dataesr/scientific-paragraphs-categorization huggingface dataset:
Cell Cycle Arrest at G2M Phase There was a significant increase (P < 0. 05) in the population of PC3 cells at the G2M phase as compared to the untreated cells when treated with the IC50 of both FD1c and FD2c extracts (Figure  8A ). The same trend was observed when the LNCaP cells were treated with the IC50 of both FD1c and FD2c (Figure  8B ). In addition, treatment with the IC50 of both plant extracts also cause a significant (P < 0. 05) decrease in the population of both LNCaP and PC3 cells at G0/G1 phase while the percentages of cell population at the S phase remains almost the same for both cell lines. The genes expressions were determined as described in RT-qPCR conditions and analysis where Control = 1. Data are mean ± SD; n = 4 experiments. * P < 0. 05, * * * P < 0. 001.
Bioguided Isolation of the Active Fraction FD1c and FD2c were chosen for further fractionation based on the IC50 values. 140 fractions were collected for each plant extracts and each fractions were examined by a TLC. Based on the TLC profiles of FD1c and FD2c (Data presented as Supplementary Materials) the eluates were then pooled into 13 major fractions (FD1c: fractions 20-23, fractions  [24] [25] [26] [27] [28] [29] [30] FD2c: fraction 16,. These fractions were subjected to another cytotoxicity study with PC3 cell lines to determine their activity. Three fractions were observed to have better efficacy than their respective plant extracts as their IC50 values for each fractions were significantly lower than their respective plant extracts before further fractionation process being done (P < 0.
Chromatographic and Mass Spectrometry Analysis MS1 dereplication is one of the first approaches in structural identification that is a common practice before MS/MS dereplication and isolation work  (Alali and Tawaha, 2009). It is established by generating molecular formula from the accurate mass data and comparing it with a bibliographical database such as DNP, Universal Natural Products Database (UNPD), and MarinLit. In this study, the custom database was created from DNP by using three taxonomy filters; species, family, and type of organism (Ficus 272 hits; Moraceae: 1,607 hits; Dicot: 107,953 hits). In addition, the type of compound indicated by the UV spectrum data was further used to reduce the number of proposed identification and improve the accuracy of the proposed identification. As an initial attempt to investigate the composition of the active extracts, focus was given only to components that gave a reasonable ELSD signal (quantitative estimate).
, 2002) , and in malignant glioma cells in vivo  (Fulda et al. , 2002). Therefore, these findings prompted scientists to   The genes expressions were determined as described in RT-qPCR conditions and analysis where Control = 1. Data are mean ± SD; n = 4 experiments. * P < 0. 05, * * * P < 0. 001. develop or find small molecules that could mimic the functions of Smac/DIABLO as therapeutic agents to induce cancer cells death or increase the apoptotic effects of the chemotherapeutic agents. This study shows that both active plant extracts (FD1c and FD2c) were able to significantly increase the expression of Smac/DIABLO gene in PC3 cells, thus contributing -in part-in activating the intrinsic pathway of apoptosis. However, upon further fractionation of the active extracts, the active fraction of FD1c (FD1c F43-51) did not show any significant effect on the expression of Smac/DIABLO.
ACKNOWLEDGMENTS Dr. Andre Mazzari  ( University College London, United Kingdom ) for training and advice on the use of RT-qPCR. Mr. Pedro Resende  (Ph. D. student) for assistance with IT and technical support. Dr. Awo Kwapong , and  Mrs. Gugu Sibandze , for their support and contribution for NMR data analysis. RA and MS for getting the permission to work with the plant materials and for the assistance in getting the funding. The authors are thankful to the  Ministry of Agriculture (MoA) of Malaysia  for granting permission to work with Malaysian herbal plant.
The difference was based on several commonly used amino acid scoring matrices and indices describing various physicochemical and biochemical properties of amino acids: conformational parameter for alpha helix and beta-sheet  67  , hydropathy  65  , polarity 66 , Grantham's chemical distance 68 , Miyata's amino acid pair distance  69  and Mohana's EMPAR matrix  70. In the case of indices, we calculated an absolute difference between the corresponding index values for given amino acids which are coded by the codon c and d. The matrices and indices were downloaded from AAindex database  108. In the case when a sense codon was replaced into stop codon, we assumed their costs as the largest value of all amino acid substitution costs in the given measure. To investigate simultaneously an optimization degree of mutational matrices according to the costs of change both in hydropathy and polarity, we applied a multiobjective optimization approach.
In particular, we considered four scenarios of optimizing these costs for mutational matrices: 1. Min, in which both costs were minimized; 2. MaxMin, in which the cost of hydrophobicity change was maximized, whereas the polarity cost was minimized; 3. MinMax, in which the cost of hydrophobicity was minimized, whereas the polarity cost was maximized; 4. Max, in which both costs were maximized. These criteria contain all possibilities in the optimization of two objectives. The mutational effect exerted by empirical and optimized artificial matrices was investigated based on protein-coding sequences from bacterial genomes, for which the empirical mutational pressures were derived. The sequences and their annotations were downloaded from GenBank database 109 -Table  S1. Since differently replicated DNA strands in bacterial chromosomes are subjected to distinct mutational pressures, we considered the derived pressures and protein-coding sequences from the leading and lagging DNA strands separately.
The location of these genes according to the DNA strands was deduced based on DNA asymmetry calculated in the Oriloc software  110. Algorithm for finding optimized solutions. Evolutionary Multiobjective Optimization (EMO) approach is used in many optimization problems due to its simplicity and flexibility. Here, we used a modified version of the Strength Pareto Evolutionary Algorithm (SPEA2)  111  , which is an efficient technique used in many multiobjective optimization problems. Moreover, SPEA2 turned out to be very effective in comparison to others and has become one of the most important reference point in various recent investigations and applications, see e. g. Zitzler, et al. 112. It produces a set of optimal solutions called Pareto set, which consists of non-dominated solutions such that none of their objective functions can be improved in value without degrading the other objective value.
The diagnostic criteria of MGD were as follows: (1) symptoms of ocular discomfort: itching or photophobia with limitations of activities; (2) clinical signs: at least 1 lid margin feature (plugging, vascularity), meibum quality: grade: ≥4, expressibility: ≥1. Potential subjects were excluded from the study if they had undergone previous corneal or ocular surgery, had any ocular pathology other than DED and DI, had systemic diseases known to affect the eye. Participants were instructed to remove soft contact lenses at least 2 weeks and rigid contact lenses at least 1 month before the examination. Data were collected from August 2015 to May 2016 in Beijing Tongren Hospital, Beijing, China. All participants signed an informed consent form in accordance with the tenets of the Declaration of Helsinki and this study was approved by the institutional review board of Beijing Tongren Hospital, Beijing, China.
Image stacks were acquired using an Axiovert 200 M microscope equipped with a Plan-Apochromat 100/1. 4 objective (Carl Zeiss) and a cooled CCD camera, ORCAII-ERG2 (Hamamatsu). Deconvolution was done according to the constrained iterative algorithm in the AxioVision 3. 1 software (Carl Zeiss).
Electron microscopy Root tips were fixed in 4% glutaraldehyde in 0. 1 M Sörensen's phosphate buffer, post-fixed in 1% OsO 4 , dehydrated in ethanol and propylene oxide and embedded in Epon 812 (Fluka). The ultra-thin sections were stained with uranyl acetate and lead citrate and examined using a JEM-1400 electron microscope (Jeol). For morphometry and image analysis, ImageJ2 software was used (9-18 cells for each mitotic stage were analyzed). For the final presentation, the brightness and contrast of the images were corrected using Photoshop software (Adobe).
15. 55 14 1. 11 + Additional file 1: Figure S1 h Nigella damascena L. 21. 10 12 1. 76 + Fig. 1b Nigella sativa L. 21. 25 12 1. 77 + [18] Lathyrus latifolius L. 21. 75 14 1. 55 + Additional file 1: Figure S1i Allium fistulosum L. 25. 05 16 1. 57 + [18] Vicia faba L. 26. 65 12 2. 22 + [29, 30] Allium sativum L. 32. 45 16 2. 03 + [21] Allium cepa L. 33. 50 16 2. 09 + [21, 30] Tradescantia paludosa 41. 25 12 3. 44 + [17] E. S. Anderson & Woodson Allium porrum L. 58. 50 32 1. 83 + Additional file 1: Figure S1j Tulipa turkestanica 87. 00 48 1. 80 + [18] (Regel) Regel Haemanthus katharinae 117. 70 18 6. 5 + [18, 31] Baker [1] ata from Plant DNA C-values Database[1].
InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0. 55 to 0. 95 with 0. 05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0. 6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE.
Generation of Artificial Sequences Using the above described library, InSiDDe generates artificial amino acid sequences with specified lengths (l) and Dt through the following steps (   8 ) repetition of steps 4 to 7 j times (with j = (l r /10) -1); and (  9 ) deletion of the extra residues in order to obtain the desired sequence length if l is not a multiple of 10. In the latter case, the final sequence of length l r provided by the program is shortened to match the desired length l by removing the appropriate number of residues from the extremity displaying the most dissimilar disorder score with respect to the chosen Dt. sequence length if l is not a multiple of 10. In the latter case, the final sequence of length lr provided by the program is shortened to match the desired length l by removing the appropriate number of residues from the extremity displaying the most dissimilar disorder score with respect to the chosen Dt.
Comparison of Figure  6A ,B definitely indicates that the second strategy generated much more acceptable sequences (≈96%) than the first (≈64%). One might question why further development of the program is necessary if the mere repetition of a bb is enough to create an artificial protein with the required |Dt -o| and ΔDo. A repetitive protein sequence would also be repetitive The rationale for generating an initial sequence made of a repetition of the same bb, rather than of different bbs from the same Dt family, lies in the requirement to start with a sequence with the smallest |Dt -Do| and ∆Do values. In a repeated sequence, the interaction between a given amino-acid and the others is constant through the entire length. As IUPred score is based on the interactions between a given residue and the adjacent ones in a defined window, a sequence based on the repetition of the same bb is the easiest way to produce an initial sequence satisfying these criteria.
Example of Use Although the artificial IDP sequences generated by InSiDDe can be used for in silico applications only, they can also be used for recombinant expression in a heterologous host in view of various ensuing applications. In order to assess the latter possibility, an artificial sequence of 100 residues with Do = 0. 6 (100-0. 6) was generated using InSiDDe and expressed in E. coli. Its sequence and IUPred disorder score are shown in Figure  9A. Note that a W was added so that the amount of protein could be measured by UV absorption at 280 nm. A BLAST search in the non-redundant protein sequence database retrieved no sequence. To functionally test 100-0. 6, we used the measles N TAIL -XD interacting system already used in our previous work  [11]. To that end, 100-0. 6 was appended to the N-terminal end of N TAIL MoRE to yield a sequence referred to as 100-0.
This effect is not ascribable to possible differences in the expression levels of NGFP-100-0. 6-MoRE and NGFP-MoRE fusion proteins (Figure  9D ). The agreement of the present results with those previously obtained using native and artificial truncated variants of N TAIL  [11] , together with the SEC and far-UV CD data herein reported, advocate for the ability of InSiDDe to generate artificial sequences whose behavior is in line with expectations. that the presence of a fuzzy appendage made of an artificial sequence of o = 0. 6 generated by InSiDDe dampens the interaction of the MoRE with XD. This effect is not ascribable to possible differences in the expression levels of NGFP-100-0. 6-MoRE and NGFP-MoRE fusion proteins (Figure  9D ). The agreement of the present results with those previously obtained using native and artificial truncated variants of NTAIL  [11] , together with the SEC and far-UV CD data herein reported, advocate for the ability of InSiDDe to generate artificial sequences whose behavior is in line with expectations.
Availability and Requirements of InSiDDE InSiDDE home page: http://insidde. afmb. univ-mrs. fr/. Operating systems: Platform independent. Programming language: Python3. Other requirements: Java 1. 5. 0 or higher, a web connection and a web browser. License: This program makes use of IUPred predictions incoming from a public web server that is run in local mode. It is provided freely and "as it is" without a warranty of any kind, either expressed or implied. Any restrictions to use by non-academics: None.
Far-UV Circular Dichroism (CD) Measurement Far-UV CD spectra were measured using a Jasco 810 dichrograph, flushed with N 2 and equipped with a Peltier thermoregulation system. One-mm thick quartz cuvettes were used. Protein concentration was 0. 075 mg/mL. Far-UV CD spectra were measured between 192 and 260 nm, in 10 mM sodium phosphate pH 8 at 20 • C. The scanning speed was 20 nm/min, with data pitch of 0. 2 nm. The buffer spectrum was subtracted from protein spectra, and the result was smoothed using the "means-movement" smoothing procedure implemented in the Spectra Manager package. Mean molar ellipticity values per residue (MRE) were calculated as [MRE] = 3300m∆A lcn ( 4 ) where l is the path length in cm, n is the number of residues, m is the molecular mass in Daltons, and c is the concentration of the protein in mg/mL.
Acknowledgments: This work was carried out with the partial support from the following agencies: European program H2020 under the  EVAg Research Infrastructure  (grant agreement  653316 ) (CB),  CNRS  (CB, SL),  Italian Ministero dell'Istruzione dell'Università e della Ricerca (Progetto di Interesse "Invecchiamento " to S. G. ) and  Sapienza University of Rome  ( C26A155S48  and  B52F16003410005  to S. G). It was also supported by the  CNRS. We wish to thank  Zsuzsanna Dosztanyi  ( Eötvös Loránd University, Budapest, Hungary ) for granting us access to IUPred in local mode,  Helena Berglund  ( Protein Science Facility, Karolinska Institutet, Sweden ) for kindly providing us with the pTH24 derivative encoding the TEV protease, and  Arie Geerlof  ( EMBL ) for providing the pETG-20A plasmid. We also thank  Vincent Bayle  (AFMB lab) for technical help in deploying InSiDDe on the AFMB server.
DESIGN METHOD Because of healthcare and child safety and privacy regulations, visually impaired pupils are a difficult public to have access to. Literature review also shows that one of the most important factors in the lack of adoption of assistive technologies and use of ICT with disabled pupil is the feeling of lack of competencies of their teachers. Therefore, we decided to focus on teachers' insights first, in order to better understand what are their needs regarding accessibility of educational games. We also have access to previous data from interviews, conducted by our collaborators, of 19 teachers. Four of the interviewed teachers answered being working in lambda schools. Two others reported being working with hospitalized children. And the other recruited answered teachers being working either in inclusive or specialized classrooms and had pupils in their class who were either sight impaired of hearing impaired or had cognitive disabilities.
While the interviews did not focus on accessibility issues, some teachers still expressed some of the difficulties they encounter while working with inclusive classes. Some of the concerns expressed include: the need for an adaptation of the study material to each student's specific situation, the lack of available accessible digital resources "There are plenty [educative video games] I don't use  […]  they are not made for sight impaired pupils", the cost in time of the preparation of ICT. This data helped us design our own user study, and we conducted three focus groups on accessibility on interactive tabletops in serious games. These focus groups and their results are described in the following subsections.
• Back to normal state: when the student removes the frame, the magnified picture goes back to its original aspect with its normal orientation. All the modifications of the magnifying frame settings the pupil made by manipulating the cursor will be saved by the cursor position and reused. The Interactive Tabletop we use for our work is a Multitaction optical table. It uses infrared sensitive video-cameras to perform touch and object detection. Object recognition is achieved through the use of squared black and white tags pasted on the bottom of the objects (see Figure  4 ) which are in direct contact with the tabletop's surface. The position of such objects and fingers is then transmitted to the tabletop's software applications thanks to a communication protocol named TUIO  (Kaltenbrunner, 2009).
Software To stick with the idea of providing such an accessibility tool for different kinds of educative games, we used Unity3D (Unity Technologies, 2017) to develop our demonstration. Unity is a broadly used game engine which allows many kind of realisations such as interactive demonstrations, commercial video games or educative games. We developed a picture exploration application featuring the frame and coded the frame interactions to be as close as possible as to the scenario proposed during the creativity sessions. Using the TUIO data transmitted by the interactive tabletop internal software, we can track the positions of the two tags which are placed under the frame and compute the size, position and orientation of a virtual window which might fit inside the frame. Thanks to the frame using two tags and not just one, we are also able to provide a more robust tracking of its position.
This is likely to have fundamental consequences for how Ca 2+signalling modules are composed, and especially how these are integrated with other cellular signalling systems. In this Review, our objectives are to use insights from genomic datasets to highlight differences between the animal and plant Ca 2+ -signalling toolkits. Rapid 'action-potential'-based electrical signalling is a phenomenon central to the evolution and success of animals, and yet this was largely lost during plant evolution. We will describe how electrical, Ca 2+ -based signalling evolved separately in plants. Finally, we will take the first steps towards identifying the nature of the selective pressures, operating over the evolutionary timescale, which have helped to dictate the complement of proteins present in the plant Ca 2+ toolkit.
ACKNOWLEDGEMENTS AMH is grateful to the  Leverhulme Trust  and the  Royal Society  for the award of an  Advanced Fellowship  and the  BBSRC  for grant support ( BB/N001168/1  and  BB/J002364/1 ). CB is grateful to the  BBSRC  ( BB/M02508X/1 ) and the  European Research Council  (Advanced Grant  670390 ) for grant support. JK is grateful for support by the  Deutsche Forschungsgemeinschaft  ( FOR964  and  KU 931/14 ) and by a  Distinguished Scientist Fellowship Program ,  King Saud University, Saudi Arabia.
Statistical analysis Data from the in vitro digestion were analyzed using SPSS version 17. 0. For all tests, the significance level was set at P < 0. 05 (2 tailed). All data are expressed as means ± SEM. Repeatedmeasures ANOVA was used to test for differences in lipid release after mastication, gastric and duodenal digestion with muffin type as a 'within-sample' factor. Differences in lipid release between the AF and AP muffin samples were analyzed by Student's paired t-test.
Patient Population University of Kansas (KU) cohort-Patients with Stage I (T≥1 cm), II and III TNBC presenting at an academic center and five community practices within the Kansas City metropolitan area were approached for participation in an IRB approved prospective registry protocol (P. R. O. G. E. C. T. NCT02302742). Eligible female patients had biopsy proven invasive breast cancer not previously treated with taxanes, anthracyclines or carboplatin for any malignancy. Triple negativity was defined as estrogen receptor (ER) and progesterone receptor (PgR) immunohistochemical (IHC) nuclear staining of less than 10% and HER2 IHC staining 0 to 1+ or fluorescence in situ hybridization (FISH) ratio<2. 0 if IHC 2+ or IHC not performed (ASCO/CAP Guideline recommendations for HER2 Testing in breast cancer)  (34).
From 2011 to 2015, 69 enrolled patients with stage I (T>1cm) II and III TNBC were treated with NAC regimen of carboplatin + docetaxel. MMJ-CAR-2014-01cohort-GOMHGUGM022011 is a prospective, multicenter, nonrandomized trial exploring the anti-tumor activity of neoadjuvant CbD (AEMPS code MMJ-CAR-2014-01, NCT01560663). Eligible patients included females with pathologically confirmed diagnosis of primary invasive breast cancer, stage II-III (T≥ 2cm) aged >18 years, and not previously treated with taxanes, anthracyclines or carboplatin for any malignancy. The patients were diagnosed at any of the participant academic institutions (see supplemental material for list of participating institutions) and were able to sign the IRB approved informed consent at each of the centers. Triple negativity was defined as ER and PgR nuclear staining of less than 1% by IHC, and HER2 IHC staining 0 to 1+ or FISH ratio < 2.
Germline BRCA1/2 Testing KU cohort-Germline testing for BRCA1/2 was done utilizing commercially available tests and laboratories. The majority of the patients (97%) had testing through Myriad Genetic Laboratories (comprehensive BRACAnalysis™ or myRisk™ Hereditary Cancer test), 3% had testing through other laboratories (BreastNext™, Ambry genetics), (OncoGeneDx™, GeneDx). Spanish cohort-Germline testing for BRCA1/2 was done at Sistemas Genómicos facilities using Targeted Next Generation by sequencing of 7 genes (BRCA1, BRCA2, PALB2, BARD1, RAD50, RAD51C, RAD51D) and MLPA by quantification of probes corresponding to BRCA1, BRCA2 genes using the MLPA kit according to the manufacturer's recommendations (MRC-Holland), fragment analysis by ABI 3730xl genetic analyzer and data normalization and interpretation of results using Coffalyser.