dataesr/scientific-paragraphs-categorization huggingface dataset:
Confocal laser-scanning microscopy Protoplast images were obtained using a Leica TCS SP8 confocal microscope equipped with a HC PL APO 20x/0. 75 IMM CORR CS2 objective (Leica Microsystems, Mannheim, Germany), with the exception of images in Supplementary Fig. 7b  and Fig. 5a  that were taken with a Zeiss LSM880 Airyscan using a 63x/1. 4 oil immersion lens. GFP was excited with a White Light Laser (WLL) at 488 nm and the emission detected at 500-550 nm. YFP was excited with a 514 nm laser line and detected at 520-555 nm. mCherry fluorescence was excited at 561 nm and emission was detected between 575-630 nm. Samples, coexpressing two fluorophores were imaged in sequential mode between frames. All images were taken as z-stacks (internal distance is 0. 5 um) and further analyses and projections were performed with either ImageJ/(Fiji) software  88  or Imaris.
For GUV experiments: Images were acquired by confocal fluorescence microscopy (Nikon Eclipse Ti-E inverted microscope using a Nikon A1R confocal laser scanning system with laser lines: 405 nm, 488 nm, 561 nm, 640 nm; 60x/1. 49 oil immersion objective; Nikon Instruments, Inc. ) and analyzed using the corresponding NIS Elements software (NIS Elements Confocal 5. 20, Nikon Instruments, Inc. ) and ImageJ (Fiji win64, Open source).
Super resolution microscopy Super resolution images were generated using an ELYRA7, structuredillumination-microscope with 3D Lattice SIM (Zeiss), equipped with a 63x/1. 4 Oil DIC objective, a Pecon incubation chamber ensuring stable temperature and processed using the Zen black software package (Zeiss). Samples were stained as indicated and imaged as z-stack with 0,091 µm interval. Each stack was processed as single plane or maximum intensity projection (MIP) using Imaris software 64×9. 9. 0. Brightness and contrast were applied equally to all images prior to quantification. For colocalization analysis, we performed 2D line scan analysis on single plane and MIP images as indicated using Zen black software and Imaris.
Acknowledgements We would like to thank  Carmen Schubert  and  Rosula Hinnenberg  for their excellent technical help and the entire Ott lab team for fruitful Article https://doi. org/10. 1038/s41467-023-35976-5Nature Communications | (2023) 14:323 discussions and providing their individual expertise throughout the course of the project. We also thank the staff of the  Life Imaging Center (LIC) in the Hilde Mangold House (HMH) of the Albert-Ludwigs-University of Freiburg  for help with their confocal microscopy resources, and the excellent support in image recording. Special thanks also to  Norbert Roos  and  Jens Wohlmann  at the  Electron Microscopy Facility, Department of Biosciences, University of Oslo, Norway , for helping with the SEM sample preparation and imaging and to  Falk Tauber  ( University of Freiburg, Cluster of Excellence livMatS ) for designing and printing a tentative indentation support.
Many thanks also to  Nicole Gensch  ( BIOSS, University of Freiburg ) for providing the pET303-EGFP-10xHis vector,  Maria Harrison  ( Boyce Thompson Institute, Ithaca, USA ) for providing the Medicago ABD-mCherry line and  Julien Gronnier  ( University of Tübingen ) for providing the AtREM2. 1  CDS  and critically reading the manuscript. J. K. , C. L. , and P. M. D. belong to the LRSV, which is part of the  TULIP LABEX  ( ANR-10-LABX-41 ). The microscopes are operated by the  Microscopy and Image Analysis Platform (MIAP)  and the  Life Imaging Center (LIC), Freiburg. Engineering Nitrogen Symbiosis for Africa (ENSA)  project currently supported through a grant to the  University of Cambridge  by the  Bill & Melinda Gates Foundation  ( OPP1172165 ) and  UK government's Department for International Development (DFID)  (T.
2CD ). Again, using a hierarchical clustering tree onto geographical coordinates of caves in the PCA (Fig. 2E , Single Clicks), we found some grouping of caves that does not fit with phylogeography. The apparent closeness of Subterráneo (Micos group) and Sabinos (El Abra group), or Molino (Guatemala group) and Chica (El Abra) rather suggests independent evolution of sound production in these different caves. In sum, our data provide strong evidence for the evolution of an "accent" in the different cavefish populations. Finally, in our Molino dataset where only 4 fish were recorded, we noticed, using unsupervised hierarchical clustering on single Clicks, the presence of 4 different groups of sounds (Fig. 2F ). Likewise, in Pachón (10 fish in net) and Subterráneo (12 fish in net) the same method yielded 8 groups and 9 groups of sounds, respectively (not shown).
The four fish taped were nevertheless productive, as 50 clicks and 50 serial clicks could be extracted from this short period for analysis. Natural soundscape in Tinaja (heavy and continuous dripping limestone ceiling) prevented to exploit overnight recordings and made us seek for a quiet pond with specimens on the second day, leading to shorter recording as well (1h30). We therefore analyzed ≤100 sounds from the audio bands from other caves, to equilibrate the comparisons and statistical analyses with the more limited Molino and Tinaja dataset. Of note, for each cave the number of sounds analyzed (50) corresponded to minimum ten times the number of variables studies, i. e. , 5 variables for the serial slicks. Sounds were extracted by ear from audio bands recordings. Each audio track was carefully scrutinized manually from sonograms magnified at a 3-4 seconds temporal window and further at a 0.
2 and 1 second bins (Fig. 1D ) allowing a visual control of each extracted sound motif while listening from T0 to end, including tracks of 11h. Clicks and serial clicks were not extracted in an exhaustive but in a systematical manner: only sounds previously described in the acoustic range of single click or serial click produced by fish in the lab or in the wild were considered, and replicates of each identified sound motif were randomly extracted. This allowed to increase the stringency and to capture the diversity of clicks and serial clicks for a comprehensive view of each cave soundscape. Sounds were digitized at 44. 1 kHz (16-bit resolution) and analysed using fast Fourrier transform (FFT) with Avisoft SAS Lab Pro 5. 2. 07 software (Avisoft bioacoustics, Glienicke, Germany)  [24]. The acoustic structure of single clicks was analyzed using a set of: -1 temporal parameter, the duration, measured from the envelop of the oscillogram, -2 parameters measured from the oscillogram: RMS amplitude, and signal to noise ratio (SNR; [RMS amplitude of the signal-RMS amplitude of noise]/RMS amplitude of noise), -5 spectral parameters obtained from power spectra (FFT, window type: Hann, window size: 512; time overlap: 90%) within a 0-22.
5 kHz bandwidth. Spectral parameters were: 1) peak frequency of the frequency spectrum (dominant frequency), 2) first quartile of energy (Q25), i. e. the frequency value corresponding to 25% of the total energy spectrum, 3) second quartile of energy (Q50), 4) third quartile of energy (Q75), and 5) interquartile, i. e. difference between Q75 and Q25. Serial clicks were examined using 5 fine temporal parameters including sound duration, pulse number, mean inter-pulse duration, mean pulse duration, and pulse rate (= sound duration/pulse number) using personal routines developed with R package Seewave  [25]. Pulses were considered "single" if they were of short duration (<20msec) and separated by >1sec interval from the next pulse (threshold defined from the histogram of the inter-pulse durations).
After calculating the correlation coefficients between the variables, we excluded highly correlated variables (r > 0. 65 or < -0. 65), retaining 3 uncorrelated variables for single clicks (duration, SNR, dominant frequency) and 5 uncorrelated variables for serial clicks. A principal component analysis (PCA; R package FactoMineR) was performed using the 3 variables retained for single clicks and the 5 variables retained for serial clicks, allowing to draw the centroïds of the 6 caves, surrounded by their 95% confidence circles (Fig. 2CD ). A permutated discriminant function analysis (pDFA; R routine from Bertucci et al. 2010  [24] ) performed on the principal components axis of the previous PCA provided a classification procedure that assigned each sound to its appropriate cave (correct assignment) or to one of the others (incorrect assignment) (Fig.
Acknowledgments Work supported by a  Lidex Neuro-Saclay  collaborative grant to SR and JA, an  Equipe FRM grant  ( DEQ20150331745 ) to SR, a prize from  Fondation des Treilles  to CH, and an  Ecos-Nord exchange Program  to SR and  Patricia Ornelas-Garcia. We thank  Luis Espinasa ,  Julien Fumey , and  Stéphane Père  and all other members of the  Rétaux's lab  for their helpful spirit in the field, and  Patricia Ornelas-Garcia  for obtaining shared fieldwork permits.
The NOW database of fossil mammals came to be through a confluence of several initiatives spanning multiple decades. The first public version of NOW database was released in 1996 and the first Advisory Board was established the year after. Originally, NOW stood for Neogene of the Old World but with the gradual expansion of the database the acronym was eventually reassigned to stand for New and Old Worlds. The structure of what would become NOW was originally cloned from the ETE database of the Smithsonian Institution and the first NOW version accessible over the internet was a node of the ETE database. The first standalone, online version of NOW was launched in 2005 and the first formal steering group was established in 2009. During its existence, NOW has been funded, directly or indirectly, by several organizations but fundamentally it has always been an unfunded community effort, dependent on voluntary work by the participants.
For terrestrial vertebrates an early manifestation of this trend was the Workshop on Computerization organized by the Society of Vertebrate Paleontology in 1989 and the resulting Guidelines and Standards for Fossil Vertebrate Databases  (Blum, 1991). The roots of the NOW database (originally Neogene of the Old World, subsequently New and Old Worlds) run deep in this fertile ground, or perhaps more accurately, it first developed as nothing but one branch of several of the Evolution of Terrestrial Ecosystems (ETE) database, developed by John Damuth and the ETE Consortium. Based at the Smithsonian, the ETE Program designed a novel kind of database for the terrestrial fossil record. Such a database would not include merely species-occurrence data for particular fossil localities, but in addition would include pertinent interpretations of sedimentary context, ecological environment and taphonomy (for localities) and biological and ecological trait characteristics (for the species).
Such a database could be used to explore terrestrial paleoecology in a way not previously possible with large compilations of data. One could ask not only, "Where/when is such-and-such a taxon found," but also questions such as, "Where during this time do we find localities with species of grazing mammals over 100 kg?" Such a database asks much of its compilers and needs frequent revision as ideas and techniques develop. But even a small set of relatively basic ecological variables opens up a wide array of avenues of research. This concept resonated with the small community of researchers involved in the beginnings of NOW. What follows here is a long and strange story, littered with coincidences and lucky breaks and not devoid of passion. One might think that databases are just neutral repositories of primary data, necessary but boring.
Instead, they seem to call forth strong personal ambitions, emotions and impulses, including the darker urges related to possession and ownership. The collective history of fossil databases is accordingly dotted with dramaat least one field catalogue of fossils even ending up as an item in divorce proceedings. But, while seemingly unavoidable and prudent to keep in mind, this dark and gossipy side is largely irrelevant to the real purpose of databases and we shall not review it further here. At the end of the story there is a moral: a public database is fundamentally really a kind of museum collection. And, like all museum collections, it needs dedicated care and curation to deliver its potential for discovery, insight, beauty, and wonder. Just as the objects in a museum and data in a database tell a story of their own, we can only appreciate the collection as a whole if we know the ambitions and quirks of those who caringly brought them together.
The Kurténian Era and the Epi-Kurténian The Setting The NOW database was long in the making. It has deep roots in the legacy of Helsinki mammal paleontologist and writer Björn Kurtén, his emphasis on function and ecology and his strong will to systematically compile and organize information about fossil mammals and environments, as in his classic books Pleistocene Mammals of Europe  (Kurtén, 1968) , The Age of Mammals  (Kurtén, 1971) , and Pleistocene Mammals of North America  (Kurtén & Anderson, 1980). Together with his then PhD students Lars Werdelin and Mikael Fortelius, Kurtén as early as the early 1980s developed a plan and a proposal for a basic database of Quaternary fossil mammals, based primarily on the raw data in the appendices to the 1968 and 1980 books, which would have run on mainframe computers using punched cards for data input (Fig.
2. 3). Thinking back to this heroic initiative one must admit that the Academy of Finland may have been right in turning the proposal down. Neither the hardware nor the software available then were quite up to the task, nor was the conceptual understanding of database structure. Nevertheless, it is undeniable that the idea was there at a very early stage. Nor can it be considered a coincidence that Kurtén's former students were later to play an important role in furthering the idea. After Björn Kurtén's death in 1988 there was a strong wish among his many colleagues worldwide to arrange a memorial meeting and publish a volume to honor his legacy. The meeting took place in Helsinki in the autumn of 1989, incidentally coinciding with the fall of the Berlin wall, and a resulting volume was eventually published as a special issue of Annales Zoologici Fennici  (Forstén et al.
, 1992). The original idea had been to publish a much more comprehensive book in the tradition of Kurtén's own synthesis volumes, but these were the days of the first enthusiasm for computerized databases and the book initiative accordingly soon evolved into a project for a database. A proposal to this effect was submitted to the European Science Foundation, which eventually funded a Network on Quaternary Mammalian Faunas for 1991-93. One explicit goal of the Network was the establishment of a database of Quaternary Mammals of Europe, a parallel to the American initiative FAUNMAP  (FAUNMAP Working Group, 1994) , with a similar concept and structure. In September 1991, Lars Werdelin hosted a technical workshop in Stockholm (Fig. 2. 4) where the properties of a Quaternary Mammal Faunas database were discussed in some detail, under the expert guidance of Russell Graham of FAUNMAP, a Quaternary fossil mammal database currently part of the Neotoma Paleoecology Database (https://www.
neotomadb. org/) and David Mayhew, a database professional with roots in mammal paleontology. An unpublished report with detailed plans was later circulated as "Report #1" of the Network  (Werdelin et al. , 1992). The Stockholm meeting fed directly into the first of three ESF-funded meetings under the Network, Mammalian Migration and Dispersal Events in the European Quaternary at Andernach on the Rhine, hosted by Wighart von Koenigswald in October of the same year. The Network was quite successful and arranged two more workshops, at Dijon in 1992 and at Sant Feliu de Guíxols, north of Barcelona, in 1993  (Agustí & Werdelin, 1995; Chaline & Werdelin, 1993; Von Koenigswald & Werdelin, 1992). Data on the occurrence of Quaternary mammals were compiled in the process.
Making It Work Anyone who has been seriously involved with the development of scientific databases will recognize a number of universals. The first and also the most trivial of them is the early obsession with technical matters, such as the choice of software platform or programming language, on which hecatombs of time and effort have been and are still being sacrificed. Interoperability, industry standard query languages, open-source software, high-level object-oriented computer languages, and the internet itself were new ideas in the early 1990s. Accordingly, there was a fear (unreasonable, as it turned out) that if one did not choose wisely, one's data would become "stuck" in a particular system and format, and could not be recovered (anyone old enough to remember trying to extract large datasets from mainframe tapes to simple ASCII files recognizes the source of that fear and frustration).
Hot on the heels of this comes the question of data access: who shall be permitted to use our incomparable database? In the present days of open access and open data it may not be obvious, but the instinctive and near-universal answer used to be some version of reciprocity: only if you contribute data will you gain access. This seemingly rational and fair choice of policy has spelled the doom of many a promising database. The population of potential contributors is simply far smaller than the population of potential users, and it is the latter that determines the visibility and perceived success of the database. The NOW database was somehow blessed in avoiding the worst of such standard mistakes. The key factor here may paradoxically have been the lack of funding and resources in general. For software we just took what happened to be available, making progress through trial and error.
The list is long and includes at least the early platforms dbase, Kman, Clarion and Paradox. Once you have built a relational database several times in different environments, passionate arguments for any one of them appear rather futile. The far more important matter of database structure and standards was never an issue for NOW, having been built originally as a clone of the ETE database. As for data contributors, it soon became clear that it was far easier to compile data on behalf of potential contributors than to persuade them to do so themselves. When actually faced with a complication of data, purportedly from her own published work, a normal scientist will be utterly unable to resist the urge to correct the mistakes. And even the few who resist this urge cannot prevent the database from compiling their data unless they (suicidally) refuse to allow public use of said data.
But by the time of the workshop, Fortelius already had one foot firmly in the world of databases and he accordingly brought up the idea of making the newly compiled high-quality data the core of a more permanent database, to be updated and offered to the scientific community in general. This idea received some support, but by the end of the meeting the matter was still undecided and no discussion of practical details had yet taken place. At this point another NOW coincidence occurred, paradoxical as in a Tang Dynasty parable, where good bad fortune cannot be told from good except in retrospect. Fortelius returned to Helsinki to learn that the Academy of Finland had unexpectedly failed to continue his main research project on the evolution of occlusal relationships in suoids and he was therefore both in acute need of a more fundable research project and free to commit himself fully to it.
Given the situation, the idea of a database project based on the Reisensburg process and data seemed an obvious choice. We quote from p. 6 of the original proposal to the Academy of Finland, submitted in January 1993 and approved in May the same year: Fossil land mammals offer both 1) a source of independent data for investigating the nature and timing of these and other similar changes, and 2) a direct window on other, related and/or simultaneous changes in the mammal communities in different habitats and on several continents. Conversely, the evolution of land mammals in relation to such an increasingly detailed background of environmental change offers challenging opportunities for evolutionary research with an ecological perspective and a geological time scale. An important step towards a more global analysis of the European fossil land mammals was recently taken by Bernor, Fahlbusch and Rietschel, who organised a roundtable workshop at Schloss Reisensburg (Germany) on the Evolution of Continental Biotopes in Central Europe and the Eastern Mediterranean (15-5 Ma) in July 1992.
For this workshop specialists were invited to revise the material for all relevant taxa and for a large number of fossil localities from Poland to Iran, and to analyse temporal and biogeographic patterns. This particular area was chosen because it can be related to the history of the Paratethys complex, and the interval because major physical and faunal changes are known to have taken place then. The Neogene land mammals are diverse enough and have a sufficiently rapid turnover to allow quantitative treatment of the data. This data will form the basis of the first scientific investigation undertaken using the NOW database, a collaborative project between Fortelius, Bernor & Mittmann (Letter 1). The funding of this project instantly created the resources needed for going ahead with the database idea.
It also raised some questions about the principles and practices of such an endeavor. In retrospect, one of them stands out as crucial: should it continue to be an informal coalition of friends and collaborators or should a more formal structure be created? In particular, should there be a formal advisory board? The fact that this question was eventually answered by affirming the latter position may have been one of the most decisive steps in the early history of the NOW database, providing it with both the scientific credibility and the sense of commitments and continuity that a fledgling database so badly needs. The original invitation to the Advisory Board members is included as Appendix 2. 1.
NOW Begins Once the database was established other developments followed naturally. In 1995, the ESF approved a new network called "Hominoid Evolution and Environmental change in the Neogene of Europe" (HOMINET). The network was coordinated by Jordi Agustí and members of the Steering Committee included, besides Mikael Fortelius, also Peter Andrews, Lorenzo Rook, Louis de Bonis and George Koufos. Although originally centered in the climatic and environmental context of the hominoid species in Europe, one of the explicit main goals of the network was to produce a database of the hominoid sites, mainly those belonging to the Vallesian and Turolian European Land Mammal Ages. In this way, the HOMINET became an early and major contributor to NOW. The original NOW was intended to include Neogene data from Spain, Italy, Germany, Hungary, Greece, Turkey and Ukraine, among other countries.
, 2005). Fortelius quickly recognized this as a welcome addition to the NOW and the data were transferred into the database, turning one of the lesser documented groups into one of the best elaborated, as it were, overnight. This was also the start of Van den Hoek Ostende becoming more involved in the NOW and taking on a role as Associate Coordinator of small mammals. Which was a quite remarkable conversion, considering that at the Senckenberg meeting he had opposed the idea of publishing the insectivores as a database in the first place.