dataesr/scientific-paragraphs-categorization huggingface dataset:
Spheroid Angiogenesis Assay HUVECs in MV medium containing 0. 25% methylcellulose were dispensed as 20-mL drops to generate spheroids that were mixed with fibrinogen (2. 5 mg/mL)-aprotinin (4 U/mL, Sigma) mixture in the presence of thrombin (50 U/mL, Sigma) and spheroids cultured for 48 hr in MV medium with CM or IMDM added to a final concentration of 40%. At least 20 spheroids per condition were photographed using a Nikon ELWD 0. 3/OD75 light microscope with Nikon DS-Fi1 digital camera, and length of sprouts were analyzed using ImageJ software.
Endothelial Cell Proliferation and Viability Assays Endothelial cell proliferation was analyzed using CyQUANTNF Cell Proliferation Assay Kit (Life Technologies) following the manufacturer's instructions. In brief, HUVECs were cultured in MV medium at 37 C for 24 or 48 hr. Subsequently, samples were analyzed using a fluorometer (Thermo Scientific) at 485-nm excitation and 530-nm emission, and data analyzed using Ascent software version 2. 5. Cell viability of HUVECs cultured in CDC-CM for 24 hr and 48 hr was determined by a colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT; Sigma) assay. Absorbance was measured at 550 nm by MultiSkan (Thermo LabSystems).
Scratch-Wound Healing Assay HUVECs were plated on a 6-well-plate at a density of 5 3 10 5 cells and incubated in MV medium at 37 C for 24 hr. A scratch ''wound'' was made with a 200-mL Gilson pipette tip. Microscope images of the ''wound'' area were taken at 0, 24, and 48 hr and rate of ''wound'' closure was calculated from the mean of six assays. Images were taken using a Nikon ELWD 0. 3/OD75 light microscope and a Nikon DS-Fi1 digital camera, and analyzed using ImageJ software. In Vivo Matrigel Plug Assay GFR Matrigel (250 mL) was seeded with MLECs and 50 mL of CM and injected subcutaneously into flanks of adult C57BL/6 mice. Plugs were harvested after 14 days and cryosections were analyzed by immunostaining.
Tissue Processing and Staining Animals were humanely killed and tissue lightly fixed in paraformaldehyde (0. 2%, overnight), equilibrated in 30% sucrose, and embedded in OCT compound. Cryosections were stained with anti-CD31 (553370, BD Biosciences), anti-SM22a (ab14106, Abcam), anti-aSMA (C6198, Sigma), and anti-phospho-histone H3 (06570, Millipore), and detected with secondary antibodies conjugated to Alexa 488 or Alexa 568. Sections were mounted with prolong Gold, imaged using an Axioimager M2 microscope fitted with an Apotome (Zeiss), and analyzed using ImageJ software.
qPCR RNA was extracted from the left ventricle using a Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. cDNA was prepared using a Tetro cDNA synthesis kit (Bioline) and Taq polymerase (Applied Biosystems). Commercial Taqman probes for Eng (Mm00468252_m1), Bmp9 (Mm00807340_ m1), Bmp10 (Mm01183889_m1), Tgfbeta1 (Mm01178820_m1), Tgfbeta3 (Mm00436960_m1), Gapdh (Mm99999915_g1), and Hprt1 (Mm00446968_m1) were from Life Technologies and used for qPCR on a Quantstudio 6&7 Flex Real-Time PCR system. Data were analyzed using comparative Ct (DDCt) to determine relative gene expression.
Western Blotting CDCs were treated with BMP9 (2 ng/mL) or TGFb1 (5 ng/mL) for 30 min before preparing whole-cell protein lysates in SDS sample buffer. HUVECs were serum starved for 4 hr before addition of CM and protein lysates prepared. Proteins were separated on 10% polyacrylamide gels and transferred onto polyvinylidene fluoride membrane before blocking with 5% powdered milk/TBST (Trisbuffered saline + Tween 20) and incubated with primary antibody to detect either phospho-SMAD1/5/8 (9516, Cell Signaling), phospho-SMAD2 (3108, Cell Signaling), phospho-AKT Ser473 (4060, Cell Signaling), phospho-AKT Thr308 (13038, Cell Signaling), AKT (4691, Cell Signaling), phospho-SMAD3 (18801, Epitomics), a-tubulin (T6199, Sigma), or b-actin (A5316, Sigma). Membranes were incubated with secondary antibody, either anti-rabbit horseradish peroxidase (HRP) or anti-mouse HRP (Dako) in blocking solution before detection using SuperSignal Chemiluminescent Substrate, and densitometric analysis using ImageQuant TL v2005 software.
Statistical Analysis Results are presented as the mean of values ± SEM unless indicated otherwise. The number of independent experiments for each study is indicated in the figure legends. The statistical significance of differences between the mean of two groups was determined using Student's t test. When more than two experimental groups were analyzed, statistical significance of differences was first evaluated by one-way ANOVA. When multiple experimental groups were compared at different time points, data were analyzed by twoway ANOVA and post hoc t tests corrected for multiple comparisons using the Holm-Sı ´dak method. Data were analyzed using GraphPad Prism software and a probability (p) value of less than 0. 05 was considered statistically significant.
Characterisation of the Time Varying Phase Shift The Time Varying Phase Shift (TVPS -a glass optical flat, Thorlabs part no. WG11050-B) used in the experiment served the purpose of erasing phase information in the pump beam between the sources S 1 and S 2 , corroborating the independence condition. It was attached to a high resolution motorised rotation stage (Newport part no. URS100BCC) and a quantum random number generator (QRNG). The QRNG system used was the Australian National University QRNG system -a secure open source implementation  [13]. We accessed their live random number stream over the internet using a Matlab R interface. To characterise the TVPS, we constructed a Michelson-Morely interferometer and placed the TVPS into one arm of the interferometer. The TVPS was set to an initial testing angle of 30 • from normal, such that the slight rotations required to vary the global phase of source S 2 would cause minimal longitudinal disturbance to the beam pumping of S 2.
Since our APDs are not number resolving, we implemented pseudo-number-resolving-detectors using spatial multiplexing. Such a device, made of two APDs and a 50:50 beamsplitter, successfully detects two-photon pulses with 50% probability. We corrected for this inefficiency in post-processing, allowing us to implement the 13 BSM required to test the B 13 bilocal inequality. Furthermore, in all the inequalities tested we account for imbalances in detector efficiencies by swapping the outcomes of for inputs x, y, z for half of the trials, effectively averaging over any bias in the outcomes for each party. We note, we make the fair-sampling assumption in the data presented in this work.
Acknowledgements. -We thank  Alastair Abbott ,  Nicolas Brunner ,  Nicolas Gisin ,  Stefano Pironio  and  Denis Rosset  for helpful discussions. This research was conducted by the  Australian Research Council Centre of Excellence for Quantum Computation and Communication Technology  (Project number  CE110001027 ). DJS and CB acknowledge  EU Marie-Curie Fellowships   PIIF-GA-2013-629229  and PIIF-GA-2013-623456 respectively. CB acknowledges a  "Retour Post-Doctorants" grant  from the  French National Research Agency  ( ANR-13-PDOC-0026 ). The authors declare that they have no competing interests. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Material. Additional data related to this paper may be requested from the authors.
The Figure  2  below illustrates this methodology for the alodine material (both sides of the iris) : A more rigorous and detailed analysis of the iris problem was made in  [2]  where the geometry of the iris was transformed into the classical 2 infinite parallel plate geometry using conformal mapping assuming that the electric field in the iris was approximately quasi-static. In parallel, a software called SEMA/MULSIM based on the Monte-Carlo approach was developed to determine the Multipactor threshold inside RF components with waveguide sections. Comparisons were drawn on the same RF component. The figures 4 and figures 5 illustrates the number of electrons after T period versus the voltage U. For the figure  4 , the calculations were realized with the SEMA/MULSIM software. For the figure  5 , the calculations were realized with the conformal mapping approach.
Using RPLP0 to normalize EWSR1-FLI1 expression, we observed important variations of EWSR1-FLI1 expression within and across the different cell lines (Figure  2a ). Importantly, highly significantly different EWSR1-FLI1 mean expression values (P o0. 001) were observed between DOX-treated and untreated shA673-1c or shSKE-17T cells hence providing a validation of single cell measurements. Using the interquartile range of the normalized expression median (EWSR1- FLI1/RPLP0 ratio) of DOX-treated shA673-1c and shSK-E17T clones, we could define an upper threshold for EWSR1-FLI1 low status. Interestingly, it is clearly apparent that EWSR1-FLI1 low subpopulations of cells can be observed spontaneously in each of the A673, SK-N-MC and TC71 Ewing cell lines. The quantification of the EWSR1-FLI1 protein expression level was also performed using three-dimensional deconvolution microscopy associated with ImageJ software of Ewing cell lines immunostained with an FLI1 antibody (Figure  2b , Supplementary Figure  S3C ), knowing these Ewing do not express wild-type FLI1.
ACKNOWLEDGEMENTS This work was supported by grants from the  Institut Curie , the  INSERM , the  Ligue Nationale Contre le Cancer (Equipe labellisée) , the  Institut National du Cancer  ( PLBIO14-237 ), the  European PROVABES  ( ERA-649 NET TRANSCAN JTC-2011 ;  01KT1310 ),  ASSET  ( FP7-HEALTH-2010-259348 ), and  EEC  ( HEALTH-F2-2013-602856 ) projects, the  German Cancer Aid  ( DKH 108128 ) and the following associations: the  Société Française de lutte contre les Cancers et des leucémies de  l'enfant et de l'adolescent, the  Etoile de Martin, Courir pour Mathieu , Dans les pas du Géant,  Olivier Chape ,  Les Bagouzamanon , Enfants et Santé, les  Amis de Claire  and M la vie avec  Lisa. Georges-Alain Franzetti  was supported by a fellowship from the  Ministère de l'Enseignement Supérieur et de la Recherche (France)  and from the  FRM  ( FDT20130928190 ).
The numerical problem is implemented with the commercial software Comsol Multiphysics™, by coupling heat equation, Navier-Stokes and continuity equations and the free boundary motion. The latter is treated with the Arbitrary Lagrangian Eulerian method, with a particular focus on the contact angle implementation. The comparison between numerical and experimental results shows a very satisfactory agreement in terms of droplet shape, thermal field and intermetallic layer thickness. The model validates our numerical approach.
Numerical Considerations The PDE equations were solved by the finite elements method, with the commercial software Comsol Multiphysics™ (V4. 4, Comsol INC, Burlington, MA, USA, 2016). Due to the deformation of a droplet and to the remeshing process (based on the mesh quality), triangular element shapes were chosen. The mesh (Figure  6 ) was built in three steps. The first meshed part is the aluminium boundaries. Then, the aluminium domain and finally, the titanium domain was freely meshed. In each domain, the elements growth factor was set at 1. 3. A 40 µm maximal length of boundary elements was set in order to allow a compromise between computational times and solution accuracy. It has been performed by a convergence study. Decreasing the size of mesh has no significant effect on the results (thermal and velocity fields).
Fieldwork phase 2 (2013) The study area was re-visited in 2013, where semi-structured interviews were conducted with a range of clinicians, nurses and laboratory staff (11) at the three HAT treatment centres north of Lake Kyoga: Dokolo Health Centre IV (Dokolo district); Serere Health Centre IV (Serere district) and Lwala Hospital IV (Kaberamaido district) on all aspects of clinical presentation, diagnosis and treatment for HAT. Again, we followed a convenience sample study design, and all staff present in the facility during our visit were invited to participate. Respondents were asked questions as regards data recording and handling and all rHAT records collected between 2009 and 2012 from these three diagnosing centers. A rapid assessment of the data recording systems present was also made.
Questions included: who is responsible for managing case data? How is sleeping sickness data recorded, shared, and reported at this facility? Who is responsible for managing case data? Is there an electronic/digital record keeping system? What challenges are there to data management at the facility? Records were obtained from Dokolo HC-IV and Serere HC-IVs (available as hand written registries in log books) and from a computerized HAT database at Lwala Hospital. Available rHAT data were entered into an Excel spreadsheet. Hand written cases were found to be incomplete and/or information was illegible, and these were excluded. Data retrieved from the national archive was compared to that from these treatment facilities. Cases that did not appear in the list from the three health facilities but which appeared in the national archive were included in the spreadsheet.
Characteristics and diagnostic capacity of the health system Seventy health facilities were identified across Dokolo, Kabaramiado, Serere and Soroti Districts in 2011: 36 HC-IIs; 29 HC-IIIs; 6 HC-IVs and 2 Hospitals (Fig. 3 ). In November 2011, these facilities employed 451 staff in HC-II -HC-IV facilities: 29 clinicians; 260 nurses; 68 midwives; 53 laboratory staff and 41 other support staff. Questionnaires were undertaken with 55% of clinicians, 20% of nurses, 18% of midwives and 40% of laboratory staff employed in these health facilities. Data relating to specific diseases could only be obtained from notebooks and/or information charts on facility walls. Data was inconsistent in some areas and largely limited to results from laboratory-based diagnostics. Across the study area, reliable records were only kept at facilities with fully functioning laboratories.
Where data were feed into an electronic database there were concerns of coding errors being carried forward (Lwala hospital). The facilities make a weekly report to the sub-county office, which feeds up to the district administration. It is the responsibility of the district health office (or HAT treatment hospitals) to report case data to the MoH. The national HAT control program updates an electronic archive and assimilates countrywide records pooled from both diagnosing and treating healthcare providers across HAT endemic districts. Between 2009 and 2012, in districts north of Lake Kyoga (Soroti, Kaberamaido, Dokolo, Lira, Amolatar and Apac) 342 people were diagnosed with rHAT  (108 cases in 2009; 104 in 2010; 70 in 2011; and 60 in 2012). Over this 4-year period, 39% of HAT cases were reported between January and March (133).
Acknowledgements We would like to thank all of the many research participants that were involved in this study, the numerous government officials and representatives from others who contributed, including three local research assistants. This work received financial support from the  European Union  seventh framework programme through the  ICONZ (Integrated Control of Neglected Zoonoses ) and  ADVANZ (Advocacy for Neglected Zoonotic Diseases)  projects (Okello et al. , 2015). The funders prayed no role in the study design and implementation, data generation and data analysis, decision to publish, or preparation of this publication.
In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes.
The use of databases is also not mandatory in this approach to decipher the coded sequences. To attain such a MS readability, the molecular structure of the polymers was carefully engineered and, in particular, two key features were implemented: the use of cleavable inter-bytes spacer that promotes programmed MS 2 fragmentation and the use of mass tags that allow identification of byte original location. The former feature allows the actual MS sequencing task to be limited to very short (8 bits) oligo(phosphodiester)s, while the latter one permits reliable reconstruction of the byte sequence. It should be noted that the reported concept is not limited to poly(phosphodiester)s and could be extended to other types of digital polymers. For instance, alkoxyamine groups are most probably not the only type of interbyte links that can be used in this approach.
All samples were prepared in a methanolic solution of ammonium acetate (3 mM), and introduced at a 10 μl min -1 flow rate in the ESI source operated in the negative mode (capillary voltage: -2. 27 kV) under a desolvation gas (N 2 ) flow of 100 l h -1 heated at 35 °C. The cone voltage was -10 or -20 V for both MS and MS 2 experiments while it was adjusted between -20 and -50 V to induce in-source fragmentation in MS 3 experiments. CID was performed in the ion trap device using argon as the collision gas after selection of the primary (in MS 2 ) or secondary (in MS 3 ) precursor ion in the quadrupole mass analyzer of the instrument. Data analyses were conducted using the MassLynx 4. 1 program provided by Waters. While fragmentation reactions occurring during the first activation stage (MS 2 experiments) mainly consist of NO-C bond homolysis, two main types of dissociation pathways were experienced by byte fragments when excited in the second activation stage (pseudo-MS 3 experiments).
Illustrative Example for the Genetic Algorithm In view of the problem NP-hardness, in the case of more than two machines apart from the initial and final buffer since they do not increase the complexity of the problem (their operating time is zero), we have proposed Algorithm 2 to solve the (  13 )-(  21 ) model. We consider the database given by Tables  4  and 5. The genetic algorithm parameters are used as follows:  100 individuals;  , 0. 95; We consider that the system produces three jobs (glass parts), which are differentiated by their color: blue (i b ), red (i r ) and green (i g ). The processing time of every job is presented in Table  4. The maintenance action periods for three machines are illustrated by Table  5.
Illustrative Example for the Genetic Algorithm In view of the problem NP-hardness, in the case of more than two machines apart from the initial and final buffer since they do not increase the complexity of the problem (their operating time is zero), we have proposed Algorithm 2 to solve the (  13 )-(  21 ) model. We consider the database given by Tables  4  and 5. The genetic algorithm parameters are used as follows: • P = 100 individuals;  On the basis of the results shown in Table  7  and Figure  13 , the GA yields a good average makespan compared to the optimal solutions given by the mathematic model. The actual computing time for each problem was nearly the same for the two resolutions of the frameworks.
In Section 5, I delineate three projects for universalization of the social sciences through IOK that result from analysis of interviews with protagonists at IIUM, realized in 2012. A few methodological indications are required here. The aim of the interviews was to understand what is at stake for scholars who teach and research in the social sciences in an institution that has as its mission the IOK in all disciplines. The interviews were conducted as expert interviews. The expert interview is the first and foremost defined by the characteristics of the interviewee: The expert. While it is generally hard to define what justifies regarding an interviewee as an expert, the particularity of the encounters realized at Kuala Lumpur was that interviewer and interviewee belonged to the same group of 'experts', for example, we were colleagues, trained in the same or neighbouring scientific disciplines (key data on interviewees is provided in Table  1  AQ5 ¶ ).
Acknowledgments I would like to thank the colleagues at  Kuala Lumpur  who have agreed to be interviewed for their time and patience and for pushing my argumentative competency to its limits. I would also like to thank  S. Farid Alatas  for the opportunity to 'debrief' my interview experiences, for his expert insights into the backgrounds of IOK and for his comments on an earlier version of this paper. I am grateful to the extended team and guests of the  BMBF-project  ' Universality and acceptance potential of social science knowledge ' at  Freiburg University -Chandni Basu ,  Ercüment Çelik ,  Christian Ersche ,  Claudia Honegger ,  José Jiménez/Tomás Elgorriaga Kunze ,  Bruno Monteiro ,  Barbara Riedel  and  Veronika Wöhrerfor  critical comments on earlier versions of this paper.
The corresponding author is responsible for ensuring that address and email details are correct for all the co-authors. Affiliations given in the article should be the affiliation at the time the research was conducted. Please see http://journalauthors. tandf. co. uk/preparation/ The underlying research materials for this article can be accessed at <full link>/ description of location [author to complete]'. If your article includes supplemental data, the link will also be provided in this paragraph. See <http://journalauthors. tandf. co. uk/preparation/multimedia. asp> for further explanation of supplemental data and underlying research materials. 6. The CrossRef database (www. crossref. org/) has been used to validate the references. Changes resulting from mismatches are tracked in red font.
Dietary protein may play an important role in the prevention of metabolic dysfunctions. However, the way in which the protein source affects these dysfunctions has not been clearly established. The aim of the current systematic review was to compare the impact of plant-and animal-sourced dietary proteins on several features of metabolic syndrome in humans. The PubMed database was searched for both chronic and acute interventional studies, as well as observational studies, in healthy humans or those with metabolic dysfunctions, in which the impact of animal and plant protein intake was compared while using the following variables: cholesterolemia and triglyceridemia, blood pressure, glucose homeostasis, and body composition. Based on data extraction, we observed that soy protein consumption (with isoflavones), but not soy protein alone (without isoflavones) or other plant proteins (pea and lupine proteins, wheat gluten), leads to a 3% greater decrease in both total and LDL cholesterol compared with animal-sourced protein ingestion, especially in individuals with high fasting cholesterol concentrations.
Methods This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement  (13). Prisma checklist is available in Supplemental Table  1. Ethical approval was not required because this was a secondary data analysis. Literature search. A systematic search of the relevant literature was performed with the use of PubMed in order to identify interventional and observational studies investigating the relation between plant-and animal-sourced proteins on markers of lipemia, blood pressure, and glucose homeostasis (glycemia and insulinemia), as well as body composition, published before March 2016. The structured search strategies used the combination of an animal-and a plant-sourced protein with an outcome related to metabolic syndrome features The search was limited to literature presented in the English language.