dataesr/scientific-paragraphs-categorization huggingface dataset:
Organism (5) Assembly merging Using the Quickmerge wrapper, and with hybrid assembly as donor and long-read only assembly as acceptor (node=1:ncpus=1:mem=6gb; cput=00:25:00;walltime=00:25:00; requires python/3): merge_wrapper. py Hybrid_assembly. fasta longread_assembly. fasta -l 10000000 -lm 10000 (6) Quiver polishing Align PB reads (in. bam format) to assembly with Pbalign (node=1:ncpus=28:mem=168gb; cput=224:00:00;walltime=08:00:00): ~/Programs/SMRTtools/smrtcmds/bin/pbalign --nproc 28 my_PBreads. bam my_assembly. fasta aligned_PBreads. bam Index aligned PB reads (node=1:ncpus=1:mem=6gb; cput=00:10:00;walltime=00:10:00): ~/Programs/SMRTtools/smrtcmds/bin/pbindex aligned_PBreads. bam Index assembly (node=1:ncpus=1:mem=6gb; cput=00:02:00;walltime=00:02:00): ~/Programs/SMRTtools/smrtcmds/bin/samtools faidx my_assembly.
fasta Run Quiver (node=1:ncpus=28:mem=168gb; cput=154:00:00;walltime=05:30:00): ~/Programs/SMRTtools/smrtcmds/bin/quiver -j 28 -r my_assembly. fasta -o my_assembly_polished. fasta aligned_PBreads. bam Run Arrow (node=1:ncpus=28:mem=168gb; cput=154:00:00;walltime=05:30:00): ~/Programs/SMRTtools/smrtcmds/bin/arrow -j 28 -r my_assembly. fasta -o my_assembly_polished. fasta aligned_PBreads. bam (7)  Pilon polishing Index the assembly file (node=1:ncpus=6:mem=6gb; cput=00:05:00;walltime=00:05:00): bowtie2-build my_assembly. fasta my_assembly nanopolish vcf2fasta -g. /my_assembly. fasta. /polished. *. vcf >. /my_assembly_polished. fasta (9) Quality assessment Quast (node=1:ncpus=5:mem=30gb; cput=05:00:00;walltime=01:00:00;requires python/3) ~/Programs/quast-4. 6. 2/quast. py -o /. / -R /path_to_reference_genome/Reference.
Experimental Apparatus An instrumented object (iBox) with 6 integrated load cells and an inertial measurement unit (IMU) was used for the purposes of this study (see Figure  1A ). This device measures 108 × 70 × 40mm and has a mass of 0. 370 kg. It enables recording of acceleration, rotational velocity, orientation of the unit as well as the forces applied normally to each of its six faces. The force of the load cell on the bottom face was calibrated so that the weight of the device, equivalent to 3. 63 N, was subtracted (i. e. , the reference force signal was zero when the object lay on the table and decreased to -3. 63 N when the object was lifted from the supporting surface). All data was sampled at a frequency of 100 Hz and transmitted wirelessly to a local computer via Bluetooth. Overall acceleration was measured as a combination of gravity and kinematic acceleration  (39).
Grip strength scores are provided in newton with values for the less affected side in brackets. Fugl-Meyer provides the total score on the upper limb evaluation with sensory and motor subscores indicated in brackets. The Jebsen Taylor provides a score in seconds, being the total time required to complete a series of manual handling tasks; the score in brackets provides the reference time for the less affected arm. task. Patients were asked to perform each grasp and place task 3 times to the best of their ability. The ensemble of grasping and holding tasks were performed first with the less affected arm and then with the hemiparetic arm. The experimenter verified the patient's initial posture and repositioned the iBox between movements as required. Visual inspection of all force, acceleration and orientation signals was carried out immediately following data acquisition.
Based upon the time-tagged data sequences, the following series of variables were extracted for analysis: • Duration and rate of grip force change for unloading and release phases • Grip force at tg, tl, tp, te (mean of the front and back load cells) • Maximal grip force and peak acceleration during the lifting phase • Time difference between maximal grip force and peak acceleration during the lifting phase • Grip force during holding (median and standard deviation of the front and back load cells during the whole period) • iBox orientation at times tg, tl, td, te (alpha angle) • iBox orientation during holding (alpha angle median and standard deviation) • Frequency of touch events before grasping and after object release and of push events during the unloading and release phases All data analysis was performed using customized Matlab scripts.
Statistical Analysis Data for continuous variables were examined using Shapiro-Wilk tests. As the ensemble of these variables was found to have non-normal distributions, Kruskall-Wallis non-parametric analysis of variance was used for statistical comparisons. Both side (hemiparetic arm/less-affected arm) and grasp configuration (pinch/precision/palmar digital/top) factors were included. Where indicated, post-hoc analysis was conducted using Dunn's method. The frequency of touch and push errors was analyzed using Chi-Squared tests. The Bonferroni method was used for correction of p-values when comparing across grasp configurations. The threshold for statistical significance was set at p = 0. 05. In order to evaluate relationships between clinical characteristics and task performance, test results from the DGS, FME, JTT, and FAT were transformed into z-scores prior to testing with Spearman correlation coefficients against the hemiparetic upper-limb variables assessed using the iBox.
Values >0. 7 or <-0. 7 were considered to represent strong correlation between clinical motor-function tests and iBox variables. In order to control for multiple correlation analysis, a resampling method with 10,000 randomized permutations of each iBox variable was used. Percentile values (2. 5 and 97. 5%) from the distribution of the resulting coefficient matrix served as a symmetric twosided 95% confidence interval  (63). Correlations of clinical motor tests and iBox variables outside of this confidence interval were considered as statistically significant. All statistical analyses were conducted using Matlab and the JASP software package (https://jasp-stats. org).
Time Courses for iBox Data Signals Time courses of force, acceleration and object orientation signals were generally consistent across the different grasp patterns used. Changes in grip forces reflected the phase progression in the grasping, lifting, holding and placement of the iBox, although the regularity and magnitude of these signals were less consistent. Figure  3  provides typical examples of these signals for two patients with contrasting functional abilities (patient 1 had a FME motor score of 66 compared to 37 for patient 7). Broadly speaking, those patients who experienced a better recovery had regular acceleration and orientation profiles. For these patients, maximal grip force occurred during lifting and a smooth decrease of force was observed before placement while the holding phase was characterized by relative stability of grip forces.
LIMITATIONS OF THE STUDY The principal limitation in the design of this study is the lack of control group. Whilst one of our previous studies involved a similar protocol, data was obtained only for young adults. In the absence of an age matched control group we have limited our analysis to differences in grasp regulation between the hemiparetic and less affected arms of patients following a stroke. Secondly, whilst the iBox affords certain advantages (ease of manipulation, multiple integrated sensors), it measures exlusively those forces normal to the surface of each face-it is unable to estimate tangential forces or torque. The choice for linear load cells was motivated by the possibility of an affordable object which could be used in the clinic or at home  (58). Finally, the design of this study allows for considerable variation in surface contact.
ACKNOWLEDGMENTS We would like to extend a special thank you to  Sara Panera ,  Ariane Bozon-Verduraz  and  Marie-Laure Descamps  of the physiotherapy department of the  Salpêtrière Hospital , as well as to  Claire Kemlin ,  Eric Moulton  and  Charlotte Rosso  of the  Institut du Cerveau et de la Moelle Epiniere  for their assistance in the recruitment of patients for this study.
conditions). Example sequences are available as Supplemental Digital Content. The sequences were sung on CV-syllables by sampled voice sounds (using Vocal-Writer software, Woodinville, WA, United States). Chords were generated by the simultaneous presentation of 3 or 4 synthetized utterances of the same syllable with different fundamental frequencies, which corresponded to the component tones of the chords. The succession of the synthetic syllables did not form a meaningful, linguistic phrase (e. g. , /da fei ku o fa to kei/), and the last syllable (i. e. , of the target) was either /di/ or /du/ to define the experimental task. The experimental session consisted of 50% of sequences ending on the related tonic target (25% being sung with /di/, 25% with /du/) and 50% ending on the less-related subdominant target (25% with /di/, 25% with /du/).
Pitch Periodicity in a Model of Auditory Short-Term Memory: Tonal Contextuality Index To further test the acoustic influences in the experimental material, we used  Leman (2000)  model (as implemented in the IPEMtoolbox v1. 02 by  Leman et al. , 2005)  that stores auditory information in a short-term memory buffer. Acoustic input is first processed in a frontend module mimicking the peripheral auditory system  (Van Immerseel and Martens, 1992). The output is then processed with a pitch module that extracts periodicities using an autocorrelation approach. Finally, the periodicity output is passed into a memory module. This model relies on the comparison of pitch images of two echoic memories, which differ in duration. With longer memory decays, the pitch images are smeared out, so that the images reflect the context echoic memory, while with a shorter decay the pitch images reflect the target echoic memory.
, 2014). The model is based on the Nucleus Matlab Toolbox (Cochlear Ltd. ), which generates patterns of electrical stimulation along the electrode array of the implant. The generated electrical field is then propagated in the cochlea to mimic current spread  (Bingabr et al. , 2008). Neural activation probability resulting from this electrical field is then calculated using approaches adapted from  Rattay et al. (2001). This time-place image is used first to examine the spectral contrast between prime and target, and then to evaluate the tonal contextuality.
Tonal Contextuality Index The electrically induced neural activation image was used as auditory image to feed into the pitch module of the IPEMtoolbox in order to extract periodicity structures. The rest of the model (memory decay and TCI computation) was identical to the one used for the acoustic/NH model. The results, shown in Figure  3B , indicate that no combination of local and global memory decay yields positive z(TCI) beyond the critical value. When applying the same linearmixed model as in the section "Pitch Periodicity in a Model of Auditory Short-Term Memory: Tonal Contextuality Index, the effect of relatedness was found to be significant [F(1,35318) = 165. 2, p < 0. 0001], with the less-related condition having a globally higher TCI. The effect of syllable was also significant [F(1,35318) = 20.
FUNDING This work was partly supported by the grant  ANR-09-BLAN-0310. This work was also supported by  LabEx CeLyA ("Centre Lyonnais d'Acoustique , "  ANR-10-LABX-0060 ) of  Université de Lyon , within the program " Investissements d'avenir"  ( ANR-11-IDEX-0007 ) operated by the  French National Research Agency (ANR).
The participants were unaware of each other's identity while the survey was being conducted. Ethics clearance was obtained from the University of Exeter before the survey was launched. Participation in the Delphi technique was based on informed consent and from the first round onwards, respondents were self-selected. We selected a total of 55 European researchers recently active (i. e. , ≥2 publications in the last 10 years) in fields of WDH and wolf conservation through two complementary searches on the Scopus 4 database. The searches were conducted on 28th February 2018 and the search terms used were ("wolf OR wolves+dog+hybrid * OR introgres * ") and ("wolf OR wolves+ecolog * +conserv * "), respectively. Two other experts were separately contacted based on a snowball sampling approach, which involves a non-random sampling method whereby respondents are asked to nominate other potential respondents (i.
ACKNOWLEDGMENTS We are grateful to experts:  H. Andren ,  M. Apollonio ,  E. J. G. Fernandez ,  O. Liberg ,  S. Nowak ,  C. Vilà , and  P. Wabakken  who participated partially in this Delphi survey and contributed their time. We are grateful to  Elleanor Gurr  from the  Royal Veterinary College (RVC)  for her help in providing ideas and shaping discussions on anthropogenic hybridization. The following funding bodies are thanked by the respective authors: GC: Formas; OG:  CNRS   Mission pour l'Interdisciplinarité through its program  Osez l'Interdisciplinarité; RG:  Portuguese Foundation for Science and Technology  ( IF/00564/2012 ); MH: post-doctoral research grant from  Estonian Research Council ; CP:  Aalborg Zoo Conservation Foundation  (AZCF: grant number 3 and 4, 2018); MP: The  Leverhulme Trust Research Fellowship  ( RF-2017-185 ); US: Institutional research funding ( IUT20-32 ) from the  Estonian Ministry of Education and Research ; JL:  Research Council of Norway  (grant  251112 ); AS: senior postdoctoral fellowship from  Insubria University in Varese, Italy ; JB:  Ramon & Cajal  research contract ( RYC-2015-18932 ) from the  Spanish Ministry of Economy, Industry and Competitiveness ; NM:  NERC  Grant/Award Number:  NE/R006946/1  and  Scriven  fellowship.
The data demonstrated successful organization of the axon fascicle segregated from the spheroids. To characterize the surface structure of the fascicle, we employed scanning electron microscopic analyses. The surface appeared to be an assembly of axon fibers running in parallel (Figures  3D  and 3E ). To assess the internal structure, we analyzed the cross-sectional morphology of the fascicle at a higher magnification with transmission electron microscopy (TEM) (Figure  3F ). This revealed that axons were packed within the fascicle. Cross sections of well-organized cytoskeletal fibers, including microtubules, were observed within the axons. The average axon diameter measured from TEM images was 338 nm, and its standard deviation was 162 nm (Figure  3G ).
ACKNOWLEDGMENTS We thank  Dr. Naoko Yoshie ,  Dr. Shintaro Nakagawa , and  Mr. Kyungmo Sung  for providing equipment and assistance for SEM analyses. We also thank  Mr. Christian Felsner ,  Dr. Miles Pennington , and members of  RCA-IIS design lab for discussion. This work was supported by  Japan Society for the Promotion of Science (JSPS)   Grants-in-Aid for Scientific Research   17H05661  and  18K19903  (Y. I. ), by  CASIO Science Promotion Foundation  (Y. I. ), by  Tanaka Memorial Foundation  (Y. I. ), and by a  Grant for Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS ) by  AMED  under the Grant Number  JP18dm0207002  (S. S. ).
Machine The TAP Biosystems' CompacT SelecT-automated cell culture platform (Sartorius Stedim, Royston, UK), which utilises an incubator carousel to store cell culture flasks, multiple peristaltic pumps to dispense cell culture reagents and a robotic arm to replicate many of the process steps involved in manual cell culture, was utilised in this study. This platform also incorporated a Cedex analyser-automated cell counter (Roche, Switzerland); the system utilises Trypan blue exclusion and automated imaging software to determine viable cell density, viability and aggregate rate. The CompacT SelecT has previously been demonstrated for the culture of hMSCs  [13, 14, 27] , hESCs  [17]  and hiPSCs  [10, 16]  as aggregates.
The flask was then 'borrowed', and the contents were weighed on digital scales. 'Borrowed' refers to the programming terminology whereby the machine is instructed by the operator to eject the flask from the machine. This step allows the operator to determine the volume of reagent dispensed, assuming that 1 mL of reagent weighs 1 g. This value can then be entered into the CompacT SelecT software in order to calibrate the peristaltic pump system, which adjusts the subsequent dispensing steps accordingly.
Dry run and automated culture emulation The CompacT SelecT-automated protocol consisted of the following: (i) dry run-a software compatibility run with each of 4 sub-protocols including media change, passaging the cells split 1:3 and 1:1 and sampling (but without cell culture media). (ii) Wet run-using PBS/ddH 2 O to emulate culture media, with each of four sub-protocols after repair service and preventative maintenance (PM).
In addition, flask-to-flask variation increased at both sites; in particular at site 2, whereby viability ranged from 66. 4 to 81. 9% at passage 5 and 48. 3 to 88. 9% at passage 6. An increase in cell viability at passage 6 was observed in 3 of the flasks expanded at site 2 only. At site 3, the experiment was terminated at passage 3 due to higher observed deviations in cell viability data and lower cell growth, most likely as a result of cell culture contamination. Specifically, cell viability at site 3 were visibly lower following passage 3 with greater flask-to-flask variation, tween 77. 7 and 93. 2% recorded. In addition, the flask-to-flask variation in cell count increased at all three manufacturing sites from passage 2 onward. The variations were more apparent in the earlier passages.
There should be an agreed acceptance across all operators and sites that contamination is an inevitable risk of cell manufacturing and should be reported immediately to the QP without questioning of the operator's cell culture practice given that there are many sources for contamination. A single database is required for the recording of contamination or process failures across all sites. A standardised format of reporting and paperwork would allow the QP to identify and analyse general trends and common areas of error or contamination. Prior to the onset of any extended processing, a detailed screening and re-qualification of banks is recommended; this should occur in a single centralised unit to avoid deviations in protocols and analysis. This process could also be blinded to avoid any potential bias in analysis and teams involved should include manufacturing and quality representatives of each site involved.
Additionally, a mathematical modelling approach can be applied to predict the growth rate and dynamics of specific cell lines and determine the critical process parameters (CPPs) that affect the metabolite concentration, viability and growth. Such parameters include cell density, composition of bulk media, presence and concentration of growth factors, the timing and frequency of feeding. This approach can also be used in predicting the effect of variation in temperature and incubation time. The results of this approach can be recorded in a centralised database to permit the establishment of agreed limits for biological process deviation across sites. During the product/process development and training processes, all operators should record and report potential areas for error, process deviation and risk.
These are to be reported using a standardised format on a centralised database to be viewed by the QP. Ultimately a single, detailed SOP that includes the risk mitigations identified should be prepared. The use of decision-process flowcharts for the SOP should be considered for steps of the process where conditional actions are acceptable. This should address the entire manufacturing process, and the conditions for terminating the culture process made explicit. Accompanying the process SOP, there is a requirement for a harmonised and uniform SOP for machine and equipment maintenance, synchronised to usage and workload. This will serve as a means to reduce points of failure regarding equipment and machine malfunction, whilst also ensuring that all processing tools are serviced, calibrated and equivalent across sites.
We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1 H-15 N HsQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method. Nuclear magnetic resonance (NMR) spectroscopy is the technique of excellence to obtain structural and dynamics atomic resolution information of macromolecules, especially proteins 1. NMR is compatible with room temperature solution measurements, a major advantage over other high-resolution structural techniques (X-ray crystallography and cryo-electron microscopy). Via NMR, protein structures can now be determined with chemical shifts data alone (employing the CS-Rosetta package) 2-6 , which is extremely important when merely sparse data is available  3, 4.
Benef ting from our previous work  [25] [26] [27] [28] [29] [30]  , we usesd dengue virus (DENV) capsid (C) protein as a model (Fig. 1a , PDB ID 1R6R)  26, 31, 32  since it possesses three distinct structural regions (Fig. 1b  and Table  S1 ): the disordered N-terminal, the flexible fold and the conserved fold. The nomenclature "conserved fold" refers to a structurally persistent fold that was.
found in the flaviviruses capsid protein structures of Dengue, West Nile and, recently, Zika viruses (with PDB IDs, respectively, 1R6R, 1SFK and 5YGH)  26, [32] [33] [34]. This approach employs a small pH variation, preserving DENV C overall structure and dynamics, which easily allows probing the backbone N-H groups' solvent accessibility (using only 1 H-  15  N HSQC peak intensities). The three DENV C structure/dynamics regions can be clearly distinguished via this method, which supports not only the current understanding of DENV C structure/dynamics properties, but also the use of this technique to access and differentiate solvent-exposed N-H groups in IDP regions. Moreover, since the solvent accessibility of each N-H group is related to its intramolecular H-bond pattern, our approach also informs on the secondary structure content.
Results Suitability of the protein to the pH-based variation approach used. Our approach is based on small variations of pH within an interval that does not lead to major protein conformational changes. DENV C (Fig. 1a, b ) was used as a model to study the relationship between the protein structure/dynamics and backbone N-H solvent accessibility (i. e. , the ability of the N-H hydrogen to exchange with water hydrogens). The interval Figure  1. DENV C structure, overall dynamics and 1 H-  15  N HSQC spectra from pH 6. 0 to 7. 5. (a) DENV C homodimer experimental structure. This protein is positively charged, with 26 cationic and 2 anionic out of 100 residues per monomer. From amino acid residue 21 to 100, it contains four α-helices named α1 to α4 (PDB ID 1R6R  32  ). The first 20 residues are not shown since they are intrinsically disordered in solution  32.
9 software  54  was used for protein structure visualization. The data agrees with the current understanding of flaviviruses C proteins structure/dynamics and biological activity  [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] 55. used is between pH 6. 0 and 7. 5, a physiological range that is suitable for most proteins, including DENV C, as described ahead. Taking advantage of the pH dependent amide N-H hydrogen exchange process  [10] [11] [12] [20] [21] [22] [23] [24]  , 1 H-  15  N HSQC spectra of DENV C were acquired at pH 6. 0 and 7. 5 (Fig. 1c, d , gray and black, respectively). Only  pecific peaks show decreased intensity and/or a chemical shift variation (Fig. 1c, d ). T e variations in intensity affect more peaks and are more pronounced than chemical shift variations, suggesting no major conformational change triggered by pH.