments: Indeed, since the inclusion in the list of results, displayed following a search made on the basis of a person's name, of a web page and of the information contained on it relating to that person makes access to that information appreciably easier for any internet user making a search in respect of the person concerned and may play a decisive role in the dissemination of that information, it is liable to constitute a more significant interference with the data subject's fundamental right to privacy than the publication on the web page.
Whilst it is true that the data subject's rights protected by those articles also override, as a general rule, that interest of internet users, that balance may however depend, in specific cases, on the nature of the information in question and its sensitivity for the data subject's private life and on the interest of the public in having that information, an interest which may vary, in particular, according to the role played by the data subject in public life. Notably, there have been a few decisions that support the interpretation that the right to be forgotten will be applied on a strict case-by-case basis. The most noteworthy case happened in the Netherlands, where a court used Google Spain to answer a request to remove links to potentially damaging information. A court in Amsterdam denied a request by the owner of an escort agency who was convicted for attempted incitement of arranging a contract killing, a matter currently under appeal (Spauwen & van den Brink, 2014).
Most of the application of the RTBF is centered towards removal of social media posts, with the top recipient of removal requests being Facebook. The second top recipient of removal requests is a website called Profile Engine, which gathers information held about individuals online. However, let us emphasize again that this analysis rests entirely on the little information available from the Google transparency report. More data is needed for a better analysis of the true impact of RTBF on freedom of expression and the public interest. Interestingly, another source of information for analysis of removal requests is to be found when third parties, which have had links to them delisted by Google, tell the public of such removals. The best source of information outside of Google at the moment is Wikipedia, as they have a reader-friendly transparency report that now includes RTBF request removals (see Wikipedia, Notices received from search engines).
The legal controversy: RTBF vs. Freedom of Expression Commentators around the world have both hailed and criticised the RTBF decision. On the one hand, opponents worry that the decision may interfere with free access to information, and that it will herald an era of abuse of these amendment orders, even if the court has specified that authorities should take into consideration the public interest aspect of the linked data (Zittrain, 2014). Supporters point out that there are valid reasons why a person would like some personal data not to show up when her name is searched, and that there should be a legal recourse to those whose privacy is being severely affected (Guadamuz, 2014). Overall, the coverage of the RTBF has been surprisingly negative. Particularly, commentary in the press and US academia has heavily criticised the decision.
It would be possible to deploy a similar regime for RTBF requests, both with more transparency and with a stronger system of protection for freedom of expression. While some of these concerns are legitimate, some critics apparently fail to understand how limited the new right is in practice. As stated before, the CJEU tried to base their decision on privacy, leaving out most of the balancing act between privacy and data protection. There is something to be said about the political power of remembrance, particularly in countries that housed secretive and repressive regimes where people were "erased" from history; but we must understand the Google Spain decision as a much more nuanced allowance to delist information to protect privacy. There has been a rush to assume that the right will affect data integrity and online archiving as mentioned in the introduction by Wikipedia founder and executives, or in a widely read blog (Hole, 2014); however, we argue that this is not what the ruling implies.
(Brügger, 2012). Commons-based solutions of peer archiving, such as the Day of Archaeology (Day of Archeology) initiative, are also developed to avoid the "digital dark age" of usergenerated content  (Jeffrey, 2012). Because of the Google Spain ruling, the RTBF and the right to erasure, and the general practices and notice and takedown, web archiving will not preserve the entire web. Does that really matter beyond open data extremists, and "memory-maniacs"? (Parmar, 2014). In reality, most of the content is not permanent. It disappears, sometimes even before it gets a chance to be archived: according to various studies, 85% within a year and 59% within a week (Ambrose, 2012), links get broken, hosting stops or dies, content gets overwritten. There is a "missing web" and web archiving is "almost always deficient" (Brügger, 2012).
" (Hockx-Yu, 2014). However, as section 3. 4 will discuss in more detail, the RTBF will be built into legislation as a new right to erasure contained in the General Data Protection Regulation, which will come into effect in 2016, and which will end-up going much further than the existing version of the RTBF contained in Google Spain. As discussed, there is currently no evidence to indicate that web archives are being affected by the RTBF, as they are already required to remove links to content. With the enactment of the General Data Protection Regulation it may be possible to foresee a future in which web archives will be required to perform actions that are more cumbersome than those already in existence. However, this is speculation, and we will need to wait and see. Web archives may have more reasons for concern in other de-listing and blocking practices, namely copyright, data materiality and mistakes.
The aforementioned General Data Protection Regulation (GDPR), which comes into force in 2016, repeals the Data Protection Directive and establishes an updated regime geared towards the digital age. One of the biggest changes present in the Regulation is that it consolidates the various rights and principles from the existing Directive that were dealing with outdated and/or erroneous data, and puts them together into a new fullfledged right, the "right to erasure. " Article 17 of the GDPR will create an obligation for Member States to provide data subjects with the right to obtain from the controller erasure of personal data where one of various requirements contained in Articles 5 and 6 have not been met. Some of these requirements relevant for the existing article are: The data is no longer necessary in relation to the purposes for which it was collected or processed.
The data subject has withdrawn his consent. The data subject objects to the processing and there is no legitimate grounds to deny this request. The data has been processed unlawfully. There is a glaring omission to the above, and it is the existing requirement that data "must be accurate and kept up to date. " While the proposed right to erase gives some more power to the user to object processing, the very founding principle behind Google Spain is no longer relevant. In some ways, this makes the right to erase very different from the RTBF version. Furthermore, Article 17 contains an inbuilt reference to balance with freedom of expression, paragraph 3 has an exception to the right to erase for the purpose of "exercising the right of freedom of expression and information. " This should hopefully lay to rest most of the criticism mentioned which see the RTBF as a possible threat to freedom of expression.
Conclusion: Forget and delete, Privacy-by-Design for web archiving While the right to be forgotten has been interpreted as a potential threat to freedom of expression, memory and web archiving, the intended application of the right to be forgotten has been limited in scope, at least as far as one can discern from the limited information available through Google's transparency report. Besides, web archiving professionals are already deleting instances on request, and other legal frameworks, namely copyright, are more likely to generate memory holes than RTBF. However, the entry into force of the General Data Protection Regulation should put most of the debate to rest, the presence of exceptions to the right to erase for both freedom of expression and archiving in the public interest serving to make potentially damaging disruption much more difficult.
ABSTRACTS This article studies the possible impact of the "right to be forgotten" (RTBF) on the preservation of native digital heritage. It analyses the extent to which archival practices may be affected by the new right, and whether the web may become impossible to preserve for future generations, risking to disappear from memories and history since no version would be available in public or private archives. Collective rights to remember and to memory, free access to information and freedom of expression, seem to clash with private individuals' right to privacy. After a presentation of core legal concepts of privacy, data protection and freedom of expression, we analyse the case of the European Union Court of Justice vs. Google concerning the right to be forgotten, and look deeper into the controversies generated by the decision.
Protein intensities were quantified using the MaxQuant software (Dataset EV1 and Data availability section) and normalized across the different conditions (see Materials and Methods). To determine whether a given detected protein was specifically associated with the CBL-OST (or CBLB-OST) bait over the course of an experiment, we compared for each time point the distribution of log-normalized intensities obtained for CBL OST (or CBLB OST ) and for wild-type CD4 + T cells. Each comparison yielded a value denoted as r(t) and specifying the enrichment observed in CBL OST (or CBLB OST ) CD4 + T cells as compared to wild-type CD4 + T cells and a corresponding P-value based on a one-way ANOVA test (denoted as P(t); Fig 2A). At a given time t, proteins were selected as specific interacting partners of the considered OST bait when both the P-value P(t) was below a set threshold and the corresponding enrichment r(t) was greater than twofold (see Materials and Methods).
In the case of the CBL signalosome, the number of interactors varied non-monotonously as a function of time, a peak of 63 interactors being detected 30 s after TCR stimulation followed by a second peak of smaller complexity 10 min after TCR stimulation. In contrast, the CBLB signalosome reached its greatest complexity 2-5 min after TCR stimulation (Fig  2E ). Therefore, the kinetics of assembly with and disassembly of the preys from the CBL and CBLB baits after TCR stimulation are not superimposable. 33 and 14% of the proteins identified as CBL and CBLB interactors, respectively, have been already reported in the BioGRID database  (Fig 2F). Such overlap corresponded to interacting proteins that in our study ranked among those with the highest maximum mean enrichment  (Fig 2C and D). Therefore, our approach provided a more comprehensive view of the CBL and CBLB signalosomes in that it encompasses a majority of interacting proteins not found the BioGRID database.
C, D List of specific interacting partners of CBLB (C) and CBL (D) ranked according to their maximum mean enrichment across all time points. Heat maps show, for each time point, the fraction of bootstrap iterations for which the corresponding proteins were detected as specific partners (denoted as "P(Detection)"). Red dots indicate the proteins that have been previously reported as CBLB (C) or CBL (D) interactors in the BioGRID database. Ubiquitin (UB) is highlighted with a black arrow.
FYN, a member of the SRC-family PTKs, interacted specifically with CBL but not CBLB, echoing its role in the recruitment of PI3K to CBL upon phosphorylation of the tyrosine residue found at position 731  (Hunter et al, 1999). Therefore, our analysis provided a comprehensive view of the CBL and CBLB signalosomes after TCR stimulation of primary CD4 + T cells, highlighting both the redundant and unique functional features of these two E3 ubiquitin-protein ligases and identifying 66 and 37 proteins not found associated with CBL and CBLB, respectively, in the BioGRID database.
Predicting PPIs using co-recruitment analysis To test whether the correlations observed in the timing of co-recruitment could be predictive of actual physical interactions between corecruited preys, we compared the interactions deduced from our CN analysis to the whole set of CBL-and CBLB-interacting partners reported in the BioGRID database. Among the 328 interactions predicted to exist on the basis of the CBL CN, 62 were already reported as physical interactions within the Homo sapiens and Mus musculus BioGRID databases  (Fig 4D). The probability of accurately predicting an existing interaction was thus 0. 19 (P = 62/328), a value largely exceeding the probability of 0. 06 (P = 302 × 2/ (98 × 97)) of finding one of the 302 reported interaction among N × (NÀ1)/2 possible interactions in a random network comprising N = 98 nodes.
TCR stimulation resulted in some CBLB degradation and in the detection of a higher molecular weight CBLB form, likely due its ubiquitylation (marked with an asterisk). In contrast, no degradation of CBL was detectable upon TCR stimulation and its molecular weight remained unchanged. Data are representative of at least two experiments. B Representation of the ubiquitin (UB) first-neighbors subnetwork within the CBL and CBLB CN. Edge width is coded according to Pearson correlation coefficient (R < 0. 8 or R > 0. 8). Red edges depict direct interactions reported in the BioGRID database. Ubiquitin (UB) is highlighted in yellow. C Immunoprecipitation of CBL from cell lysates of CD4 + T cells isolated from WT or CBLB-deficient mouse (Cblb À/À ) and kept unstimulated (À) or stimulated as in (A). Immunoprecipitates and whole-cell lysates (WCLs) were analyzed by immunoblot with antibodies specific for the proteins specified in the left margin.
Molecular masses are shown (kDa). Data are representative of at least two experiments. D Immunoprecipitation of CBLB from cell lysates of CD4 + T cells isolated from WT or CBL-deficient mouse (Cbl À/À ) and kept unstimulated (À) or stimulated as in (A). Immunoprecipitates and whole-cell lysates (WCLs) were analyzed by immunoblot with antibodies specific for the proteins specified in the left margin. to CBL or CBLB. Consistent with that view, immunoprecipitation of CBL from lysates of TCR-stimulated CD4 + T cells isolated from CD5-deficient mice showed that the absence of CD5 resulted in a drastic reduction in the extent of ubiquitylated proteins that coimmunoprecipitated with CBL as compared to TCR-stimulated wildtype CD4 + T cells (Fig  7A ). PIK3R1 (also known as PI3K p85a) is found in the sole CBL signalosome and akin to CD5 constituted a first neighbor of ubiquitin within the CBL CN (Pearson correlation coefficient of 0.
Flow cytometry Stained cells were analyzed using an LSRII system (BD Biosciences). Data were analyzed with the Diva software (BD Biosciences). Cell viability was evaluated using SYTOX Blue (Life Technologies). The following antibodies were used: anti-CD5 (53-7. 3), anti-CD4 (RM4-5), anti-CD8a (53-6. 7), and anti-CD45R (R3-6B2), all from BD Biosciences. For analyzing, the relative intracytoplasmic amounts of CBL and CBLB in double-positive thymocytes and CD4 + T cells from the spleen, cells were stained with antibodies directed at CD5 (53-7. 3), CD8a (53-6. 7), and CD4 (RM4-5), permeabilized with BD Cytofix/Cytoperm (BD Biosciences) for 30 min at 4°C, and then stained with saturating amount of Strep-Tactin APC (IBA GmbH).
Protein identification and quantification Raw MS files were processed with MaxQuant software (version 1. 5. 0) for database search with the Andromeda search engine and quantitative analysis. Data were searched against Mus musculus entries in the UniProt protein database (release UniProtKB/Swiss-Prot 2014_09; 16,699 entries). Carbamidomethylation of cysteines was set as a fixed modification, whereas oxidation of methionine, protein N-terminal acetylation, and phosphorylation of serine, threonine, and tyrosine were set as variable modifications. Specificity of trypsin digestion was set for cleavage after K or R, and two missed trypsin cleavage sites were allowed. The precursor mass tolerance was set to 20 ppm for the first search and 4. 5 ppm for the main Andromeda database search. The mass tolerance in tandem MS mode was set to 0.
5 Da. Minimum peptide length was set to seven amino acids, and minimum number of unique peptides was set to one. Andromeda results were validated by the target decoy approach using a reverse database at both a peptide and protein false discovery rate of 1%. For label-free relative quantification of the samples, the match between runs option of MaxQuant was enabled with a time window of 0. 5 min, to allow cross-assignment of MS features detected in the different runs.
Identification of specific binding partners To identify specific CBL-and CBLB-binding partners, we used the intensity metric from the MaxQuant protein group. txt output (sum of peptide intensity values for each protein) normalized by iRT standard peptides (Dataset EV1). Protein intensities were first normalized by adjusting the mean log intensities corresponding to all the proteins that were detected at all times points and in all biological and technical replicates of CBL OST , CBLB OST , and wild-type origins. To replace missing protein intensity values, we estimated the statistics of background signals from protein intensities of wild-type samples. Accordingly, for each detected protein, the mean and standard deviation of log-transformed wild-type intensities were calculated. Missing values were then replaced by sampling from a log normal distribution centered on the 5-percentile of the distribution of mean log wild-type intensities with a standard deviation set to the mean standard deviation of log wild-type intensities computed across all detected proteins.
Pie charts showing the percentages of CBL and CBLB interactors detected in both the present study and the BioGRID public database. The size of the pie charts is proportional to the numbers of interactors per bait. Molecular Systems Biology 12: 876 | 2016 ª 2016 The Authors Molecular Systems Biology Assembly dynamics of the CBL and CBLB signalosomes Guillaume Voisinne et al overrepresentation of annotations related to "signaling adaptor activity" and "role in protein degradation" was observed (Fig EV3).