dataesr/scientific-paragraphs-categorization huggingface dataset:
Thermal shift assay Thermal shift assay experiments were performed on a MiniOpticon Real-Time PCR System MJ Mini (Bio-Rad). The protein sample (4 lM) was incubated in 20 mM Tris/ HCl pH 8. 0, 100 mM NaCl with 1 mM of potential ligands in a total volume of 23 lL for 30 min at room temperature. The samples were heated from 20 °C to 94 °C at 0. 1 °CÁs À1 after addition of 7 lL Sypro Orange 259 (Thermo Fisher Scientific). The fluorescence intensity was plotted as a function of temperature using the MJ OPTICON MONITOR ANALYSIS software. Melting temperature (T m ) was given by the inflection point of the fluorescence curve.
SAXS experiments and data processing zPRMT2 73-408 SAXS data were collected on a BioSAXS-1000 camera (Rigaku, Ettlingen, Germany) mounted on a MicroMax 007 HF Rigaku rotating anode at a sampledetector distance of 500 mm, covering the range of momentum transfer 0. 008 < q < 0. 65 A À1 (q = 4p sin(h)/k, where 2h is the scattering angle and k = 0. 154 nm is the X-ray wavelength) in four frames (30 min each) to check for possible radiation damage. The q scale was calibrated by silver behenate powder diffraction and all data were collected up to a maximum q of 0. 35 A À1. Scattering measurements were carried out at 20 °C in a thermostated quartz capillary with a diameter of 1. 5 mm. zPRMT2 full-length SAXS data were collected at the SAXS beamline P12 at the PETRA III storage ring (Deutsches Elektronen-Synchrotron, Hamburg, Germany).
The exposure time was 0. 045 s. All zPRMT2 samples were solubilized in 20 mM Tris/ HCl pH 8. 0, 100 mM NaCl, 5 mM TCEP, 1 mM SAH and measured at several concentrations. The SAXS data were processed by standard procedures using the ATSAS software package (version 2. 7. 2). The scattering intensity I(0) and the radius of gyration R g were evaluated using the Guinier approximation with PRIMUS  [64]. These parameters were also determined from the entire scattering pattern using GNOM which computes the distance distribution function P (r) and the maximum particle dimension D max  [65]. The program CRYSOL was used to fit the theoretical scattering pattern to the experimental data  [66]. For ab initio model construction, multiple runs were performed using the program DAMMIF  [67]  to verify the stability of the solution.
MS and MS/MS conditions on SYNAPT mass spectrometer The MS and MS/MS analyses were performed on the SYNAPT TM , a hybrid quadrupole orthogonal acceleration time-of-flight tandem mass spectrometer (Waters) equipped with a Z-spray ion source and a lock-mass system. The capillary voltage was set at 3. 5 kV and the cone voltage at 35 V. Mass calibration of the TOF was achieved using Glu-fibrino-peptide B fragments obtained at 27 V on trap cell on the  m/z range in positive mode. Online correction of this calibration was performed with Glufibrino-peptide B as the lock-mass. The ion (M + 2H) 2+ at m/z 785. 8426 is used to calibrate MS data and the fragment ion (M + H) + at m/z 684. 3469 is used to calibrate MS/MS data during the analysis. For tandem MS experiments, the system was operated with automatic switching between MS and MS/MS modes (MS 0.
5 s/scan on m/z range [250-1500] and MS/MS 0. 7 s/ scan on m/z range ). The three most abundant peptides (intensity threshold 60 countsÁs À1 ), preferably doubly and triply charged ions, were selected on each MS spectrum for further isolation and CID fragmentation with two energies set using collision energy profile. Fragmentation was performed using argon as the collision gas. The complete system was fully controlled by MassLynx 4. 1 (SCN 566; Waters). Raw data collected during nanoLC-MS/MS analysis were processed and converted with ProteinLynx Browser 2. 5 (Waters) into. pkl peak list format. Normal background subtraction type was used for both MS and MS/MS with 5% threshold and polynomial correction of order 5, and deisotoping was performed.
MS/MS data interpretation The peak list has been searched against a Swiss Protderived combined target-decoy database using MASCOT (version 2. 4. 1; Matrix Science, London, UK). The database contained sequences of human proteins including common contaminants (human keratins) and porcine trypsin and was created using an in-house database generation toolbox (http://msda. u-strasbg. fr). During database search, up to one missed cleavage by trypsin and four variable modifications [oxidation of methionine (+16 Da), carbamidomethylation of cysteine (+57 Da), and methylation or dimethylation on arginine] were considered. The search window was set to 15 ppm for precursor ions and 0. 05 Da for fragment ions. MASCOT result files (. dat) were imported into SCAFFOLD 3 software (version 3. 6. 5; Proteome Software Inc.
Acknowledgements This work was supported by grants from  CNRS ,  Universit e de Strasbourg, INSERM, Instruct , part of the  European Strategy Forum on Research Infrastructures (ESFRI)  supported by national member subscriptions as well as the  French Infrastructure for Integrated Structural Biology (FRISBI)  ( ANR-10-INSB-05-01 , grant  ANR-10-LABX-0030-INRT ), a  French State  fund managed by the  Agence Nationale de la Recherche  under the  frame program Investissements d'Avenir labeled   ANR-10-IDEX-0002-02  to JC and IGBMC, grants from the  French Proteomic Infrastructure  ( ANR-10-INBS-08 ;  ProFI  project) to SC and grants from  Association pour la Recherche contre le Cancer (ARC)  (No. A09/4/5005 , No. SFI20121205902 ). We thank the members of the IGBMC common services and the members of the structural biology platform of IGBMC for technical assistance.
Highly purified enzymes are also a prerequisite for further enzyme characterization and for structure analysis. The goal of this work was to provide more modification-dependent REases for molecular biology and diagnostic applications. Here we report the cloning and expression of the BisI restriction enzyme gene in E. coli. BisI is the prototype for a new family of methylation-dependent REases since BisI does not share any significant amino acid (aa) sequence homology to the other known Type IIM restriction enzymes such as the DpnI, MspJI, McrBC, Mrr, McrA, ScoA3McrA or SauUSI families. By using the BlastP server at NCBI to search genome sequences in GenBank, we identified over 150 BisI homologs in bacterial genomes with 17% to 100% aa sequence identity. We cloned/expressed some of these genes in E.
Results Searching for the BisI restriction gene (bisIR) in the B. subtilis T30 genome. The B. subtilis T30 genome was sequenced using a Pacific BioSciences RSII sequencer and the sequences were assembled into a single circular contig of 4. 03 Mbp with 4,138 predicted genes (GenBank accession number CP011051)  19. Initially, one small putative HNH endonuclease gene (Bis30_20225, 124-aa, a. k. a. BspT30 HNH endonuclease) and one phospholipase D (PLD) family endonuclease gene (Bis30_09935, 221-aa) were considered as candidate genes for BisI. The partially purified gpBis30_20225 displayed strand-specific and sequence-specific DNA nicking activity with the specificity 5′ RCG ↓ GT 3′ in Mg 2+ buffer and a more relaxed specificity under star conditions  22. The gpBis30_20225 nicking specificity is similar to that of phage Gamma HNH endonuclease (N.
subtilis T30 strain is still unknown. Bacillus subtilis subsp. Spizizenii strain W23 (ATCC 6633) encodes a protein (Bsu6633_05694) identical to BisI, but its activity has not been tested. Other highly similar BisI homologs ranging from 67% to 88% aa sequence identity are also found in sequenced Bacillus subtilis (WP_024573623) and Bacillus sp. genomes (WP_053358749, WP_035432006) that remained to be evaluated. Cloning/expression and purification of BisI homologs. We used the BisI aa sequence to query GenBank using BlastP and found over 156 homologs (103 homologs with > 25% aa sequence identity; E value < 0. 004; 53 homologs with 19% to 25% aa sequence identity, E value > 0. 005) in March 2016 in more than 60 bacterial genera and mega-genome sequences (data not shown). Thus, BisI homologs are present in many bacteria.
One homolog is the Eco15I endonuclease (active, see below), which has an N-terminal 160-aa with significant similarity to BisI. However, it also contains an extra C-terminal domain of ~130-aa that shows significant similarity to some putative HNH endonucleases (COG1403 and COG 3183, Pfam01844). In some bacteria, the homologs of the C-terminal domain of Eco15I exist as separate small proteins 88 to 129-aa long whose function remains to be determined. A total of 34 Eco15I homologs (263 to 294-aa residues long) were found in GenBank mainly among Gram-negative bacteria, including some pathogens. In the shot-gun sequence of the DNA fragment encoding Eco15I, the restriction gene is located next to an XRE family transcription regulator, two putative DNA transposases (COG1662 and COG3677) and an IS1 protein InsA.
We evaluated some of the homologs for modification-dependent restriction activity. These BisI homologous genes were cloned into pTYB1 as fusions containing an intein and a CBD so that the target protein could be purified quickly from affinity chitin columns and DTT/intein cleavage (one BisI homologs, Rfl17I, was 6xHis-tagged at the N-terminus and was purified from Ni-NTA affinity column, data not shown). Figure  1  shows some partially purified BisI homolog proteins. The purified enzymes were used to digest pBRFM which contains two and three modified m5 C in GCNGC sites or phage XP12 DNA in which all C residues are replaced by m5 C. We also used DNA duplex oligos with two, three, or four m5 C in a GCWGC site for enzyme digestion (see below). BisI-L (long form, 178 aa) was poorly expressed and showed a low activity (Fig.
Because RGNCY sites are not modified in pBR322, this result suggests that Bce1273I may have lost some of its specificity for m5 C modification. We performed run-off sequencing of Bth171I-digested pBR322. Four cut sites are shown in Supplementary Figure  S9A. The consensus recognition sequence and cut sites (RS ↓ NSY) are shown in Figure  S9B. The cut sites were similar to those derived from Bce1273I, except that Bth171I generated more complete digestion. It is noted that M. Fnu4HI-modified site G m5 CNGC is a subset of RSNSY sites and the modified site is cleaved by Bth171I at a low efficiency. Sve396I prefers to cleave GCNGC sites with three to four m5 C. But its star activity at high enzyme concentration can cut unmodified sites at GC ↓ GAC (data not shown). To reduce star activity on unmodified sites for the BisI family enzymes, it is best to perform restriction digestion in high salt buffer (NEB buffer 3.
Other REases recognizing GCNGC, GCWGC, or GCSGC. Another enzyme, only remotely related to BisI, is the recently described EcoBLI that cleaves GCNGC sites containing two to four m5 C 30. More than 30 homologs are present in GenBank with > 30% aa sequence identity to EcoBLI by BlastP search. There are a number of Type IIP REases cleaving unmodified GCNGC sites (Fsp4HI)  31  , GCWGC (ApeKI and TseI), or GCSGC (TauI) sites  7. The aa sequences of these enzymes and other homologs have very low sequence similarity to the BisI family enzymes (less than 15% identity), suggesting that Type IIP enzymes cleaving BisI-related sites evolved independently.
Acknowledgements We thank  Priscilla Too  and  Mike Dalton  for purification of the native BisI enzyme;  Vernissia Tam ,  Priscilla Too ,  Siu-Hong Chan ,  Alexey Fomenkov , and  Penghua Zhang  for evaluation of the putative PLD endonuclease;  Tom Evans  for useful suggestions;  Tamas Vincze  for initial bioinformatics assistance;  Rick Morgan ,  Peter Weigele ,  Yu Zheng , and  Nick Guan  for providing plasmids, phage DNAs and the XP12 sequence;  Victoria Hull  for help with Rfl17I purification;  Tom Evans ,  Lise Raleigh  and  Bill Jack  for helpful discussion and critical comments. Funding for publication processing fee was provided by  New England Biolabs, Inc.
DATA A N D N O I S E C RO S S -C O R R E L AT I O N S The Valhall LoFS network is a permanent ocean-bottom cable array made of 2320 four-component sensors (a three-component geophone and a hydrophone) installed on the seafloor in the North Sea (Fig. 1 ), above Valhall reservoir. We use 400 min (∼6. 5 hr) of continuous ambient noise records on vertical (Z), south-north (N) and west-east (E) component of geophones for this study. The data set was recorded at 250 samples per second with the low-cut filter that removes almost all energy at periods longer than 2. 5 s. The interstation distance between the sensors along cable is 50 m and intercable distance is 300 m. For three component sensors more than 10 millions of interstation cross-correlations (CCs) are computed between all possible pair of sensors for vertical-vertical (ZZ) component along with north-north (NN), east-east (EE), north-east (NE) and east-north (EN) components combinations.
The new misfit is calculated and new n c cells are chosen to be resampled. The last step is repeated and algorithm stopped after n i iterations. When the model space is considered to be well sampled, the ensemble of tested models and their respective misfits can be used statistically to characterize the solution of the inverse problem. The selected parameters bounds are [150, 550] m s -1 for V 0 [0. 08, 0. 28] for α and [550, 1350] m s -1 for V n. We run NA with n 1 = 10 000, n s = 1000, n 5 = 5 and n i = 8, that is, a total of 50 000 models are tested. For that, we use computer with 24 cores and 45 GB internal memory and Matlab as a platform to run the NA code written in C language that took around 15 min to run the inversion for a point. Finally, we select 1000 the best-fit models and take average of these 1000 models for defining the final velocity profile.
A M B I E N T N O I S E S U R FA C E WAV E T O M O G R A P H Y O F S C H O LT E A N D L OV E WAV E S After constructing the average 1-D velocity model, we proceed with 3-D tomography. At this stage, we retain only the fundamental-mode measurements and do not use the first overtone data because it is too noisy, when considering individual station pairs. The surface wave tomography is done using a common three-step approach (e. g. Ritzwoller et al. 2011 ). In the first step, the frequency-dependent phase traveltime is measured for all noise CCs computed of every individual virtual source. In the second step, the phase traveltime is inverted to construct 2-D phase-velocity maps for Scholte and Love waves at different frequencies using eikonal tomography technique  (Lin et al. 2009 ). In the final step, we invert the local dispersion curves computed from 2-D phase-velocity maps for depth structure.
C O N C L U S I O N S Only 6. 5 hr of continuous recording of noise data at Valhall LoFS network allowed us to image Valhall structure down to 600 m depth and to observe high-resolution 3-D S-wave velocity structure with the depth-dependent radial anisotropy information. A set of 2-D phase-velocity maps of Scholte wave at periods 0. 7-1. 6 s and of Love wave phase-velocity maps at periods 0. 8-1. 5 s were constructed to image the near-surface structure of Valhall using the eikonal tomography method. Near-trace stacking helps us to improve SNR for Love wave signal. A Monte Carlo inversion is applied to invert average dispersion curves of Scholte and Love waves to get 1-D isotropic velocity (V S ). Our depth inversion results show good agreement with the geological structure already found using controlled source seismic observations  (Sirgue et al.
In addition, patients maintained a median trough level of 13. 4 IU/dl FIX activity on weekly prophylaxis. Overall, 97. 2 % of bleeding episodes were successfully treated with one or two injections of rIX-FP (95 % CI: 92 % to 99 %), 88. 7 % with one injection, and 96 % of the treatments were rated effective (excellent or good) by the Investigator. No patient developed FIX inhibitors and no safety concerns were identified. These results indicate that rIX-FP is safe and effective for preventing and treating bleeding episodes in children with haemophilia B with weekly prophylaxis. Routine prophylaxis with rIX-FP at treatment intervals of up to 14 days are currently being investigated in children with severe and moderately severe haemophilia B. Clinicaltrials. gov.
Trial design This was a prospective, non-randomised, international, open-label phase 3 study, with all patients assigned to weekly prophylactic treatment (▶ Figure  1 ). Patients underwent up to one-month screening followed by active treatment for 12 months or longer. All patients participated in PK evaluation of 50 IU/kg rIX-FP at study entry. Patients also participated in PK evaluation of 50 IU/kg of previous FIX product unless PK data were available in the medical records. The patients were assigned a dose of 35-50 IU/kg rIX-FP for weekly prophylaxis, at the investigator's discretion. The dose could be adjusted higher or lower, based on bleeding phenotype, physical activity level, and clinical outcome, while maintaining a weekly treatment interval. The active treatment period for the evaluation of safety and efficacy was extended up to 18 months to allow patients to receive continuous treatment with rIX-FP until enrolment in the subsequent extension study.
Therefore, as an acceptance criterion, the lower limit of the two-sided 95 % CI was set at 80 %. The PK analysis was performed by standard non-compartmental analysis using Phoenix WinNonlin ® software version 6. 2 (Pharsight). Four main PK parameters (incremental recovery, terminal half-life, AUC and total body clearance normalised to body * Nucleotide and codon numbering according to Human Genome Variation Society (HGVS)  (23, 24) , in which the first codon is the first residue (Met) of the 46-residue signal peptide/propeptide, and the first residue of the mature protein is 47. † The number of patients reporting the mutation as captured in the Factor IX Variant Database, available at www. factorix. org. (13). ‡ Report of this mutation is in the CDC Hemophilia B Mutation Project (CHBMP) F9 Database only  (25).
Patient characteristics Overall, 27 male patients with haemophilia B (FIX activity ≤2 IU/ dl) from 17 sites in 10 countries provided informed consent and were enrolled and treated with rIX-FP between January 2013 and October 2014. Patient enrolment and a study flow diagram are presented in ▶ Figure  1. Enrolment was evenly distributed be- no patients had the same mutation, as shown in ▶ Table  2. The majority of mutations identified were point (missense) mutations; one mutation (Arg294Stop) in one patient causing a large deletion has been reported to be associated with the development of inhibitors in the Factor IX Variant Database  (13).
Low AsBRs, effective treatment of bleeding episodes, and clinical improvement of target joints suggests that weekly routine prophylaxis with rIX-FP may provide an improved option for the prevention and treatment of bleeding episodes in children with haemophilia B. Following completion of this study, 24 patients chose to continue treatment with rIX-FP in the extension study (Clinicaltrials. gov number NCT02053792). In addition, approximately 50 % have switched to a longer treatment interval of once every 10 or 14 days with 75 IU/kg of rIX-FP. Longer treatment intervals of up to 14 days are currently being investigated in children with severe and moderately severe haemophilia B which will continue to provide further clinical efficacy and safety data, in addition to the investigation of rIX-FP in previously untreated paediatric haemophilia B patients and in perioperative management.
Acknowledgements The authors thank all of the patients and their families who contributed to this study, and all of the participating research nurses and data coordinators; the Independent Data Monitoring Committee members:  Barbara Konkle  (chairperson),  Puget Sound Blood Center, Seattle, WA, USA ;  Mike Makris ,  Royal Hallamshire Hospital, Sheffield, UK ;  Amy Dunn ,  Nationwide Children's Hospital, Columbus, OH, USA. The authors thank  Annette Feussner ,  CSL Behring/Germany  for central laboratory testing support,  Christine Joch  and  Denise Wolko ,  CSL Behring/Germany  for data analysis,  Grace Cole  and  Amanda Stetka CSL Behring/United States  for operational management, and  Tharin Limsakun ,  CSL Behring/United States  for PK review.
Background: Cerebellar atrophy and developmental delay are commonly associated features in large numbers of genetic diseases that frequently also include epilepsy. These defects are highly heterogeneous on both the genetic and clinical levels. Patients with these signs also typically present with non-specific neuroimaging results that can help prioritize further investigation but don't suggest a specific molecular diagnosis. Methods: To genetically explore a cohort of 18 Egyptian families with undiagnosed cerebellar atrophy identified on MRI, we sequenced probands and some non-affected family members via high-coverage whole exome sequencing (WES; >97 % of the exome covered at least by 30x). Patients were mostly from consanguineous families, either sporadic or multiplex. We analyzed WES data and filtered variants according to dominant and recessive inheritance models.
Bioinformatics, databases A variant filtering pipeline was systematically applied to narrow down the number of putative causative variants. All the possible inheritance patterns were tested. Briefly, common (>1 % minor allele frequency) variants were filtered out by using dbSNP, 1000 genomes databases and our in house exome collection, which includes more than 7000 exomes. Functional (protein-altering) alleles were prioritized versus non-functional. Potentially pathogenic variants in known disease genes were identified if flagged as damaging by polyphen2 (http://genetics. bwh. harvard. edu/pph2/), Sift (http://sift. jcvi. org/) or mutation taster (http://www. mutationtaster. org/). Remaining variants were compared with those in the public databases EXAC (http://exac. broadinstitute. org/) and EVS (http:// evs.
gs. washington. edu/EVS/) exome database. The presence of candidate recessive variants in homozygous intervals was checked by identifying predicted regions of SNP homozygosity from exome data with the unifiedgenotyper tool from GATK (https://www. broadinstitute. org/ gatk/). In order to identify fully penetrant dominant mutation in singleton WES data we used the following method. We filtered out variants that were present in control individuals from our in house exome database and not predicted to be pathogenic by at least two prediction programs: PolyPhen, SIFT or Mutation-Taster. When a single rare variant predicted to be deleterious was observed in a single known cerebellar atrophy gene and associated with a dominant mode of inheritance, it was considered as potential candidate. When the same rare variant has been previously associated with disease, this was considered strong evidence that it was likely to be pathogenic.
Acknowledgments This project was funded by grant  ANR-12-PDOC-0026  that supported also VC and MN salary and by grant  ANR-10-IAHU-01. We are grateful to  Campus France  that allowed the French-Egyptian collaboration and supported some travel and accommodation fees for HM. We acknowledge the assistance and expert advice from collaborators at the genomic and bioinformatics cores of the Imagine institute. We thank  L. S. Nguyen  and  C. Gordon  for critical reading of the manuscript.
Participants We measured a sample of professional SIs [principally interpreting from English (L2) to German (L1), totally 12, 10 women, mean age = 37. 9 years, SD = 6. 9 years] and multilingual controls participants (totally 12, 9 women, mean age = 39 years, SD = 4. 7 years). All participants were consistently right-handed, as revealed by the Annett Handedness Inventory  (Annett, 1970) , and were native German speakers with a good English listening comprehension (DIALANG 1 ). 1 http://www. lancaster. ac. uk/researchenterprise/dialang/dialang_technical The two groups were matched for age, gender, L2 proficiency, age of L2 acquisition, and education (i. e. , University degree). None of the participants reported a history of neurological, psychiatric or audiological disorders (Home Audiometer Software 2  ) and all participants denied consumption of illegal drugs or regular medication.