dataesr/scientific-paragraphs-categorization huggingface dataset:
broadinstitute. org/allpaths-lg/blog/?p=647. Admixture and introgression analyses. Short read data for Hybrid, Baltic gray seal, Baltic ringed seal, and Saimaa ringed seal were mapped to the Weddell seal reference genome. Similarly, the reference Weddell seal individual's short read data was mapped to its reference genome. The mapping was conducted using bwa mem (v. 0. 7. 15), samtools rmdup (v. 1. 3. 1) and GATK IndelRealigner (v. 3. 7). The resulting bam files were used for introgression and admixture analyses. To examine the hybrid, an admixture analysis was carried using NgsAdmix  (Skotte et al. , 2013)  and the pipeline at: http://www. popgen. dk/software/index. php/NgsAdmix. To reduce computational burden, a random sample of 3. 6 million markers (10% of the data) were used to reduce the computation burden.
NgsAdmix was run 10 times with K=2 clusters on the hybrid, gray and ringed seals. Each of these runs converged to identical clustering. Introgression was studied using Patterson's D-statistics  (Green et al. , 2010)  that, other than requiring the ancestral population to be randomly mating, is robust to variables such as variations in population size  (Durand et al. , 2011). D-statistics was calculated by abbababa2 module of ANGSD  (Korneliussen et al. , 2014)  using the first 1,000 scaffolds of the Weddell genome (over 50% of the genome) and the default pipeline at: http://www. popgen. dk/angsd/index. php/Abbababa2. To examine individual differences, the D- Genetic distances. To obtain a relatively robust and comparable measure of genetic distances between the hybridizing species pairs, we analyzed fourfold degenerate (ffd) sites from a large number of orthologous genes.
As substitutions on ffd sites do not alter the encoded amino acid, they can be considered a proxy of the neutral evolutionary process and thus be relatively free of biases due to selection. A list of single-copy human genes and their orthologs in cat, dog, horse and chimpanzee were fetched from Ensembl BioMart (v. 83)  (Kinsella et al. , 2011). 4,826 complete gene sets with unambiguous orthology ("Homology Type" is "ortholog_one2one"; "Orthology confidence" is "high") were retained and, for each reference species, nucleotide and peptide sequences of every transcript were fetched using the Ensembl REST API  (Yates et al. , 2014). Using last (v. 658)  (Kiełbasa et al. , 2011) , scaffold-level genome assemblies of tiger, Weddell seal and donkey were aligned against the genomes of cat, dog and horse, respectively.
Lift-over chains were built using the Kent source utilities  (Kent et al. , 2002). Short read data for donkey and lion were mapped to the horse and tiger genomes using bwa mem (v. 0. 7. 15), samtools rmdup (v. 1. 3. 1) and GATK IndelRealigner (v. 3. 7)  (Li and Durbin, 2009; McKenna et al. , 2010). Locally generated short read data for Baltic gray seal and Baltic ringed seal were mapped to the Weddell seal genome. The data for the Neanderthal human individual were obtained as bam alignment files. Data sources are listed in Table supp. 2. The gene annotations were divided into individual coding exons, removing split codons where necessary, and the exon coordinates in reference species (human, cat, dog, horse) were transferred to related non-reference genomes using CrossMap (v. 0. 2. 4)  (Zhao et al.
The exon regions of each transcript were extracted and combined into one sequence. Sequence data were obtained for 4,329 genes. These sequences were aligned, selecting the longest transcripts, with Pagan's translated pileup alignment. To remove artefacts of low quality sequence (for example, due to assembly errors), resulting multiple sequence alignments were filtered and regions where two neighboring codons contain more than one non-identical base among all the study species were masked. For different species sets, gene sequence alignments of at least 100 columns in length after filtering and removal of sites with missing data were concatenated, and ffd sites were extracted using R package rphast (v. 1. 6. 5) (Hubisz et al. , 2010). Pairwise genetic distances were computed using R package ape (v.
3, 4. Dental material and analyses. Baltic gray and ringed seal material was used in comparisons to the hybrid as the parents were reported to be from the Baltic Sea (Dataset supp. 1, Table  supp. 5 ). Postcanine teeth of seals are laterally compressed resembling early mammalian morphologies, and the lateral views capture most of the shape variation  (Jernvall, 2000). Images were taken from the lingual views from a distance (approximately ten times the length of the tooth row) and the number of cusps and top-cusp angles were tabulated using ImageJ (version 1. 51). The angle captures the relative height of the tallest cusp, and correlates with cusp number because cusp spacing and number are developmentally linked  (Jernvall, 2000; Salazar-Ciudad and Jernvall, 2010). For teeth that had only one or two cusps, the line was drawn to the maximum anterior or distal ends at the crown base.
3B, Table supp. 7 ). These different combinations basically simulate how additively the parameters function, but do not imply that each parameter would have one underlying locus. Rather, we consider the simulations to approximate the overall developmental effect of the genetic backgrounds. ToothMaker software, is freely available for Windows, MacOS, and Linux (available from the authors and with default seal parameters at https://github. com/jernvall-lab/ToothMaker). Analysis of the crania. 31 ventral and 22 dorsal 3D landmark coordinates were acquired from skulls of complete ontogenetic series (from newborns to adults) of gray and ringed seals from the collections of Finnish Museum of Natural History (Helsinki, Finland) using a Microscribe G2X digitiser with 0. 2 mm accuracy (Immersion). These data were merged together into a full configuration of 46 landmarks using FileConverter  (Klingenberg, 2011) (Figure supp.
5A). The hybrid was compared to the geometric morphometric mean and differences were visualised via warping and heatmaps  (Figure supp. 5B and C). A multivariate quadratic regression of shape onto centroid size was used to investigate the main patterns of allometric growth for each species that were visualised with warped 3D microCT-scans of a newborn gray and ringed seal using Landmark Editor 3. 6 and function 'warpmovie3d' (Figure  5 , Movie supp. 1)  (Wiley et al. , 2005; Gerber and Hopkins, 2011; Schlager, 2017). All analyses were performed with MorphoJ 1. 06d  (Klingenberg, 2011) , custom R (R Core Team, 2009) and Python scripts.
review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available understatistics were calculated for each Baltic individual in addition to the Baltic sample. The Saimaa ringed seals were set as P1, Baltic ringed seals as P2, and Baltic gray seals as P3. The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB25679.
Acknowledgements. We thank  S. Mallick  and  S. Martin  for discussions and advice on genome related analyses,  J. Laakkonen ,  M. Kunnasranta , and  M. Olsen  on seal biology. We thank the members of the Saimaa Ringed Seal Genome Project for help, for collections access and specimen loans we thank  I. K. Hanski  and  E. -S. Hyytiäinen  from the  Finnish Museum of Natural History (Helsinki, Finland)  and  D. Kalthoff  from the  Museum of Natural History (Stockholm, Sweden) , who also helped us to locate the hybrid specimen. We thank  UH  librarians for help with old reprints, and  H. Suhonen ,  A. Kallonen ,  M. Christensen , and J. CC-BY-NC-ND 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available understatistics were calculated for each Baltic individual in addition to the Baltic sample. The Saimaa ringed seals were set as P1, Baltic ringed seals as P2, and Baltic gray seals as P3. The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB25679. certified by peer The copyright holder for this preprint (which was not this version posted April 29, 2018. ; https://doi. org/10. 1101/310789 doi: bioRxiv preprint. CC-BY-NC-ND 4. 0 International license a.
Introduction The local newspaper can be regarded as an enormous database  (Mathien 1986 ) that contains information regarding the type, location, time and duration of natural hazards occurring in the newspaper's catchment (e. g. ,  Guzzetti et al. 1995 Guzzetti et al. , 2003;; Hilker et al. 2009; Petrucci et al. 2010). The newspaper content also contains details regarding damage and loss. As a result, Russell Blong's source book on volcanic hazard  (Blong 1984) , for example, draws heavily on information contained in newspaper reports to document societal impacts of eruptive events. The newspaper also records scientific, governmental, service-provider, responder, and community actions, responses and reactions during a volcanic emergency  (Harris et al. 2012 ). However, agenda-setting, spin and framing are all part of creating the news  (Cohen, 1963; McCombs and Shaw 1972; McCombs 2014a, b; Vu et al.
In this regard, media reporting can be viewed as a key means to educate a population allowing it to better prepare for, and respond to, a natural hazard  (Coppola 2015). In step 2, we assess whether the newspaper format is tabloid. From the point-of-view of the volcanologist this is important because, if a volcanic event is deemed newsworthy for the tabloid, then the event will be reported, and hence information will be disseminated. Finally, in step 3, we use the newspaper content to build a database regarding the impacts of the event on the impacted population, as was done for example by  Blong (1984)  for volcanic hazards and by  Sterling (1997)  and  Séchet (2004)  for weather-related hazards, thereby creating a timeline for the societal impacts of the natural hazard. Understanding how information is filtered and represented informs on how we can interact with the media to maximize the effectiveness, and correctness, of the message delivered.
As a result, there was extensive coverage. Based on databases we have for newspaper reporting of natural hazards in the USA, the UK, France and Italy, we argue that extensive coverage of volcanic eruptions, landslides, and storms impacting the readership is indeed a feature of tabloid coverage (e. g. ,  Harris et al. 2012; Harris et al. 2015a, b; Harris and Lanfranco 2017; and other unpublished data). For example, during the air space closure due to the 2010 eruption of Eyjafjallajökull, the British tabloid, The Sun, published by far the greatest amount of information of seven newspapers analyzed, devoting around 30,000 cm 2 of newspaper space to the event over eight days, as opposed to just 1000 cm 2 of information that appeared in the French broadsheet, Le Monde  (Harris et al. 2012 ). The tabloid thus provides an enormous amount of information to its readership regarding natural hazards.
Conclusion Generally, reporting of the April 2007 eruption of Piton de la Fournaise in JIR can be viewed as close to a blueprint for hazard communication through a newspaper. The April 2007 eruption and its effects received high volume-news status, appearing on the front page as each new eruptive phase and associated hazard unfolded. This was due to the fact that a volcanic eruption, especially one which impinges on the local population, fits many (if not all) of the tabloid-newspaper news values. Reporting was accurate, well-supported and researched, and followed the evolution of the eruption, reviewing each new hazard as it evolved, with quotes mainly expressing warning, followed by alerts and impacts, and then response. It was, thus, an exceedingly useful educative tool. In terms of a database and information source for natural hazards, when tabloid newspapers are involved, the local newspaper is an enormous and valuable resource.
Acknowledgements We thank  Francois Martel-Asselin  for answering our many questions about reporting during the eruption of April 2007. We are also exceedingly grateful to  Philippe Le Claire  (Director of the JIR) for granting us permission to reproduce JIR material and front pages to support this study. Two anonymous reviewers, the associate editor ( Ilan Kelman ), and the editor-in-chief (Jan Lindsay) provided excellent advice on how to better communicate this work. This is ANR-LAVA contribution no. 2.
Funding This work was funded by the  Agence National de la Recherche  (ANR: www. agence-nationale-recherche. fr) through project  ANR-LAVA  ( ANR Program :  DS0902 2016 ; Project:  ANR-16 CE39-0009 , Link: www. agencenationale-recherche. fr/?Project=ANR- 16-CE39-0009 ).
| DISCUSSION The first part of this Statement focuses on the possibility of HIV transmission during specific acts that are commonly considered in prosecutions: sexual activity, biting or spitting  [3]. It does not reference other ways HIV may be transmitted, for example, through blood transfusion, needle stick injury, injecting drugs or breastfeeding. An initial meeting in Seattle (February 2017) decided the contents and framing of this Consensus Statement. A detailed literature review was prepared based on a search for literature published in English using the PubMed online database up to April 2017. Specific search terms relating to the possibility of HIV transmission were used, including "HIV and viral load, " "HIV sexual transmission risk per act, " "oral sex HIV transmission, " "anal sex HIV transmission, " "vaginal sex HIV transmission condom per act, " "anal sex HIV transmission condom per act, " and "anal sex HIV transmission circumcision per act.
Interpretation of phylogenetic results for forensic purposes requires expertise about phylogenetics and the distinction between virus evolutionary trees and transmission histories. This is not straightforward and methodologies have not yet been standardized  [155]. The reliability of evidence derived from phylogenetic analysis depends on a number of methodological factors including use of adequate "local controls"  [164] [165] [166]  and database sequences  [167] [168] [169]  which must be selected using consistent selection criteria  [155]. International research shows that phylogenetic evidence used in criminal trials has not always satisfied these requirements  [155].
Since its launch for the treatment of erectile dysfunction in 1998, a particularly strong evidence base for the efficacy and safety of sildenafil in the treatment of ED has been established, comprising the highest number of studies and published scientific papers in this drug class. For example, more than twice as many clinical studies assessing the use of sildenafil in men with ED are indexed in the MEDLINE database than for the nextmost-studied PDE5-I, tadalafil. In a review of clinical trial data, it has been shown that w80% of men taking sildenafil in the dosage range of 25e100 mg report improvements in erections, compared with 25% of men taking a placebo, a highly statistically significant finding. 8 9e13 Data show that 50% of men stop their treatment with firstgeneration PDE5-Is (sildenafil, tadalafil, vardenafil) in traditional formulations within a year, although data are limited for the second-generation PDE5-I, avanafil, which was designed to overcome some of the limitations of first-generation agents.
ACKNOWLEDGMENTS We thank  Ray Hill , an independent medical writer acting on behalf of  Springer Healthcare Communications , who provided medical writing support funded by  IBSA Institut Biochimique SA, Switzerland. Corresponding Author:  Emmanuele A. Jannini, MD , Chair of Endocrinology and Medical Sexology (ENDOSEX),  Department of Systems Medicine, University of Rome Tor Vergata ,  Via Montpellier , 1, E Tower South. Floor 4,  Room E413 ,  00133 Rome ,  Italy. Tel :  þ39-06-7259-6613 ; Fax:  þ39-06-7259-6934. ; E-mail: eajannini@gmail. com.
Background: Collecting data on the localization of users is a key issue for the MASK (Mobile Airways Sentinel networK: the Allergy Diary) App. Data anonymization is a method of sanitization for privacy. The European Commission's Article 29 Working Party stated that geolocation information is personal data. To assess geolocation using the MASK method and to compare two anonymization methods in the MASK database to find an optimal privacy method. Methods: Geolocation was studied for all people who used the Allergy Diary App from December 2015 to November 2017 and who reported medical outcomes. Two different anonymization methods have been evaluated: Noise addition (randomization) and k-anonymity (generalization). Results: Ninety-three thousand one hundred and sixteen days of VAS were collected from 8535 users and 54,500 (58.
Data analysis We initially mapped the data in order to validate the fact that the geolocation data of the App users is an identifying process (https://folium. readthedocs. io/en/latest/). Experiments have been conducted by using the Folium Python Library and Leaflet maps (http://leafletjs. com/). Folium builds on the data wrangling strengths of the Python ecosystem and on the mapping strengths of the Leaflet. Folium visualizes data on an interactive Leaflet map. It enables the binding of data to a map for choropleth visualizations and Vincent/Vega visualizations as markers on the map. Clustering image pixels is an important image segmentation technique. We used the algorithm of Hou et al. [29]  who combined DSets (dominant sets) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) to generate the clusters of arbitrary shapes without any parameter input.
We then assessed geolocation methods. A first experiment was to apply a random anonymization technique to the data set. We used noise addition by replacing the last two digits of the geolocation data by a zero value, which corresponds to blur geolocation data in a 10 by 10 km area  [14]. A second set of experiments used a k-anonymization  [26]  method. k-anonymity allows the tolerable disclosure risk to be selected at the outset. For k-anonymity, the risk of identity disclosure is upper-bounded by 1/k. ε-Differential privacy can ensure a very low identity and disclosure (especially for small ε), but at the expense of an important utility loss. However, k-anonymity does not protect against attribute disclosure in general (e. g. if the values of a confidential attribute are very similar in a group of k records sharing quasi-identifier values).
Random anonymity By including a zero value for the last two digits of the localization data, we could blur the location zone. When distinct users were close to each other (as in an urban zone), this process enabled the merging of different VAS data (of distinct users) in a single location zone. But in areas where only one user was using the App, miles away from the other closest user, the reported VAS data was linked only to this individual user at that location (Fig. 3 ). In these circumstances, the random method by noise addition did not enable the dissociation of the VAS data days from their owner. Figure  3a  and b  show data collected on one of the five "testers". Figure  3b  shows the data collected from one of the five "testers" when the random method by noise addition has been considered.
It shows that it does not enable the dissociation of the VAS data days from their owner. Even if it is not possible to determine the precise location of the user, it is possible to infer his/her main location. The point is now located at the barycentre of all the previous locations. This method was tested on the three data subsets that were analyzed. We observed that 70% of the users declared symptoms within a circle of 1 to 9 km. This method is therefore not a de-identification method in our data set.
For users having declared only 1 day of VAS, it is mandatory to merge their geolocation data to at least one other user in order to de-identify their information. The algorithm could merge the one VAS day-user's location with up to 5 users if they had all declared only 1 day of VAS. But even if the users declare only 1 day of VAS, the k-anonymity method allows the de-identification of the related results since all the results are aggregated to get a virtual position as the barycentre of the circle. This method does not alter the initial quality of the VAS data but creates a location zone big enough to respect users' privacy. When more users are identified in this area, the algorithm will be automatically adjusted to create a sharper location zone to fit the above condition. Below is an example of k-anonymity applied to the users of Valenciennes (France).
Discussion of methods The General Data Protection Regulation (GDPR) still recognizes quantification and gradation of anonymization methods. For the Allergy Diary App, pseudonymizing cannot be considered as an anonymization technique because linking information data sets (such as pollen exposure) cannot guarantee that the initial sensitive data will not be recovered  [23]. For random approaches (i) Permutation of data was not considered, as it would alter the quality of the database (DB); (ii) Differential confidentiality would imply the calculation of an aggregation estimator on sensitive data. We did not investigate this option since the DB could no longer be used to fit the MASK project objectives; (iii) Noise addition was tested. Using a zero value for the two last digits of the geolocation data, we were able to blur geolocation data in a 10 by 10 km area.
t-proximity  [13]  is even more stringent than the k-anonymity and l-diversity methods but we would need to know the general distribution of the sensitive data. This method would also imply the segregation of the data to obtain homogenous distribution classes. These data treatments would be too restrictive, and the overall DB quality would be affected. The general strengths and weaknesses of the tools should be compared in terms of the three basic requirements proposed by WP29  [13]  (Table  3 ). k-anonymity applied to the MASK DB is sufficient to guarantee the users' anonymity, not only on the current medical data set but also considering the integration of environmental data sets (e. g. pollen counts and pollution risks) yet to be gathered. No other DB containing personal data will be merged to our current data set in the future for the allergic rhinitis worldwide survey.
We therefore recommend the k-anonymization method (with our selected conditions/parameters) to anonymize this kind of geolocated medical data since this method does not interfere with the overall DB quality. This post treatment of sensitive data is an irreversible way of de-identifying the data collected through the App. The individualization of data is therefore respected, since even with k = 2, the probability of getting 5 days of identical VAS values is extremely low and, so far, has never been observed in our dataset. Considering the other data collected in our DB (such as the impact of allergic symptoms on daily activities), no correlation is possible with other data sets. Even if we integrate pollen counts and pollution risks, no personal data will be added to our database that could question the anonymization of our data set.
Perspectives Privacy of information is an increasing concern with the availability of large amounts of data from many individuals. In the Allergy Diary App, the mandatory data retrieved to use the app only include age, sex and country of living. This information is essential for adjusting the list of treatments available in the country of living. This is why the privacy concern has to focus only on geolocation data. In the future, we plan to apply our de-identification method, allowing us to merge our database with other sources of information that include precise geolocation data (for example: pollen and pollution exposition), while respecting users' life privacy. These results are applicable to other DBs using geolocated data for any field of medicine. The DB anonymization of "trajectories" (i.