dataesr/scientific-paragraphs-categorization huggingface dataset:
Coevolutionary analysis Sequence extraction and preprocessing To perform direct-coupling analysis we used the same sequence extraction protocol as in  (Malinverni et al. , 2015) , reported hereafter:. Initial seeds were built for both protein families, containing sequences from all kingdoms: Bacteria, Eukaryotes and Archaea. Hidden Markov models of the alignments were built, using the hmmbuild utility of the HMMER (version 3. 1b2)  (Mistry et al. , 2013)  suite, with default parameters. The union of the Swissprot and the Trembl databases (release 2015_08) was scanned against these two profiles , using the hmmsearch  (Mistry et al. , 2013)  utility, with default parameters. For both retrieved MSAs, all sequences having more than 10% gapped positions were removed from the datasets. The Hsp70 sequences were restricted to the NBD and linker region, by trimming the C-terminal part of the alignment.
Taxonomic identifiers for all sequences were retrieved from the NCBI taxonomy database. This resulted in multiple-sequence-alignments for the Hsp70 and Hsp40 families containing, respectively, 20061 and 26254 homologues, with the following taxonomic distribution: The number of paralogs per organism varies widely (Table  2 , Figure  6 ), with bacteria having fewer paralogs for both Hsp40 and Hsp70. All organisms were included in the full dataset, both those having multiple paralogs and organisms possessing a single copy of Hsp40-Hsp70 pairs (3701 organisms). The resulting MSAs covered the following ranges of the E. coli DnaK/DnaJ proteins: DnaK (Uniprot ID: P0A6Y8) I4-T395, DnaJ (Uniprot ID: P08622) K3-G78. Both sequence alignments and taxonomic identifiers for the Hsp40 and Hsp70 families are available as supplementary material (Supplementary file 1À5).
We observed that in this case, only a fraction of the strongest coevolutionary signals predicted from the full-dataset are recovered. Recently, two methods to simultaneously pair interacting paralogs and predict inter-protein coevolving contacts have been developed  (Bitbol et al. , 2016; Gueudreet al. , 2016). Both these involved methods tackle the combined objective of deciphering the paralog interaction network as well as determining coevolving residue across protein interfaces through iterative schemes. We observed that the strongest inter-protein contacts predicted by the two methods  (Bitbol et al. , 2016; Gueudreet al. , 2016)  strongly overlap with those obtained using our random-matching strategy (Figure  7 -figure supplement 1). To allow comparison with other inter-protein interactions studied by DCA, we report here an empirical inter-protein score introduced in  (Feinauer et al.
The dotted circle represents residue E75 of the J-domain, absent from the structures used in the simulations (see Materials and methods). The depicted conformation is the final frame of one of the three 1 À s HPD-IN FL-ATP simulations. DOI: 10. 7554/eLife. 23471. 017 The following figure supplements are available for figure 5: Figure supplement 1. J-domain per-residue contribution to the binding energy with DnaK. DOI: 10. 7554/eLife. 23471. 018 Figure supplement 2. Frequency of appearance of the coevolutionary inter-protein contacts (see Materials and methods), for the dataset containing full-length Hsp70s. DOI: 10. 7554/eLife. 23471. 019.
Acknowledgements DM thanks the  Swiss National Science Foundation  (http://www. snf. ch/) for grants  2012_149278  and  20020_163042/1. AJL and GH were supported by the  Max Planck Society. AB acknowledges the support of the  French Agence Nationale de la Recherche (ANR) , under grant  ANR-14-ACHN-0016. This work was supported by a grant from the  Swiss National Supercomputing Centre (CSCS)  under project  s684.
The intensity of the Pr55Gag band on immunoblots did not radically differ between the three samples (data not shown). A quantitative, luciferase-based assay of extracellular VLPs was then performed. The principle of this assay resides in the co-packaging of Vpr (and Vpr-fused proteins) with Pr55Gag into membrane-enveloped VLPs banding at a density of 1. 18. This co-packaging is mediated by the specific interaction between the Gag p6 domain and Vpr  53, 54. The co-expression of the Luciferase-Vpr fusion protein together with Pr55Gag by co-infection of Sf9 with the recombinant vectors AcMNPV luc-vpr and AcMNPV gag showed that the activity of luciferase co-incorporated with Pr55Gag into VLPs directly reflected the amounts of VLPs released in the extracellular medium  33. Control Sf9 cells, Sf/(Myr+)αRep4E3-GFP and Sf/(Myr+)αRep9A8-GFP cells were co-infected with AcMNPV gag and AcMNPV luc-vpr , and harvested at 48 hrs pi.
Acknowledgements The work in Thailand was supported by the  Centre of Biomolecular Therapy and Diagnostics (CBTD) , the  Thailand Research Fund   Basic Research Grant   BRG5480004 , the  Senior Research Scholar Grant   RTA5980007. SH was supported by the  PhD Franco-Thai scholarship program  ( SIAM 2013 ) from the  French Government , the 50 th  CMU Anniversary PhD Program , and the  Faculty of Pharmaceutical Sciences, Burapha University. SN was supported by the  Franco-Thai Junior Research Fellowship Program  (2012). KC was supported by the  Thailand Research Fund  through the  Royal Golden Jubilee PhD program  (Grant  PHD/0146/2556 ). KF was supported by a post-doctoral fellowship 2016 from  Chiang Mai University. The authors express their gratefulness to the  Research Institute for Health Sciences  for providing the viral propagation facility.
In the data set of SCI-containing genomes, Vibrio genomes are overrepresented, reflecting the general bias toward human pathogen species. We therefore repeated this analysis after exclusion of Vibrio genomes and found that this difference remained significant (Fig. S1 ). (ii) Cassette lengths. Cassette lengths were investigated as another means of control over their excision dynamics. When simultaneous folding of both flanking attC sites is promoted, e. g. , when the distance between both sites was smaller than the length of ssDNA found between two Okazaki fragments or smaller than the size of supercoiled plectonemes, cassette excision is likely to be favored. Therefore, we decided to analyze the cassette length. We used two independent proxies for the length of cassettes to test this hypothesis: CDS length and the distance between identified attC sites.
On the one hand, CDS length underestimates cassette length but is highly correlated with it, since most cassettes have one single CDS and small adjacent regions. On the other hand, the distance between attC sites provides an exact measure of cassette length but is affected by inaccuracies in the detection of attC sites (a missed attC can lead to the doubling of a cassette length). We performed these analyses for the 393 integrons identified by the IntegronFinder program (10) (Materials and Methods) and their respective replicons. CDSs in MIs and SCIs are significantly shorter than CDSs in replicons (median CDS lengths were 575, 362, and 818 bp, respectively [Fig. 3A] ). Moreover, CDSs in SCIs are significantly shorter than those in MIs. We also performed this analysis by excluding known antibiotic resistance genes (ARGs) because they are overrepresented in MIs (500 out of 851 CDSs), upon which we observed a significant decrease in median MI CDS lengths.
4B  and S4B ). We did not observe any correlation between the length and the pfold values of attC sites, even when excluding the Vibrio attC sites (Fig. S5A ). Our previous study of 263 MI attC sites from the INTEGRALL database  (33)  showed that the ΔG of the folded bottom strands (ΔG bs ) is on average 2. 12 kcal/mol lower than the ΔG of the folded top strands (ΔG ts ), suggesting that folded bottom strands are more    4C] ). Surprisingly, the analysis of 1,744 SCI attC sites shows that ΔG bs is on average 1. 71 kcal/mol higher than the ΔG ts , suggesting that folded top strands are more stable. Once again, this effect was due to the attC sites of Vibrio spp. : their exclusion reversed the trend toward higher ΔG ts (differences of 3. 13 kcal/mol). This value was not significantly different from the one observed for MI attC sites (Fig.
4C ). We observed a negative correlation between the length of attC sites and the ΔG bs Ϫ ΔG ts in MIs and in SCIs without Vibrio attC sites (Fig. S5B ). This correlation was reversed for SCI attC sites, which is expected, given that their increased length is mostly due to a longer VTS, which together with the UCS produces this difference in ΔG (Fig. S5B ). As previously described, the bottom strands of MI attC sites are enriched in purines, especially in guanines, which contribute to the difference in folded strand stability  (17). Indeed, purines have a higher self-stacking tendency, thus stabilizing secondary structures  (34). We confirmed negative GC and AT skews for MI attC sites from our data set (the skews were calculated relative to the top strands) (Fig. 4D ). However, for SCI attC sites, we observed positive GC and negative AT skews, meaning that the bottom strands were C and A rich.
MATERIALS AND METHODS In silico analysis. (i) Data. The sequences and annotations of complete genomes were downloaded from NCBI RefSeq (last accessed in November 2013, http://ftp. ncbi. nih. gov/genomes/refseq/bacteria/). Using the IntegronFinder program (https://github. com/gem-pasteur/Integron_Finder), we analyzed 2,484 bacterial genomes, including 2,626 replicons labeled as chromosomes and 2,006 replicons labeled as plasmids. IntegronFinder ensures an automatic and accurate identification of integrons, cassette arrays, and attC sites. (ii) SCI and MI classification. Several criteria were used to determine the integron classification  (10). Briefly, integrons were considered SCIs when they were present in the genomes of all the available sequenced strains of the species or when they contained more than 19 attC sites.
They were considered MIs when they were absent in more than 40% of the sequenced genomes of the species, when they were present on a plasmid, or when the integrase was from one of the five classes of MIs. (iii) CDS analysis in sequenced strains containing integrons. The set of MIs had 851 CDSs, whereas the set of SCIs had 2,856 CDSs, together belonging to 393 integrons. The replicons containing integrons Cassette Excision in Integrons had 472,225 CDSs. Leading and lagging strands were determined using the information from the OriC prediction database  (48). The leading strand was defined as the strand with an increasing gradient of GC disparity (the GC disparity is a measure of the Z-curve representing the excess of G over C, a similar measure to the GC skew). The complementary strand was defined as the lagging strand.
(vi) attC site folding, ⌬G and pfold predictions, and skews. All folding predictions were obtained by RNAfold program from the ViennaRNA 2 package  (49)  with the set of DNA folding parameters derived from reference 50. We used the -p option to compute the partition functions and the -c option to add constraints required for a recombinogenic structure: pairing of the L' and L'' sequences and pairing of the 4 bases 5=-YAAC-3= in the R' sequence with the 4 bases 5=-GTTR-3= in the R'' sequence. We report the structures and ΔG values of the minimal free energy (MFE) structure. In order to obtain the pfold (probability of folding a recombinogenic structure) values, folding predictions were performed with and without constraints. pfold was calculated as the Boltzmann probability of the constrained (recombinogenic) structure in the ensemble: Pfold ϭ e E u Ϫ E c RT , where E u is the Gibbs free energy of the unconstrained (total) ensemble, E c is the Gibbs free energy of the constrained (recombinogenic) ensemble, R is the gas constant, and T is the absolute temperature  (51).
ACKNOWLEDGMENTS We thank  Claire Vit  for helpful discussions and  Sebastian Aguilar Pierlé  for reading the manuscript. This work was supported by the  Institut Pasteur , the  Centre National de la Recherche Scientifique, Fondation pour la Recherche Medicale  (project  DBF20160635736 ), the  French Government Investissement d'Avenir program Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases"  ( ANR-10-LABX-62-IBEID ), the  French National Research Agency  ( ANR-12-BLAN-DynamINT ), the  European Union   Seventh Framework Program  ( FP7-HEALTH-2011 -single-stage), the  "Evolution and Transfer Of Antibiotic Resistance" (EvoTAR) ;  Paris Descartes University-Sorbonne Paris Cité, Fondation pour la Recherche Medicale  ( FDT20150532465 ) and  École Doctorale Frontières du Vivant (FdV)-Programme Bettencourt  (to A.
Cultured cells were grown on glass coverslips. Living or fixed cells were imaged as described  (Pinilla-Macua et al. , 2016). Images from tumor sections or cultured cells were acquired using a spinning disk confocal imaging system based on a Zeiss Axio Observer Z1 inverted fluorescence microscope (with 63x Plan Apo PH NA 1. 4) system, controlled by SlideBook6 software (Intelligent Imaging Innovation, Denver, CO) as described previously  (Pinilla-Macua et al. , 2016). The montages of multiple images were generated using SlideBook6. All image acquisition settings were identical for all experimental variants in each experiment.
Acknowledgements We are grateful to  Drs. Sara Sigismund ,  Adam Kwiatkowski  and  Steffi Oesterreich  for the gifts of reagents. We thank  Dr. Roberto Weigert  ( National Cancer Institute ) for the valuable advice and discussion of intravital imaging experiments,  Dr. David Drubin , ( University of California Berkeley ) for generous help with gene-editing, plasmid sharing and advice; and  Mr. Greg Gibson  ( Center for Biological Imaging, University of Pittsburgh ) for technical help with the multiphoton microscope imaging. Supported by  NIH/NCI  grants  CA089151  and  GM124186  (AS), and  UPCI HNC SPORE IO1-BX003456  (UD).
The level of ionization suppression, determined at about 50% only, highlights the effectiveness of the fractionation protocol. It can be related to the complementarity between the high-pH fractionation and low-pH reverse phase chromatography, and the optimized washing and elution conditions during SPE. Quantification based on cetuximab calibration standards, processed similarly and simultaneously to the clinical samples, coupled to internal standardization by SIL-peptides spiked at an early step in the protocol demonstrated high repeatability and reproducibility, in line with the latest bioanalytical recommendations, and method's performance in terms of analytical range and sensitivity was fully in line with available data regarding circulating cetuximab concentrations in patients with cancer  [3] [4] [5].
1% formic acid, centrifuged for 5 min at 20000 g and transferred into an LC vial. LC-MS/MS analysis. LC-MS/MS analyses were performed on a XEVO TQ-S triple quadrupole mass spectrometer (Waters, USA) controlled by Masslynx software (version 4. 1). The instrument was linked to an Acquity I-Class LC system (Waters, USA). Chromatography was performed using a gradient combining solvent A (0. 1% formic acid in water) and solvent B (0. 1% formic acid in acetonitrile). Peptides were separated on an Acquity UPLC BEH Shield C18 column, 2. 1 mm × 50 mm, 1. 7 μm, (Waters, USA). Peptide separation was achieved using a gradient from 5 to 33% B over 10 min, at a flow rate of 500 μl/min and a temperature of 50 °C. MS data were acquired in positive mode with an ion spray voltage of 3000 V, a source and a desolvation temperature set to 150 °C and 225 °C, respectively.
Cone voltage was set to 40 V and optimal collision energy (CE) was determined at 15 and 16 eV (Table  1 ). Scheduled SRM acquisitions were performed with Q1 and Q3 quadruples operating at unit resolution. The dwell time for HT4 and LT3 was set to 0. 052 and 0. 025 s, respectively corresponding to about 15 acquisition points per LC peak. MS data from measurements in patient samples have been deposited in the PeptideAtlas SRM Experiment Library (PASSEL) (Identifier PASS00983)  30. Peak area measurements of cetuximab peptides from the calibration curve illustrated in Fig. 3  and from all patient samples are illustrated in Tables  S1  and S2. Quantification protocol. An external calibration curve was prepared in pooled human plasma spiked with cetuximab. To overcome the impact of partial recovery during trypsin digestion or peptide extraction, the calibration curve was processed similarly and simultaneously to the clinical samples.
Acknowledgements This work has been partly performed thanks to the support of  AM*IDEX  project ( MARS Project ,  Aix Marseille Univ. 2014-2017 ) funded by the  Investissement d' Avenir French government program. We do thank  Mr Freddy Delsenne  ( Waters, Paris France ) for his constantsupport and encouragement throughout this project. We thank  Merck France  for nothing.
A genomic relationship matrix (GRM) has limited dimensionality due to small effective population size, resulting in infinite number of generalized inverses of GRM for large genotyped populations. A specific inverse called APY requires only a small fraction of GRM, is sparse and can be computed and stored at a low cost for millions of animals. With APY inverse and PCG iteration, GBLUP and ssGBLUP can be applied to any population. Both tools can be applied to GWAS. When the system of equations is sparse but contains dense blocks, a recently developed package for sparse Cholesky decomposition and sparse inversion called YAMS has greatly improved performance over packages where such blocks were treated as sparse. With YAMS, GREML and possibly singlestep GREML can be applied to populations with >50 000 genotyped animals.
GREML and APY GREML is REML using a GRM. Similarly, REML using matrix H can be called single-step GREML (ssGREML). In the past, the success with REML in animal populations was due to sparse inverse of A -1 and sparse matrix factorization/ inversion  (Misztal and Perez-Enciso, 1993; Pérez-Enciso et al. , 1994). If G is dense and large,  Masuda et al. (2015)  showed that GREML with the old sparse matrix package is inefficient and unstable. A new package called YAMS recognizes dense blocks in MME, rearranges computations accordingly, allowing also for parallel computations for large dense blocks. With YAMS, GREML was much faster and more reliable.
Conclusions In conclusion, common operations in genetic selection are computationally feasible for an almost unlimited number of genotyped individuals using appropriate algorithms. Solving 'SNP' equations is best accomplished by iteration on data using either a special form of GS iteration or the PCG algorithm. Solving ssGBLUP is best accomplished by iteration on data using the PCG algorithm. For GREML, a sparse matrix package needs to account for dense blocks. Computations in the two latter cases greatly benefit from efficient (and sparse) inverse of the GRM.
Electrophysiological recordings by intracellular microelectrodes Soon after removal, EDL muscles were tied at each tendon on a glass rod in a 25-ml chamber and perfused with the normal physiological solution at 30°C gassed with 95% O 2 /5% CO 2. The resting total membrane conductance (gm) was determined using the two intracellular microelectrodes technique in current-clamp mode as detailed elsewhere. 44 Briefly, fibre diameter and membrane resistance (Rm) was calculated applying a hyperpolarizing square current pulse into the muscle fibre through one microelectrode and recording the resulting voltage deflection with a second microelectrode inserted at two different distances from the current electrode. The current stimulation and data acquisition and analysis were carried out under computer control.
Histology For histological studies, EDL muscles were dissected by surrounding tissue, then covered with tissue-tek O. C. T. (Bio-Optica) and frozen in isopentane cooled by liquid nitrogen. Samples were stored at À80°C until processing. Serial cross sections (7-8 μm thick) were cut in a cryostat microtome set a À20°C (HM525 NX, Thermo Scientific). Haematoxylineosin (HE) staining was performed on transverse muscle sections to examine the general morphology. Sections were examined using Olympus CX41 microscope. Morphometric analysis was performed by using the Image J analysis software semi-automatic method. The percentage of total damage (necrosis + inflammatory infiltration + non-muscle area) was calculated on 6-7 fields at 10× covering more than the 80% of the entire muscle section. Furthermore, crosssectional area (CSA) of individual fibres was measured as the internal H&E-stained area.
Acknowledgements This work was supported by  Università degli Studi di Bari  " Aldo Moro" (Project "Fondi Ateneo 2012 " to AL) and by  Duchenne Parent Project  NL (Project 2015 to ADL). The authors certify that they comply with the ethical guidelines for authorship and publishing of the Journal of Cachexia, Sarcopenia and Muscle. 79.
Statistical analyses For data related to drone life traits (e. g. , survival, maturity, and semen volume), the following 2-step statistical analyses were performed: 1) a linear model plus analysis of variance to determine the potential effects of each rearing method and treatment on different parameters; and then 2) a post hoc Wilcoxon test because the small number of data points required a nonparametric test for confirmation. To analyze semen parameters, statistical analyses were performed using a generalized linear mixed model with a random effect on the hive/cage from which the drones were obtained. These statistical analyses were performed using the package lme4 in R software  [33].
Food collection and consumption The amount of food collected in the feeders was measured daily to assess the effect of fipronil on worker feeding behavior. Regardless of the rearing method, fipronil did not affect the amount of syrup and pollen that was gathered by the bees (data not shown), as was previously observed in bees grown under semifield conditions  [26]. A comparison of the amount of food that was gathered by workers between bees reared using different methods was not relevant because the feeding methods were different. Bees reared under laboratory conditions did not need to fly to gather food because food was directly supplied in the cage, whereas food was not directly supplied to the bees reared under semifield conditions. When the bees were reared in a cage or in a hive, the amount of food assessed by individuals within a hive/cage was not possible because most of the food that was gathered was stored in comb cells.
Acknowledgment-The present study was supported by the  French National Institute for Agricultural Research (INRA) , the  Region PACA (Provence Alpes Côte-d'Azur) , and the  Apiculture Remuaux Company. The authors thank J. S en echal,  W. Oberstar ,  J. Gauthier , and  C. Baudrier  for their technical assistance. Data availability-The dataset is available from: https://figshare. com/s/47d5bcce8e849d453e47 or from the corresponding author (jean-luc. brunet@inra. fr).
Surface Plasmon Resonance Measurements To investigate dynamic interactions of GST-CNF1 with Lu the Biacore X100 system (Biacore, Little Chalfont, UK) was used. Lu-Fc was amine-coupled to a CM5 sensor chip, according to the manufacturer's instructions (10 mM sodium acetate pH 4. 5). Around 1300 response units were achieved. Sensorgrams were performed using 1 × running buffer (10 × HBS-EP+buffer: 0. 1 M HEPES, 1. 5 M NaCl, 0. 03 M EDTA and 0. 5% Surfactant P20), with a flow rate of 30 µL/min at 25 • C. Up to six different concentrations of pure ligand (GST-CNF1) were injected. GST-CNF1 was purified via gel filtration on a Superdex 200 10/300 GL column (GE Healthcare) prior to Biacore measurements. With the help of Biacore X100 Evaluation software (version 2. 0) kinetic constants were calculated.