dataesr/scientific-paragraphs-categorization huggingface dataset:
A decision was eventually made to turn the book into two volumes and to go ahead with the taxonomic groups with all of the contributions in place, and in 1998 the first volume (TM1 Carnivores, Ungulates, and Ungulate-Like Mammals; Janis et al. , 1998) was published by Cambridge University Press. The second volume (TM2 Small Mammals and Marine Mammals; Janis et al. , 2008) was published a decade later, this time with new contributing editors, Gregg Gunnell and Mark Uhen. This second volume also had some updates of both the locality information (including additional localities and some new dates) and the taxa covered in the first volume. Although this book was not originally devised as an online database, the hope always was that somebody would make such use of the information. Starting in 2008-2009, in the aftermath of the publication in the Proceedings of the National Academy of Sciences of the United States of America of a paper entitled Distribution history and climatic controls of the Late Miocene Pikermian chronofauna  (Eronen et al.
, 2009) , Janis began corresponding with Fortelius and others about North American chronofaunas. This turned into an endeavor to include TM1 and TM2 into the NOW database. The work started in late 2009, and went through 2010 and 2011, producing the first synthesis papers soon after  (Eronen et al. , 2012; Figueirido et al. , 2012). Laura Säilä-Corfe and Jussi Eronen were responsible for the correspondence and much of the work in addition to Mikael Fortelius and Susanna Sova. The locality-related work and issues (see below) took much time, correspondence and travel. For example, Eronen and Janis were working on the TM1 and TM2 data in Providence when hurricane Sandy hit the Eastern Seaboard of the United States in 2012. The process of incorporating the Tertiary mammals data into NOW concluded in 2016, when they were made public, and the North American data have been subject to normal updates since then.
A potential problem with converting the TM locality data to the NOW format is that Janis had not separated all the localities to the level of individual sites as was done in NOW (and in other databases such as the ETE or the Paleobiology Database. So, for example, locality CP110 (the Olcott Formation in Nebraska) includes around three dozen separate quarries or sites of varying sizes and quality (which are named in the locality list but not separately numbered). At least 10% of the localities are of this nature. This 'lumping' approach was taken for several reasons: (1) contributors often did not provide the necessary detailed information; (2) it was considered that, for the purposes of the book, a degree of locality lumping would actually be more informative, rather than reporting on every little sample individually; (3) given that Janis was working essentially alone, and at least for the first volume without the type of computerized assistance (e.
Running NOW From the beginning, the NOW interface was designed to be as intuitive as possible so that the users can concentrate on its essential reason for beingthe data. The aim was that even a lazy but excited researcher can insert the data smoothly. Adding data was made as straightforward as possible, human mistakes were minimized, and collecting information in different ways was steadily improved. Rules were enforced at both the interface and the database levels, restricting the range of possible entries in many fields, and enforcing the integrity of relationships between the various fields. Gudrun Evans was the main person behind this thinking and Jouni Vepsäläinen continued on the same track. We were very lucky to get Jouni just before Gudrun and Alistair Evans left Helsinki for their native Australia.
It has been a surprise how much abstract thinking in three dimensions database development requires and Jouni had that ability in spades. Jouni quickly took the technical aspects in hand and his meticulous work enabled the development of NOW without compromising the safety and robustness of the database. NOW officers all had database-related projects of their own, which made them alert to errors and inclined to think about improvements. Thus, the interface was continually improved in many small steps. Localities with unknown coordinates no longer ended up in the Gulf of Guinea, under the armpit of Africa and the Map-and Export-functions became easier to use and adapted for a range of different purposes. The biggest improvement to the user interface may have been the Import-function. Previously, large, curated datasets had required a great deal of manual labor in harmonizing the data exactly to the NOW format, but with the improved Import-function, automatic format checking and reformatting was introduced.
Jussi Eronen was the first brave NOW participant to actually use it, successfully as it turned out, for importing the North American data described above. This import significantly increased the records in the database, which in turn made it important to further develop checks on the consistency of logic as well as the formal validity of entries. History has shown the value of these improvements again and again, as many datasets still come to NOW as Excel-files that may have grown over years or even decades, with changes in usage that typically occur over time. From 2009 onwards, the NOW office has worked together with the taxonomic coordinators, updating and unifying taxonomic information of all families, under the umbrella of 'NOW synonymy project' (ridding the database of synonymous entries).
This was initiated by Laura Säilä during her post-doctoral period in the Academy of Finland funded research project Extinction dynamics of taxa in the fossil record. This has vastly improved the taxonomic accuracy of the NOW database and how it can be reliably used for large-scale evolutionary studies that rely on taxonomic data. Additionally, improvements in how changes are recorded, and can be viewed, in the references of each locality and taxon entry and how synonymies and other taxonomic issues are detected in the database were implemented. Simultaneously, enhancements took place in search functions for taxonomic entries and their geographic/temporal occurrences in both the main database and its Export and Maps interface, and the types of data that could be exported out of the NOW database were increased.
One late but crucial development must be mentioned here, even though it falls outside the temporal scope of the main narrative. One of the main challenges of running NOW during its first two decades was the lack of an employed curator to provide stability and continuity. This was finally remedied when, in the autumn of 2016, the University of Helsinki received a major donation from the Ella & Georg Ehrnrooth Foundation and decided to use this, in accordance with the wish of the donor, for furthering the research into hominin paleoenvironments that had sprung up as a collaboration between Fortelius and Meave Leakey's research network centered on the Kenyan Turkana Basin. This donation both allowed the university to establish a professorship of Hominin Environments and to finally establish, in the Finnish Museum of Natural History, a permanent technical data coordinator position that includes responsibility for the maintenance of the NOW database.
For this position Kari Lintulaakso was fortunately available, a person already involved with NOW for many years and intimately familiar with the structure and purpose of the database. This way, NOW finally achieved an administrative position in accordance with its international role and weight. As is evident from this narrative, NOW came together gradually, through an unplanned and rather amorphous process of collaboration between friends and colleagues who for various reasons shared an interest in developing this common resource. In retrospect it seems clear that what gave NOW direction, coherence and credibility in the critical early phase was the establishment of an Advisory Board of respected scholars, many of whom had also been active during the gestation period that preceded the formal launching of the database (cf.
It doesn't have to be right, consistency is everything! has always been a key slogan for NOW data development and in this NOW differs significantly from other leading databases, for example the Paleobiology Database (https://paleobiodb. org/), which instead favors recording of alternative scientific opinions. While both systems have their advantages, the dictatorially induced consistency of NOW definitely makes it easy for users to locate all occurrences of a species, but inevitably also creates extra work for users who disagree about synonymy. Needless to say, few if any decisions of this kind have ever been made without consultations among coordinators and with the approval, implicit or explicit, of the general coordinator. NOW was always very much a consensus-based community effort. Originally, NOW had no administrative organs, there was just the somewhat misnamed Advisory Board, an Overall Coordinator and an Associate Coordinator.
When executive decisions had to be made, this was done by the signatories of the founding document (Appendix 2. 1), ironically self-styled as the NOW Mafia. As NOW grew and new members joined the Advisory Board it was gradually realized that some more transparent administrative structure was desired. A new structure was accordingly put in place in December 2013 with a Steering Group appointed by the now renamed General Coordinator and approved by the Advisory Board. At this time a five-year cycle of membership in both the Steering Group and the Advisory Board was also introduced. The main task of the Steering Group has been to decide on major issues such as the appointment of new board members or updating the stratigraphic reference for the NOW Time Unit Table. Thus, the daily running of the NOW database gradually caused its administrative structure to stabilize and mature.
Looking at the structure of the NOW and the people involved, it is clearly an international consortium serving a global community. At the same time, history leaves no doubt that the main office of this consortium is in Helsinki. As is clear from the narrative above, it was this firm ground that allowed the database to develop all of its technical and conceptual aspects, supported by the Finnish academic infrastructure. Many colleagues and students travelled to Helsinki over the years and these visits were the basis for fruitful discussions and collaborations. However, they were still individual visitors enjoying the hospitality of the Finnish team. A major step towards creating a stronger community feeling came, when in 2016 NOW switched to a creative commons license, expressing the role of the community in each reference made to the database.
This was the beginning of a second wave of computer science collaboration based on the NOW data that would eventually see Žliobaitė transformed into a paleontologist in her own right and the successor of Fortelius as the General Coordinator of NOW. But this is another story. Email: gem_dig@gaia. pc. helsinki. fi  Dear colleague, 15. 10. 1997  The first years of the NOW database have gone, and with them the years of highly coherent and organised data entry. NOW, such as it was used for the synthetic chapters of Bernor-Fahlbusch-Mittmann (and is available on request from gem_dig@gaia. pc. helsinki. fi), is far from free of errors, but it is still a uniquely up-to-date source of information regarding the occurrence and attributes of the Miocene mammals of Europe on a continental scale. It was never complete, and it still isn't.
Several taxa (notably Proboscidea) are missing altogether, and most localities have incomplete faunal lists. The selection of localities is also somewhat random (the case of Austria was especially remarked upon in this regard). We are gradually filling in holes but there is no concerted effort comparable to the "Reisensburg Process". In our opinion the database is already a valuable resource, and we would like to contribute to its being more extensively used than has been the case so far. In the long run, such databases have the potential of bringing fossil mammals into contact with neighbouring fields, for example palaeoclimate and biodiversity modeling and research. Meanwhile, we know from first-hand experience that the database is already a wonderful resource for many mundane, everyday tasks involving Eurasian Neogene mammals.
We feel strongly the need to continue the process of building the database as well improve the quality of the data. We are writing to you in the hope that you might share our interests and be willing to participate in the next step of developing the NOW database. To begin with, there are currently four main sources of new data into NOW: 1. Specific research projects that need to augment the existing data in some way (especially "ecomorphological" attributes of the animals) 2. The ESF "HOMINET", which is revising and adding (primarily) the hominoid-bearing localities of Europe 3. A collaboration project with the IVPP to database all Chinese later Cenozoic mammal localities 4. Data extracted from the literature by our students and ourselves. In addition to these and somewhat different in nature are plans to fuse NOW with other existing databases with a similar structure (EUQUAM, ETE, FAUNMAP).
Such plans will proceed independently of our development of NOW, and will not change the basic principles outlined below. Not all the data arriving to the database are of equal quality, and not all specialists agree on the details of taxonomy or dating, to say nothing of interpretation that is more speculative. Only some relatively powerful verification mechanism can prevent the growing database from decaying into a chaotic state, with taxa represented by multiple nomina and perpetuation of various long-since-recognised errors. In establishing such a verification mechanism one must balance several factors. It is important that the database retains a broad base in the field, so that it can grow as a common resource. On no account must it be seen as the toy, or worse, the exclusive research tool, of some small clique! It is also important to minimise the workload put on single individuals.
On the other hand, for a database more important even than correctness is consistency. This means that once a certain classification and nomenclature has been adopted, any competing scheme must be put aside until, perhaps, it is verified and a conscious decision is made to adopt it. A similar principle applies to stratigraphic correlation and related issues, and these factors argue against having too many individuals directly involved with the supervision of the data. What we propose here is the creation of an Advisory Board for NOW, consisting primarily of the core group from the original Reisensburg Process, augmented (or replaced) by colleagues who have since joined the project. The Board would feature specialists and taxa, on stratigraphy, and on particular regions, and would complement itself as required.
General coordination and development Overall coordination and data entry -Mikael Fortelius Database structure and technical development -John Damuth Associate NOW coordinator -Suvi Viranta *** A few words about the "data policy" that we have in mind. As agreed during the preparation of the Bernor-Fahlbusch-Mittman volume, all contributors are entitled to the full data set that was produced. It was also agreed that this data set would become public with the publication of the volume, and this is the basic principle that we intend to maintain. New data deposited in the NOW database can be kept under restricted access until a project is completed, but will eventually join the growing mass of public data available to all bona fide researchers. Another basic principle is that the NOW data should not be distributed directly to third parties.
Everybody is required to get their data directly from NOW (gem_dig@gaia. pc. helsinki. fi), to ensure that the currently available version is used, and to allow us to keep track of how and where NOW data are being used. (Backup copies of older versions will, of course, be kept and made available for verification purposes. ) In the future, a version of the public data will also be available on the world wide web, probably as a collaboration project with the ETE database. We hope that you will accept our proposal and join the NOW database Advisory Board. Whether you do join or not, we hope that you will let us know your opinion and any suggestions you may have, including suggestions for additional people you feel should be involved. With our highest hopes and best wishes, Mikael Fortelius, Ray Bernor, Hans de Bruijn, Sevket Sen, Lars Werdelin.
Acknowledgments Although there has been some dedicated funding for  NOW , including the  Academy of Finland  grant  1993-1996  that made the first implementation possible, NOW was always overwhelmingly an unfinanced community effort. Most of the work has been contributed by NOW participants in their own time, and much has no doubt been sponsored by a large number of academic employers worldwide, knowingly or otherwise. In addition to the  Academy of Finland  we would like to acknowledge generous support from the  European Science Foundation , the  Volkswagen Foundation , the  Finnish Society of Sciences and Letters , the  Finnish Museum of Natural History , the  University of Helsinki , the  Naturalis Biodiversity Center , the  Hanken School of Economics  and the  CSC -IT Center for Science.
All samples were preserved in ethanol. A total of 4158 occurrence records of H. viridiflavus (at a 5 arc-minutes resolution, ∼10 × 10 km resolution) were used to model the ecological niche of the species (Figures  1  and S2 ). Occurrence records were obtained from the online GBIF Portal (n = 3853; https://www. gbif. org/es/species/2458916, accessed on 25 June 2023) and from personal (n = 304) datasets. The GBIF dataset was carefully examined to delete records that were potentially erroneous, which were determined as those falling outside the species range determined by the IUCN  [37].
Phylogeographic Analyses A total of 224 H. viridiflavus ND4 (NADH dehydrogenase subunit 4) sequences were considered to estimate the phylogenetic relationships and create haplotype networks (Table  S1 ). We generated 80 unpublished sequences in this work (GenBank accession numbers to be added after acceptance) (see Supplementary Text S1 for laboratory procedures), and 144 sequences were retrieved from previous studies (GenBank accession numbers: LN552045-LN552095,  [31] ; FJ430621-FJ430660,  [34] ; KY923281-KY923287,  [35] ; and MW297553-MW297679,  [36] ; see Table  S1 ). Hierophis gemonensis (Laurenti, 1768), considered to be the closest related species to H. viridiflavus  [31] , was included as an outgroup (accession number: LN552113,  [31] ) in the phylogenetic analyses. Sequences were manually aligned and edited using Geneious v 4.
Paleoclimatic Modelling To predict the potential species distribution in the current and past conditions, we used the maximum entropy approach, which was implemented in the Maxent ver. 3. 3. 3k software  [50, 51]. This algorithm only requires presence data, performs well compared with other methods  [52] , and has been used successfully in modelling snake species distributions, e. g. ,  [15, 19, 31]. Occurrence data and climatic variables were imported into Maxent software, where 50 replicates were run with random seeding, 70%/30% training/testing partition, and bootstrap with replacement. Before running the final models, a test calibration process using the Maxent parameters was carried out to address the model parameterization, which was performed using the R package ENMeval  [53]  (further details in Table  S2 ).
Data Availability Statement: Not applicable. Acknowledgments: Special thanks to Universitat de Barcelona (UB) and Museu de Ciènces Naturals de Barcelona for facilitating samples from collections and also to Marco Zuffi and one anonymous reviewer for constructive comments in an early version of this manuscript. I. R. -I. acknowledges Alberto Gosá, Enrique Ruiz Ara, Iñaki Sanz Azkue, and Ander Izaguirre for providing tissue samples, as well as Ion Garin-Barrio, Xabier Rubio, and Marie Delbasty (from Aranzadi Zientzia Elkartea) who helped during the fieldwork campaigns. P. G. acknowledges all of the people who provide tissues samples for the Collection BEV, especially Marc Cheylan.
Author Contributions: Conception and design, I. R. -I. , F. M. -F. and M. G. -P. ; data collection, I. R. -I. and P. G. ; analysis and interpretation of results, I. R. -I. , F. M. -F. , Y. J. -R. and I. F. ; manuscript writing, I. R. -I. , I. F. , Y. J. -R. , M. G. -P. , P. G. and F. M. -F. ; supervision, M. G. -P. and F. M. -F. All authors have read and agreed to the published version of the manuscript. Funding: I. F. and F. M. -F. are supported by FCT-Fundação para a Ciência e a Tecnologia, Portugal (ref. SFRH/BD/148514/2019 and DL57/2016/CP1440/CT0010, respectively). This work has been funded by the Spanish Government under project-grant PID2019-110243GB-100/AEI/10. 13039/501100011033 (Ministerio de Ciencia e Innovación), awarded to M. G. -P. Institutional Review Board Statement: Fieldwork to obtain the tissue samples and occurrence data was conducted in accordance with permits from the Provincial Council of Gipuzkoa (ref.
Sample collection and measurements of oxygen Samples from the shallow oxygen maximum, lake interface, anoxic zone, and shallow sediments (17 samples total) were collected in mid to late October each year from 2017 to 2019. Prior to sampling, oxygen concentration and saturation were measured through the water column with a SDOT dissolved oxygen data logger (NKE Instrumentation). All water column samples were collected using a 12-l Niskin bottle. Between 3 and 5 bottles were taken for each water column sample (36-60 liters total), and all the water from one depth was pooled and filtered by tangential flow filtration (0. 2-μm cartridge) to yield concentrate. The 12-m and 57-m samples from 2019 were pre-filtered before tangential flow filtration with a 20-μm filtration tissue to exclude larger eukaryotic organisms.
Metagenomic assembly, coverage calculation, gene prediction, and preliminary annotation Metagenomic assembly was performed following the procedures of He et al. 2021  [12]. Briefly, sequencing reads were rid of Illumina adapters using BBTools and were trimmed using Sickle  [13]  (default thresholds). Quality-filtered reads were then assembled using MEGAHIT (v. 1. 2. 9 , default parameters)  [14]  and scaffolded using IDBA-UD  [15]. Reads were mapped back to the entire assembly for each sample using bowtie2  [16]  to compute scaffold coverage values. Assembled scaffolds were subsetted to those ≥1000 bp for gene prediction and binning. Genes were predicted using Prodigal (meta mode)  [17] , and predicted proteins were annotated using USEARCH against the KEGG (v. 74. 0), UniRef (release-2015_10), and UniProt (release-2015_05) databases.
Genome binning, refinement, taxonomic assignment, and relative abundance calculation Genome binning was performed using both a manual and an automated approach. For the manual approach, scaffold information was loaded into ggKbase (ggkbase. berkeley. edu) and scaffolds were binned on the basis of coverage, GC content, taxonomic affiliation, and inventories of bacterial "single copy" genes. For the automated approach, reads were cross-mapped against every other assembly within each biome type using bowtie2. Sediment and water column samples were binned separately. Coverage tables were generated using the jgi_summa-rize_bam_contig_depths script (bitbu cket. org/ berke leylab/ metab at/ src/ master) and passed to MetaBAT2 (minimum contig size 1500 bp)  [18]  for automated bin generation. Bins derived from the manual and automated approaches were reconciled with DAS Tool  [19]  to create the best merged set of bins for downstream analysis.