What's new? (December 2015)
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It is hard to believe but the Reptile Database turned 20 years a few weeks ago. Peter Uetz posted the first list of reptile species on the web server of the European Molecular Biology Laboratory (where he was a graduate student) in November 1995. Coincidentally, the EMBL also maintained the EMBL DNA sequence database and thus the first searchable reptile database went online just a few months later, using the same interface as the sequence database (now hosted by the European Bioinformatics Institute in Cambridge, UK). In fact, soon after that we had a function to retrieve DNA sequences of reptile species! Our database is therefore probably one of the oldest taxonomic online databases worldwide, just 5 years younger than the WWW itself (which went online with the first web page on Dec 20, 1990). A more detailed history of the database has been submitted to Herpetological Review and will be published in their first issue of 2016.
The current release features 10,309 reptile species, 40 more than the previous release (Aug 2015) which had 10,269 species, and 190 more than the Dec 2014 released one year ago. However, we have added “only” 102 species described in 2015. The remaining additions are revalidations of synonyms and elevations of former subspecies. See our checklist including a list of changes for details. In addition, 8 more species have been described since the deadline for this release about a week ago (!) but are not available in the online database yet, namely Cyrtodactylus petani RIYANTO et al. 2015, Cyrtodactylus soudthichaki LUU et al. 2015, Synophis bogerti, S. zamora, and S. insulomontanus TORRES-CARVAJAL et al. 2015, Synophis zaheri PYRON et al. 2015, Amphisbaena metallurga COSTA et al. 2015, and Japalura vela WANG et al. 2015. Let us know if we missed any other ones!
Since the Dec 2014 release we have added 2,502 references, increasing the number of papers and books from 35,614 to 38,116 in the current release. That is, on average we have added about 7 papers per day, even though “only” 1,507 of these have been published formally in 2015. The others were publications from previous years, including some historical papers and books. Over the past 10 years we added an average of 1220 new references per year, i.e. 3-4 every day!
Not surprisingly, we need more curators! If you like reading reptile papers (and extracting the gist of them) please let us know (inlcuding your field of interest). We have a backlog of more than a 1000 papers right now. Some instructions can be found on our curator page.
The Reptile Database also contains a number of extinct species, especially species that went extinct in recent history (within the past couple of hundred years). However, there is no precise number as several dozen species haven not been found for decades and are “probably” extinct. Once in a while such “extinct” species are re-discovered. (Our literature database has 142 references that contain the term “rediscovery” in their title evern though some of them refer to “rediscoveries” in certain localities). You can search for “extinct” or “possibly extinct” species using the quick search on our home page.
By the way, Ceballos et al. 2015 reviewed the number of species that have been evaluated by the IUCN (100% of mammals and birds, 88% of amphibians, but only 44% of reptiles, many of which are threatened.
We have uploaded 784 photos of 280 species since the last release, increasing the number of photos to 8,840, representing 3,292 species (not including those species that we display through external sources such as Flickr or CalPhotos). The new photos were submitted by a total of 50 photographers. However, the bulk of photos came from just two individuals this time, Sebastian Lotzkat (519 photos) and Uwe Schlüter (129 photos). Sebastian is now on par with Paul Freed (our photo editor) as the number 1 photographer (both with 576 photos -- congratulations!). The other photographers this time were Alex Slavenko, Ashok Captain/A. Biju Kumar, Awal Riyanto, Brad Maryan, Chris Harrison, Conrad Hoskin, Diego Demangel, Eli Greenbaum, Fanomezana Ratsoavina, Federico Arias, Fenoy Xavier, Javier Torres Lopez, Jian-Huan Yang, Jim Conrad, Josef Kiechle, Laurie Vitt, Levi Gray, Luke Verburgt, Mark O’Shea, Nicole Schneider, Niranjan Sant, Pablo Venegas, Patrice Hugues, Patrick Prévost, Paul Carter, Prathamesh Dange, Raimundo Lopez-Silvero Martinez, Regina Ribeiro, Reinaldo de Medeiros Jr, Robert Sprackland, Roy Santa Cruz Farfán, Salvador Carranza, Samuel Lalronunga, Shai Meiri, Stephen Busack, Thasun Amarasinghe, Tomas M. Rodriguez Cabrera, Tomas Mazuch, Truong Quang Nguyen, Victor Acosta Chaves, Vimukthi Weeratunge, Vivek Philip Cyria, cVivek Sharma, Vladimir Bobrov, Yehudah Werner, and Zeeshan Mirza. Thanks to all of you!
If you have submitted photos but are not listed, your photos will be uploaded with the next release -- sorry!
We have updated the checklists for the following geographic areas: Argentina: Chubut (following Minoli et al. 2015), Australia (Cogger 2014), Brazil: Bahia (Freitas 2014), Cambodia (Grismer et al. 2008), Europe (Kwet 2015, Kwet & Trapp 2014), Guyana (Cole et al. 2013), India: Tamil Nadu (Bhupathy, Subramanian & N. Sathishkumar 2013), Kerala (Palot 2015), Mexico: Chiapas (Johnson et al. 2015), Thailand (Chan-ard et al. 2015, but see the critical review by Pauwels 2015).
Note that we do not curate County records (most of the Geographic Distribution notes in Herpetological Review), but we add new state and country records. If you are interested in curating checklists or older issues of Herpetological Review (now open access, please let us know (e.g. as student project in class).
Selected taxonomic news
An updated squamate phylogeny was presented by Zheng & Wiens 2015.
Colli et al. (2015) reorganized the family Gymnophthalmidae with redefinitions of the subfamily Ecpleopodinae, a novel subfamily Bachiinae (to include the genus Bachia, previously Cercosaurinae), included Riolama in Cercosaurinae, and redefined the Gymnophthalminae with the tribes Chirocolini, Iphisini, and Gymnophthalmini.
New reptile genomes
The first gecko genome (that of Gekko japonicus) and that of the corn snake were published recently.
The authors of the corn snake genome also created a Reptilian transcriptomics database.
Other things of interest
• Russell Mittermeier et al. investigated turtle hotspots around the world.
• Mario Schweiger tracked down many references and information (e.g. distribution) on Podarcis subspecies, and posted many of the original descriptions on http://www.vipersgarden.at (links are in our species accounts).
Phylogenetics editor wanted
Although taxonomy depends on good phylogenies, we have neglected that area due to the lack of manpower. If you are interested in phylogenetics and want to help us with trees, please let us know. There are a number of ways to go about this, e.g. linking to trees online, extracting them from the literature and posting them on our site, or posting them to other sites such as Wikipedia and link there. In addition, we would love to list species that are included in published trees, but since it is usually a pain to retrieve such species lists from papers we often don’t do it (even though we do cite the papers in at least one species account, often type species or genera). We also would love to work with the Open Tree of Life and other initiatives but need help to do so.
Master’s theses and student projects
If you are a student (or professor) interested in biodiversity informatics or a taxonomy-related project for a master’s thesis, please let us know.
Students interested in programming (Perl, Python, Filemaker, etc.) are especially encouraged as we have numerous projects to be solved but too little manpower.
If you are teaching a spring class in herpetology, please consider using some of our teaching materials or suggest others that make use of the Reptile Database.
New books received
Pough et al. (2015) Herpetology, Sinauer, 591 pp.
We will have a detailed review in our next newsletter (let us know if you have an opinion or if you have found errors).
Grants and funding
Although we made great progress during our 20 year history, obtaining funding turned out much more difficult. We only had two small grants from the European Union (as part of their Species 2000 and 4D4Life initiatives) which expired a long time ago. Ironically, when we submitted a grant proposal to the US National Science Foundation several of the reviewers criticized that the database had no long-term maintenance plan. Yes, admittedly — it’s difficult to have long-term plans without funding. But hey, I (PU) am only halfway on my way to retirement, so there is a decent chance that we can keep going for another 20 years without funding.
However, if you happen to submit grants to any agency that have a significant taxonomic or databasing component (e.g. the Genealogy of Life FY 2016 program), please consider budgeting a few k$ for the Reptile Database. We are happy to collect and store your data, even long term (currently we have older versions on figshare). Mere mortals can also donate through Paypal on our home page.
Although we planned to release this database version earlier, actually before the SSAR herp meeting in Lawrence, Kansas, the amount of new data delayed us more than expected. But finally, after a longer hiatus (since our last newsletter from 23 March 2015), we just released a new version of the Reptile Database. The wait was worth it because it seems like we have a record amount of new data, including ...
10,269 species, 91 up from 10,178 in March. 72 new species have been added in 2015 so far, and another 19 revalidated or elevated from subspecies status (see below for details).
37,093 references, 815 up from 36,278 in March (including 761 published this year).
2014 was hottest year in history. As with climate change, the last 10 years were the hottest in history, but especially in reptile taxonomy. Every year in the past decade had at least a 100 new species described, a number that was reached only 5 times before 2005 (namely in 1758 with Linnaeus himself, then in 1854, 1863, 1864, and 1887). It turns out that a record 180 species were described in 2014. This number includes a few species that we added only recently (in fact, we received the 180th species, Cynisca ivoirensis, only after our deadline yesterday, so it will show up only in the next release).
Species with changed information. As far as changes go, we have updated or added information to about 2000 species just this year. Given the large number of small changes, additions, corrections, etc. it’s practically impossible to produce a list of all individual changes. However, we have added a list of name changes to our checklist (downloadable as Excel spreadsheet). This list shows the 128 species names that were added, revalidated from synonymy, elevated from subspecies, or changed their genus.
More higher taxa. Recently, we have added several categories to the higher taxa field in our database. You can now search for these keywords in the higher taxon field: Squamata, Caenophidia, Alethinophidia, Anguimorpha, Scincoidea and a few others. These keywords essentially follow the classification of Pyron et al. 2013 (but do not include the most recent groups suggested by Reeder et al. 2015 such as Teioidea). We will add those once we have sifted through their 70+ supplemental figures and tables :)
Buy a species name! Most of you have probably heard of the BioPat initiative that allows you to help taxonomists and in return they will name a species after you (or after your suggestion). Now you can also buy a species name on eBay, as various media have reported. If you can afford it, that is: http://go.nature.com/ziq152.
Species Named After BHL. Although you can buy a species name, it may be more original to name it after a really useful service like the Biodiversity Heritage Library (or the Reptile Database, just to name a few:). This is exactly what some malacologists have done: A new land snail species from Laos, Vargapupa biheli was named in honor of BHL to express thanks for "the multitude of rare literature made available to us. The name 'biheli' is an acronym derived from the name BIodiversity Heritage LIbrary."
New checklists. We have updated several species lists based on recently published checklists, e.g. those for chameleons and Phelsuma geckos (after Glaw & Rösler 2015), lizards of the Amazon (Ribeiro-Júnior 2015a,b), lizards of Togo (Segniagbeto et al. 2015), lizards (or reptiles) of the Mexican states of Jalisco (multiple sources), Morelos, Hidalgo, and Oaxaca, and pythons (Barker et al. 2015).
New photos and photographers. Thanks to the tireless help of our photo editor, Paul Freed, we have added 711 photos illustrating 556 species (!) by 41 photographers since the last release (including 419 photos by Paul himself!). The photographers who donated photos this time are Abhinava Mukherjee, Alexandre Teynie, Bhargavi Srinivasulu, Bruno Gattolin, César Luis Barrio Amorós, Claudia Koch, Daniel Velho, David Alfonso Bejarano Bonilla, Dhofir Tri Dharmawan, Frank Glaw, Miguel Vences, Geoff Patterson, Helianne de Niemeyer, Herbert Becker, Hinrich Kaiser, Ibrahim Elkhalil Mohamed, Jaime Troncoso-Palacios, James Culverwell, Jean-Claude Jamoulle, Joe Tuck, Johan Chaves, Juan Salvador Mendoza, Luciano Avila, Mauro Hernan, Ngo Van Tri, Nigel Voaden, Nikolay Poyarkov, Patrick David, Patrick Prevost, Paul Freed, Pier Cacciali, Ricardo Buff, Ross Wanless, Ryan van Huyssteen, Sandy Leo, Si-Min Lin, Soheila Javanmardi, Stephen Schmidt, Trent Bell, Vishal Santra, and Young Dae Kim. Thank you all for your generous help! If you have submitted photos which are not in this batch, please be patient — we will add them soon!
We now have 7675 photos of 3064 species on our server, with photos of another 3000 species or so linked in and displayed from Calphotos (~800), Flickr (~900), and many other sites. This translates to more than 6000 species in the database that have photos. We are pretty sure that this is the most comprehensive database of reptile photos online (not counting search engines such as Google images).
Neverthless, there are still 4000 species to go — please help us to get photos of those too!
More reptile genomes. Among the latest reptile genomes published is that of Ophisaurus gracilis, now Dopasia gracilis, an anguid (limbless) lizard (Song et al. 2015).
Books received: Gunther Köhler & Hannes Zorn (2015) Chuckwallas, Herpeton Verlag, 142 pages + 199 color photos. This definitive guide to chuckwallas (genus Sauromalus) provides a comprehensive survey of the taxonomy, biology, and husbandry of the 5 species in the genus. It describes even fossil species, the climate, diet, behavior, ecology and conservation of this groups of lizards. Detailed instructions describe how to keep and breed chuckwallas. The only limitation is that it is in German, but you can still enjoy the nearly 200 color photos if you cannot read the text.
Herpetological bibliography of Europe. The Field Herpetology special interest group of the German Herpetological Society (DGHT) has released an illustrated Herpetological bibliography of Europe that features almost 900 illustrations of European herps (in German).
Forgotten species wanted: Christopher Kemp, a science writer, is looking for “forgotten species”, i.e. they're collected in the field and then wait decades, or even centuries, in collections until they're finally described and named. We have provided some but for a book project he is especially interested in species that are morphologically distinct, not just cryptic species. Let him know at <firstname.lastname@example.org>. BTW - the subject has been addressed by Fontaine et al. 2012 who found that the average “shelf life” of species was 21 years between collection and description.
Use the Reptile Database in class. If you happen to teach a class in Herpetology, the end is near — at least of the summer break. Please consider giving some homework to your students that benefits their readings skills as well as our data collection efforts. For more information see our Teaching page. We have many more ideas, e.g. having your students involved in a small research project using bioinformatics, data mining or analysis, or other data-driven studies. For instance, we need help finding the coordinates of type localities. Let us know if you are interested.
10,178 species, up from 10,119 in December (plus 59, including revalidations and elevations). 165 species were described in 2014 and 13 described so far this year.
36,278 references, up from 35,615 in December (plus 663, including 96 published this year, and a record 1,652 published last year).
Bibliographic database. Of the 36,000+ references now in the database, about 21,000 have links to online sources, although many of them are admittedly still behind pay walls. However, many are not, including about 3000 papers and books with links to the Biodiversity Heritage Library. Let us know if you see any papers that are online but have no links (and send the URLs to us, so we can include them). Among the new literature that went online for free is the Biology of the Reptilia.
Selected taxonomic news
Turtle phylogenetics. A new phylogenomic analysis of turtles has been published by Crawford et al. 2015 who provide the first genome-scale analysis of turtle phylogeny which includes 32 turtle taxa representing all 14 recognized turtle families.
The first reptile species that has been created in the lab. Aspidoscelis neavesi is the first known tetraploid amniote that reproduces through parthenogenetic cloning by individual females. Aspidoscelis neavesi originated through hybridization between Aspidoscelis exsanguis (triploid parthenogen) × Aspidoscelis inornata (diploid bisexual or gonochoristic species) in the laboratory. The authors speculate that such tetraploids may also be found in nature.
As announced previously, we have started to recruit editors (or curators) to keep up with the large number of papers published and the number of photos submitted. We welcome Vivek Sharma as new editor for India, Sebastian Lotzkat for Panama and Costa Rica, Mark O’Shea for the snakes of Papua New Guinea, Andrew Durso for freshwater reptiles, and Amr Salah for Egyptian reptiles. If you are interested in acting as an editor please let us know. Your job will require to look through recent papers and to send us relevant bits and pieces of information from these papers (we can send papers!). See our editor page for more details.
Photos and photo editors. Paul Freed and Sven Mecke are our new photo editors and have processed their first 400+ hundred photos which will be going online in a few days.
Photographers whose photos are being uploaded this time include Alan Giraldo, Alessandro Catenazzi, Ar Shakti Nanda, Arne Rasmussen, Brad Maryan, Breno Hamdan, Bruno Miranda, Cameron Siler, Carmelo Lopez, Chiramjib Debnath (via Joydeb Majumder), Chris Rego, Claudia Koch, Colin Bryant, Dick Sage, Diego Ramirez, Henrik Bringsøe, Jaime Troncoso-Palacios, Jakob Hallermann, J. Cairos, Jean-Claude Jamoulle, Jorge Alberto Zuñiga Baos, Joydeb Majumder, L. David, Luis Alberto Rueda Solano, M.R. Low, Marco Freitas (via Breno Hamdan), Nathanaël Maury, Nigel Voaden, Rick West, Subhendu Mallik, Thomas Calame (via Vin Luu), Tom Ferrara, Tony Wales, William W. Lamar (via Rick West). Many thanks to all of you! (Those who are not in the list, will have their photos uploaded soon. Please be patient or send more photos :)
New country checklists: We have updated the database using a number of recently published checklists, including those for Nicaragua (Sunyer 2014), Honduras (Solis et al. 2014, McCranie 2015), Guinea, Sierra Leone, Ivory Coast, Liberia, Ghana, Togo, Benin, Nigeria (snakes, Trape et al. 2014), and Iran (lizards, Smid et al. 2014). Note that when you search for distribution = Guinea you will also find Papua New Guinea and Equatorial Guinea, so we suggest to combine this search with a keyword from the title of Trape et al. 2014, e.g. reference = “Philothamnus”.
Kenya Reptile Atlas: There is also a new atlas for Kenyan reptiles.
Other herpetofaunal sites: Our Link page has a links to various herpetofaunal sites. Let us know if you know of others that we should add.
Genera and type species: You can find all type species of all reptile genera in the Reptile Database now. Unfortunately we do not have a separate data field for that information (yet), so you will have to use a workaround to find the type species in the Comments field: use the quick search to find a genus name plus "type species", e.g. “Pogona type species”. The type species is often the oldest name in that list, here Pogona barbata (CUVIER, 1829). However, you can also find a list of type species in our updated downloadable checklist.
Why is this relevant? Although we do not have a separate database for higher taxa, you can often find information about a genus (or family etc.) in the species entry of the type species. For instance, several hundred type species have diagnoses for the genus. For instance, the diagnosis of the genus Pogona is in the entry of its type species, Pogona barbata.
Currently the type species remain unclear for only 3 genera, namely Dalophia, Pseustes, and Phrynonax. Let us know if you can provide insight into those.
User survey. We are planning a conduct a user survey soon to get more feedback about how we can improve the Reptile Database. If you have experience with online surveys, please let us know. We would appreciate some help, including the analysis of the results.
With an unusually long delay since our last newsletter, we would like to inform you about the latest release of the Reptile Database which was released a few days ago. This version features
10,119 species (including 139 described this year), up from 10,038 in August,
35,615 references (including 1,203 published this year), up from 34,104 in August, which resulted in almost 200 new and changed names.
You can download a complete list as an Excel spreadsheet. The checklist also contains a list of changes (in a separate sheet). The format is not perfect but we are working to improve it. The next release should have a complete and detailed list of changes in the format “old name > new name”.
Homalopsidae: Murphy and Voris (2014) suggested a number of new genera and revalidated a few more, leading to 28 genera for just 53 species.
Boidae: Pyron et al. 2014 suggested to split the monophyletic boas into multiple families; we did not follow this suggestion following a discussion with the Scientific Advisory Board (see below). However, the new suggested families (such as “Sanziniidae) can be found in the database.
More species and genera split, including Lampropeltis, Blanus, Crotalus triseriatus, Hemidactylus fasciatus, and Pelomedusa subrufa. Guo et al. (2014) split the fairly large genus Amphiesma (43 species) into 3 genera: Amphiesma, Hebius, and Herpetoreas. Only Amphiesma stolatum remains in the genus.
For other changes, please search the database (e.g. year or reference = 2014) or take a look at the updated species checklist.
We have finally completed the import of all Herpetology Notes papers (i.e. references) even though not all papers are completely indexed. We are also indexing the new journal BioGecko.
The almost 1,000 papers of the journal Sauria are now cross-referenced individually so you can order individual articles (or journal issues). Please support the publisher (and us) by ordering a few papers :)
Stipala, J. 2014
Mountain Dragons - In search of chameleon diversity in the highlands of Kenya.
Jan Stipala, 124 pp., ISBN: 978-0-9928176-0-2
Recently we constituted a Scientific Advisory Board (SAB) who will advise the Reptile Database on general strategic decisions but also on controversial taxonomic issues. One of the first recommendations of the SAB was not to adopt the suggested Boid taxonomy suggested by Pyron et al. (2014, see above). We continue to consult individual experts in more special cases, e.g. on individual species or genera. There is a consensus that all published taxonomic changes should be in the Reptile Database but when it comes to valid names we can only show one “accepted” name for any given species even if several are in use. Instead of flip-flopping between names with each new publication, the result will be a bit more conservative but also more stable.
In order to manage data curation and data import better, we have started to recruit editors for special tasks.
Photo editor. Paul Freed and Sven Mecke are our first volunteer photo editors. They will receive the photos we get, edit them, verify correct identifications with experts, find photos of species not pictured etc. This will also allow us to process photos faster. We are still looking for a photo editor taking care of turtles. Let us know if you are interested. See also the note about photos under “Other News”.
Taxonomic editors: Similar to the photo editors, we are looking for volunteers who are willing to help with the curation of papers. Initially we will start with editors for turtles, crocodiles, and squamate families (or genera if they have a substantial number of species). The taxonomic editors will receive papers from which they are supposed to extract information that is relevant for the database such as taxonomic or nomenclatural changes, new distribution records, or databasable life history data. Please let us know if you are interested in helping with any particular taxonomic group.
The Reptile Database in teaching. You can help to improve data curation for the Reptile Database by using it in your class. If you are teaching a herpetology (or taxonomy) class, you can have your students curate papers, editing Wikipedia pages (that link to the Reptile Database), ID species, or find and analyze other information. We always have a large backlog of papers that need to be curated, including simple cases with new distribution data or more complicated ones. Please get in touch if you are interested. We have designed a few exercises and assignment for classroom use. Please let us know what you think and if you have suggestions for improvements.
Photos. We have again a large number of new photos (>1,500). However, they are added to the database independently of text, and thus have not been updated yet. This will probably take another few weeks or so, just in case you do not see the photos that you have submitted. In any case, more photos are always welcome! Please send photos (with location or coordinates) to email@example.com. You can find more instructions at the bottom of this page: http://www.reptile-database.org/db-info/introduction.html.
Bounced emails. This mailing list returns an increasing number of bounced emails, reaching a total of about 300 now or almost 10% of all recipients. Please take a look at this list and let us know if you recognize any of the email addresses. Please inform these people or send us their current email addresses. Also, some of you may not have received our last newsletter because it has ended up in your spam folder.
Google Maps. We often use Google Maps to verify the localities reported in papers. However, Google Maps shows different maps in different countries. For instance, Google Maps in India shows Arunachal Pradesh as part of India. However, Google Maps in China shows Arunachal Pradesh as part of China. Although we will replace our current approximate maps by “real" distribution maps sooner or later, such details are important when you search the Reptile Database for geographic areas (or if you need a list of all Indian or Chinese reptiles). Right now, we treat Arunachal Pradesh as part of India. Finally, there are different names in different Google Maps versions. For instance, in the international version you can see the “Persian Gulf”. However, in Arabian countries it is called the “Arabian Gulf”. There are a number of other contentious borders or names, so please keep this in mind when you search the database.
New countries and states. In the course of history new countries keep forming, such as the new countries that used to be Yugoslavia or North and South Sudan (which used to be Sudan). However, there are also new states, such as the new state of Telangana in India, and the Indian government apparently discusses the creation of another 21 new states (the current states are fairly new too, many having been formed only in 1956). Obviously, this can cause headaches for us as we try to keep tabs on reptiles in those states, especially when they are species-rich such as those in India. Keep us posted if you see discrepancies or errors.
JournalMap: This new web service and database offers a scientific literature search engine that empowers you to find relevant research based on location and biophysical attributes combined with traditional keyword searches. Give it a try.
Funding. We still do not have funding for the Reptile Database. If you plan to submit a grant related to reptile taxonomy or with databasable information, please consider including the Reptile Database as a subcontractor or collaborator. Of course, you can also budget personnel to curate data for us.
Donations: Since it is gifting season, we also offer (or rather accept) donations now. We usually use the little available money we have to buy literature, travel to libraries, or pay students to enter, scan, or process data. If you have a few spare bucks, you can donate them to the Reptile Database via Paypal:
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