dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic inference Analyses were carried out for the data set of the three genes combined, as well as for the separate COI data set. Phylogenetic trees were inferred using maximum likelihood (ML). Model selection was determined according to the hierarchical likelihood ratio test as implemented in ModelTest 3. 06  (Posada and Crandall 1998) , with the starting tree obtained by maximum parsimony to estimate model parameters. The data were analyzed in MEGA X  (Kumar et al. 2018)  with the GTR + G + I model of sequence evolution and 10,000 bootstrap replicates to estimate branch support. We performed a divergence time estimation using the StarBEAST 2 v. 0. 15. 5 package  (Ogilvie et al. 2017 ) available in BEAST2 suite v. 2. 6. 3  (Bouckaert et al. 2019) , which implements the Bayesian multispecies coalescent method to infer calibrated species trees  (Ogilvie et al.
2. 5. 2  (Bouckaert et al. 2019 ) with a selected burn-in of 25% to build the maximum clade credibility tree, and posterior probabilities (pp) were calculated as branch support. Chain convergence was further assessed with Tracer v. 1. 6 (Rambaut et al. 2014)  to confirm sufficient effective sampling size (ESS > 200) (BEAST Developers 2017). Node support is defined as low/weak (pp < 0. 50), moderate (pp: 0. 50-0. 84), high (pp: 0. 85-0. 94), or strong (pp ≥ 0. 95). The trees were visualized using Figtree v. 1. 4 (Rambaut 2009 ). To plot the ultrametric tree, the R package Strap  (Bell & Lloyd 2015)  was used, and the resulting trees were refined in Inkscape 0. 92. 3 (https:// www. inksc ape. org). We used secondary calibrations to time-calibrate the species tree (see  Peña et al. 2011; Chazot et al.
Acknowledgements We would like to thank  Haydon Warren-Gash  ( London, UK ) for critical reading of the manuscript and  Akito Kawahara  (FLMNH) and the  ButterflyNet Consortium  (supported by  National Science Foundation   DEB-1541500 ) for providing the sequences of nuclear genes of P. homoeodice. Nomenclature ZooBank Registration: urn:lsid:zoobank. org:pub: B5FC1030-BEFF-4F68-B6C5-6B47495BFC2F.
The characterization and measurement instruments were shared through social networks using Google forms; permission was obtained from the authors to use the instruments. The average time to answer the instruments was 20 min. The study was approved by the ethics and research committee of the Faculty of Nursing at Universidad Autónoma de Coahuila and the electronic informed consent was applied. Among the measurement instruments, a data card was applied where participant personal data was considered, as well as the presence of COVID-19 in the family, having been diagnosed with the disease, and the number of risk factors for complication regarding this disease, such as suffering from hypertension, diabetes, tobacco use, chronic obstructive pulmonary disease, heart disease, immunosuppression, chronic kidney disease, overweight or obesity.
80 and it is interpreted that the higher the score, the greater the self-care activities during the COVID-19 confinement. (16) e statistical analysis used the SPSS program version 25, which applied descriptive statistics by using means, standard deviation, frequencies and percentages. Correlations were explored among continuous variables from Spearman's statistic, with prior compliance of normality requirements. To test the mediation model based on regression, the Macro Process was used for the SPSS statistical program  12  to examine the direct and indirect effects of the COVID-19 risk factors on self-care mediated by concern and fear (Figure  1  for the model). A multiple mediation analysis was performed with two mediating variables forming a causal chain. The PROCESS program is a macro (computational) tool that simplifies implementation of mediation, moderation, and analysis of conditional processes using manifest variables.
Study design This was a post-hoc study, analyzing data collected previously by the AFHEM study, a French, prospective, observational, cross-sectional study conducted between September 16, 2013 and October 25, 2013  [10]. French hematological units of university hospital and cancer medical centers were invited to participate. The study was conducted in accordance with the Declaration of Helsinki and with Good Epidemiological Practices. Approvals from national review boards (Comité Consultatif sur le Traitement de l'Information en matière de Recherche dans le domaine de la Santé and Commission Nationale de l'Informatique et des Libertés) were obtained. Patients hospitalized in participating units were required to provide written informed consent prior to inclusion in the study. The 2008 EORTC/MSG criteria were used to define IFDs  [13].
In this game, children learn to recognise animal sounds, discriminate sounds and understand simple orders. Particularly, eye tracking was the mechanism to interact with the game, in which the youngest children needed additional help. However, after the experiment, the authors concluded that neither eye tracking nor VR headset led to difficulties for individuals in the sample, which turned them into proper devices for this kind of training. Another proposal for hearing impairment was from  Bouzid et al. (2016) , who proposed the computer game MemoSign to teach sign language. This game is based on the Memory Match Game, which includes a 3D human character who reproduces signs to facilitate the learning process for users. In this experiment, nine deaf users reported good experiences towards the game and found it useful.
Search string: (game-based learning) AND (special education). Game-based learning substring: game-based learning OR educational games OR serious games OR educational gamification OR gameful learning OR gamified learning. Special education substring: special education OR learners with special needs OR students with special needs OR learners with disabilities OR students with disabilities. The literature search was undertaken using Taylor & Francis Online, IEEE Xplore Digital Library, ScienceDirect, and Web of Science. After searching the relevant databases, two authors analysed the retrieved papers by title, abstract and if necessary, by full text based on a predefined inclusion and exclusion criteria defined in Table  1. Because of the novelty of the topic and the aim to provide comprehensive insights into game-based learning for learners with disabilities, conference papers were considered.
Third, snowball sampling can be used to tap more users by "asking participants to pass along recruitment information to other potential participants"  (Ghanouni et al. , 2020). Lastly, working with local schools may also increase sample size, but consideration and caution must be given to learners' prior knowledge and learning environments. In this context,  Valentini et al. (2017)  and  Ghanouni et al. (2020)  mentioned that universities should collaborate with associations to enhance accessible learning. (Buzzi et al. , 2019) , and (e) unspecified  (García-Redondo et al. , 2019). Figure  6  shows that half of the games were played on a PC or laptop using Windows (e. g. ,  Bendak, 2018) , Linux (e. g. ,  Groenewegen et al. , 2008)  or MacOS (e. g. ,  Pontes et al. , 2020). About 32% of the studies used mobile game-based learning, where 19% were on Android (19%) while 13% were on iOS (e.
Recommendations It is encouraged to use cross-platform design frameworks when developing game-based learning so that they can be deployed in devices with a wide range of operating systems, including iOS, Android, Linux and Windows. Additionally, to minimise technical problems, studies must select the appropriate experimental environment and context, such as games that involve slow narration where time lag is not significant. In this context, a usability experiment should be conducted in advance to test the application of technology in a given game-based learning application. Furthermore, as shown in Figure  7 , not too many game-based learning applications were multiplayer. Therefore, to promote social interaction and collaboration within learners with disabilities, more multiplayer game-based learning scenarios should be developed.
" It should be noted that the current study, while providing some crucial insights into improving learning experiences for learners with disabilities, has several limitations. For instance, the findings were based on the reviewed studies, which depend on the search keywords and electronic databases during the review process. However, despite these limitations, this study has provided a solid basis for understanding the design and effects of game-based learning for learners with disabilities. Future research directions could focus on developing game-based learning environments for learners who have the less investigated disabilities according to the findings of the current systematic review, such as specific language impairment. This could help to investigate how game-based learning impacts those learners, as well as the associated advantages and challenges.
a Phylogenetic tree of selected evolutionarily divergent actins based on amino acid sequences. Leishmania major parasite actin (LmActin) and α-skeletal muscle rabbit actin (Oryctolagus cuniculus, RbActin) used in this study are highlighted in bold. See the Source Data file for the sequence accession codes from Uniprot. b Pairwise comparison of the sequence identity between selected actins. c Methods applied to assemble and visualize LmActin filaments in microfluidics-coupled TIRF microscopy experiments. BE barbed end, PE pointed end. d Examples of observed actin filaments assembled using the methods described in panel c. e Typical "segmented" filaments assembled by alternating between a solution of Alexa-labeled RbActin (green) and a solution containing equimolar concentrations of unlabeled Lm-G-actin and LmProfilin.
Methods Phylogenetic tree and sequence alignments. The phylogenetic tree was generated in Geneious Prime (Build 2020-01-14). Alignment was based on the blosum45 score matrix and genetic distance model from Jukes-Cantor. Protein sequences were obtained from Uniprot, and the accession codes are provided in the Source Data file. To compare sequence identity and similarity between rabbit and Leishmania actins, sequences were pairwise aligned in Geneious Prime (Build 2020-01-14) with the "Clustal Omega" function using blosum45 score matrix with a threshold 2. Cloning. We synthesized a codon-optimized actin gene (Thermo Scientific) of Leishmania major (LmActin) for insect cell expression based on reported Uniprot sequence Q9U1E8, corresponding to TriTrypDB:LmjF. 04. 1230 entry in Tri-TrypDB. Another entry, P45520, reported in 1995 is 100% similar and 99% identical (disagreements Q9U1E8  93  EL  94  , P45520 93 DV  94  ).
The gene fragments were synthesized at TWIST Biosciences (San Francisco, USA), and then PCR-amplified and the overlapping regions of varying lengths were introduced on both ends of the fragments for further assembly reactions. The vectors were also PCR-linearized. All PCR reactions were carried out with KAPA HiFi HotStart ReadyMix (Roche, #7958927001), following the standard manufacturer protocol. Linear vectors were assembled with linear synthetic fragments with overlaps using NEBuilder HiFi DNA Assembly Master Mix (NEB, #E2621) following standard manufacture protocol. All final constructs were confirmed by Sanger-sequencing, and the primers and database references used to generate the constructs are described in Supplementary Table  3. Generation of baculovirus strain. pFastBac-1-LmActin vector (Thermo Scientific) was transformed to MAX Efficiency DH10Bac (Thermo Scientific) to recombinantly generate the bMON14272 shuttle vector for insect cell transfection.
-Polymerization/depolymerization with twinfilin: we compared the length of segments assembled for n minutes with actin-profilin alone, with or without extra m min of actin-profilin and twinfilin. The polymerization rate with twinfilin was calculated as the difference in length, divided by the duration m (Fig. 7a ). In all cases, the elongation rate was normalized from μm/s to subunits/s by dividing by the effective monomer length of 2. 7 nm. Individual measurements were finally averaged and plotted with the Python package Numpy and Panda. Barbed end depolymerization and Pi-release. The depolymerization rate of RbActin and LmActin was measured by exposing filaments to F-buffer only. To measure the depolymerization rate of ADP-Pi F-actin, F-buffer was modified by replacing KCl with 40 mM K 2 HPO 4 and 10 mM KH 2 PO 4.
This depolymerization rate vs time v(t) was then fitted on Python (curve_fit function from Scipy package) with the following function 87 : 1 vðtÞ ¼ 1 v ADP þ e ÀtÃk off 1 v ADPÁPi À 1 v ADP ð1Þ where v ADP and v ADP•Pi are the depolymerization rates of purely ADP and ADP•Pi actin filaments, and k off is the Pi-release rate. These three constants are always left as free parameters. Supplementary Fig. 2b, c  show the fitted parameter for two typical movies, with LmActin and RbActin, labeled with ATP-ATTO or Alexa568, respectively. Pointed end depolymerization rate. The microfluidic chamber was passivated with 1% biotinylated PLL-PEG or BSA following the previous method. The surface was then exposed to 5 μg/mL neutravidin for 5 min, and 10 nM biotin-gelsolin in F-buffer supplemented with 0. 4 mM CaCl 2 for ~2 min.
We then used the Kaplan-Meier estimator to calculate the fraction of severed actin segments (Python packages Numpy and Lifelines). Likewise, we used the "exponential" Greenwood formula to calculate the 95% confidence interval (shown as shaded surfaces)  88. The fraction curve was fitted (Python function curve_fit, in scipy package) with a single exponential: F t ð Þ ¼ 1 À e Àk sev ÃLÃt ð2Þ where L is the mean segment length and k sev is the global severing rate (unit: /s/μm, Figs. 5b, 6e and Supplementary Fig. 5 ). Likewise, the lower and upper values of the 95% confidence interval were fitted to estimate error on the fit (error bars, Figs. 5b, 6e and Supplementary Fig. 5 ). Cryo-EM sample preparation. For preparing LmActin for plunge-freezing, the ADP-Pi sample was polymerized in PBS supplemented with 0.
For the actincofilin complex, 3 μl of 12 μM Leishmania actin was applied on the grid and left to settle for 15 s at room temperature. This grid was then mounted to the Vitrobot and 1 μl of the sample was withdrawn. On top of the remaining 2 μl of Leishmania actin, 1 μl of Leishmania cofilin at 77 μM concentration was added and plungefreezed immediately. The grids were stored in liquid nitrogen. Cryo-EM data collection. Data for ADP-Pi actin filament was collected on a Talos Arctica (Thermo Scientific) operated at 200 kV with a C2 aperture of 50 μm and an objective aperture of 100 μm. Movies were recorded at a nominal magnification of 150,000x corresponding to a calibrated pixel size of 0. 97 Å yielding a total dose of ~45 e/Å² fractionated into 45 frames. The target defocus for acquisition ranged from -0.
8 to -3 μm. The data were collected using the EPU software (Thermo Scientific) with the Falcon 3 detector (Thermo Scientific) in counting mode in two separate sessions yielding 1998 movies in total. Data for ADP-actin filament (with or without cofilin-bound) was collected on a Titan Krios G2 (FEI Thermo Scientific) equipped with a BioQuantum/K3 energy filter (Gatan) operated at 300 kV in zero-loss mode (slit width 20 eV) with a C2 aperture of 50 μm and an objective aperture of 100 μm. Movies were recorded at a nominal magnification of 105,000x corresponding to a calibrated pixel size of 0. 86 Å and a total dose of ~55 e/Å² fractionated into 50 frames. The target defocus for acquisition ranged from -0. 75 to -2. 5 μm. The data were collected using the EPU software (Thermo Scientific) with the detector in counted super-resolution mode using a binning factor of 2.
The total amount of movies collected was 8138. Image processing. Cryo-EM data were processed in Relion 3. 1 software  89. Movie frames were first aligned with MotionCor2 90 or Relion's own implementation of motion correction and CTF estimated by CTFFIND 4. 1  91. Filaments were picked manually in Relion for ADP-Pi, ADP-actin, and cofilin-decorated filament reconstructions. For the ADP-Pi sample, manually picked segments were used as templates to automatically pick the final particles from two data sets collected on different days. ADP-actin filament was reconstructed from the same sample as cofilin-decorated actin filaments. This was possible since we observed that only ~5-10% of the images contained filaments that were decorated with cofilin at specific grid locations. This was likely due to the addition of cofilin to actin filaments without mixing just before plunge-freezing.
Local resolution of the cryo-EM reconstructions was estimated with Relion. Finally, we applied helical symmetry on the map in real space using the highest resolution region (z-length of 50%) by using the relion. helix. toolbox. This map was input to AutoSharpen in Phenix  92 (v. 1. 19. 2)  to produce the primary map for model building. Model building. To build ADP-state Leishmania actin filament, the asymmetric unit from chicken muscle actin (PDB ID: 6DJO) was manually docked into the cryo-EM density in Chimera  93  (v. 1. 14 build 42094). To transform actin monomer to L. major actin sequence, the sequence was automatically assigned in Phenix with the "Map-tomodel" function. After mutation to L. major sequence, the model was manually curated and built per amino acid in Coot  94  (v. 0. 8. 9.
1) and refined in Phenix (v. 1. 19. 2). In all cases, a helical assembly consisting of five actin monomers was built in Chimera. ADP-Pi state was built based on the ADP-state model and flexibly fitted to the cryo-EM map in Namdinator molecular dynamics webserver (https:// namdinator. au. dk)  95. The initial model for LmCofilin was obtained from Leishmania donovani cofilin (PDB ID: 2kvk)  96  , which was manually mutated to L. major cofilin and then docked to the cryo-EM map in Chimera. Then a monomer from LmADPactin reconstruction was docked to the cryo-EM density and relaxed to LmCofilinbound conformation in Namdinator. After these steps, the models were manually curated in Coot. Ramachandran and side-chain rotamer outliers were fixed by using the iSolde  97  (v. 1. 1. 0) package in ChimeraX (v.
Acknowledgements We thank  Benita Löflund  and  Pasi Laurinmäki  ( University of Helsinki ) for technical assistance from the  HiLIFE Cryo-EM unit at the University of Helsinki , a member of  Instruct-ERIC Centre Finland, FINStruct, Biocenter Finland , and  Finnish Cryo-EM bag  ( CEM00362 ). We also thank  Dustin Morado  and  Cryo-EM Swedish National Facility  funded by the  Knut  and  Alice Wallenberg ,  Family Erling Persson  and  Kempe Foundations, SciLifeLab ,  Stockholm University and Umeå University. Andrea Vizcaino-Castillo  is acknowledged for critical reading of the manuscript. The model in Fig. 7c was created with BioRender. com. This work was supported by  Jane and Aatos Erkko Foundation  ( 4708679 ) and the  Academy of Finland  (grant  302161 ) to P. L. ,  ERC  (grand StG-679116) to A.
Data availability The cryo-EM reconstructions generated in this study of the L. major ADP-actin filament, ADP-Pi-actin filament, and ADP-actin filament-cofilin complex have been deposited in the Electron Microscopy Data Bank (EMDB) under ID accession codes EMD-13864, EMD-13863, and EMD-13865, respectively. The corresponding atomic models generated in this study have been deposited in the Protein Data Bank (PDB) under accession codes 7Q8C, 7Q8B, and 7Q8S, respectively. The coordinates corresponding to the muscle actin filament structures, cofilin-decorated actin filament structure, yeast cofilin, and malaria actin filament structure shown in this article are available from PDB under accession codes 6DJO, 6DJN, 5YU8, 1QPV, and 6TU4, respectively. The sequence data used in this study was obtained from Uniprot and the accession codes are described in the Source Data file.
Cells were plated and cultured to confluency before a 10 µl pipet tip was used to create a cross-shaped wound across the monolayer. Samples were imaged on a widefield microscope (IX-81, Olympus) equipped with an LED lamp (Excelitas Technologies), an Orca 16-bit chargecoupled device camera (Hamamatsu), an automated z-drift compensation IX3-ZDC (Olympus), an automated stage (Prior Scientific), an environmental chamber (Live Cell Instrument) and using a 10X objective (MPlanFL N 10X, 0. 3 NA, Olympus). Cell motility was recorded at 10 min intervals over 48 h. Manual cell tracking was performed using the TrackMate plugin through Fiji  53. The track number, the spot coordinates and the frame number were exported. Computation of the velocity and persistence were done using a custom made Matlab code.
Computation of the distance index was done using a custom made Matlab code (available upon request). Mean-squared displacement analysis of cells. Coordinates of individual cell trajectories were obtained by particle tracking with the origin of each spheroid at (0,0), and were transformed from the Cartesian {x,y} to {r,ϕ} polar coordinate system. Mean squared displacements (MSDs) were then calculated in radial and angular directions, averaged over different spheroids and experimental repeats for different conditions. The MSD data were then fit to a power law, in both directions, namely r À r 0 À Á 2 D E ¼ Γ r t α r ð1Þ and ϕ À ϕ 0 À Á 2 D E ¼ Γ ϕ t α ϕ ð2Þ where ðr 0 ; ϕ 0 Þ correspond to the origin of each trajectory in the polar coordinate system, Γ r;ϕ correspond to the amplitudes of the power laws, and α r;ϕ are the exponents, in radial and angular directions, respectively.
For lung clonogenic assay (https://doi. org/10. 5281/zenodo. 6639302), lungs were minced, digested in a collagenase type IV/elastase cocktail (Worthington Biochemical) and filtered through a 70 μm mesh. Then, the cell suspension from each lung was split into two tissue culture plates. One plate was incubated with a combination of 6-thioguanine (Cayman Chemicals) and puromycin, for growth of Tks5-CTL and Tks5-KD cells. The other plate was incubated with a combination of 6-thioguanine, puromycin and geneticin for growth of 4T1 Tks5-KD cells only, or with a combination of 0. 5 µg/ml puromycin and 500 µg/ml geneticin (Invitrogen) for growth of MDA-MB-231 D2-KD. After 14 days at 37 °C and 5% CO 2 , the colonies were fixed in methanol, stained using 0. 03% (w/v) methylene blue (Sigma-Aldrich) and counted (4T1 and 67NR), or counted using fluorescent labeling (D2-KD).
RStudio software was used to perform all statistical analyses. The distribution of each data set was analyzed, and the Shapiro-Wilk test was performed to test for normality. For normally distributed data sets, an F test was performed to compare the variances of two data sets. Based on the results from the F test, a Welch two-sample t-test or a two-sample t-test was done to compare the means of the two data sets. For non-normally distributed data sets a Wilcoxon rank sum test was performed to compare the two data sets. Unless stated otherwise, all tests were performed using unpaired and two-sided criteria. All data are represented as line graphs or boxplots with median (line), 25th/75th percentiles (boxes) and maximum/minimum (whiskers). Statistical significance was defined as *p < 0. 05, **p < 0.
Acknowledgements We would like to thank the flow cytometry core at  Lewis Katz School of Medicine  for assistance with cell sorting, and the members of  Temple Bioengineering  and  Fox Chase Cancer Center Biology  for valuable discussions. Funding was provided by  NIH   R00 CA172360 ,  R01 CA230777  (B. G. ) and  R01 GM121679 (E. T. ) ;  American Cancer Society   Research Scholar Grant   134415-RSG-20-034-01-CSM (B. G. )  and  Conquer   Cancer Now/ Young Investigator Award  (B. G. ).