dataesr/scientific-paragraphs-categorization huggingface dataset:
The fixed set consists of data pairs with one random 64-bit value and one fixed 64-bit value chosen randomly in advance. The random set is completely composed of random values. A random input is fed into the PRINCE implementation before each encryption so that the circuit is in a random state before encrypting each value from a given set. For all the encryption operations, the three 64-bit masks for TI are generated randomly. To conduct the t-test, we used 10 million power consumption traces observed during the encryptions for each data set. Furthermore, to suppress the effect of changes in the circuit temperature and other environmental factors during the power observations, we fed the two data sets into the circuit in a randomized interleaved manner so that a single observation of the fixed or random sets was made with a probability of 1/2.
This work was supported in part by the  Japan Science and Technology Agency (JST) Core Research for Evolutional Science and Technology (CREST)  under Grant  JPMJCR19K5 ,  Japan , and in part by the  Japan Society for the Promotion of Science (JSPS) KAKENHI  under Grant  17H00729  and Grant  19K24336. The associate editor coordinating the review of this manuscript and approving it for publication was Prof.
KSM-P15 and from Caldicellulosiruptor bescii (PDB entries 1EE6 and 3T9G, respectively)  (27, 28). It carries the same invariant residues with Lys227 acting as the catalytic base and Lys252 and Arg255 implicated in the binding of the substrate (Fig. 2  and Fig. S3 ). In the catalytic site of Pel3 1m , a sulfate ion was detected, which forms salt bridges with Lys227, Lys252, and Arg255 mimicking the hydroxyl groups of the natural substrate, polygalacturonic acid (Fig. S4 ). In addition, a structural calcium ion was present in the monomer B of Pel3 2m where it coordinates the main-chain carbonyl O of Ile195 and Pro221, the side-chain Oδ atom of Asp194 and Asn216, and two water molecules, which complete the pentagonal bipyramidal geometry (Fig. S3A ). Superimposition of monomers A and B of Pel3 2m indicated that the Ca 2+ ion seems to be necessary for a proper fold of loop T3.
Structure-function analysis of Pel3 Figure  5. Phylogenetic tree of Pel3 and the PL-3 family proteins. Phylogenetic tree topology was obtained by using bootstrapped maximum-likelihood approach with PhyML (55) as described in "Experimental procedures" and visualized with iTOL software  (56). Bootstrap values ≥70 are indicated below the branches. Colored branches and boxes show the PL-3 protein groups from Bacteria (blue), Nematodes (green), Fungi (orange), and Oomycetes (magenta). Red circles show the occurrence of disulfide bonds, numbered from #1 to 5, as in Pel3. Green and blue triangles indicate the substitutions of substratebinding residues equivalent to K252T/S and K252R of Pel3, respectively. Full species names and some other features of the proteins used are listed in the Table  S2.
Crystallization Crystallization screening was carried out at 293K (vapordiffusion by the sitting-drop method), with commercially available crystallization kits. For screening, a mosquito crystallization robot from TTP Labtech was employed (150 nl + 150 nl drops equilibrated against 70 μl). Pel3 crystals suitable for X-ray analysis grew within 3 months either in a solution containing 1 M succinic acid, 0. 1 M HEPES pH 7. 0, 1% (m/v) PEG MME 2000 (4U4B) or 0. 2 M lithium acetate, 20% (w/v) PEG3350 (4U49). For cryoprotection, crystals were soaked in a reservoir solution supplemented with 15% (v/v) ethylene glycol during 2 to 5 min. X-ray diffraction data were collected at beamline X06DA at the SLS (Paul Scherrer Institute, Switzerland), at a wavelength of 0. 979 Å for 4U49 (Pel3 2m ), or at beamline ID29 at the ESRF (Grenoble, France), at a wavelength of 0.
939 Å for 4U4B (Pel3 1m ). Pel3 crystals diffracted Xrays to 2. 10 Å resolution for 4U4B and 1. 80 Å resolution for 4U49. They were both indexed and scaled with the program XDS. The crystal structure of Pel3 was solved by the molecular replacement method with the program PHENIX-AutoBuild (47) using the refined structure of PelI from D. dadantii (PDB 3B4N) as search model. The structure was then refined with the program PHENIX-Phaser and visualized with COOT software  (48). The refined structure was validated with PRO-CHECK (49) before depositing.
Phylogenetic analysis Candidate homologs were searched at a protein level by using BLAST  (50)  and Pel3 as a query sequence. Search was done against the UniProtKB database. Three different BLAST searches were done, respectively, against Bacteria, Fungi, and Nematodes. All sequences that aligned at least on 80% of the length of the Pel3 catalytic domain were kept for multiple sequence alignment. Sequences were then clustered with CD-HIT in order to keep a significant number of sequences for each group. Some other sequences were then manually added, namely two oomycota sequences from NCBI database (entries XP_024585360_1 and XP_024581403_1), since only two oomycota representatives are available in UniprotKB database (September 2020) and three sequences corresponding to the available protein structures from the PL-3 family (entries O50325, B9MKT4, and Q9RHW0, corresponding to the PDB entries 3B4N, 3T9G, and 1EE6, respectively).
Multiple sequence alignments were done with MAFFT program  (51)  and conserved blocks were selected by using BMGE 1. 12 (52), using the BLOSUM30 (53) matrix with both programs. In total, 154 sites were kept for further analysis after the character trimming method performed by BMGE  (52). Phylogenetic analyses were performed, with the LG model and a gamma correction, using two approaches: a Bayesian method with mrBayes (54) and a bootstrapped maximum-likelihood approach with PhyML  (55). By default, 100,000 generations were run when using mrBayes, and we ran 100 bootstrap replicates when using PhyML. Phylogenetic tree was generated and visualized with iTOL software  (56).
Acknowledgments-We are grateful to  Yvan Rahbe  for help with phylogenetic analysis. We thank  Guy Condemine  and other team members for comments and suggestions. We are grateful to  Valerie James  for critical review and English proofreading. Author contributions-L. B. , C. P. , and V. E. S. conceived and designed the experiments described in the paper. C. P. , N. G. , F. R. , and V. E. S. performed all the experiments. L. B. and I. G. performed phylogenetic analysis; X. R. , P. G. , and L. B. performed structural data collection and analysis. L. B. and V. E. S. wrote the article. Funding and additional information-This research was supported by funding from  CNRS  ( Centre National de la Recherche Scientifique ) and a grant from  ANR  ( Agence Nationale de la Recherche )  SYNERGY_T2SS ANR-19-CE11-0020.
The results of this analysis presented in Table  2  identified some transcripts that were not among those with FCs > 100 listed in Additional file S2 and summarized in Table  1. All cuticle protein genes in Table  2  only showed a single transcript in the RNA-seq analysis. Some transcripts with top ten rpms in the three structures in FW are expressed with FC < 1, likely reflecting a relative down regulation in expression of the corresponding genes in BW. There was also a marked shift towards more RR-2 transcripts RR-2 increased in expression only in gut, or structureshared e. g. an AAEL004746 transcript for a RR-2 increased in expression in all three structures. Cuticle proteins encoded by most of the top ten abundant transcripts in all three structures in FW were detected by proteomics in shed L4 cuticles (proteomics data are presented in a separate section below).
Shed BW and FW L4 cuticles are different by proteomics analysis There were 607 unique proteins consistently identified in all three technical replicates of a biological replicate in both BW and FW shed L4 cuticles by proteomics (Additional file S3). Of these, 266 were detected only in BW cuticles and 23 only in FW cuticles. Among the 607 proteins, there were 103 cuticle proteins of which 21 were detected only in BW cuticles and none only in FW cuticles. Amongst the 103 cuticle proteins, the more numerous were 33 RR-1s, 32 RR-2s, ten CPLCGs, nine CPAPs, and seven CPCLWs (Additional file S3). The 21 BW cuticle-specific cuticle proteins were composed of 10 RR-1s, seven RR-2s, three CPLCGs and one CPAP1. Many OPACs were amongst the 504 proteins other than cuticle proteins uniquely identified in cuticles (data in ProteomeXchange repository).
Membrane receptors Transcripts for a notch homologue receptor (FC > 100 anal papilla and carcass; FC 40 gut) and a frizzled transmembrane receptor (FC > 100 carcass; FC 31 gut; FC 32 anal papilla) were prominently increased in all three L4 structures, while transcripts for two G-protein-coupled receptors and a putative odorant binding protein were strongly decreased in gut (FC 0. 01) and with FC < 1 in anal papilla and carcass (Additional file S2). Transcripts for a ppk301 sodium channel protein with a salinitysensing role in oviposition  [43]  were expressed with FC 1 and very low rpm of 0. 1 in all three structures (Additional file S4). None of these proteins were detected in shed L4 cuticles (data in ProteomeXchange repository).
Transcription regulatory proteins Transcripts for a zinc finger and a bHLH transcription factors, CREB regulatory factor, speckle-type transcription regulator, a putative RNA-binding protein, and a different transcriptional regulator were markedly increased in all three structures (Additional file S2). A POU-domain containing transcription factor class 3 transcript was increased modestly in all three structures (Additional file S4). These proteins were not detected in shed cuticles (data in ProteomeXchange repository).
Signalling pathway proteins Transcripts for a rho guanine nucleotide exchange factor in carcass, a cell polarity regulator protein par-6, a Nmyc downstream regulator and a target of myb1 in membrane trafficking in anal papilla were greatly increased with FC > 100 (Additional file S2). Nine different serine/threonine protein kinases in gut and two others in carcass were strongly decreased (FC ≤ 0. 01). These proteins were not detected in shed cuticles (data in Pro-teomeXchange repository). Transcripts coding for MAP3K interacting protein, tak1-binding protein, MAP2K, Jun kinase, Jun, Kras GTPase and Rho GTPase were implicated in a shortterm salinity response in anopheline L4  [44]. These seven proteins were not detected in shed L4 cuticles (data in ProteomeXchange repository), and their transcripts in BW L4 were either unchanged or modestly increased in the case of MAP2K, Jun kinase, Jun, and Kras GTPase with more marked increases in Rho GTPase (Additional file S4).
Cytochrome P450 Transcripts from 135 cytochrome P450 genes were identified in the RNA-seq analysis (Additional file S1). Transcripts from two cytochrome P450 genes annotated as CYP18A1 in Ae. aegypti (FCs 11-111) and homologue of CYP4G17 in An. gambiae (FCs 14-71) were markedly increased in all three structures in BW L4 (Additional file S4). They were not found in shed L4 cuticles (data in ProteomeXchange repository).
Aquaporins (AQPs) Transcripts for AQP3 and a putative AQP (AAEL021132) with FCs of 5-12 and 4-7 respectively, were increased in all three structures in BW L4 (Additional file S4). AQP1 and AQP4 transcripts were increased in anal papilla and carcass with FCs < 3. AQP6 transcript was decreased in anal papilla (FC 0. 3). Only a single aquaporin, AQP2, was detected in both BW and FW shed L4 cuticles (data in ProteomeXchange repository).
Anion exchange protein The protein had multiple transcripts. The majority of transcripts were either unchanged or modestly increased in the three structures in BW. One transcript RL was markedly increased in all three structures, and another RK was relatively prominently increased in anal papilla in BW (Additional file S4). The protein was not detected in shed L4 cuticles (data in ProteomeXchange repository). Na + /H + antiporters NHE1, NHE2 and NHE3 proteins were not detected in shed L4 cuticles (data in ProteomeXchange repository). Many transcripts for NHE1 and NHE2 were expressed with relatively unchanged FCs in all structures in BW L4. The numerous transcripts of NHE3 were expressed with relatively low rpms but increased up to FC7, 5 and 12 in gut, anal papilla and carcass respectively, except for transcript RC which was markedly increased in gut (FC 44), anal papilla (FC 45) and carcass (FC 34) in BW L4 (Additional file S4).
NH 4 + and amino acid transporters The four NH 4 + transporters AeAmt1, AeAmt2, AeRh50. 1 and AeRh50. 2 were not detected in shed L4 cuticles (data in ProteomeXchange repository). Their transcripts were relatively unchanged, except for AeRh50. 2 which was markedly reduced (FC 0. 1-0. 4), in all three structures in BW L4 (Additional file S4). Transcript for a cationic amino acid transporter was however highly increased in anal papilla (FC 142) and also increased in gut (FC 8) and carcass (FC 21) in BW L4 (Additional file S2) but the protein was not identified in shed L4 cuticles (data in ProteomeXchange repository).
Other enzymes Two transcripts for a very long chain fatty acid elongase (AAEL024147) were markedly increased in BW L4 in anal papilla (FC 145,126), gut (FC 33, 26) and carcass (FC 37, 28); for a fatty acid synthase (AAEL002228) in carcass (FC 113), gut (FC10) and anal papilla (FC 7); and for a fatty acyl CoA reductase (AAEL008125) in carcass (FC 138), gut (FC 6) and anal papilla (FC10), as shown in Additional file S2. These three enzymes were not detected in shed L4 cuticles (data in ProteomeXchange repository). Transcripts for several proteolytic enzymes were highly increased (FC > 100) notably in gut, but only one protein, a serine protease (AAEL001675) whose transcripts were increased in all three structures in BW L4 (Additional file S2), was detected by proteomics in both BW and FW shed L4 cuticles (data in ProteomeXchange repository).
aegypti Liverpool AGWG strain transcripts AaegL5. 1 in VectorBase (www. vectorbase. org) with the Galaxy Interface bowtie tool (www. usegalaxy. org) using default parameters allowing up to two mismatches per 28 bp seed (Galaxy version 1. 1. 2). Summary of mapping statistics are provided in Additional file S5. Transcript abundance were extracted as read counts using SAMTools pileup  [78]. Reads per million mapped reads (rpm) and the ratio of rpms in BW to FW termed fold change (FC) were calculated for every transcript. Cuticle protein annotation was according to VectorBase or manually done where necessary with the CutProtFam-Pred tool (http://aias. biol. uoa. gr/ CutProtFam-Pred/home. php)  [79, 80].
4 (Thermo Fisher Scientific) to match the acquired MS/ MS spectra to a protein database of the full mosquito taxon available from Uniprot, downloaded on 1 April 2019 (UniprotKB + TrEMBL, total 237,216 entries). The following parameters were used: trypsin digest with two maximum missed cleavages; six and 144 amino acids as minimum and maximum peptide lengths, respectively; a tolerance of 10 ppm/0. 02 Da for precursors and fragment ions, respectively; cysteine pyridyl-ethylation was set as a fixed modification; C-terminal protein amidation, methionine and tryptophan oxidation were set as variable modifications. The identification confidence was set at a false discovery rate of 1%. Proteins consistently identified across a series of three technical replicates were considered correctly identified.
Availability of data and materials The datasets supporting the conclusions of this article are available as follows (i) Illumina sequencing data as BioProject PRJNA629452 with BioSample accession SAMN14771163 and SRA accessions SRR11661571 to SRR11661576 for the six libraries at NCBI (https://www. ncbi. nlm. nih. gov/ bioproject), and (ii) the mass spectrometry proteomics data at ProteomeXchange Consortium (http://www. proteomexchange. org) via PRIDE partner repository under accession PXD018397 and Project doi:https://doi. org/10. 6019/PXD018397. Other data supporting the conclusions of this article are either included within the article or provided in Additional files 1, 2, 3, 4 and 5.
METHODS This retrospective study involved nine participating centers across six countries (Belgium, Canada, France, New Zealand, Switzerland, and the United States,) and was approved by the institutional ethics review board of each participating center and the procedures followed the tenets of the Declaration of Helsinki. Patients were identified through the respective internal databases. Inclusion criteria were: (1)  female or male subjects with retinal degeneration, (2) biallelic pathogenic or presumed pathogenic variants in BBS1 or BBS10 genes, and (3) availability of ocular and systemic phenotype information for at least one visit. The patient's evaluation and genetic counseling were provided according to the best standard of care practice of each institution. For those countries in the European Union, the Oviedo Convention and the Treaty of Lisbon were honored.
Data collected and analyzed included de-identified demographic information, ocular and medical history, systemic phenotype, DNA genetic results and parameters of the ocular phenotype (visual acuity [VA], Goldmann kinetic perimetry [VF], and electroretinography [ERG]). In selected cases, optical coherence tomography (OCT) scans were also reviewed. Full data sets were not available for all subjects for all testing parameters and some patients only had data from one visit (Table  1 ).
Visual Function Assessment Data available from full field ERGs were collected from patient' charts at different ages when possible. ERGs were performed incorporating standards of The International Society for Clinical Electrophysiology of Vision (ISCEV) using Diagnosys LLC system (Canada, France, and the United States) or RETI-port system, Roland Consult (Belgium and New Zealand). 38, 39 ERG results were interpreted by each principal investigator and categorized as RCD, CORD, COD, or non-detectable (ND) at first visit. The RCD pattern referred to the reduced rod and cone photoreceptor responses with predominantly reduced rod ERGs; the CORD pattern referred to reduction in cone and rod ERG responses but predominantly reduced cone responses; and the COD phenotype referred to a reduction in cone responses with preserved rod responses.
Visual Acuity The methods of VA assessment included preferential looking Teller acuity cards for preverbal children and Snellen acuity charts, or decimal (France), for older individuals. VA data for children ≤ 5 years of age were excluded due to poor reliability. All VA measurements were converted to logarithm of the minimum angle of resolution (LogMAR). Because refractive errors were not documented for all patients in some cases it was uncertain if the best correction was used. For this reason, we refer to VA and not BCVA. For the purpose of data analyses, patients who could only count fingers (CFs), perceive hand motion (HM), had only light perception (LP) or no light perception (NLP) were assigned LogMAR values of 2. 6, 2. 7, 2. 8, and 2. 9, respectively. 40, 41 Acuity of each eye was measured separately but, for analyses, VA results are presented as an average of both eyes.
bwh. harvard. edu/pph2/). § Allele frequency across multiple populations from Genome Aggregation Database (GnomAD: https://gnomad. broadinstitute. org/). Splicing predictor (Splice prediction by Neural Network; https://www. fruitfly. org/seq_tools/splice. html). ¶ ClinVar (archive of reports of the relationships among human variations and phenotypes, with supporting evidence; https://www. ncbi. nlm. nih. gov/clinvar/intro/) or Uniprot (highquality and freely accessible resource of protein sequence and functional information; https://www. uniprot. org/). Pat-, pathogenic; Lik. Pat. , likely pathogenic; Unc, unconclusive. Downloaded from iovs. arvojournals. org on 03/03/2022 BBS1 and BBS10-Related Visual Function Differences IOVS |.
Then, we performed first evaluations of the CATHARE code abilities to model thermal-hydraulic transient in cryogenic devices of a tokamak. Two cases of helium flow in a CICC of a JT-60SA toroidal field coil have been studied, and comparisons were performed with experimental data and the THEA code developed by CryoSoft. Simulations focusing on the behaviour of a device protected by a safety valve against incidental pressure increase were also performed. CATHARE results were compared with available experimental data on supercritical helium discharge through the safety valve of a tank in case of failure of the insulating vacuum.
Additional correlations have been implemented in the code to perform thermal-hydraulic calculations of supercritical helium flow in a cable of a superconducting magnet. Then, a pure hydraulic experimental test performed on a coil has been modelled with the CATHARE code to carryout a primary validation of the model. A comparison with the THEA code  [2]  has also been realised on a case of a high heat load deposition on the cable and the discrepancies between the two codes were investigated. The second modelling part focuses on the protection of cryogenic facilities by a safety valve against incidental pressure increase. An experimental device  [3]  has been modelled in the CATHARE code and results were compared with available experimental data on supercritical helium discharge through the safety valve of a tank in case of failure of the insulating vacuum.
The non-linear system is solved with the Newton-Raphson iterative method. In this study, as only monophasic supercritical helium is considered, CATHARE-3 is used with monophasic calculations  [9]. Development for monophasic simulations mainly consists in reducing the six standard balance equations to three balance equations for the gas phase only and insure compatibility with the different modules and sub-modules. The benefits of using single-phase flow calculation are a shorter computing time and a better convergence of the results. Moreover using different fluids than water is possible through the coupling with the Reference Fluid Thermodynamic and Transport Properties Database (REFPROP) developed by the NIST  [10]. REFPROP can compute properties of more than 100 fluids and enables the use of real gas properties.
Two correlations have been implemented to calculate the pressure drop in the CICC. The first one is the Darcy-Forchheimer correlation and is based on a porous media analogy  [13] : f bundle = φ 2 C F D h 2K 0. 5 + φ D h 2 2K 1 Re K = K 0 φ 3 (1 -φ) 2 C f ̅̅̅ ̅ K √ = C 0 φ n (1) With K the cable permeability, C F the drag factor and φ the void fraction. The multiplying constants K 0 and C 0 are given in Table  2. They depend closely on the strands arrangement in the CICC and have been calculated in  [13]  to obtain the best fit with datasets. Due to the large dependence of the pressure drop on the cable geometry, scattering of the hydraulic characteristics of the different DP were detected during tests  [14]. JT-60SA conductor samples used in the manufacture of the different TF coils have been extracted directly from the production line and tested with the OTHELLO test facility  [15].
This profile is consistent with heat propagation in the CICC due to pure advection of the warm front of helium, and the delay between the inlet and outlet temperature increases corresponds to the time needed by helium for flowing through the entire cable. For the CATHARE-3 simulation with the inter-turn model, the outlet temperature profile is close to the experimental one. The characteristic time of the transverse heat conduction is well evaluated by the code. Except during the first 350 s, THEA gives an outlet temperature similar to the one simulated by CATHARE-3 all along the transient (Fig. 7 ). The gap observed at the beginning of the simulation is only due to difference in the initialization of the calculation in the two codes. In CATHARE-3, the transient does not start directly from the initial state defined in the dataset.