dataesr/scientific-paragraphs-categorization huggingface dataset:
New forms of evaluation were put into practice, closer to the peer review system used in highly reputable academic journals. The biggest consequence of the new project-based funding procedure in the ANR grant system is the considerable change in outlook brought about by a radical change from a system in which teams had to work with the more or less generous amount allocated on a quadrennial basis, to a new system in which supplementary resources could be obtained through competitively funded projects. Unfortunately, this revolution only affects the SSH in a limited way, partly because of the long-lived reflexes of managing penury, partly because the available funds are much more limited than the investments in other scientific domains or in technological development. ANR priorities clearly favour scientific domains, which are considered as better contributing to industrial leadership and in responding to societal concerns.
1). 11 Depending on his or her status, two to four 'first-class publications' ('productions de rang A') by period of four years are supposed to earn a researcher the 'produisant' label; patents, databases and other similar products are accepted as an equivalent. The problem is that there is no clear reason for the number of publications requested (why not one or six, for instance?), while the rigid classification of the outputs is inappropriate in many disciplinary fields (see infra). Besides, the thorough characterization of journals and books, recommended initially by the AERES to define the channels of first-class publications, proved to be highly complicated. Even a simple glance at the produced lists, displayed on the AERES site, reveals tremendous problems. On one hand, these lists have evolved, following major criticisms from the academic community, from being graded league tables (A, B and C or international, national and limited reputation) to a collection of titles whose very inclusiveness 12  is at odds with the 'first-class publications' claim.
The evolution of the French higher-education system during the last years, as well as the external and the internal pressure, has opened the field for initiatives like the DisValHum and the IMPRESHS projects. The starting point for the DisValHum and IMPRESHS projects is the realization that many of the problems observed in research evaluation in France stem from an insufficient-and, in certain cases, nonexistent-observation of the domain to be assessed and a lack of engagement with the stakeholders, principally the researchers themselves. The situation is even more acute for the SSH, where the preliminary analyses rarely go further than a few platitudes ('SSH publish more books than articles', 'SSH journals are not included in international databases', 'workshops and conferences are important in the SSH'), clumsily taken into account in the various evaluation activities.
Our aims are: First: to analyse the forms of dissemination, starting from what researchers do (as reflected in their CVs), and not from various preconceptions, based, in most cases, on practices in other fields or on the personal experience of the category designer. The idea is to avoid Procrustean solutions like those imposed by the official reporting, which asks all academics, irrespective of their field, to classify their production in fixed categories. Such categories are not necessarily clear, as there is, for example, no precise definition about what constitutes an international or a national conference. They are also incomplete. Among the most visible gaps are the lack of a category for critical editions or translations, frequent in the SSH, and also the nonexistence of categories such as databases or websites for scientific information.
The channels will be further characterized by using objective descriptors, such as presence in international databases or not (for journals), and international distribution or not (for publishing houses), etc. Once again, the aim is to start from the bottom and not from top-down defined lists. Fifth: to understand the reasons motivating the choice of these channels, as well as of the publication formats adopted. On one hand, we try to understand if maximising the scientific impact constitutes a preoccupation of Breton researchers when they publish; on the other hand, the requirement is to track their ideas about how and why they interact with the wider public. To fulfill these aims, our first concern has been to build a research products database. A preliminary study was conducted on a small number of CVs published online by researchers in French literature, linguistics, history and law, since these are the domains covered as a priority by the projects.
The study was meant to identify the types of research products created by SSH researchers, whether as written material or not. This pilot study was completed by a study of categories selected by various information systems, such as CRISTIN in Norway, VABB-SSH in Flanders (Belgium), or RIN in the United Kingdom. These categories were then tested on a larger scale with the help of the students from the Master of Digital Humanities in Université de Bretagne-Sud. These gathered as many CVs of Breton researchers as possible in the considered domains, helped refine the categories and the structure of the database, and provided the first statistical calculations. For all these reasons, the number of categories finally selected is much larger than that of any of the considered CVs; the differences have proved interesting in themselves as both the focus groups and inter-views have demonstrated that the non-inclusion of an item in a CV does not translate necessarily into the nonexistence of such a product in the activity of the considered researcher.
Its absence is merely a form of self-censorship, sometimes related to the perceived expectations of the external evaluation bodies. 17 In such situations, topdown criteria imposed without a preliminary study of the ground clearly result in a loss in information and, moreover, of potential arguments for demonstrating the social impact of the SSH. The database, which is currently under development, is organized into four main sections: books, articles (whether in journals or collected works), other written material and non-written material. A comparative list in the appendix of this article shows the types of products it covers, compared to those taken into account by the UK RIN analyses. Authors are characterized by their affiliation (institution and research unit) and by domain (CNU section); a CNU section is conventionally attributed to foreign researchers who cooperate with Breton academics.
This has the disadvantage that CNU sections are extremely broad, but does mean that precision can be reached a posteriori using a study of dissemination types and focus group output rather than imposing further subdivision. Co-authorship characterization allows for social network analysis, which will be confronted with a similar analysis conducted on institutional contacts of research units. Moreover, geographical information is available (city and country of authors, and country of publication), making it possible to map visualizations of research contacts. The basic information as to who, what, where and when is entered in the database. In each section, broad classes of channel and type are used. These remain sufficiently broad to handle all the data included in an individual CV. Only when the database has reached a reasonable size will work start on trying to classify the input in more detail.
This is particularly the case with the 'other' section, which contains a rich variety of outputs that probably have a wider social impact than those in a standard CV. As the aim is to get an overall picture of different research groups and different disciplines, we are not concerned with individual researchers, but will look at individual cases when necessary. The highly time-consuming operation of establishing a database was necessary because information about the SSH production of the researchers in our perimeter is incomplete, unusable, or inaccessible. The institution in charge of producing indicators for research and innovation in France, namely, Observatoire des Sciences et des Techniques, covers the SSH production only on an exceptional basis (Filiatreau  2010) and in doing so relies on the Thomson-Reuters database.
If this choice is justified by the benchmarking purposes of the report, it proves clearly inadequate to answer the practical questions listed previously. As a responsible scientific organization, the CNRS is fully aware of the need for quality checks. Consequently, it has put into place its own internal survey, called RIBAC (Dassa and Sidéra 2011). Unfortunately, this information system concerns only CNRS, and despite talk of imposing on universities, it is more than probable that the current government will abandon the idea. This is not altogether a bad thing, as it is far from certain that RIBAC categories are adapted to the EC. The typology of research products also tends to be very restrictive. A full comparison with other databases has not been possible as yet as the CNRS has not made access to the structure publicly available.
It is however clear that the non-written material, as well as research reports of all types and forms, are underestimated, which does handicap impacts studies as that envisaged here. A national database of research output, HAL 18  -Hyper articles en ligne-that collects research outcomes from French researchers, has existed since 2006 ('HAL:  Accueil', 2013) as an open repository. HAL SHS, a specific site for the SSH managed by the CNRS, is used by researchers wishing to put data online. This is not compulsory and, given the extreme lack of user-friendliness, many researchers do not submit; thus, its coverage is only partial. Data can be exported in csv format, but an attempt to nourish our database showed that a great deal of what was necessary, coupled with the non-compulsory nature of the repositories, meant that such an operation is not feasible in the immediate future.
The imposed categorization also introduces a further difficulty, as researchers either leave out aspects of their work or misinterpret the categories. Technological changes, as well as policies of major research groups, are rapidly rendering the HAL database redundant. Lastly, research group activity reports, established for the quadrennial evaluation performed by AERES, have appeared unsatisfactory as evaluation research tools. Not only do many laboratories not publish these reports, but when the reports do exist, the laboratories list only the productions of the previous four years. Inside each report, bibliographical references are far from unified, rendering impossible an automatic translation of the information into our database. Parallel to the building of the database, which is still in the long phase of manual data entry, a series of group interviews with SSH scholars from various research units in Brittany are being conducted.
Outcomes Following initial focus groups and observations of the database, one thing is very clear: there is an enormous mismatch between what goes into CVs, what is accepted by AERES and how researchers see the dissemination of their research. The interpretations of the AERES classification codes vary widely, between those researchers who put in all their activities, no matter how trivial, and those who leave out activities such as speaking to the general public-considering that the CV deals only with 'research'. This is summed up neatly by an English language specialist who asked whether pedagogical dissemination (course material) could be treated as research dissemination: 'Est-ce que la dissémination pédagogique compte, est-ce que les cours comptent?' [Does pedagogical dissemination count, does teaching courses count?] This is a delicate question to ask in that many SSH scholars write material for the French competitive exams governing entry into the secondary school system as teachers.
We try to collect precise identifications of these partners to conduct cross-interviews in the manner of those recommended by the ERiC method. In quantitative terms, the image about SSH publication coming from the database is, for the moment, as in Table  1. The dominance of books and book chapters is clear in history and literary studies, but these figures must be treated with care. Published chapters may be, in fact, published proceedings, something that is rarely declared in English, but is always noted in the sectors of law and history. The AERES classification lumps together books and book chapters and groups papers in proceedings with either national or international conferences. It is possible that the book section is considered more prestigious by English specialists, hence the preference to declare a chapter to a proceedings article.
2a ) in the presence and absence of bound zinc. Zinc release was monitored at 500 nm using the PAR assay. The two methods showed good agreement for the bimolecular rate constant for diamide-induced oxidation of RsrA red. Zn 2 þ (183±6 and 195±11 M À 1 s À 1 , respectively). (b) Zinc release from the RsrA red. Zn 2 þ -s R complex (2 mM) on treatment with increasing concentrations of diamide under pseudo-first-order conditions monitored by the PAR assay; 25 mM (filled diamonds), 50, 100, 150 and 200 mM (open diamonds). Inset shows variation of k obs with diamide concentration (with associated error bars). Data were fitted to the Michealis-Menten equation, with fitted parameters of K 1 ¼ 0. 7 mM and k 2 ¼ 0. 15 s À 1 (Supplementary Fig. 2b ). The corresponding bimolecular rate constant (k 2 /K 1 ¼ 214 M À 1 s À 1 ) is in reasonable agreement with values obtained in a.
Data collected as ellipticity in millidegrees were converted to mean residue ellipticity, (y; degrees cm 2 per dmol residue). Native state mass spectrometry of protein complexes. Intact mass spectrometry measurements were performed on a Waters Synapt G2 HDMS modified for high mass transmission (ref. 41). Samples were buffer exchanged into 25 mM ammonium acetate using BioSpin 6 (Bio-Rad) columns before mass spectrometry (MS) analysis. Typically, each measurement was performed by loading 3 ml of protein sample into gold-coated nanospray capillaries prepared in-house  42  and loaded into a static nanospray block providing the spray voltage. Electrospray was induced by applying a potential of between 0. 9 and 1. 2 kV to the capillary. A sample cone of 50 V was used to capture the charged droplets, with a source backing pressure of 5.
5 mbar. The instrument was operated in time-of-flight mode (no ion mass spectrometry separation), with the trap and transfer collision cells held at an acceleration voltage of 10 and 5 V, respectively (with an argon pressure of 2 Â 10 À 2 mbar). Data were processed using the MassLynx software. For high-resolution MS measurement, a Thermo Scientific Q-Exactive hybrid quadrupole-Orbitrap mass spectrometer was used to measure the presence/absence of the disulfide in the RsrA* Cys11His-s R complex. The instrument was modified for high mass measurement as described elsewhere  43, 44  and optimized for retention of non-covalent interactions. Hardware alterations include a lower radio-frequency (RF) applied to the selection quadrupole and a gas line allowing higher pressures to be achieved in the higher-energy collisional dissociation (HCD) cell.
Glutathione and glutathione disulfide were from Sigma-Aldrich. Fluorescence titration experiments were carried out in 50 mM Tris (pH 7. 5) buffer and 100 mM NaCl at 25 °C. All buffers were degassed and purged with N 2 gas before the use. In all experiments, GSH was kept constant at 0. 5 mM, while GSSG was varied from 100 mM to 100 mM. The RsrA red. Zn 2 þ -s R complex was at 2 mM. All samples were incubated with the redox couple for 2 h before data collection. Two hours was deemed as having reached equilibrium since longer incubations had no effect. Data were corrected for the inner-filter effect, as described  45. Inclusion of the PAR reagent does not influence redox titration experiments, since its affinity for zinc is several orders of magnitude lower than that of RsrA  46. Positive and negative controls were collected at each redox couple concentration.
The concentration of diamide at various time points was computed by determining the ratio of diamide consumed relative to a control in which 25 mM diamide was converted to the hydrazine form using 500 mM DTT. Raw data were then linearized by plotting the variation of 1/ [diamide] against time from which the second-order rate constant for diamideinduced oxidation was determined. Zinc release from the RsrA red. Zn 2 þ -s R complex on oxidation with diamide was measured using 100 mM PAR, which absorbs at 500 nm on zinc binding  46. The second-order rate of diamide-induced release of Zn 2 þ was determined as described above using the PAR assay. For pseudo-first-order experiments, only zinc release was monitored from the RsrA red. Zn 2 þ -s R complex (2 mM), where diamide was varied from 25 mM to 20 mM.
Charge states 1 þ and 2 þ were excluded from HCD fragmentation. MS data were converted into mgf format using MSconvert from the ProteoWizard toolbox  50  and searched using the pLink software  51. The database contained the target proteins only (RsrA and s R ). Search parameters were as follows: maximum number of missed cleavages ¼ 2, fixed modification ¼ carbamidomethyl-Cys, variable modification 1 ¼ oxidation-Met, variable modification 2 ¼ Glu to pyro-Glu, mass shift of BS2G-d 0 ¼ 96. 02113, mass shift of BS2G-d 4 ¼ 100. 04583, mass shift of BS3-d 0 ¼ 138. 06809, mass shift of BS3d 4 ¼ 142. 09279, mass accuracy filter ¼ 20 p. p. m. for precursor ions with consideration of the first five isotopic peaks, MS2 tolerance ¼ 20 p. p. m. Data were initially filtered by E-value (Eo1. 98e À 4). Crosslinks were further inspected by checking the presence of the peak pair in the MS spectra generated by the d 4 /d 0 mixture, as well as fragmentation patterns.
With the exception of experiments to measure residual dipolar couplings (RDCs; see below), all the NMR experiments were performed on a Bruker Ultrashield 700 MHz spectrometer with triple ( 1 H,  15  N and 13 C) nucleus (TXI, Bruker Biospin) probe equipped with z gradient coils, running TopSpin (Bruker BioSpin) software and belonging to the University of York Centre for Magnetic Resonance. All experiments were performed at 298 K with NOESY mixing times of 100-150 ms and a TOCSY mixing time of 50 ms. Processing and assignment of NMR spectra. All spectra were processed using NMRPipe  55. Backbone and side-chain assignments were made using a standard suite of three-dimensional (3D) triple resonance experiments HNCA, CBCANH and CBCA(CO)NH, HNCO and HN(CA)CO in addition to 3D  15  N-1 H-HSQC-NOESY and  15  N-1 H-HSQC-TOCSY.
NOEs were assigned using 3D NOESY and two-dimensional 1 H-1 H NOESY experiments. Assignments were made using CcpNmr Analysis version 1. 0 (ref. 56). Chemical shift assignments were deposited at BMRB (accession numbers 25,955 and 25,956 for RsrA red. Zn 2 þ and RsrA Ox , respectively). Residual dipolar couplings. The 1 H-15 N RDCs 57 were recorded using antiphase/in-phase experiments 58 at 14 T ( 1 H larmor frequency of 600 MHz) at the University of Southampton using a 5% C12E6/hexanol (r ¼ 0. 64) liquid crystalline medium as an alignment medium  59. Data in the isotropic and aligned state for both the RsrA red. Zn and RsrA ox samples were acquired at 298 K with sweep widths of 10,000 and 1,800 Hz, and acquisition times of 51 and 100 ms, for 1 H and 15 N, respectively. The observed deuterium splitting in the aligned state was 24 Hz for both the zinc-bound and oxidized samples.
The data were processed with NMRPipe 55 and were further analysed with Sparky 60 using the built-in peak fitting module to determine the peak positions. Errors were estimated to be 1 Hz. The RDCs (40 restraints for RsrA ox and 29 for RsrA red. Zn 2 þ ) were analysed using Module  61  and incorporated into the structure calculations during refinement. Structure calculation and validation. One hundred structures were calculated using the program CNS  62  (Table  1 ). The Ser42-Pro43 peptide bond was modelled in the cis-conformation (using the CIPP patch) in the structure of RsrA red. Zn, based on the presence of an NOE between the Ha atoms of Ser42 and Pro43 and between Hb of Ser42 and Ha of Pro43 and on the lack of NOEs between Ser42 Ha and Pro43 Hd that would be characteristic of a trans-conformation.
In RsrA ox , however, this bond was modelled in the trans-conformation based on observed NOEs between Ser42 Ha and Pro43 Hd. An additional patch was generated for inclusion of the zinc atom and modification of the zinc ligands (Cys11, His37, Cys41Ser and Cys44) in RsrA red. Zn. Estimates of backbone dihedral angles were obtained using TALOS  63  ; only restraints for residues that had 'good' predictions were included. Accessible molecular surface areas on a per residue basis (averaged over the 10 lowest-energy structures for RsrA red. Zn 2 þ and RsrA ox ) were calculated using WHAT IF  64. Structure coordinates of RsrA ox and RsrA red. Zn 2 þ have been deposited in the Protein Data Bank (5frh and 5frf, respectively). determined NMR structures of RsrA. J. Y. , J. T. S. H. , S. M. and C. V. R.
Acknowledgements We thank  Nick Housden  and  Grigorios Papadakos  ( Department of Biochemistry, Oxford ) for guidance on the kinetic and thermodynamic measurements in this paper. We are indebted to  Mark Buttner  and  Morgan Feeney  ( John Innes Centre, Norwich ) for comments on the manuscript,  Joseph Gault  ( Department of Chemistry, Oxford ) for help with acquiring high-resolution MS data and  David Staunton  ( Molecular Biophysics Suite, Oxford ) for help with biophysical measurements. This work was funded by  BBSRC  grant  BB/I008691/1. J. R. P. holds a  British Heart Foundation Senior Basic Science Fellowship  ( FS/12/36/29588 ), J. M. W. and L. P. would like to thank the  Wellcome Trust  for support of the  Southampton NMR centre  (grant no. :  090658/Z/09/Z ) and the  MRC for support of the Biomedical NMR Centre at Mill Hill  (grant no.
Data availability. Structure coordinates of RsrA ox and RsrA red. Zn 2 þ have been deposited in the Protein Data Bank (5frh and 5frf, respectively). NMR assignment data have been deposited at BMRB (accession numbers 25955 and 25956 for RsrA red. Zn 2 þ and RsrA Ox respectively). All other relevant data are available from the authors on request.
Fog is considered to be a primary challenge for free space optics (FSO) systems. It may cause attenuation that is up to hundreds of decibels per kilometer. Hence, accurate modeling of fog attenuation will help telecommunication operators to engineer and appropriately manage their networks. In this paper, we examine fog measurement data coming from several locations in Europe and the United States and derive a unified channel attenuation model. Compared with existing attenuation models, our proposed model achieves a minimum of 9 dB, which is lower than the average root-mean-square error (RMSE). Moreover, we have investigated the statistical behavior of the channel and developed a probabilistic model under stochastic fog conditions. Furthermore, we studied the performance of the FSO system addressing various performance metrics, including signal-to-noise ratio (SNR), bit-error rate (BER), and channel capacity.