dataesr/scientific-paragraphs-categorization huggingface dataset:
Regulatory features of the Tst core promoter and exon 1 region To define the location of the core promoter sequences we used the Eukaryotic promoter database (EPD) tools that located it within a 59 bp-long interval overlapping the transcription initiation site (TSS, Fig. 2ablack ). No TATA-box or CG box consensus sequences were identified around this core promoter segment. Genetic variation in the mouse genome in this segment identified 14 SNPs, one of which mapped to the evolutionary constrained element (Fig. 2b ) and one SNP to the core promoter (Fig. 2c , presented as red lines). SNPs occurring in highly conserved functional regions may affect expression and phenotypic variability in strains harbouring the mutant alleles. The open chromatin region (Fig. 2d ) harbours four transcription factor binding sites (TFBS) for transcription factors ZFX, E2F1, KLF4 and NELFE (Fig.
Regulatory features of the Tst intronic region Our bioinformatics analysis revealed strong evidence for the existence of the second regulatory region within intron of the Tst gene (Fig. 1 ). Introns can affect transcription by acting as repositories for transcriptional regulatory elements (i. e. enhancers and repressors). We narrowed a segment potentially important in the regulation of Tst to a region between 78402750 -7840000 bp. Using different tools and databases we identified regulatory elements or features such as constrained elements (Fig. 3a ), open chromatin site (Fig. 3c ), two histone modifications specific for transcribed portions of genes and associated with enhancers and other distal elements (Fig. 3d ), and also one TFBS (Fig. 3e ). Additionally, the frequency of DNA methylation sites (Fig.
Funding This study was funded by grants from the  Slovenian Research Agency : core funding program  P4-0220 ,  J3-6804 , and  Young Investigator Grant  for  Jasmina Beltram. N. M. Morton  was supported by an  Investigator Award  from the  Wellcome Trust  ( 100981/Z/13/Z ) The funders had no role in the design of the study and collection, analysis, decision to publish, interpretation of data or preparation of the manuscript.
Acknowledgements This publication arises from the project  Pro-Health 65+  which has received funding from the  European Union , in the framework of the Health Programme (2008)(2009)(2010)(2011)(2012)(2013). The content of this publication represents the views of the authors and it is their sole responsibility; it can in no way be taken to reflect the views of the  European Commission  and/or the Executive Agency for Health and Consumers or any other body of the  European Union. The  European Commission  and/or the  Executive Agency do(es)  not accept responsibility for any use that may be made of the information it contains. Publication co-financed from funds for science in the years 2015-2017 allocated for implementation of an international co-financed project.
The 'Aerobiology Over Antarctica' Consortium With recent agreement to co-ordinate weather and climate monitoring at the XIth Scientific Committee on Antarctic Research (SCAR) symposium -Life in Antarctica: Boundaries and Gradients in a Changing Environment, Barcelona, 15-18th, July 2013, the necessary foundation exists to enable establishment of a pan-Antarctic sampling initiative. For the first time, this initiative encompasses a co-ordinated program to produce (i) a global dataset on aerobiological diversity and (ii) contextualized environmental data aimed at clarifying the relationship between aerial biodiversity and terrestrial ecosystem stability. At the XXXIIIth SCAR Open Science Conference, Auckland, New Zealand, 23rd August -3rd September 2014, a workshop was held to discuss the structure, sampling, and environmental data recording methodologies, and common approaches to data analyses that would be fundamental to the success of such a program, and would render it technically feasible while also minimizing costs.
The key challenge in this type of study, as for many studies in microbial ecology, is that the abundance and composition of airborne communities is variable across time and space. This means that a large area (global or pan-continental) aerobiological sampling initiative could be compromised by the specific methods selected and the techniques used in different regions. To overcome such challenges, we propose the use of standardized minimal air collection and sample processing methodologies and statistical analyses, in order to identify and detect patterns in aerobiological datasets obtained from a wide variety of sources and approaches.
CONTEXTUAL DATA Meteorological Data In order to make sense of the aerobiological diversity, it is important to collect environmental context data. In combination with backtrack analyses, researchers also need to consider the conditions the air mass has or will experience en route between two regions, not just those at the 'landing site' , as these will determine survival during transfer. Collaboration with current platforms, such as the MCM TON (McMurdo Terrestrial Observation Network -these networks are being designed to monitor key physical and biological processes associated with changing ecosystems across regional to continental spatial scales by facilitating coordination and comparability of measurements) and ANTOS (SCAR Antarctic Nearshore and Terrestrial Observing System) initiatives, would help generate a standard suite of environmental parameters.
Modeling Different numerical models have been used in aerobiology over a range of applications, including pollen dispersal (and allergy susceptibility), species invasions, spread of diseases and air pollution (see e. g. ,  Garcia-Mozo et al. , 2009). These models represent useful tools to test current ecological hypothesis. For example, data from the Antarctic Mesoscale Prediction System (AMPS) and the application of NOAA HySPLIT system could be used to create back trajectories over the Antarctic continent, indicating the sources of particular air masses and, potentially, their contained biota. The co-ordinated sampling approach outlined here would provide observational data for use in modeling studies (including community compositions and species distributions), particularly if combined with meteorological data  (Westbrook, 2010).
Data Management The datasets likely to be generated by this initiative are large but not necessarily complex. A number of data management initiatives are already underway though SCAR, and would be appropriate to utilize here. For example, the Microbial Antarctic Resource System (mARS) for sequence data (using MIMARK environmental data format guidelines), the Polar and Alpine Microbial Collection (KOPRI, Korea), the collection of polar cyanobacteria BCCM/ULC (Liege, Belgium), the DNA repository for long term DNA storage (University of Waikato, New Zealand), the SCAR Antarctic Terrestrial Biodiversity Database (Australian Antarctic Data Centre), and the Antarctic Plant Database (held at the British Antarctic Survey).
Next Steps To get involved, register your project with the consortium. We will develop and host a metadata repository to identify ongoing and prospective studies, that can be used to suggest links and collaborations that can lead to enhanced datasets. Registrants will have the opportunity to become contributors to a coordination workshop to analyze and develop the next stage of implementation of the project 'Gathering large scale spatial and temporal airborne microbial samples to understand the role of airborne input to continental Antarctic ecosystem function, its resilience and stability'.
SUBJECTS AND METHODS A prospective study was conducted with retrospective data analysis of all patients having undergone PN for T1-T2 renal tumors from January 2010 to the end of December 2015. The tumor was removed with the standardized minimal healthy tissue margin technique. After resection and immediately before performing hemostasis, US control of the surgical margins was performed: • In the open surgery, PN the specimen was immersed in a saline solution and a sequential US was performed to evaluate in three dimensions if the tumor's capsule was intact • In the laparoscopic approaches the specimen was placed into a laparoscopic endobag (EB-200; Brightness Medical, Jiangsu, China) filled with enough saline solution to cover the specimen. The laparoscopic US probe was then placed into the endobag and an US was performed.
RESULTS In 177 PN(s) on 147 patients were included (seven patients were operated bilaterally, and 17 had multifocal tumors on the same kidney). Patients' characteristics and data are described in Table  1. Open surgery was performed in 144 PN(s) and 30 by laparoscopic approaches (20 laparoscopy and 10 robot-assisted laparoscopy). Hilar clamping was done in 32 cases with a mean warm ischemia time of 19 ± 6 min. Parenchymal clamping was done in 48 procedures and clamping was not needed in 74 cases. Mean operative time was 112 ± 31 min and the mean estimated blood loss was 230 ± 160 ml. US control of surgical margins of the specimens was positive in four patients. As described above these patients had an extra rim of renal parenchyma resected. Mean US examination time was 41 ± 7 s. In only one case, the US control was not possible because no capsule was visible.
Cost data collection We collected CPPW cost data quarterly from the 44 ARRA-funded communities via a web-based Cost Study Instrument (CSI)  (6). We provided each community with access to the CSI to report quarterly costs for the program award period (2010 through 2013); the first reporting period covered the first year of funding. We obtained cost data for 1) labor, 2) consultants, 3) materials, travel, and services, 4) overhead activities (ie, indirect expenditures), and 5) partner organization work (ie, contracted services). In addition to actual expenditures, we collected information on voluntary or in-kind contributions from communities and their partners. Each community developed a CPPW community action plan that included multiple community-defined objectives to improve population health.
Cost data aggregation We estimated community costs at the most disaggregated level by generating objective-and MAPPS strategy-level costs. For example, if a community had 10 objectives, and each objective had 2 MAPPS strategies linked to it, we estimated costs for 20 objective and strategy combinations. Communities also allocated costs to administration or evaluation. We assigned administrative costs to program cost estimates in proportion to spending on each objective or strategy. We also estimated evaluation costs but excluded them from program cost estimates. CPPW interventions were defined after the programs were under way and were usually more specific than MAPPS strategies. For example, "healthy vending" was an intervention linked to the broader MAPPS strategy "healthy food/drink availability.
If multiple interventions supported an objective, we calculated intervention costs by weighting the relevant objective costs (eg, including one-half of costs for objectives supported by 2 interventions). We summed community intervention costs across all communities to estimate aggregate costs for each CPPW intervention. To estimate the cost per person reached, we needed estimates of the number of people reached by each intervention. Because data on reach was not collected at the intervention level, we estimated in-tervention reach using objective reach data that communities submitted to the Centers for Disease Control and Prevention (CDC). These data were supplemented with narratives on program accomplishments written by CDC program staff, then reviewed and validated by CPPW program officers, subject matter experts, and evaluation contractors.
Reviewers used US Census Bureau, school, and other local data sources to validate reach estimates. If an intervention was linked to only one objective, we assumed intervention reach was equal to objective reach. If an intervention was linked to multiple objectives, we used the maximum objective reach to approximate intervention reach. Objectives were marked as complete or incomplete by the end of the grant period. We used an estimate of "interim reach" for incomplete objectives, but we dropped interventions for which data on interim reach were not available. Of the 768 community interventions for which we collected cost data, 120 were eliminated because of missing reach data; costs assigned to the dropped interventions totaled $33 million. We calculated intervention costs per person reached as aggregate intervention costs across implementing communities divided by aggregate intervention reach.
We verified quarterly total costs entered in the CSI against quarterly expenditures reported in ARRA financial reports; however, we could not verify the accuracy of allocations to objectives and strategies or in-kind contributions. The initial study goals were 1) to determine how cost data for prevention activities could be collected, 2) to understand the challenges of collecting cost information, and 3) to build an accurate tool for cost data collection. An important challenge was collecting uniform cost data that could be aggregated and standardized across communities, given changes during the study in community activities. As more community prevention programs collect and report intervention costs, it will be important to compile and disseminate cost estimates to inform program design and provide input for cost-benefit evaluations.
Acknowledgments This report was prepared by  RTI International , under contract to the  Assistant Secretary for Planning and Evaluation (ASPE). The findings and conclusions of this report are those of the authors and do not necessarily represent the views of ASPE, the  Centers for Disease Control and Prevention , the Office of the Assistant Secretary for Planning and Evaluation, or the  US Department of Health and Human Services. No financial disclosures were reported by the authors of this article. The findings and conclusions of this article are those of the authors and do not necessarily represent the views of the Office of the Assistant Secretary for Planning and Evaluation or the  US Department of Health and Human Services.
The effects of inhibiting these nodes alone or in combination on cell growth were studied using a WST-1 assay (Roche Diagnostics, Burgess Hill, UK). Experiments were carried out in triplicates. Statistics. Data are reported as means ± s. d. Statistical significance was evaluated by non-parametric Mann-Whitney's tests. Results were subjected to statistical analysis by using the GraphPad Prism software package, v6. 01 (GraphPad Software, La Jolla, CA, USA).
ACKNOWLEDGEMENTS This work was supported by  Cancer Research UK  (grant number  C309/A11566 ), the  Experimental Cancer Medicine Centre award  (grant number  C12540/A15573 ), and the  National Institute for Health Research Biomedical Research Centre  award. SB has received the support of  Fondation de France -Unicancer  (Aide ala mobiliteinternationale de medecins ou pharmaciens). Dr UB has received research funding from  AstraZeneca.
To characterize the mechanism of action of CPM against hRSV, we selected CPM-resistant viruses and identified that a single R151K mutation on the hRSV M2-1 protein was able to confer resistance to the compound. Our data are consistent with previous studies which demonstrated that this residue is critical for RdRp activity. Indeed, an R151D substitution in M2-1 resulted in 70% reduction of M2-1-dependent transcription  21, 26. In an hRSV RdRp-specific minigenome functional assay CPM potently inhibited RdRp activity. The R151K variant was significantly less sensitive to CPM, demonstrating that the R151K mutation is responsible for CPM resistance. An analysis of 486 wild-type sequences reported in GenBank showed that R151 is fully conserved in all human M2-1 sequences (data not shown). Furthermore, virus supernatants were unable to recover from a sharp increase of cyclopamine concentration.
IC 50-90-95-99 values were determined by focus counting (viral entry) or focus size measurement (viral propagation, treatment post-adsorption) and were obtained using non-linear regression analysis using GraphPad Prism (GraphPad Software, La Jolla California USA). Compound cytotoxicity was assessed using a CellTiter-Glo Luminescent Cell Viability Assay (Promega, Madison, WI), following the manufacturer's instruction in the conditions of the focus reduction assay. Selection of hRSV resistance to CPM. CPM-resistant viruses were generated by blind-passages with increasing concentration of compound. Infections were started at an MOI of 0. 1 for the first round and infections were stopped after 72 h or when about 50% CPE was observed. The infection media were subsequently clarified and 100 μ L of supernatant were used to inoculate cells during the next passage.
Coverslips were mounted in Prolong Gold Antifade reagent (Invitrogen, Carlsbad, CA), observed with a Nikon TE200 microscope equipped with a CoolSNAP ES2 (Photometrics, Tucson, AZ) camera, and images were processed using the Meta-Vue (Molecular Devices, Sunnyvale, CA) and Fiji 57 softwares. Immunoassays. Proteins from SDS-PAGE were transferred onto nitrocellulose membranes which were incubated with primary rabbit polyclonal anti-P 58 , -N 58 ; -M2-1  26  , and mouse monoclonal anti-tubulin-α antibodies (Sigma-Aldrich, Saint-Quentin Fallavier, France) for 1 h, followed by appropriate HRP-conjugated secondary antibodies for 1 h. Immunodetections were performed using an enhanced chemiluminescence (ECL) substrate (GE Healthcare GMB, Vélizy, France). Protein levels were determined from Western blots using the GeneTools software after acquisition of the signals with a GeneGnome Digital Imager (Syngene, Frederick, MD, USA).
(d) Mapping of the three mutation sites on a monomeric M2-1. Left: Surface representation of a full-length M2-1. Right: Surface (top) and cartoon (bottom) representations of the C-terminal side of M2-1 core domain. The RNA and P binding sites described by Blondot et al. 21 are colored in red and blue respectively. The amino-acids that belong to both binding sites are colored in magenta. The three sites of mutation are indicated with black arrows. The models (PDB accession code 4C3B) were rendered using the PyMOL Molecular Graphics System, Version 1. 7. 1. 0, Schrödinger, LLC.
Acknowledgements We thank  Christina Sizun  ( Gif-sur-Yvette ) for NMR assays with M2-1 and CPM,  Jill Grenier  for assistance with high throughput screenings,  Rong Chen  for providing HEp-2 cells and hRSV Long strain and  José Melero  ( Madrid ) for providing M2-1 22K4 antibodies. This work was supported by the  Institut Pasteur Shanghai -Chinese Academy of Sciences  and the  Li Ka Shing Foundation  [R. A. ], the  French Agence Nationale de la Recherche ,  specific program ANR Blanc 2011  " Bronchioliteaserl " [ ANR-11-BSV8-0024 , J. F. E. ], and in part by funding from  National Natural Science Foundation of China  [ 31400148  to G. Z. ] and the  Science and Technology Commission of Shanghai Municipality  [ 14YF1407600  to G. Z. ] A Doctoral Grant from the  Institut Pasteur International Network  and a  Griffith University Post-Graduate Scholarship  are also acknowledged [B.
The black arrows indicate the sites of clear mutation. (d) Mapping of the three mutation sites on a monomeric M2-1. Left: Surface representation of a full-length M2-1. Right: Surface (top) and cartoon (bottom) representations of the C-terminal side of M2-1 core domain. The RNA and P binding sites described by Blondot et al. 21 are colored in red and blue respectively. The amino-acids that belong to both binding sites are colored in magenta. The three sites of mutation are indicated with black arrows. The models (PDB accession code 4C3B) were rendered using the PyMOL Molecular Graphics System, Version 1. 7. 1. 0, Schrödinger, LLC.
These vortices are convected towards the downstream cylinder. As the previous review shows, the flow structure and dynamics in the gap region are still ambiguous and indeterminate, especially at larger pitch ratios within the reattachment regime. This is mainly due to the scarcity of data from quantitative imaging techniques such as high speed PIV, which may enable the resolution of both the spatial structure and temporal evolution of the gap flow. The aim of our ongoing experimental works, part of which is presented in this article, is to provide such data. In addition, the tandem configuration provides an excellent test for turbulence modeling validation. Thus, these PIV measurements may also provide a large database that can be used for comparison with numerical simulations, as in the study by  Perrin et al.
For each location the time series from the ten acquisitions were concatenated in order to form a sufficiently long time series. The PSD of these time series was computed using spectral averaging on multiple windows  (Marple (1987) ) with nonoverlapping Hamming windows of a size corresponding to 1024 samples. The image processing and the cross-correlation analysis were realized by using the DAVIS 8 software of La Vision. A slight inhomogeneity gradient of the Laser's light appears in the measuring plane, which is due to an intrinsic characteristic of the Laser source related to the nominal distribution of the energy in the Laser's beam. Furthermore, one of the cameras used, the RS3000 type, presents an intrinsic slight inhomogeneous intensity response yielding a slight absorption of the signal's intensity in the borders of the measuring plane.
Acknowledgments This study has been accomplished in the context of the  French research program  of the " Agence Nationale de Recherche" -ANR BARESAFE, "Simulation of Safety Bareer reliability ", coordinated by  EDF  and under the partnership of EDF,  CEA, AREVA, "Institut de Recherche en Informatique de Toulouse" -IRIT, "Institut de Mécanique des Fluides de Toulouse" -IMFT , " Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie ",  Université de Strasbourg -ICUBE. Part of this study was carried out in.
The signals were amplified and filtered (×10,000; 0. 1-10 kHz) using a DigitalLynx (Neuralynx, USA) amplifier, digitized at 32 kHz and saved on a PC for post-hoc analysis using custom-written functions in Matlab (MathWorks, USA) as described previously  [3]. The Mann-Whitney and t tests were used for the group data comparisons with a level of significance set at p < 0. 05.
Methods We conducted a retrospective consecutive case series review of 53 patients (74 eyes) who received one or more courses of IVB injections (Avastin, Roche Registration Limited, Welwyn Garden City, UK) for the treatment of DME at the Royal Surrey County Hospital (Guildford, UK) during the period May 1, 2011 to December 31, 2013, who had at least 1 year of follow-up. Each IVB injection (1. 25 mg/0. 05 mL) was prepared by the hospital pharmacy as a prefilled syringe containing 0. 10 mL, with only 0. 05 mL being injected into an eye. This study was approved by the Royal Surrey County Hospital Research Ethics Committee (outcomes of retinal disease: RSCH/12DEV0010). Due to the observational and retrospective nature of the study, for which data were obtained from review of medical charts, with no intervention or deliberate modification of treatment, patient informed consent was waived by the committee.
statistical analysis All data was entered into a Microsoft Excel 2010 spreadsheet (Microsoft Corporation, Redmond, WA, USA). Analyses and graphs were constructed using GraphPad Prism v5. 01 (La Jolla, CA, USA), and PASW Statistics 18 (v18. 0. 0; SPSS Inc. , Chicago, IL, USA). A P-value #0. 05 was accepted as statistically significant. Changes in variables were compared by Wilcoxon and Mann-Whitney test; proportions between groups were compared using the χ 2 test, Fisher's test, or McNemar test. Logistic regression was used to evaluate potential predictors of response, generating odds ratios.