dataesr/scientific-paragraphs-categorization huggingface dataset:
MALDI-MS/MS and database search analysis Mass spectrometry analyses were performed on an AB 4800 MALDI TOF/TOF analyzer using a 200 Hz solid-state laser operating at 355 nm  (Szopinska et al. , 2011). MS spectra were obtained using a laser intensity of 3,200 and 2,000 laser shots per spot (100 shots/subspectrum) in the m/z range of 800-4,000, whereas MS/MS spectra were obtained by automatic selection of the 15 most intense precursor ions per spot using a laser intensity of 4,000 and 2,000 laser shots per precursor (100 shots/sub-spectrum). Collision-induced dissociation was performed with an energy of 1 kV with air as the collision gas at a pressure of 1. 10 6 Torr. Data were collected using the ABSciex 4000 Series Explorer TM software. MS data from the soluble and the microsome fractions were pooled and analyzed as a single data set using ProteinPilot software v.
4. 0 with the Paragon TM search algorithm  (Shilov et al. , 2007)  (AB SCIEX). The MS data were searched against the S. symbiotica CWBI-2. 3 T database (containing 3,397 protein sequences downloaded on Augustus 08th 2015, GenBank accession number: CCES00000000). The searched options in ProteinPilot were ''thorough search'', ''MMTS'' as the cysteine modification, ''trypsin'' as the digestion enzyme. All reported proteins were identified with 95% or greater confidence, as determined by ProteinPilot unused scores (>1. 3). This corresponds to a stringent threshold of false discovery rate, lower than 1%. The ''unused'' score is a measurement of the protein identification confidence taking into account peptides from spectra that have not already been used by higher scoring proteins. All identified proteins were analyzed by PSORTb version 3.
Proteome map The reference proteome map was built through the analysis of the soluble and the microsome fractions from three independent S. symbiotica CWBI-2. 3 T cultures using a gel-free approach. Due to their low abundance and poor solubility, membrane proteins are generally poorly represented on two-dimensional gels  (Geert Baggerman, 2006). We therefore decided to rely on a gel-free approach. Soluble and membrane proteins were separated by ultracentrifugation and the microsome fraction was stripped at alkaline pH to remove soluble proteins  (Wu et al. , 2003). Overall, spectral data were pooled and analyzed as a single data set. This led to the identification of 720 different proteins (Table  S1 ), corresponding to 19. 7% of all theoretically expressed proteins of the recently sequenced strain S.
Culturomics approach allowed to isolate 295 new bacterial species from the human gut  [1]. As a part of culturomics study in September 2016, we isolated from a fresh stool sample of a 26-year-old healthy French woman two bacteria strains (Marseille-P3369 T and Marseille-P3385 T ) that could not be identified by our systematic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (http:// mediterraner-infection. com/article. php?laref=256&titre=urmsdatabase) on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany)  [2]. This study was approved by the ethics committee of the Institut Hospitalo-Universitaire Méditerranée Infection under number 2016-011, and the patient provided signed informed consent. The fresh stool sample was inoculated in an anaerobic blood culture bottle (Becton Dickinson, Le Pont-de-Claix, France) incubated for 3 days at 37°C.
The colonies are white and circular, and 0. 5 mm in diameter. Cells were Gram positive, small rod shaped, and slightly curved, ranging in diameter from 350 to 400 nm. Strain Marseille-P3369 T did not exhibit catalase or oxidase activities and grew optimally at 37°C and pH 7. 5. 16S rRNA gene sequence-based identification demonstrated that strain Marseille-P3385 T exhibited 96. 31% sequence identity with Prevotella disiens JCM 6334 T (GenBank accession no. NR_113103. 1) [3]  (Fig. 1 ), and strain Marseille-P3369 T exhibited a 16S rRNA gene sequence similarity of 98. 25% with Varibaculum cambriense strain CCUG 44998 (GenBank accession no. NR_114873. 1), its closest related species with standing in nomenclature  [4]  (Fig. 2 ). These values are under the thresholds of 98. 7% separating new species established by Stackebrandt and Ebers  [5].
MATERIALS AND METHODS 2. 1. Materials. Acetaminophen (Paracetamol, BioXtra, ≥99%, Sigma-Aldrich) and isopropyl alcohol (IPA; technical grade (99%), VWR) has been used in this study. 2. 2. Methods. 2. 3. Particle Count Measurement: Focused Beam Reflectance Measurement. The FBRM probe (model G600) from Mettler Toledo was used to measure in situ the particle count and the chord length distributions (CLD). The iC FBRM software (version 4. 4) was used for the data acquisition and analysis. The scan speed of the unit was set to 4 m/s with measurement interval of 5 s in all experiments. Both primary mode and macromode are available to analyze the FBRM data. The count data reported here are based on primary mode which means that the count data have high sensitivity for the edges detected. Mean squared chord length data from FBRM is used for reporting the mean particle size as measured by the FBRM.
2. 4. Particle Size Distribution: Laser Diffraction. A laser diffractometer (Mircotrac S3500) was used for particle size measurement using dry mode sample measurement. Samples for particle size distribution analysis were prepared by filtering the slurry. The residue containing the product crystals was washed with a small amount of IPA and left overnight for drying in an oven maintained at 30 °C. The samples have also been pictured under a microscope. 2. 5. In Situ Concentration Measurement. An ATR probe, model K1 Katana 6 mm supplied by Hellma, connected to a deuterium light source (model DH-2000-BAL) and to a spectrometer (HR2000+CG), both supplied by Ocean Optics, has been used to measure the absorption spectra of paracetamol in IPA. The concentration of paracetamol in IPA is estimated from the spectra collected by Spectrasuite software (Ocean Optics), by calculating the absorbance between the wavelengths of 255 up to 270 nm.
The parameter estimation was done by a least-squares optimization. The model parameters obtained are a 1 = -0. 398, a 2 = 0. 214, a 3 = 1. 55e -5, a 4 = -2. 89e -3 and a 5 = 2. 26e -3. The concentration measurement and the calibration procedure adopted here are as reported in the literature in a previous study. 22 Figure  1  shows the measured concentration of sample with known concentration of paracetamol in IPA against the saturation data reported in the literature. 23 The measured values are in line with literature values. The error between the measured and the estimated concentration was ascertained using a validation set prepared separately. Validation experiments were performed to test the calibration by heating a slurry of paracetamol IPA in steps in a temperature range similar to the calibration curve.
Microwave Assisted Direct Nucleation Control Structure. Figure  3  provides the overview of the implementation of process monitoring and control. CryPRINS (crystallization process informatics system) software which has the DNC approach implemented has been used to obtain the feedback of the particle count via the FBRM. For information about DNC using CryPRINS, literature can be referred to. 24 The temperature set point output by CryPRINS is linked to a Labview program (developed in-house) which controls and communicates the temperature set point of the thermostat and the microwave unit. Based on the temperature set point received by the microwave unit, an internal PID controller on the Labotron unit itself switches the microwave on or off and regulates the power level (maximum 2 kW) Primarily due to nucleation or dissolution events, the particle count deviates, which (detected via the FBRM) triggers a heating or cooling response in the form of a new temperature set point for the crystallizer.
In experiment MW 1, the tight control over the number of particles during nucleation and dissolution allows for the batch to approach the desired count set point closely. 4. 2. Particle Size Distribution with Rapid Temperature Cycling. To assess the final product crystals, the size distribution of crystals at the end of each experiment has been determined, by measuring the dried sample in a forward laser diffraction instrument. In addition, samples have been imaged under the microscope and the chord length distribution data measured by the FBRM are also available. Figure  9  shows the normalized volume distribution for microwave assisted DNC experiments carried out at various count set points. Unimodal distribution is observed, with a small shoulder at large sizes. The shoulder could be due to agglomerated crystals resulting during the sampling process which involves filtration and drying.
For our initial assembly, we used BLATq version 1. 02  (Henderson & Hanna, 2016a) , which was a modification of BLAT version 35  (Kent, 2002; Kent, 2012) , to find Illumina reads that aligned to the Ninox novaeseelandiae mitochondrial genome (GenBank Accession AY309457. 1) (Harrison et al. , 2004)  (Supplemental Material 1. 1. 1) and extracted those matching reads using excerptByIds version 1. 0. 2 (Henderson & Hanna, 2016b ) (Supplemental Material 1. 1. 2). We then used SOAPdenovo2 version 2. 04  (Luo et al. , 2012)  to assemble those sequences (Supplemental Material 1. 1. 3). We used the web version of the NCBI BLAST+ version 2. 2. 29 tool BLASTN  (Altschul et al. , 1990; Zhang et al. , 2000; Morgulis et al. , 2008; Camacho et al. , 2009)  to search the NCBI nucleotide collection  (Johnson et al.
, 2008; Boratyn et al. , 2013; Benson et al. , 2015; NCBI Resource Coordinators, 2015)  (NCBI-nt) to assess the completeness of the resulting assembled continuous sequences (contigs) by aligning them to available mitochondrial genome sequences (Supplemental Material 1. 1. 4). We confirmed that we had assembled a contig with the genes for tRNA Phe through cyt b to tRNA Thr that was approximately 18,000 nucleotides (nt) in length, but lacked the complete control region sequence. We used GNU  Grep version 2. 16 (Free Software Foundation, 2014)  to search the Illumina reads for matches to the assembled sequence of tRNA Phe or tRNA Thr (Supplemental Material 1. 1. 5). We found three reads that spanned tRNA Phe and combined them using the Geneious version 9. 1. 4 de novo assembler  (Kearse et al.
, 2012; Biomatters, 2016) (Supplemental Material 1. 1. 6). We then extended this assembled contig using a targeted assembly approach with the software PRICE version 1. 2  (Ruby, Bellare & DeRisi, 2013; Ruby, 2014)  (Supplemental Material 1. 1. 7). This PRICE run produced an improved and lengthened assembly after 31 cycles, but the assembly still lacked the complete control region sequence. We used BLATq version 1. 0. 2 to align Illumina sequences to the assembly output by PRICE (Supplemental Material 1. 1. 8) and extracted aligned reads using excerptByIds version 1. 0. 2 (Supplemental Material 1. 1. 9). We then performed another PRICE assembly with the same initial contig as before, but with the extracted additional Illumina sequence data (Supplemental Material 1. 1. 10). This run produced an assembly of one contig of length 18,489 nt after 26 cycles.
In order to use all of the available Illumina sequence data to verify our mitochondrial genome assembly, we took the draft whole genome assembly of S. o. caurina  (Hanna et al. , 2017)  and replaced scaffold-3674, which was the incomplete assembly of the mitochondrial genome, with the 19,889 nt mitochondrial genome assembly from our targeted assembly methodology (Supplemental Material 1. 3. 1). We aligned all filtered Illumina sequences to this new draft reference genome using bwa version 0. 7. 13-r1126  (Li, 2013a)  and then merged, sorted, and marked duplicate reads using Picard version 2. 2. 4 (http://broadinstitute. github. io/picard) (Supplemental Material 1. 3. 2). We filtered the alignment file to only retain alignments to the preliminary targeted mitochondrial genome assembly using Samtools version 1.
3 with HTSlib 1. 3. 1  (Li et al. , 2009; Li et al. , 2015). We then used Samtools and GNU Awk (GAWK) version 4. 0. 1  (Free Software Foundation, 2012)  to filter the alignments (Supplemental Material 1. 3. 3-1. 3. 4). We next visualized the alignment across the reference sequence in Geneious version 9. 1. 4 to confirm that the sequence evidence matched our assembly (Supplemental Material 1. 3. 5). We annotated the final assembly using the MITOS WebServer version 806  (Bernt et al. , 2013)  (Supplemental Material 1. 4. 1) followed by manual inspection of the coding loci and comparison with predicted open reading frames and sequences from Gallus gallus (GenBank Accessions NC_001323  (Desjardins & Morais, 1990)  and AB086102. 1  (Wada et al. , 2004) ) in Geneious version 9. 1. 4. We annotated the repetitive regions using the web version of Tandem Repeats Finder version 4.
09  (Benson, 1999; Benson, 2016)  (Supplemental Material 1. 4. 2). We used bioawk version 1. 0  (Li, 2013b)  and GAWK version 4. 0. 1 to find goose hairpin sequences in CR1 and CR2 (Supplemental Material 1. 4. 3). We compared the sequences of the annotated genes in our final mitochondrial genome assembly with those of the incomplete mitochondrial genome assembly that was output as a byproduct of the S. o. caurina whole nuclear genome assembly  (Hanna et al. , 2017)  in order to evaluate the efficacy of the nuclear genome assembler in assembling mitochondrial genes. We aligned all of the nucleotide sequences of the genes in the final mitochondrial genome against a database of the scaffold-3674 gene nucleotide sequences using NCBI BLAST+ version 2. 4. 0 tool BLASTN  (Altschul et al. , 1990; Zhang et al.
Strix varia mitochondrial genome assembly In order to assess the divergence between S. occidentalis and S. varia across all genes of the mitochondrial genome, we constructed a complete S. varia mitochondrial genome assembly. We did this by utilizing available whole-genome Illumina data from two S. varia individuals collected outside of the zone of contact of S. varia and S. o. caurina  (Haig et al. , 2004). The main set of S. varia whole-genome Illumina data originated from sequencing of a tissue sample collected in Hamilton County, Ohio, United States of America (CNHM<USA-OH>:ORNITH:B41533; Table  1 ), hereafter ''CMCB41533''. The paired-end Illumina sequence data was from a genomic library constructed, sequenced, and the data processed as described in  Hanna et al. (2017). The raw sequences are available from NCBI (SRA run accessions SRR5428115, SRR5428116, and SRR5428117).
The second S. varia individual was from Marion County, Indiana, United States of America (CAS:ORN:95964; Table  1 ), hereafter ''CAS95964''. Sequence data from this individual informed the assembly process, but none of these data are included in the final S. varia mitochondrial genome assembly (Supplemental Material 1. 6. 1). The raw sequences are available from NCBI (SRA run accession SRR6026668). We performed adapter and quality trimming of these sequence data using Trimmomatic version 0. 30  (Bolger, Lohse & Usadel, 2014)  (Supplemental Material 1. 6. 2). For use in only the SOAPdenovo2 assembly, we trimmed the sequences using a different set of parameters and performed errorcorrection of the sequences using SOAPec version 2. 01  (Luo et al. , 2012)  (Supplemental Material 1. 6. 3). We constructed the complete S.
2 with the larger CMCB41533 Illumina sequence dataset (Supplemental Material 1. 11. 1). After four cycles, this assembly produced one contig (ContigInput2) of length 17,073 nt. We performed a final assembly using PRICE version 1. 2 and the 9,690 nt ContigInput1 and the 17,073 nt ContigInput2 as the initial contigs (Supplemental Material 1. 12. 1). After two cycles, this assembly produced one contig of length 19,589 nt. We then used Sanger sequencing to confirm the sequences of CR1 and CR2. We PCR-amplified CR1 with primers cytb-F1 and 17122R (Table  2 ), which primed in cyt b and ND6, respectively (Supplemental Material 1. 12. 2). We then sequenced the fragment using the original external primers as well as the internal primers CR1-F1, CR1-F1-RC, CR1-R2, CR1-R2-RC, and N1  (Barrowclough, Gutierrez & Groth, 1999)  (Table  2 ).
We annotated the assembly using the MITOS WebServer version 605 (Supplemental Material 1. 12. 4) followed by manual inspection of the coding loci and comparison with predicted open reading frames and sequences from Gallus gallus (GenBank Accessions NC_001323  (Desjardins & Morais, 1990)  and AB086102. 1  (Wada et al. , 2004) ) in Geneious version 9. 1. 4. We annotated the repetitive regions using the web version of Tandem Repeats Finder version 4. 09  (Benson, 1999; Benson, 2016)  (Supplemental Material 1. 4. 2). We used bioawk version 1. 0  (Li, 2013b)  and GAWK version 4. 0. 1 to find goose hairpin sequences in CR1 and CR2 (Supplemental Material 1. 4. 3).
Avian mitochondrial gene order comparisons We downloaded the mitochondrial genome sequences of Gallus gallus (GenBank Accession NC_001323. 1) (Desjardins & Morais, 1990) , Melopsittacus undulatus (GenBank Accession NC_009134. 1) (Guan, Xu & Smith, 2016) , Falco peregrinus (GenBank Accession NC_000878. 1) (Mindell et al. , 1997; Mindell, Sorenson & Dimcheff, 1998a; Mindell et al. , 1999) , Bubo bubo (GenBank Accession AB918148. 1) (Hengjiu et al. , 2016) , Ninox novaeseelandiae (GenBank Accession AY309457. 1) (Harrison et al. , 2004) , Tyto alba (GenBank Accession EU410491. 1) (Pratt et al. , 2009) , Strix leptogrammica (GenBank Accession KC953095. 1) (Liu, Zhou & Gu, 2014) , Glaucidium brodiei (GenBank Accession KP684122. 1) (Sun et al. , 2016) , and Asio flammeus (GenBank Accession KP889214.
RESULTS We deposited the complete mitochondrial genome sequences of Strix occidentalis caurina sample CAS:ORN:98821 and Strix varia sample CNHM<USA-OH>:ORNITH: B41533 as NCBI GenBank Accessions MF431746 and MF431745, respectively. The lengths of the final S. o. caurina and S. varia mitochondrial genome assemblies were 19,889 nt and 18,975 nt, respectively. As for all typical avian mitochondrial genomes, they are circular and code for two rRNAs, 22 tRNAs, and 13 polypeptides (Figs. S1  and S2 ). The annotations produced by MITOS identified a 1 nt gap that split ND3, which is consistent with the untranslated nucleotide and translational frameshift seen in ND3 in some other bird species  (Mindell, Sorenson & Dimcheff, 1998b) , including owls (Strigiformes)  (Fuchs et al. , 2008). Both the S. o.
varia CR1 is 1,686 nt long. In both species, the 5 end of CR1 borders tRNA Thr and the 3 end is adjacent to tRNA Pro , then ND6, and then tRNA Glu (Fig. 1 ). The initial 1,104 nt of the S. o. caurina CR1 are identical to a S. o. caurina partial control region sequence (GenBank Accession AY833630. 1) (Barrowclough et al. , 2005). All of the top 100 matches of the BLASTN searches of the S. o. caurina CR1 to NCBI-nt were to either S. occidentalis or S. varia control region sequences deposited by other researchers, as we expected. CR2 follows tRNA Glu and is 2,319 nt in length in S. o. caurina and 1,719 nt long in S. varia. The initial 549 nt of the S. o. caurina CR2 matches the beginning of the D-loop sequence of an annotated complete genome of a Bubo bubo mitochondrion (GenBank Accession AB918148.
1) (Hengjiu et al. , 2016). One of the top 100 matches of the BLASTN searches of the S. o. caurina CR2 to NCBI-nt, which had the highest total score (2,177) and query coverage (96% versus 36-41% for the other matches) of the top 100 matches, was to a S. uralensis control region sequence (GenBank Accession AB743794. 1) The numerical coordinates at the top of each panel correspond to the coordinates of the alignment. Black rectangles for each control region denote continuous sequence, whereas intervening horizontal lines denote gaps in the alignment. The sequence identity rectangle is green at full height when there is agreement between the sequences, yellow at less than full height when the sequences disagree, and flat in gap regions. The location of the goose hairpin sequence in each control region is annotated in blue.
DNA Deposition The following information was supplied regarding the deposition of DNA sequences: Complete mitochondrial genome sequence of Strix occidentalis caurina CAS:ORN:98821 deposited as NCBI GenBank Accession MF431746. Complete mitochondrial genome sequence of Strix varia CNHM<USA-OH>:ORNITH: B41533 deposited as NCBI GenBank Accession MF431745. The raw sequences for Strix varia sample CAS:ORN:95964 are available from NCBI (SRA run accession SRR6026668).
Data Availability The following information was supplied regarding data availability: BLATq deposited at Zenodo DOI: 10. 5281/zenodo. 61136 available at https://github. com/calacademy-research/blatq. excerptByIDs deposited at Zenodo DOI: 10. 5281/zenodo. 61134 and available at https://github. com/calacademy-research/excerptByIDs.
The BRIght Target Explorer (BRITE) Constellation is the first nanosatellite mission applied to astrophysical research. Five satellites in low-Earth orbits perform precise optical two-colour photometry of the brightest stars in the night sky. BRITE is naturally well suited for variability studies of hot stars. This contribution describes the basic outline of the mission and some initial problems that needed to be overcome. Some information on BRITE data products, how to access them, and how to join their scientific exploration is provided. Finally, a brief summary of the first scientific results obtained by BRITE is given.
Encircled stars have been proposed for BRITE observations. The sky areas labeled and encircled in pink have been observed by BRITE to date (cf. Table  1 ). Almost the whole galactic plane has been sampled. the respective data set is suitable for stand-alone publication), and a final report after one year. After this oneyear proprietary period has passed, the data will become public, unless an extension of the proprietary period of up to half a year has been approved in exceptional cases. A list of fields observed, stars measured therein, the respective contact PIs, and links to public data can be found at http://brite. craq-astro. ca/doku. php. Even if a data set is still in the proprietary phase, the contact PI can be approached for possible collaborations, as each contact PI is free to set up their own network of co-workers.
Acknowledgments The Polish contribution to the  BRITE  project is supported by the  NCN  grants  2011/01/B/ST9/05448 ,  2011/01/M/ST9/05914 ,  2011/03/B/ST9/02667  and  2015/18/A/ST9/00578. GAW and SMR acknowledge  Discovery Grant  support from the  Natural Science and Engineering Research Council (NSERC)  of  Canada. AFJM is grateful for financial aid from  NSERC  and  FQRNT (Quebec). KZ acknowledges support by the  Austrian Fonds zur Förderung der wissenschaftlichen Forschung (FWF , project  V431-NBL ). BTr operations are supported through a  Canadian Space Agency (CSA)  Academic Development grant. RK and WW acknowledge financial support by the  Austrian Space Application Programme (ASAP)  of the  Austrian Research Promotion Agency.
5 ). In LEO the Earth's magnetosphere provides substantial shielding from high-energy Fig. 2  Irradiance spectrum of the Sun from 100 to 2500 nm. (From the Sorce web database, http://lasp. colorado. edu/lisird/sorce/) Fig. 3  Time series for Lyman α and 200 nm daily averaged irradiance between 2003 and 2013, measured with the SOLSTICE instrument on the SORCE spacecraft  (Pankratz et al. 2005; Rottman 2005 ). The high frequency modulation is due to the 27 days solar rotation period. (From the Sorce web database, http://lasp. colorado. edu/lisird/sorce/) charged particles, including a majority of the charged-particle flux from SEPs, and to a lesser extent GCRs, as per the local geomagnetic cutoff rigidity. The geomagnetic cutoff rigidity Fig. 4  Flux of cosmic ray particles as a function of their energy at the top of the Earth atmosphere.