dataesr/scientific-paragraphs-categorization huggingface dataset:
Instead, treating the SLB with 55% FBS medium the same initial changes were restored to the initial value after washing. The NR profiles for analogue SLB samples treated with in situ NPs and pure FBS solutions are displayed in Fig. 5. A direct comparison between the two cases showed a decrease of intensity of the fringe at 0. 1 Å -1 with respect to the pattern of the untreated SLB for both samples, the effect was enhanced in the presence of the NPs (Fig. 5b ). A summary of the parameters and the scattering length density profiles obtained by fitting the data with the five slabs model can be found in Table  4  and in Fig. 5c , respectively. The presence of the NPs led to a significant increase of the hydration of the lipid bilayer mostly in the tail region together with a small swelling of such a region as shown by the values reported in Table  4.
13, 51 The NR characterisation of DOPC SLB agrees with data reported in literature. 49, 52-54 Curves are characterized by a minimum between 0. 15 and 0. 20 Å -1 related to the thickness of the bilayer, due to interference arising between the reflected waves at the top and the bottom of the SLB. The defects in the SLB can be evaluated from the amount of hydration water in the hydrophobic tails region of the SLB. The averaged value of tail hydration was less than 1% (0. 8±0. 3%) indicating essentially defect free layers. The thickness value of SLBs determined with the two techniques is the same (46 ± 6 Å and 46 ± 5 Å, respectively). NR allows higher molecular resolution to distinguish between hydrophilic and hydrophobic regions: the hydrophobic tail region was 28. 3 ± 0. 6 Å, slightly larger than that provided by Nagle et al.
They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.
jcm. riken. jp/cgi-bin/nbrp/nbrp_list. cgi). e Automated prediction. f Diploids. g Number of unigenes determined from RNA sequencing, genome sequence unpublished, data taken from GenBank: ANFW000000000. 2. Assembly size suggests hybrid genome. h Dubious number, average CDS size (1024 bp) is significantly shorter than that of other yeast genomes (1500 bp), suggesting sequencing errors (frameshifts). i Unpublished data taken from http://genome. jgi. doe. gov (nonpublic). other by a short AT-rich interval (CDEII), contrast with the 3to 5-kb-long regional centromeres observed in the CTG clade  (Sanyal et al. 2004; Padmanabhan et al. 2008; Kapoor et al. 2015; Chatterjee et al. 2016) , in Y. lipolytica  (Vernis et al. 1997 (Vernis et al. , 2001;; Lynch et al. 2010) , and in the methylotrophs  (Morales et al.
c Total numbers of predicted protein-coding genes (CDS) are taken from original publications or subsequent annotations, as most appropriate. Data not found indicated by -. d Unpublished data taken from the National BioRecource Project (www. jcm. riken. jp/cgi-bin/nbrp/nbrp_list. cgi). e Unpublished data taken from GenBank: LCTY00000000. 1. f Unpublished data taken from GenBank: MDSA000000000. 1. g G. candidum and L. starkeyi are listed here despite their large number of scaffolds because each genome represents the only reference available, so far, in its respective lineage. h Automated prediction based on comparisons to the CTG clade. i Unpublished data taken from http://genome. jgi. doe. gov (nonpublic). j Unpublished data taken from GenBank: LWLF00000000. 1. k These are listed here for convenience and are the few sequenced yeast species not included in the four major subgroups of Saccharomycotina defined in this review.
Numbers of chromosomes are indicated in bold type when known. Figures in brackets correspond to numbers of scaffolds in assemblies. c Total numbers of predicted protein-coding genes (CDS) are taken from original publications or subsequent annotations, as most appropriate. Figures in brackets represent estimate from incomplete sequence. d Unpublished data taken from https://yjx1217. github. io/Yeast_PacBio_2016/data/. e Sequence data taken from http://ygob. ucd. ie. f Unpublished data taken from GenBank: CCBQ000000000. 1. Unpublished data taken from the National BioRecource Project (www. jcm. riken. jp/cgi-bin/nbrp/nbrp_list. cgi).
Acknowledgments While writing this review article, the authors' laboratories were supported in part by the  Centre National de la Recherche Scientifique  ( UMR3525 ),  Université Pierre et Marie Curie  ( UFR927 ) and the  L'Agence Nationale de la Recherche  (contract  DYGEVO from program  blanc  2011 SVSE6 ) for B. D. ; and by the  Biotechnology and Biological Sciences Research Council  and the  University of Leicester  for E. J. L. The authors declare no conflict of interest.
Numbers of chromosomes are indicated in bold type when known. Figures in brackets correspond to numbers of scaffolds in assemblies. c Total numbers of predicted protein-coding genes (CDS) are taken from original publications or subsequent annotations, as most appropriate. Figures in brackets represent estimate from incomplete sequence. d Unpublished data taken from https://yjx1217. github. io/Yeast_PacBio_2016/data/. e Sequence data taken from http://ygob. ucd. ie. f Unpublished data taken from GenBank: CCBQ000000000. 1. Unpublished data taken from the National BioRecource Project (www. jcm. riken. jp/cgi-bin/nbrp/nbrp_list. cgi). b g Unpublished data taken from GenBank: CP014248. 1. h.
Deregulation of b Cell lncRNAs in Human T2D The identification of functional lncRNAs led us to explore whether some lncRNAs are abnormally expressed in human T2D and might thus be relevant to the pathogenesis of this disease. We therefore analyzed our new set of 2,373 lncRNAs in a recently reported gene expression dataset that includes human islet samples from donors diagnosed with T2D or impaired glucose tolerance (IGT)  (Fadista et al. , 2014). Our results showed that, despite the fact that gene expression across human islet donors is highly variable, the expression of 15 and 100 lncRNAs was significantly altered in islets from T2D and IGT versus nondiabetic donors respectively (adjusted p < 0. 05) (Figure  S6A ; see Table  S7  for a complete list). This finding suggests a potential role of functional b cell lncRNAs in driving some of the b cell gene expression changes that are associated T2D.
Gene Expression Array Analysis RNA was hybridized onto HTA2. 0 Affymetrix arrays. RMA normalization was carried out using Expression Console (Affymetrix). Gene-based differential expression analysis was done using Transcriptome Analysis Console (TAC, Affymetrix). Enhancer cluster genes were defined by genes that were associated with clustered islet enhancers that show top 50 percentile binding by TFs (PDX1, FOXA2, NKX2-2, NKX6. 1, and MAFB) as defined previously  (Pasquali et al. , 2014). Pancreatic islet gene sets used for enrichment analysis are shown in Table  S5. A list of isletenriched genes was generated as those with more than two SDs higher expression in human islets than the average expression in 16 human tissues (Table  S5 ). Differential Expression in IGT and T2D Islets RNA-seq data have been described previously  (Fadista et al.
ACKNOWLEDGMENTS The research was supported by the  National Institute for Health Research (NIHR) Imperial Biomedical Research Centre. Work was funded by grants from the  Wellcome Trust  ( WT101033  to J. F. ),  NIH-BCBC  ( 2U01 DK072473-06  to J. F. and P. R. ),  Ministerio de Economı ´a y Competitividad  ( BFU2014-54284-R  to J. F. ), and  Horizon 2020  ( 667191  to J. F. ). Work in IDIBAPS was supported by the  CERCA Programme, Generalitat de Catalunya. J. Y. was supported through a Berg and  Unity Biotechnology  fellowship. The authors are grateful to  Helena Raurell Vila  for experimental help and  Romain Derelle  and  Loris Mularoni  for advice regarding bioinformatics analysis. P. R. is a shareholder and consultant for  Endocells/Unicercell Biosolutions. Z. T. receives financial support from  Berg Pharma  and  Unity Biotechnology  as a consultant.
-Location and ancillary instrumentation The present work utilizes data from Granada and Valladolid (both located in Spain). Valladolid is an urban area, surrounded by rural areas, sited in North-Central Iberian Peninsula (150 km North from Madrid) with a population of ~300. 000 inhabitants. Román et al. [2014b]  characterized the predominant aerosol at Valladolid as -continental clean‖ obtaining monthly mean values of the AOD at 443 nm ranging from 0. 10 to 0. 24, and Angström Exponent (AE) from 0. 9 to 1. 5, showing higher/lower AOD/AE values in summer due to episodic Saharan dust events  [Cachorro et al. , 2016]. Granada, located in the South-East of the Iberian Peninsula, is a medium-sized and nonindustrialized city situated in a natural basin surrounded by mountains and with a population similar to Valladolid; the local aerosol sources are mainly the heavy traffic (particularly diesel vehicles) together with the re-suspension of material available on the ground, especially during the warm season.
s. l. ) and on the rooftop of the Andalusian Institute for Earth System Research (IISTA-CEAMA; 37. 16ºN; -3. 61ºW; 680 m a. s. l. ). The mentioned ceilometers belong to the Iberian Ceilometer Network, ICENET, which processes raw data and provides information about the vertical attenuated backscatter at 1064 nm  [Cazorla et al. , 2017]. This information helps to detect possible changes in the aerosol properties at night. The CE318-N photometer takes measurements of Sun irradiance and sky radiance, and CE318-T photometer also measures lunar direct irradiance, performing daytime and night time photometric measurements  [Barreto et al. , 2016]. The photometer #914 (CE318-T) was available for a short campaign at Valladolid and used in this work. For the rest of the period, the photometer #788 or the photometer #383 (both CE318-N), located at the same station, were used.
Both photometers belong to the RIMA network (Iberian network for aerosol measurements), which is federated to AERONET. The #918 (CE318-T), used for this work at Granada, belongs to I-AMICA (Infrastruttura di Alta Tecnologia per il Monitoraggio Integrato Climatico-Ambientale of Italy) and operates within AERONET. These instruments are periodically calibrated, following the AERONET protocol, ensuring high quality data. In addition, AERONET processes the photometer data providing a wide set of products such as daytime AOD at 8 wavelengths, aerosol size distribution, fraction of spherical particles (sphere fraction) and refractive indices  [Holben et al. , 1998; Dubovik et al. , 2000 Dubovik et al. , , 2006]]. Regarding night time measurements, AOD is obtained at 6 wavelengths (440, 500, 675, 870, 1020 and 1640 nm) following the method described in  Barreto et al.
3. 1. 2-Sky coordinates of each pixel SONA sky camera position is fixed, thus every pixel measures the same region of the celestial vault. Hence, the zenith and azimuth angles corresponding to all the pixels can be calculated to locate any celestial body in every image (in this work we focus on the position of the Moon and its aureole). The zenith and azimuth matrices have been calculated using a dataset of sky images under cloud-free conditions and visible stars and planets whose celestial coordinates are well-known in these images. The stellar bodies used at Granada have been Arcturus, Jupiter and Vega; while for Valladolid they have been Altair, Arcturus, Jupiter, Saturn, Vega and Venus. The pixel positions of these stellar bodies have been correlated with their sky coordinates, finding a relationship between the zenith and azimuth with pixel position.
As a result, a linear HDR image gives, for each channel and pixel, a signal proportional to the incoming irradiance to the CCD  [Stumpfel et al. , 2014]. In this work, the sky cameras have been configured to record 16 consecutive sky images with exposure times following a doubling sequence. The first image (im 1 ) is taken with an exposure time, ET(im 1 ), then the second image (im 2 ) is taken with an exposure time, ET(im 2 ), equal to 2*ET(im 1 ), then the third (im 3 ) with an exposure time equal to 2*ET(im 2 )=2 2 *ET(im 1 ) …, and finally the last image (im 16 ) is taken with a exposure time, ET(im 16 )=2 15 *ET(im 1 ), around 2. 5 seconds. The elapsed time obtaining the 16-image dataset is about 30 seconds. The gain (ISO) used for these images has been set to constant at at night time, and equal to the one used for obtaining the dark frames (Section 3.
3. 2. 3-Background correction The nocturnal sky images also recorded part of the city background light (city lamps, buildings and others). As a consequence, the sky is not fully dark even without Moon. The lunar aureole viewed by the camera can be contaminated by these lights, hence, in order to detect the Moon aureole, the city lights need to be characterized and removed for the original HDR image. With this aim, a data base of background images (BG) has been constructed from images taken under cloud-free conditions and with both Moon Zenith Angle (MZA) and Solar Zenith Angle (SZA) above 100º. In these conditions, we guarantee that the images are not contaminated by the Moon nor the Sun light and neither the clouds. Note that these BG images have been taken at low illumination and they usually are quite noisy.
To partially correct for this effect, all the BG images have been smoothed by an averaging filter of 5x5 pixels. As a first guess, we could assume that the signal of background images depends on the aerosol load, since aerosols can scatter part of the city lights back to the camera. The data base of BG images has been analyzed and correlated to the closest AOD value measurement (note that there are no simultaneous measurements of AOD since BG images are taken under skies without the Sun and Moon). The maximum gap allowed between BG images and AOD measurements has been 3 hours for Granada and 4 hours for Valladolid due to the lower number of images available in the latter. AODs at 440, 500 and 675 nm have been assigned to the blue, green and red channels of the camera, respectively. The determination coefficient (r 2 ) between the pixel signal of each channel and its AOD value has been calculated using the chosen BG images for both cameras (151 images for Granada and 61 for Valladolid).
, 2014]. Aerosol refractive indices, both real (RRI) and imaginary (IRI), have been assumed as constant (non spectral variation); this assumption has been done due to the lack of information regarding the diurnal retrievals which consider that refractive indices can vary with wavelength. As a result, for each HDR image and 6-AOD dataset, the following parameters have been obtained: bilognormal size distribution, real and imaginary refractive indices, single scattering albedo (SSA) at the same wavelengths than input values, and sphere fraction. The retrieved bilognormal size distribution is described by six independent parameters  [Torres et al. , 2016] : volume concentration of the fine (C f ) and coarse mode (C c ); volume median radius of the fine (r f ) and coarse mode (r c ), and geometric standard deviation for both modes: σ f (fine) and σ c (coarse).
5. 1. 2-Statistical analysis In addition to the analyzed case, seven other nights have been added to the dataset for comparison, with a total of 8 nights (4 cases with fine aerosol predominance and 4 coarse aerosol cases), 5 at Granada and 3 at Valladolid. The normalized radiances have been simulated for the eight nights as in the previous case using the parameters of the AERONET retrievals (corresponding to the afternoon before or to the morning after) shown in Table  1. Clean cases (low aerosol load) have not been considered due to the uncertainties in the aerosol parameters under low aerosol load. In fact, the aerosol parameters retrieved by AERONET present quality assurance only when the AOD at 440 nm is higher than 0. 4  [Holben et al. , 2006] ; however, due to the lack of coincident cases with high AOD values and camera measurements under stable and constant aerosol conditions along a full night, AERONET data used were retrieved with AOD at 440 nm higher than 0.
Acknowledgements This work was supported by the  Andalusia Regional Government  (project  P12-RNM-2409 ) and by the  -Consejería de Educación" of "Junta de Castilla y León"  (project  VA100U14 ); the  Spanish Ministry of Economy and Competitiveness  and  FEDER  funds under the projects  CGL2013-45410-R ,  CMT2015-66742-R ,  CGL2016-81092-R  and - Juan de la Cierva-Formación‖ program  ( FJCI-2014-22052 ); and the  European Union 's  Horizon 2020 research and innovation programme  through project  ACTRIS-2  (grant agreement No  654109 ). The authors thankfully acknowledge the  FEDER program  for the instrumentation used in this work. The technical support given by  Ying Li  is acknowledged. The authors acknowledge the use of GRASP inversion algorithm (www. grasp-open. com). Tom Stone  is also acknowledged for the ROLO calculations used in this work.
9 ] [17] [18] [19]  In this review, we discuss the main characteristics and limitations of molecular imaging technologies to investigate cellular biodistribution and fate. The primary focus was on SPION labeling methods for stem cells tracking in a myocardial infarction model, but we also discussed other models, markers, and molecular imaging techniques. We have reviewed the literature in the field and also provided unpublished data on mesenchymal stem cells labeling and tracking in the myocardial infarction model. For this review, we consulted relevant articles published on prominent journals for each specific area covered in the topics, provided that they were indexed on PubMed, Wiley's Library, Science Central, and/or Google Scholar. We used the following keywords for our search: SPIONs, nanoparticles for cell labeling, cell tracking, tracking cells in myocardial infarction, in vivo cellular imaging, MRI, molecular imaging technologies, and nanoparticles toxicity.
Furthermore, technetium-99m ( 99m Tc)-labeled bone marrow-derived mononuclear cells delivered by intracoronary injection in chronic chagasic patients are detected in the heart 24 hours after injection. 126 These data suggest that labeled cells injected in situ can be detected by different in vivo imaging modalities at least within hours of cell injection. Recently, Martens et al evaluated the biodistribution of pluripotent stem cells after intramyocardial injection in infarcted mice, by in vivo bioluminescence analysis. The authors could reveal and quantify massive early stem cell loss in heart and accumulation of them in the lung. When they increased the cell concentration, much larger numbers of cells were counted in the heart, although pulmonary accumulation still persisted. 127 In our studies with chagasic mice injected systemically with mesenchymal cells, we also observed a preferential migration to the lung, liver, and spleen, but with a beneficial cardiac effect as well.
They reported that the technique was not toxic to the cells. The authors performed an intracoronary injection of ferumoxytollabeled rat cardiosphere-derived stem cells in rats, with and without magnetic targeting. The authors reported that magnetic targeting improved cardiac homing of transplanted cells as assessed by fluorescence imaging, MRI, and quantitative polymerase chain reaction 24 hours after cell transplantation. 128 ere, we present previously unpublished qualitative data on stem cell tracking in infarcted rats. We used immunostaining analysis by fluorescent or confocal microscopy to observe Feridex-labeled mesenchymal stem cells in a rat model of myocardial infarction. The animals were submitted to infarction by the ligation of the left anterior descending artery, and 24 hours later received an intramyocardial injection of 1×10 6 labeled stem cells in the left ventricle wall.
Acknowledgments This study was supported by grants from the  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) ,  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) , and  Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). The authors wish to thank  Janet W. Reid  from  JWR Associates, USA  for revising and editing the language in the text.
Emerging insects Emerging insects were sampled during 2 periods, from March 2002 to October 2002 and from March 2003 to October 2003. Surface-level funnel emergence traps (Figure  1D  and Supplemental Data, SI-1, Figure  S4 ) containing formaldehyde at 4% were placed along each mesocosm at 2 and 16 m. Every 2 wk, the lid of the traps was opened, and the organisms were retrieved using a plastic pipettor. Identification of the individuals was performed to the lowest practical taxonomic level (family or subfamily taxonomic level except for chironomids, which were identified to the tribe level  [37] [38] [39]. An overview of all the compartments, populations, and communities sampled throughout the experiment along with the methodologies is given in Table  S2  of the Supplemental Data (SI-1).
Statistical analysis Prior to analysis, the abundance data for zooplankton, macroinvertebrates, and emerging insects were Ln (a Â X þ 1) transformed, where X stands for abundance. The value of a was chosen in such a way that when the lowest value of the dataset above 0 was taken for X, a Â X yields 2. This was done to downweight high-abundance values and to approximate a normal distribution of the data (for rationale, see Van den Brink et al. [40] ). For total abundance, taxa richness and abundance of certain species of zooplankton, macroinvertebrates, and emerging insects, a Williams test was used to determine the eventual differences between the control and treatments  [41]. This test is an analysis of variance (ANOVA) that assumes that the mean response of the variable is a monotonic function of the treatment, and thus greater effects are expected with increasing dose  [41].
The tests were performed using the TOXSTAT 3. 0 computer program  [42]. The responses of the communities to copper treatment were analyzed using the principal response curve (PRC) method  [43]. As sampling of emerging insects was discontinuous, 2 PRC analyses were performed for 2002 and 2003. To test the significance of the treatment effects on communities, a Monte Carlo permutation was done following the PRC. Monte Carlo permutation was also performed for each individual sampling date, to test for the significance of the treatment effects. To know which treatment differed from the control for each sampling date, principal component analysis was used. Then a Williams test was applied to the first principal component to determine the NOEC at the community level (NOEC community ). In addition, NOECs at the population level were calculated for the taxa that had the highest species weight in the PRC.
Surprisingly, C. sphaericus abundance was higher in the low and medium treatments compared with the control in June and July 2002. Taxa with a negative weight increased in abundance. This was the case for the protozoan Vorticella sp. (Figure  4F ); negative weight appeared in January 2003 and developed mainly in the medium and high treatments at high abundances. The NOECs for each taxon are presented in Table  2  and vary with time. The raw data are available in the Supplemental Data (SI-3, Zooplankton raw data).