dataesr/scientific-paragraphs-categorization huggingface dataset:
IMPLEMENTATION AND RESULTS Implementation. BOLDR consists of QIR, host languages, and databases. To evaluate our approach, we implemented the full stack, with R and SimpleLanguage as host languages and PostgreSQL, HBase and Hive as databases. Table  1  gives the numbers of lines of Java code for each component to gauge the relative development effort needed to interface a host language or a database to BOLDR. All developments are done in Java using the Truffle framework. 1 : BOLDR components and their sizes in lines of code. As expected, the bulk of our development lies in the QIR (its definition and normalization) which is completely shared between all languages and database backends. Compared to its 4000 l. o. c. , the development cost of languages or database drivers, including translations to and from QIR is modest (between 700 and 1000 l.
conf", "tpch") revenue = tableRef("revenue", "PostgreSQL", "postg. conf", "tpch") max_rev = function() max(subset(revenue, TRUE, c(total_revenue))) q = subset(merge(supplier, revenue, function(x, y) x$s_suppkey == y$supplier_no), total_revenue == max_rev(), c(s_suppkey, s_name, s_address, s_phone, total_revenue) )[order(s_suppkey), ] print(executeQuery(q)) BOLDR was able to inline this query, whereas the equivalent in SQL+UDFs could not be inlined by the optimizer of PostgreSQL. Table  2. B illustrates the overhead of calling the host language evaluator from PostgreSQL by comparing the cost of a non-inlined pure PL/SQL function with the cost of the same function embedded in a host expression within the query. While it incurs a high overhead, it remains reasonable even for expensive queries (such as TPCH-1) compared to the cost of network delays that would happen otherwise since host expressions represent expressions that are impossible to inline or to translate in the database language.
RELATED WORK The work in the literature closest to BOLDR is T-LINQ and P-LINQ by Cheney et al. [7]  which subsumes previous work on LINQ and Links and gives a comprehensive "practical theory of language integrated queries". In particular, it gives the strongest results to date for a language-integrated queries framework. Among their contributions stand out: (i) a quotation language (a λ-calculus with list comprehensions) used to express queries in a host language, (ii) a normalization procedure ensuring that the translation of a query cannot cause a query avalanche, (iii) a type system which guarantees that well-typed queries can be normalized, (iv) a general recipe to implement language-integrated queries and (v) a practical implementation that outperforms Microsoft's LINQ. Some parts of our work are strikingly similar: our intermediate representation is a λ-calculus using reduction as a normalization procedure.
However, our work diverges radically from their approach because we target a different kind of host languages. T-LINQ requires a pure host language, with quotation and anti-quotation support and a typesystem. Also, T-LINQ only supports one (type of) database per query and a limited set of operators (essentially, selection, projection, and join, expressed as comprehensions). While definitely possible, extending T-LINQ with other operators (e. g. , "group by") or other data models (e. g. , graph databases) seems challenging since their normalization procedure hard-codes in several places the semantics of SQL. The host languages we target do not lend themselves as easily to formal treatment, as they are highly dynamic, untyped, and impure programming languages. We designed BOLDR to be target databases agnostic, and to be easily extendable to support new languages and databases.
We also endeavored to lessen the work of driver implementers (adding support for a new language or database) through the use of embedded host language expressions, which take advantage of the capability of modern databases to execute foreign code. This contrasts with LINQ where adding new back-ends is known to be a difficult task  [10]. Lastly, we obtained formal results corresponding to those of T/P-LINQ by grafting a specific SQL type system on our framework. QIR is not the first intermediate language of its kind. While LINQ proposes the most used intermediate query representation, recent work by Ong et al. [16]  introduced SQL++, an intermediary query representation whose goal is to subsume SQL and NoSQL. In this work, a carefully chosen set of operators is shown to be sufficient to express relational queries as well as NoSQL queries (e.
g. , queries over JSON databases). Each operator supports configuration options to account for the subtle differences in semantics for distinct query languages and data models (treatment of the special value NULL, semantics of basic operators such as equality,. ). In opposite, we chose to let the database expose the operators it supports in a driver. Grust et al. [12]  present an alternative compilation scheme for LINQ, where SQL and XML queries are compiled into an intermediate table algebra expression that can be efficiently executed in any modern relational database. While this algebra supports diverse querying primitives, it is designed to specifically target SQL databases, making it unfit for other back-ends. Our current implementation of BOLDR is at an early stage and, as such, it suffers several shortcomings.
Some are already addressed in existing literature. First, since we target dynamic programming languages, some forms of error cannot be detected until query evaluation. This problem has been widely studied and, besides T-LINQ, works such as SML#  [15]  or ScalaDB  [11]  use the static type system of the language to ensure the absence of a large class of runtime errors in generated queries. Second, our treatment of effects is rather crude. Local side effects, such as updating mutable references scoped inside a query, work as expected while observable effects, such as reading from a file on host machine memory, is unspecified behavior. The work of Cook and Wiedermann  [8]  shows how clientside effects can be re-ordered and split apart from queries. Third, at the moment, when two subqueries target different databases, their aggregation is done in the QIR runtime.
CONCLUSION AND FUTURE WORK We presented BOLDR, a framework that allows programming languages to express complex queries containing application logic such as user-defined functions. These queries can target any source of data as long as it is interfaced with the framework, more precisely, with our intermediate language QIR. We provided methods for programming languages and databases to interface with QIR, as well as an implementation of the framework and interfaces for R, SimpleLanguage, PostgreSQL, HBase, and Hive. We described how QIR reduces and partially evaluates queries in order to take the most of database optimizations, and showed that BOLDR generates queries performing on a par with hand-written SQL queries. Future work includes the creation of a domain-specific language to define translations from QIR to database languages, leaving the implementation details to the language itself, with the associated gains of speed, clarity, and concision.
Currently, queries targeting more than one data sources are partially executed in the host language runtime. We plan to determine when such queries could be executed efficiently in one of the targeted data sources instead. For instance, in a join between two distinct data sources, it could be more efficient to send data from data source to the other will complete the join. ORMs and LINQ can type queries since they know the type of the data source. BOLDR cannot do it yet since QIR queries may contain dynamic code, and we do not want to type-check the whole host language. While we cannot foresee any general solution, we believe that to exploit any type information available we could use gradual typing  [20] , a recent technique blending static and dynamic typing in the same language. In particular, we would be able to use type information from database schemas (when available) to infer types for the queries.
Here, we present the genome of a new thraustochytrid species, which is highly similar to Aurantiochytrium limacinum/mangrovei and Schizochytrium aggregatum. The taxonomic position of this new species will be determined later, after more thorough analyses. The pollen grain bait isolation method (5) was used to obtain monospecific axenic cultures from coastal seawater samples gathered in Mayotte (Indian Ocean, 12°48=51. 8ЉS, 45°14=21. 7ЉE). Once the culture was proved to be monospecific and axenic, it was deposited at the Culture Collection of Algae and Protozoa (CCAP) under the accession number CCAP_4062/3. Cells were propagated in M1 medium (6) at 30°C under agitation (140 rpm). Genomic DNA was extracted and purified using a Quick-DNA Miniprep Plus kit (Zymo Research) according to the manufacturer's instructions.
Quality and concentration were estimated using the Quant-iT PicoGreen dsDNA assay kit. Shotgun sequencing libraries were prepared and sequenced as paired-end reads (100 bp) on an Illumina HiSeq platform (Illumina, Inc. ). The quality of the raw reads was assessed with FastQC (http://www. bioinformatics. babraham. ac. uk/projects/fastqc). About 137,997,490 paired-end reads were de novo assembled using SPAdes version 3. 10. 1 (7) with a multi-k-mer approach (k ϭ 27, 31, 35, 41, 45, 49, and 53). Contigs were scaffolded with Satsuma using the genome of Schizochytrium sp. CCTCC M209059 (GenBank accession number JTFK00000000) as the reference. The final assembly consisted of 4,503 contigs Ն300 bp assembled in 2,232 scaffolds. The N 50 value was 236,568 bp, and the overall GC content was 57%. AUGUSTUS version 3.
gene prediction  (8). A total of 11,853 coding sequences were recorded. BUSCO  (9)  analysis showed that 10% of the eukaryotic conserved gene core is not represented and that 85. 1% is represented by complete single-copy genes in our genome. Functional annotation was carried out using AHRD (https://github. com/groupschoof/ AHRD) after a BLAST search against the UniProt Eukaryote and Protist TrEMBL protein database was performed. A description was associated with 7,861 sequences (66%), while a gene ontology (GO) annotation was assigned to 7,269 transcripts (61%). Analysis with barrnap software (https://github. com/tseemann/barrnap) identified three copies of the 5. 8S gene, eight partial copies of the 28S gene, and seven partial copies of the 18S gene. The 18S and 28S sequences were finally reconstructed by PCR amplification and direct Sanger sequencing.
The taxonomy and systematics of this strain are under study. This genome is considered of high interest, because metabolic pathways potentially suitable for the bioproduction of different high-added-value molecules can be identified. Other Labyrinthulomycetes genomes have been sequenced, and comparative analyses of closely related taxa can lead to a better understanding of the evolutionary success of thraustochytrids, particularly their ability to produce considerable amounts of lipids. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under BioProject PRJNA396017. The version described in this paper is the first version. The 18S, 5. 8S, and 28S rRNAs have been deposited at GenBank under the accession numbers MF766427, MF766428, and MF766429, respectively.
ACKNOWLEDGMENTS Olivier Bastien  ( LPCV, Grenoble ) is acknowledged for helping in 18S rRNA gene identification. K. S. and A. A. thank  Sylvaine Roy  for her substantial support and precious advice. E. M. was supported by the  Oceanomics program  ( Investissements d'Avenir, Biotechnology & Bioresources ) from  ANR. This work was supported by a Fermentalg-CEA partnership and the  Trans ' Alg Bpifrance  project.
The dyes were sequentially imaged (Alexa 647 first, followed by Alexa 532) to collect the desired single molecule frames and to avoid photo bleaching. Multi-color fluorescent microspheres (Tetraspeck, Invitrogen) were used as fiducial markers to register long-term acquisitions and correct for lateral drifts and chromatic shifts. A spatial resolution of 14 nm was measured using centroid determination on 100 nm Tetraspeck beads acquired with similar signal to noise ratio than d-STORM single molecule images. Details of experimental procedure and data analysis was followed as described before  (Nair et al. , 2013). Tesselation analysis of d-STORM experiments are done as described in the original paper  (Levet et al. , 2015). uPAINT 13-14 Days in vitro (DIV)-dissociated neurons were imaged at 37˚C in an open Ludin Chamber (Ludin Chamber, Life Imaging Services, Switzerland) filled with 1 ml of Tyrode's.
Electrophysiology recordings on cell culture Coverslips of transfected neurons were placed in a Ludin Chamber on an inverted motorized microscope (Nikon Eclipse Ti). Extracellular recording solution was composed of the following (in mM): 110 NaCl, 5. 4 KCl, 1. 8 CaCl 2 , 0. 8 MgCl 2 , 10 HEPES, 10 D-Glucose, 0. 001 Tetrodotoxin and 0. 05 Picrotoxin (pH 7. 4; 245 mOsm). Patch pipettes were pulled using a horizontal puller (P-97, Sutter Instrument) from borosilicate capillaries (GB150F-8P, Science Products GmbH) to resistance of 4-6 MW and filled with intracellular solution composed of the following (in mM): 100 K-gluconate, 10 HEPES, 1. 1 EGTA, 3 ATP, 0. 3 GTP, 0. 1 CaCl 2 , 5 MgCl 2 (pH 7. 2; 230 mOsm). Transfected neurons were identified under epifluorescence from the GFP signal. Recordings were performed using an EPC10 patch clamp amplifier operated with Patchmaster software (HEKA Elektronik).
Whole-cell voltage clamp recordings were performed at room temperature and at a holding potential of À70 mV. Unless specified otherwise, all chemicals were purchased from Sigma-Aldrich except for drugs, which were from Tocris Bioscience. Data were collected and analysis of miniature EPSCs was performed using a software developed by Andrew Penn, the matlab script is available on MATLAB File Exchange, ID: 61567; http://uk. mathworks. com/matlabcentral/fileexchange/61567-peaker-analysis-toolbox).
Bicuculline (20 mM) was added to the aCSF to block inhibitory currents and DNQX (100 nM) was added to control epileptic activity. Series resistance was always lower than 20 MW. Paired-pulse ratio was determined by delivering two stimuli 50 ms apart and dividing the peak response to the second stimulus by the peak response of the first one. For recordings aEPSCs, extracellular CaCl 2 was substituted to equimolar SrCl 2. aEPSCs evoked within 500 ms after the stimulation, were analyzed off-line with Mini Analysis software (Synaptosoft). In all cases, at least 20 sweeps per recording were analyzed with a detection threshold set at 5 pA.
Co-localization analysis Co-localization analysis was performed using custom written program in Matlab (Mathworks, UK). Manders' coefficients were chosen as co-localization measure because they do not depend on the relative intensity difference between two component images, therefore bypassing alteration in labeling efficiency of different cellular structures. Here, we perform pairwise analysis between coincidental objects observed in two image components. Thus, our Manders' coefficients represent fraction of the intensity belonging to co-localizing super-resolution pixels of a given object. Manders' coefficients are calculated using following equations: M 1 ¼ P n i I 1i;coloc P n i I 1i M 2 ¼ P n i I 2i;coloc P n i I 2i Where i is a pixel index, 1 and 2 stands for two image components and n is the number of pixels in an object for which coefficient is evaluated.
Acknowledgements We acknowledge  E Gouaux  for the anti-GluA2 antibody;  J-B Sibarita  and  C Butler  for providing single particle analysis software,  I Gauthereau  for anti-GFP nanobody production;  C Breillat ,  B Tessier ,  S Benquet  and  E Verdier  for cell culture and plasmid production;  E Normand  and  S Daburon  for virus tests; and  M Goillandeau  and  A Penn  for mEPSC analysis software ( Detection Mini ). This work was supported by funding from the  Ministe  ` re de l'Enseignement Superieur et de la Recherche  ( ANR NanoDom  and  AMPA-T) ,  Centre National de la Recherche Scientifique, FRM  to BC,  ERC Grants nano-dyn-syn  ( 232942 ) and ADOS ( 339541 ) to DC, the  Conseil Regional de Nouvelle Aquitaine and SyMBaD -ITN Marie Curie , Grant Agreement n˚238608 - Seventh Framework Program  of the  EU  to KH.
Context. The Class 0 protostellar binary IRAS 16293-2422 is an interesting target for (sub)millimeter observations due to, both, the rich chemistry toward the two main components of the binary and its complex morphology. Its proximity to Earth allows the study of its physical and chemical structure on solar system scales using high angular resolution observations. Such data reveal a complex morphology that cannot be accounted for in traditional, spherical 1D models of the envelope. Aims. The purpose of this paper is to study the environment of the two components of the binary through 3D radiative transfer modeling and to compare with data from the Atacama Large Millimeter/submillimeter Array. Such comparisons can be used to constrain the protoplanetary disk structures, the luminosities of the two components of the binary and the chemistry of simple species.
1995)  and prebiotic molecules  (Jørgensen et al. 2012)  were detected. The source IRAS 16293A appears to be highly active with several detected outflows, while IRAS 16293B is more quiescent, with no known outflows (e. g. ,  Chandler et al. 2005; Kristensen et al. 2013). Alves et al. (2012)  find that the magnetic field strengths in IRAS 16293 are comparable to the outflow ram pressure, and thus that the magnetic field is dynamically important for this system. Both components are embedded within a larger, circumbinary envelope of dust and gas, which has been well studied in previous works using single-dish data and 1D radiative transfer modeling  (Schöier et al. 2002; Jørgensen et al. 2005b; Crimier et al. 2010). These models all use a single central radiation source, where disks or complex structures, such as a dust and gas filament, have never been included in the radiative transfer calculations.
In this paper, we construct a 3D model, including disks, a filament and two radiation sources using high angular resolution data from the ALMA Protostellar Interferometric Line Survey (PILS) as observational constraints. The impact of the binary nature of IRAS 16293 on the temperature distribution is evaluated as opposed to that of a single star. As stellar binaries are abundant, especially in the Class 0 stage  (Tobin et al. 2016) , this temperature evaluation of IRAS 16293 is useful as a case study on the temperature distribution in the environment of protostellar binaries in wide orbits, found in large fractions of starforming regions (e. g. ,  Duchêne et al. 2004) , as well as a retrospective analysis on the validity of previous works approximating a binary as a single protostar in their radiative transfer modeling, which will be useful for data-mining.
588 GHz, Klapper et al. 2000) , C 18 O (329. 331 GHz, Klapper et al. 2001) and C 17 O (337. 061 GHz,  Klapper et al. 2003)  were extracted from the dataset, using the entire pixel map, after the lines were identified. The source A LSR velocity of 3. 1 km s - 1   (Jørgensen et al. 2011)  was used for all lines. Channels within ± 5 km s -1 of each line were combined into an integrated intensity (moment zero) map for each isotopologue, using the image analysis software MIRIAD. Using this approach, the vast majority of the observed line emission was extracted, while avoiding major line-blending from other species.
Dust radiative transfer modeling This Section describes the setup of the radiative transfer code RADMC-3D, including a description of the dust opacity, model grid and the envelope dust density model used. At the end of the Section, we present our investigation of the temperature structure difference between a single-and a binary protostar, where the envelope dust density model was used. We constructed 3D dust and gas line radiative transfer models consisting of a large envelope with a radius of 8×10 3 AU based on  Schöier et al. (2002) , two disks around the protostars, as well as a dust filament between the two protostars. The disk's dust densities were mod-eled with both the model protoplanetary disk (PP-disk) structure known from Class II sources (e. g. ,  Andrews et al. 2012 ) and the density solution from the angular momentum conservation of an infalling, rotating collapse  (Terebey et al.
RADMC-3D To determine the dust temperature and to produce continuum images, the radiative transfer code RADMC-3D (Dullemond et al. 2012, v. 0. 40) 1 was used. RADMC-3D uses the  Bjorkman & Wood (2001)  algorithm to perform a Monte Carlo simulation of photon propagation from one or more radiation sources, through a predefined grid of dust density cells, in order to estimate the dust equilibrium temperature. This equilibrium is a balance between the incoming radiative energy and the blackbody emission from the dust cell itself. The code setup in this work assumed that all the dust energy originated from the protostars through irradiation, and not from any internal energy source such as viscous accretion, or any external radiation source. The precision of the resulting dust equilibrium temperature depends, among other parameters, on the number of photons used in the radiation simulation (this differed between model setups, see Table  1 ).
In LIME, the number density of the colliders is approximated as n H 2 , as H 2 is by far the most abundant species in the dense molecular cores where star formation takes place (e. g. ,  Genzel & Stutzki 1989). LIME performs non-LTE (Local Thermodynamic Equilibrium) line radiative transfer modeling, where the rotational level populations are found iteratively. The CO isotopologue data files containing collisional rate coefficients  (Yang et al. 2010)  were downloaded from the LAMDA 2 database  (Schöier et al. 2005). The collisional rate coefficients of the CO isotopologues with H 2 in these files include collisions with both ortho-and para-H 2. In this work, we assumed that the dust and gas temperatures are coupled, which is usually a good approximation in the dense inner environments of the envelope  (Schöier et al.
This work illustrates the importance of using complex, full 3D radiative transfer modeling together with subarcsecond observations of young stellar objects such as IRAS 16293 in order to constrain the physical parameters of such Class 0 disks and their environment. It also illustrates the need for even higher resolution observations of the gas and dust in the disks around source A and B in order to do a full quantitative investigation with parameter confidence intervals, to determine the exact CO isotopologue abundances and the parameters of the dust filament enveloping both sources. We also suggest that gas dynamics, including outflows and magnetic fields, are investigated in future modeling efforts. Having a detailed and robust physical model is critical for the interpretation of ALMA spectral data of the various hot corino species.
Acknowledgements. The authors are grateful to  Søren Frimann ,  Jonathan Ramsey  and  Attila Juhasz  for useful discussions about 3D radiative transfer modeling. We would also like to thank the anonymous referee for helpful suggestions, which improved the presentation of this work. This paper makes use of the following ALMA data: ADS/JAO. ALMA# 2013. 1. 00278. S. ALMA is a partnership of  ESO  (representing its member states),  NSF (USA)  and  NINS (Japan) , together with  NRC (Canada)  and  NSC and ASIAA (Taiwan)  and  KASI (Republic of Korea) , in cooperation with the  Republic of Chile. The Joint ALMA Observatory is operated by  ESO ,  AUI/NRAO  and  NAOJ. The group of J. K. J. acknowledges support from a  Lundbeck Foundation   Group Leader Fellowship  as well as the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No.