dataesr/scientific-paragraphs-categorization huggingface dataset:
Concentration and purity of both the RNA and cDNA samples were determined using a NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific). To exclude the amplification of genomic DNA, primers were designed to span introns near the 3'poly-A tail using Primer3 software (Table  1 ). Quantitative RT-PCR (qRT-PCR) assays were run in a ViiA7 TM Fast Real-Time PCR System (Applied Biosystems) in MicroAmp® Optical 384-Well Reaction Plate (Applied Biosystems). Reactions were performed in a final volume of 10μL using 5μl of Power SYBR® Green PCR Master Mix (Applied Biosystems), 0. 4μM final concentration of primers and 1l (up to 1g) of cDNA. Thermocycling conditions were as follows: an initial denaturation at 50°C for 20sec and 95°C for 10min, followed by 40 cycles at 95°C for 15sec and at 60°C for 1min.
Acknowledgments The authors are grateful to  Domingos Henrique ,  Joaquin Rodriguez Leon ,  Solveig Thorsteinsdottir  and  Kim Dale  for reagents, to  Sérgio Dias  for helpful discussions and to  Interaves Portugal  for contributing with quail fertilised eggs. This work was supported by  Fundação para a Ciência e para a Tecnologia (FCT) , project  PTDC/SAU-BID/115264/2009. M. Figueiredo received two research fellowships from  FCT.
Fermi-LAT data analysis The Large Area Telescope (LAT) on board the Fermi satellite is a pair conversion telescope sensitive to photons with energies from 20 MeV to more than 300 GeV. For the analysis presented here we used data which were recorded between 2008 August 4 and 2014 August 8 and which are reconstructed with pass 7 reconstruction. The data were analysed using Fermi ScienceTools V9r32p5 with the python interface enrico  [6]. Events of the "source" class falling within a circular region of interest (ROI) of 10 • radius centred on the source position were selected. Events with zenith angles of more than 100 • and time intervals when the rocking angle was larger than 52 • have been rejected. In order to reduce the background and investigate the GeV regime a minimum energy threshold of 3 GeV was considered.
To date no longitudinal study has been performed in T1D. We measured SAF in 300 patients with T1D during year 2009. Our baseline results, which show that SAF was related to retinopathy, nephropathy and long term past glucose control, have been published elsewhere  [12]. In the present study, we investigated whether SAF was related to their cardio-renal outcome within 4 years of follow-up: cardiovascular events, estimated GFR (eGFR), and AER. Data were available in 243 patients after 4 years of follow-up.
Design and patients We analyzed the data from two hundred and fortythree patients with T1D included during the year 2009 after written informed consent. The following data were recorded at inclusion, on the day of SAF measurement: age, sex, body mass index (BMI), duration of diabetes, hypertension (defined by a blood pressure ≥140/90 mm Hg and/or treatment with antihypertensive drug) and smoking history. Smokers included patients with past and current smoking history. The biological data recorded included HbA 1c levels, serum creatinine levels, eGFR calculated with the CKD-EPI formula and AER.
Data Collection and Processing Livestock Data Formal questionnaire censuses were conducted with all livestock owners present in the study area in 2003 and 2012. The census asked owners to list pasture locations and water sources used by their large stock and small stock (separately) over 12 month periods starting from October 2002 and October 2011. Overall, 118 unique livestock owners were recorded. Of these, full livestock ownership information was available for 80 owners in 2003 and 84 in 2012 (58 appeared in both years). According to the census data, 49 owners used the Moiynkum desert at some period of the year in  2002-2003, and 30 in 2011-2012  (note that due to the practice of collective herding several owners may use the same sites, just as one owner may use more than one site). The information on stock type, numbers, water source, and monthly location name were entered into a database.
Interviews were used to gather livestock owners' perceptions on site selection and to identify important variables affecting decision-making. The results are discussed in detail elsewhere  (Kerven et al. 2016b ) and summarised here briefly in relation to our hypotheses and findings. During interviews conducted in 2013 and in spring 2014 a number of additional occupied wells were recorded, including some which were newly occupied and a small number missed during the original census, but exact dates of use and livestock numbers were not recorded. Thus, livestock presence data were available for wells occupied in 2002-03 and between the end of 2011 and the start of 2014 (concerning mainly the years 2012 and 2013), whilst density (stocking rate) information was available on a monthly basis for two single year periods running from the months of October 2002 and 2011.
Concerning the exact locations of used sites, many of the surveys and interviews were conducted at grazing sites, recorded by GPS. Livestock owners and other knowledgeable interviewees identified additional used locations on a set of 1:50,000 Soviet era topographical maps. The majority of these sites were then visited by vehicle with key informants and recorded by GPS. The locations of those sites that could not be visited were digitised directly from the georeferenced topographical maps on which all wells are shown, many with names. Most such locations were verified on the maps by more than one interviewee. All locations, with their coordinates, were inputted into a relational database, thus providing exact locations for every site listed in the livestock survey table. Livestock presences were recorded as locations having any stock presence over the year, whilst absences were defined as locations having wells that existed in the Soviet era, but which were not recorded as occupied either in 2002-3, or between 2011 and 2014.
Therefore, some analyses were also performed on this subset of sites alone, concerning 102 potential sites. Most of these have been re-occupied from Ulan bel' village as Malye Kamkale is virtually abandoned. Overall, livestock were present at 26 locations in 2002/ 2003 and 40 during the full fieldwork period of 2011-2014 (of which 37 were within former sovkhoz boundaries and 30 in Chu sub-district). Twenty-seven of these were recorded with full livestock number information for our specific census period October 2011-October 2012. The rest were recorded as having livestock presence at some point between October 2011 and April 2014. These data represent two snapshots of well occupation in a complex 20 year-long process of well occupation and abandonment. Our data do not include information on the exact dates and length of occupation periods between the two study periods.
However, the year of first occupation since the collapse of the sovkhoz was obtained for a subset of 29 wells for more detailed investigation of site sequencing. The sets of occupied sites are different in the two time periods, altering the choice of unoccupied sites. This is addressed by explicitly comparing site characteristics between sites occupied in 2011-2014 alone, occupied in 2003 and then abandoned, and occupied in both periods. Resource Density The remote-sensing derived Normalised Difference Vegetation Index (NDVI) is used worldwide as an indicator of green biomass  (Pettorelli et al. 2011). We employed a gapless 250 m 16 day NDVI dataset generated from the MODIS MOD13Q1 product  (Vuolo et al. 2012)  for the years 2001-2012, from which we extracted annual averages both over the entire period and for the years 2003 and 2012 alone (see supplementary materials 1).
By integrating NDVI over the year, we are looking at the overall attractiveness of a site as a 'base' regardless of the season in which it was used at the time of the study. Resource Depletion In many arid areas of Central Asia, forage is relatively homogeneous around wells; wells and shelter are located in the same place and forage availability tends to increase, and grazing pressure to decrease, away from this single central point  (Alimaev et al. 2008; Kanchaev et al. 2003; Nechaeva et al. 1979). Differences between NDVI at 0-2 km and 3-5 km from wells, or NDVI gradients, were measured using the annual average NDVI data for 2003 and 2012. These gradients may be interpreted as a measure of resource depletion and have been shown to be closely related to stocking density metrics elsewhere in the region  (Behnke et al.
Statistical Analysis Relationships between distance from settlement and NDVI, date of first occupation and NDVI, stocking rate and NDVI gradient, and well depth and first date of occupation were explored by ordinary least squares linear regression. Differences in mean NDVI, NDVI gradient, distance from settlement, well depth and snow cover between locations with stock presence and absence were assessed using Welch's t-test; differences in these variables between the four site stocking categories (used in 2003 alone, 2011-14 alone, both periods or unused) were assessed using one-way ANOVA. All statistical analyses were carried out in R (R Core Team 2014). Image processing and analysis were carried out using the Raster package for R  (Hijmans and van Etten 2013)  and ARCGIS  (ESRI 2011).
Resource Depletion We now therefore turn to our hypotheses concerning NDVI gradients outwards from wells. As hypothesised, average NDVI gradients were steeper at occupied than at unoccupied sites in both 2003 and 2012 (Fig. 4c ). Secondly, we examined average NDVI gradients in 2012, at sites with different occupation histories, to address the hypothesis that more recently occupied, or more briefly occupied, sites should exhibit less resource depletion. Within sovkhoz boundaries, sites occupied only in recent times (appearing in the 2011-2014 dataset alone) exhibited no discernible difference in NDVI gradient in 2012 from unoccupied sites, which, as would be expected, have a median gradient of around zero (Fig. 4d ). Sites occupied in both periods exhibited high levels of depletion. The difference between sites occupied in both periods and those appearing only in the 2011-2014 dataset is particularly strong.
This may be because stocking rates are not variable enough to cause detectable differences in depletion level. Overall, at least by 2012, site occupation appears more likely to be causing resource depletion than to constitute a response to variability in vegetation density, consistent with the scenario that distance-related costs were the dominant factor determining site selection. However, although the MVT prediction that the most resource dense sites would be occupied first has not been shown to be correct, it is difficult to refute convincingly because we are essentially dealing with two temporal 'snapshots. ' Our dataset does not have the fine temporal detail of occupation and abandonment dates which could perhaps have been used with associated NDVI data at dates of initial occupation to untangle these two factors.
If relationships between resource density and date of first occupation do exist, they are most likely to be negative, as those sites occupied first are furthest north, where precipitation is lowest. Those sites occupied in 2003, but abandoned before the subsequent study period, have low NDVI gradients (little depletion) in 2012 (Fig. 4d ), but also have low long-term average absolute NDVI values (Fig. 4b ), suggesting that these sites may be generally resource-poor in a way not related to depletion alone. This may also explain why the difference between NDVI at occupied and unoccupied sites was so much greater for the 2003 dataset (significant at 6 km) than for the 2011-14 dataset (non-significant at 6 km). A second prediction of classical MVT, that movement away from sites would occur once they had been grazed down to the landscape average resource density, appears not to be supported, at least for the 2003 dataset.
5 ). These data are circumstantial at bestthe set of wells for which information could be gathered represents that for which informants had knowledge, and the limit of our research resources. Most data for wells unoccupied in 2003 concern those which were in fact occupied later on (hence existence of knowledge about these wells in 2012-2014 interviews). There are very few data for wells unoccupied in either period. This is because herders are unsure about the status of wells that have not been visited for a long time. However, interviews do confirm that pumping costs increase with well depth and that water quality is an important pull factor in site selection  (Kerven et al. 2016b). Lastly, we examined the effect of water source type on livestock presence. The Soviet-era grazing plan of Ulan bel' shows all major shaft wells and bore holes (n = 58).
Acknowledgements This paper is a contribution to Imperial College's Grand Challenges in Ecosystems and the  Environment initiative. We are very grateful to the following individuals for their support, advice, and assistance:  Resgul Adushov ;  Ilya Ilytch Alimaev ;  Kydrbai Atabaev  and all his family;  Cara Kerven ;  Bulgyn Koitai ;  Igor Lysenko ;  Zheksinbai Sisatov ;  Aidos Smailov ;  Sayat Temirbekov ;  Sean Webber ;  Aigul Zharas; Nurgul  and  Nazgul Zhumasheva. We appreciate the comments and suggestions from two anonymous reviewers.
Statistical analysis and treatment outcomes Malaria burden Clinical data from all enrolled children were entered into Excel spreadsheet. The analysis was performed using Epi-info 6. 04 (Centres for Disease Control and Prevention, Atlanta, GA) to determine the percentage of febrile children attending public health facilities with malaria parasites detected with either microscopy or RDT. The performance of microscopy, as compared to RDT, was assessed by calculating the sensitivity (Se), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV). Cohen's kappa coefficient (κ) was determined to measure the degree of agreement between the two diagnostic tests  [21]. The 95 % confidence intervals [95 % CI] of the proportions of positive thick films and RDT, Se, Sp, PPV, and NPV were determined using the exact binomial method.
a This study focused only on facilitators of and barriers to implementation experienced by key stakeholders in the health care, schools, and early care and education sectors. Data on community recreation departments are not included, because intervention activities were being conceptualized during intervention year one; data on restaurants and on factors affecting family engagement with CA-CORD are described elsewhere (28,29). b To be eligible for CA-CORD, school-aged children needed to attend one of these schools. c Early care and education intervention activities were conducted in 2 temporally distinct waves; this study includes only the 13 early care and education centers that participated in intervention year-one CA-CORD activities. "Some teachers didn't even take their kids out to PE.
Thus, although nucleolin and B23 have different structural domains, they share similar functions, not only in the nucleoli, but also related to the centrosome and microtubules. Recently, B23 has been shown to stabilize microtubules in vitro by inhibiting the kinesin Eg5  [6]. Although the association of nucleolin with microtubules has been identified in a proteomic study, (supplemental Table S1 in  [18] ), the interaction and the effects of nucleolin on microtubule dynamics have not been addressed. Here we have addressed the consequences of nucleolin expression (depletion by siRNA or over expression of exogenous protein) on parameters of microtubule dynamics by analyzing EB3 kinetics, a microtubule plus end binding protein. For this analysis, we used a Matlab-based open source software package to track EB3 and measure microtubule dynamics.
Microscopic image acquisition and treatment Twelve-bit images were acquired using a Cool Snap HQ charge-coupled-device (CCD) camera mounted on a Zeiss Axio-Imager Z1 equipped with a 63x oil-immersion objective lens (numerical aperture = 1. 4 / working distance 0. 19mm) and flImager Z1 filters suited for the visualization of DAPI, Atto488 and Alexa555. For each field of view, z-stacks of about 25 images with a pixel size of 102 nm were obtained by setting the z-step at 200 nm. Images stacks were processed using a 3D constrained iterative deconvolution module running under Metamorph (Meinel Algorithm on Metamorph [iteration: 7x / σ: 0. 7 / frequency: 5 / without auto background]), using the Point Spread Functions (PSF) measured for the different channels under similar acquisition conditions for PS-speck beads (Molecular probes) mounted in the same mounting medium.
Signal was then tracked in each individual cell using Matlab (MathWorks R2012b) and the PlusTipTracker open source software package  [25, 26]  with the following parameters: σ1 = 1 / σ2 = 4 / K = 3 / Search radius range = 1-5 pixels / Minimum sub-track length = 3 frames / Maximum gap length = 30 frames / Maximum shrinkage factor = 1. 5 / Maximum angle forward = 30°/ Maximum angle backward = 10°/ Fluctuation radius = 2 pixels. Results tables were then exported and further analyzed using Excel (Microsoft Office). Growth, pause and catastrophe events were analyzed by selecting all the type 1, 2 or 3 subtracks respectively. EB3-TagRFP movies were acquired in three independent experiments.
All image manipulations and computations are performed with the software Igor pro 6. 36 (WaveMetrics). For the cell shape analysis, single cell or cell agglomerates were analysed using the Analyze-Particles operation (Igor software) to determine their surface area, circularity and perimeter. Circularity is define as the ratio of the square of the perimeter to (4 Ã π Ã Area). Numbers of cell were determined by counting the DAPI labelled nuclei.
For high-throughput measurement, we analyzed the dynamics of EB3-tagRFP signal using PlusTipTracker, a Matlab-based open source software package, which automatically detects and tracks thousands of EB3-tagRFP comets on the movies  [25, 26]  and provides microtubule characteristics during growth phases (Fig 1B, see polymerization). We were also able to deduce microtubule characteristics during pauses and catastrophe events, in which the EB3-tagRFP comets temporarily disappear (Fig 1B, see pause and catastrophe)  [29]. Altogether, this assay allows the analysis of the effects of changing nucleolin and B23 protein levels on global microtubule dynamics in live cells. We first analyzed the effects of nucleolin and B23 protein levels on microtubule dynamics during polymerization phases (Fig   expression [B23-GFP] n = 15 cells).
Nucleolin inhibits catastrophes We then analyzed microtubule parameters during catastrophe events (Fig 6  and Table 2 ) which are characterized by a temporarily disappearance of the EB3-tagRFP signal and a reappearance (see Fig  1B, catastrophe ). The PlusTipTracker software detects catastrophe events by linking temporally close growths, spatially spaced out by a Backward Gap (Bgap). Like pause frequency, catastrophe frequency was significantly lower in nucleolin over expressing cells (P<0. 005, Fig  6A ). In addition to being less frequent, catastrophes in nucleolin over expressing cells were also found with a slower depolymerization speed (P<0. 1, Fig 6B  )  and a    In conclusion, catastrophe events are more frequent when cells over-express nucleolin and depolymerization speed is anti-correlated to the amount of nucleolin level, as for polymerization events.
Acknowledgments The authors thank  Cendrine Moskalenko  for her help in the process of using PlusTipTracker software package. The authors also thank the  PLATIM (PLAteau Technique d'Imagerie et de Microscopie ,  UMS3444 ,  Lyon, FRANCE ) for assistance in the acquisition and analysis of microscopic data. We are grateful to  Eric Denarier  for his expertise on microtubule image analysis. M. Bornens  for the gift of U2OS-centrin-1-GFP cells and  T. Pederson  for the gift of the pEGFP-hB23-C1 plasmid. This project was funded thanks to the  Ligue contre le Cancer (Allier and Saone et Loire), FINOVI , the  CNRS and Ecole Normale Supérieure de Lyon.
Introduction Many models of physics beyond the Standard Model (SM) predict the existence of new spin-1 gauge bosons that could be discovered at the Large Hadron Collider (LHC). While the details of the models vary, conceptually these particles are heavier versions of the SM W and Z bosons and are generically called W ′ and Z ′ bosons. In this letter, a search for a W ′ boson is presented using 3. 2 fb -1 of pp collision data collected with the ATLAS detector in 2015 at a centre-of-mass energy of 13 TeV. The results are interpreted in the context of the benchmark Sequential Standard Model (SSM), i. e. the extended gauge model described in Ref. [1] , in which the couplings of the W ′ SSM to fermions are assumed to be identical to those of the SM W boson. The decay of the SSM W ′ to SM bosons is not allowed and interference between the SSM W ′ and the SM W boson is neglected.
No additional uncertainty is assigned in the muon case as the multijet background is small. The electron and muon reconstruction, identification and isolation efficiencies as well as their corresponding uncertainties were evaluated from data using tag-and-probe methods in Z boson decays up to a p T of O(100 GeV). The ratio of the efficiency measured in data to that of the MC simulation is then used to correct the MC prediction. For electrons, these ratios are measured following the prescriptions of Ref. [25] , with adjustments for the 2015 running conditions. For higher-p T electrons, an additional systematic uncertainty of 2. 5% is assigned to the identification efficiency. This is based on differences observed between data and simulation, and their propagation to the simulated electrons.
3 NNLO  [35]  PDF sets. Normalisation uncertainties in the top-quark background are found to add a negligible contribution to the total background uncertainty. The modelling of the top-quark background is verified in a data control region defined by requiring the presence of an additional muon (electron) in events passing the electron (muon) selection. The uncertainty in the diboson background is found to contribute negligibly to the total background uncertainty.
In addition, individual groups and members have received support from  BCKDF , the  Canada Council, CANARIE ,  CRC ,  Compute Canada, FQRNT , and the  Ontario Innovation Trust ,  Canada ;  EPLANET ,  ERC ,  FP7 ,  Horizon 2020  and  Marie Skłodowska-Curie Actions ,  European Union ;  Investissements d'Avenir Labex and Idex ,  ANR ,  Région Auvergne  and  Fondation Partager le Savoir, France ;  DFG and AvH Foundation ,  Germany; Herakleitos ,  Thales  and  Aristeia  programmes co-financed by  EU-ESF  and the  Greek NSRF ;  BSF, GIF and Minerva, Israel; BRF, Norway ;  Generalitat de Catalunya, Generalitat Valenciana, Spain ; the  Royal Society and Leverhulme Trust ,  United Kingdom. The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from  CERN , the ATLAS Tier-1 facilities at  TRIUMF (Canada) ,  NDGF (Denmark, Norway, Sweden) ,  CC-IN2P3  (France),  KIT/GridKA (Germany) ,  INFN-CNAF (Italy) ,  NL-T1  (Netherlands),  PIC (Spain) ,  ASGC (Taiwan) ,  RAL (UK)  and  BNL (USA) , the Tier-2 facilities worldwide and large non-WLCG resource providers.