dataesr/scientific-paragraphs-categorization huggingface dataset:
Thus, a value of zero indicates there is no nutritional offset relative to the median, while positive and negative offsets represent excess or deficits in the intake, respectively (as in  [32] ). We then analysed the effect of species, P:C ratio, and assay time on each macronutrient offset using linear models. We chose to pool the data of both time points, even if time had a significant effect for protein consumption, because the main macronutrient differences between species were relative to carbohydrates (Additional file 4: Tables S1, Additional file 5: Table  S2 ). We compared the different macronutrient offsets slopes by comparison of the least squared trends, adjusting for multiple comparisons with sequential Bonferroni (Holm) correction. Finally, we assessed adult oviposition preference in relation to substrate macronutrient composition and substrate hardness in two separate assays.
Differences in font type (regular versus italic) between letters represent significant differences across least squared trends for a protein and b carbohydrates between the two species. C Amount of protein and carbohydrate ingested in the two-choice assay. Each dot represents the mean value of 10 replicates, except the triangles, which represent the average intake target for both species calculated from the pooled data of all treatments/time points. Error bars are 95% confidence intervals of the means. Twenty larvae were offered a choice between two protein to carbohydrate (P:C) ratios in three different combinations. Larvae were able to forage for 2 or 4 h and each time point was replicated ten times. The quantity of food in the larval gut was determined by spectrophotometer. D The figures show the percentage of the total amount of food ingested that corresponded to the higher protein food (1:1 for the first and second food pairs, and 1.
5:1 for the third food pair) found in the guts of D. suzukii and D. biarmipes larvae in the two-choice assay. Black asterisks represent significant differences to no choice (50%-dashed black line-see Additional file 13: Table  S10 ) and grey asterisks represent significant differences between species for the same diet (Least squared means comparison, see Additional file 14: Table  S11 ) foods and fed preferentially on the protein rich food, with a higher proportion of larvae doing so in D. biarmipes relative to D. suzukii (Additional file 3: Figure  S3 ; Additional file 11: Table  S8 ). This result agrees with our nochoice assay results where larvae prioritized protein over carbohydrate regulation. Our spectrophotometric dataset, allowing the quantification of protein and carbohydrate ingested in pooled larva, showed significant differences between the two species after 4 h of choice assay (Fig.
Taken together, these datasets imply that these species use different foraging strategies when offered a choice between food types. While D. biarmipes larvae select between food types, in D. suzukii larvae the preference for protein rich food was weaker and rather then choosing the protein rich food they compensated by altering their food intake when feeding on protein poor diets. The latter observation contrasts with results from D. melanogaster, whose larvae mix between unbalanced foods to achieve an intermediate P:C ratio  [8]. This suggests interesting differences in foraging strategies between these three species, with D. suzukii and D. biarmipes preferring to forage in a single food and regulating their macronutrient intake through the volume of food ingested. We also found that both D.
The two cameras mounted on Scheimpflug adapters (TSI Powerview Plus 4MP, 12-bit output and 2048 × 2048 pixels 2 ) are oriented perpendicular to the laser sheet. They are located on the same side of the latter. The angle between the two cameras is limited to 30 °because of optical access constraints. Band-pass filters centered at 532 nm with a 10 nm bandwidth (50%) are used to collect Mie light scattering. A precision-machined twin level calibration target with dot pattern, perfectly centered over the burner inner diameter, is used for calibration. A host computer captures 500 pairs of image frames for each camera continuously with each frame covering a flow area of about 115 mm (width) x 95 mm (height). Nikon AF Micro-Nikkor 105 mm F/2. 8 lenses are used to collect the PIV signal. TSI Insight 3 G software is used to analyze S-PIV images and a background extraction scheme is applied to reacting case images as pre-processing step.
Ampelographic comparison between somaplants and 'Hencha' mother plant. After 2 years, all acclimatized somaplants were also checked for the conformity using ampelography analysis. Phenotypic characterization involving ampelographic description was applied on 50 'Hencha' somaclones for eight foliar descriptors (Table  2 ). The comparison of ampelographic data between the somaclones and the mother plant showed identical characteristics and a complete uniformity in 46 somaclones, except for somaclones H20, H21, H24 and H37, this corresponds to a per- According to the OIV descriptors, true-to-type vines 'Hencha' and progenitors showed identical characteristics in shoot tip. The length of the tendrils was short and the same at 'Hencha' and progenitors, between 12 and 15 cm, density of prostrate hairs between main veins on lower side of blade is absent.
This procedure reduces somaclonal variation event and permit to develop in a short time healthy grapevine somaplant. In fact, 92% of regenerated somaplants were morphologically uniform. The developed method appears to be suitable for the application of this in vitro process to other endangered local grapevine cultivars, because of diseases. In addition the virus-free 'Hencha' somaplants preserved in the insect proof permit to the ampelographer to built up rigorous ampelographic and ampelometric data matrices for endangered native local grapevines. In addition, virus-free material is necessary for evaluating germaplasm potentialities. Ampelographic investigations will be supported, in a future work, by molecular marker analysis to reevaluate the progenitors of grapevine 'Hencha' cultivar.
Regarding the OCTA, we set the reference at the level of the choriocapillaris, defined as a 20 μm band below the RPE-Bruch's membrane complex. Manual adjustment of the segmentation level was used to improve visualization. In OCTA images, we assessed the retinal and choroidal blood flow, mainly the presence of abnormal flow in a choroidal neovascularization network. Two experienced OCTA readers evaluated the images independently to determine morphological characteristics of the retina and choroid, to identify a CNV network, and to confirm the diagnosis. Only very high quality data (>60 signal strength index) were taken to analysis. 2. 1. Statistical Analysis. Numerical traits were described by way of the measures of location-mean, median, and quartiles, and measures of dispersion-interquartile range, standard deviation, standard error of mean, 95% confidence interval, and minimum-to-maximum values.
Bioeconomy and its sectors Bioeconomy have been categorized in many sectors and the role of regional specialization has been highlighted. Many comparisons has been made in different regions in order to better understand synergies and interactions of the various elements involved in the formation of bioregions, generic term indicating capacity building of some advanced region in terms of adherence to this new paradigm. According to BERST research project ( http://www3. lei. wur. nl/BerstPublications) there are eight important sectors such as: biomass, food and feed, construction, chemicals and polymers, pulp and paper, textile and clothing, energy, R&D services. Since it implies various sector economy is considered as well a meta sector worth 2 trillion euro in Europe, creating 22 million jobs, representing 9% of the overall workforce, according to the data released by the European Union.
For the formation of the bimetallic nanoparticles, the same deposition conditions were maintained such that the coverage of Au and Pd on TiO 2 (110) could be estimated from the volume of the nanoparticles measured with STM. The coverage of Pd and Au is expressed in equivalent monolayers (MLE), defined as the surface concentration of Pd(111) and Au(111), respectively (for Pd 1 MLE ~ 1. 53 × 10 15 atoms/ cm 2 , while for Au 1 MLE ~ 1. 39 × 10 15 atoms/cm 2 ). STM images were recorded in constant current mode using W tips prepared by electrochemical etching and conditioned by outgassing at 500 K as well as voltage pulses in STM. The STM images were analyzed using WSxM software  [48]. For determining the average height, at least one hundred nanoparticles were measured. Deposition of eight monolayer equivalents (MLE) Pd onto TiO 2 (110) results in the formation of a continuous multilayer film of Pd that dewets partially after annealing at 953 K for 1 h (Fig.
Acknowledgements We acknowledge fruitful discussions with  Professor Michael Bowker. The UCL group is supported by a  European Research Council   Advanced grant ENERGYSURF , and the  Royal Society  through a  Wolfson Research Merit Award. The Szeged group is supported by research grant  NKFIH-OTKA-120115. This collaboration was funded by a  European Cooperation in Science and Technology Action :  ECOST-STSM-CM1104-030815-063692. The  ELI-ALPS  project ( GINOP-2. 3. 6-15-2015-00001 ) is supported by the  European Union  and co-financed by the  European Regional Development Fund.
A good way to deal with reversed causality is to use time-lags between the independent and dependent variables. However, with annual waves, such a lagged model cannot address well the short-term effects of work on health and vice versa. In our study, a lagged analysis was not feasible since data on three consecutive measurements were not available for all participants and the proportion of persons who entered paid employment was small. Larger studies are needed to determine the causal relation of employment transitions on perceived health. The study population consisted of a very specific group of long-term unemployed persons with common mental health problems, diagnosed by a physician, primarily living in the four largest cities of the Netherlands. This may limit generalizability of the study findings to other populations, such as unemployed persons with other health problems.
5). The quality and quantity of the genomic DNA was checked with a Nanodrop (ND-1000, Thermo Scientific, United States) and a Promega fluorometer (Quantus, Promega, United States). Purified genomic DNA was sequenced using the MiSeq sequencing system of Illumina  (Zerbino and Birney, 2008) , yielding 250 bp paired-end reads with a mean library size of 400 bp. De novo assembly was performed using Velvet  (Zerbino and Birney, 2008). Prediction of protein-encoding regions and automatic functional annotation was performed using the Rapid Annotations using Subsystem Technology (RAST) server  (Aziz et al. , 2008). Genes for tRNAs and rRNAs were predicted with tRNAscan-SE  (Lowe and Eddy, 1997)  and RNAmmer server  (Lagesen et al. , 2007)  respectively, with the prokaryotic default setting. Insertion sequences (ISs) were identified by BLASTN searches against the ISfinder database  (Siguier et al.
, 2006). Prophage regions were identified using the PHAST web server  (Zhou et al. , 2011). Orthologous protein coding sequences in B. mycoides ATCC 6462, B. mycoides EC18, and B. mycoides SB8 were analyzed by the OMA (Orthologous Matrix) orthology database  (Altenhoff et al. , 2014). In addition, the functionality analysis of all the genes was performed by searching against protein domain databases, including GO  (Harris et al. , 2004)  and COG (clusters of orthologous groups)  (Tatusov et al. , 2003).
RNA Sequencing and Data Analyses RNA sequencing was conducted at PrimBio Research Institute (Exton, PA, United States). The raw RNA-Seq reads were trimmed from the adapter sequences and mapped against the reference genome sequence of each strain. The RPKM (Reads Per Kilobase Million) table of the core genome of the three strains (4743 genes) was generated. Differential gene expression analyses were carried out with the web server pipeline T-REx  (de Jong et al. , 2015) , in which the RPKM values of the B. mycoides strain grown in the presence of root exudates was compare with that grown in the absence of root exudates. The significance threshold was p-value < 0. 05 and fold-change > 2 ("TopHits" in T-Rex). Functional categorization including GO, InterPro, KEGG and PFAM domains, was performed on the Genome2D web server 2.
Genomic Analyses of B. mycoides Stains The Whole Genome Shotgun sequence of strains EC18 and SB8 has been deposited at GenBank under the accession MRWW00000000 and MRWS00000000, respectively. The general features of the genomes of EC18, SB8 and the reference strain ATCC 6462 are listed in Table  1. EC18 has a genome size of 5. 75 Mb (Mega Base pairs) and SB8 has a genome size of 5. 98 Mb, both of which are bigger than the type strain ATCC 6462 (5. 64 Mb). The GC content of all three strains is around 35%. EC18 encodes 6,014 proteins, 77 RNA genes (7 rRNA and 70 tRNA genes) and 71 prophage-associated genes, while the SB8 genome comprises 6,250 protein-coding genes, 47 RNA genes (3 rRNA and 44 tRNA genes), and 177 prophage-associated genes. As shown in Figure  2 , the core genome of the three strains consists of 4,743 orthologous groups and a pan-genome size of 7,234 genes, among which 357 genes are unique to EC18 and 646 genes are unique to SB8.
Of those, 408 genes were upregulated and 307 genes were downregulated (Figure  3C ). 193 out of the 715 altered genes were represented in the COG database and hence used to perform ortologanalyses. As shown in Figure  4 , a large part of the genes are poorly characterized and belong to the group [R] (General function prediction only) or [S] (Function unknown). Apart from this, the upregulated genes were mainly implicated in amino acid metabolism and signal transduction, while many of the significantly downregulated genes were involved in cell cycle control, amino acid transport and amino acid metabolism, cell wall and membrane biogenesis, transcription, and carbohydrate transport and metabolism. The soil strain SB8 responded to the root exudates with an upregulated of 261 genes,whereas 219 genes were significantly downregulated.
109 of the in total 480 altered genes were found in the COG database. The largest group of altered genes were again clustered in [R] and [S], thereby leaving their function unknown or only providing an insight into a generally assumed function. The genes represented by COG classes with known function were mostly categorized in amino acid transport and metabolism, cell cycle control, and energy production and conversion. Taken together, the results showed clear differences in gene expression changes between EC18 and SB8 in response to potato root exudates.
mycoides-plant interactions. In general, the endophytic strain showed a more complex response than the soil isolate. The DEGs are categorized based on GO, COG, and Pfam databases. The endophytic strain responded to the root exudate with a significant upregulation of genes related to amino acid transmembrane transport, while genes involved in sugar transport including BG05_RS27120 (cellobiose PTS transporter IIA) and BG05_RS26300 (arabinose ABC transporter permease) were downregulated (Figure  7 ). However, as shown in Figure  8 , several genes related to the PTS (phosphohistone-sugar phosphotransferase system) were significantly upregulated in the soil isolate SB8, i. e. , those genes including sugar ABC transporter (BG05_RS11820), PTS lactose transporter subunit (BG05_RS06025), PTS cellobiose transporter subunit (BG05_RS27110 and BG05_RS27115), and PTS sugar transporter (BG05_RS27275).
Studies on fish embryo models are widely developed in research. They are used in several research field such as drug discovery or environmental toxicology. In this article, we propose an entirely automated assay to detect cardiac arrest in Medaka (Oryzias latipes) based on image analysis. We propose a multi-scale pipeline based on mathematical morphology. Starting from video sequences of entire wells in 24-well plates, we focus on the embryo, detect its heart, and ascertain whether or not the heart is beating based on intensity variation analysis. Our image analysis pipeline only uses commonly available operators. It has a low computational cost, allowing analysis at the same rate as acquisition. From an initial dataset of 3,192 videos, 660 were discarded as unusable (20. 7%), 655 of them correctly so (99.
Computer and software We used the Python 2. 7 environment under Windows 7 (64 bits) in an HP computer with a 3. 60GHz Intel R Core TM i7-4790 CPU and 32 GB of RAM. We used Numpy, Scipy, and Scikit-image  [27] , Python Imaging Library (PIL), Pink  [28] , and Open CV for Python  [29]. Platform control and image data acquisition were performed using FEI Visilog 7.
Ground truth establishment In the context of our test validation, two possible types of ground truth exist: observations under a microscope and those directly acquired on videos. Each present different advantages and drawbacks. The strongest way of assessing the quality of the complete embryo analysis process, including plate preparation, data acquisition, and data treatment, is to compare our results to the observations of embryos under a microscope. On the other hand, the automated method we developed works on video sequences whose information may be much different from the observations made under microscope. Several aspects linked to the experimental protocol or the acquisition method can explain this fact. (i) Video quality is such that some weak heart beats may be undetectable on video even if they are visible under a microscope.
We refer to these observations as "Dataset 0". The expert identified each case as a living or dead embryo by checking for the presence of a heartbeat. After that, another expert ("expert 1 ") analyzed the resulting 3,192 acquired videos ("Dataset 1"). He began manually assessing the usability of the videos, by checking that they were complete, wellrecorded, that the well was not empty, and that the embryo was not too close to the well boundary. In this manner, 655 unusable videos were identified. Then, for the remaining 2,537 usable sequences only, this expert determined if the embryo was alive or dead. However, whereas determining videos usability is easy and thus reliable, detecting a beating heart is sometimes difficult and therefore subject to errors. For this reason, we selected a subset of only 200 usable videos ("Dataset 2") so that the health status of the embryo could be reassessed by two other independent observers ("experts 2 and 3").
Validation of the method Using the 200 Dataset 2 videos, we can now compare the results of our program with the previously established consensus data. We consider the program to be erroneous if it detects a dead embryo that was identified as alive according to expert consensus (false negative) or if, on the other hand, it detects a living embryo that was identified as dead by expert consensus (false positive). We detected 3 errors made by the program for a corresponding error rate of 1. 5%. (see Table  3 ). Moreover, this error rate only corresponds to false negatives. In toxicity tests, this is a more acceptable type of error since it does not provide a false sense of security with regard to the molecule tested. In Table  3(.
25 × 10 -4 ). However, this low error rate is based on video-based ground truth and is only representative of the quality of the program itself. To assess the reliability of the entire procedure, including preparation, acquisition, and treatment, we need to establish ground truth by observing embryos under a microscope. Nevertheless, as we explained in part 5. 1, we still face video quality and accuracy issues with the current acquisition procedure. For example, when comparing the manual health status determination under microscope on Dataset 0 and the videos on Dataset 1, we noticed a discrepancy in 282 cases, for a rate of 11%. To improve upon this, we are investigating the use of the VAST system: http://www. unionbio. com/vast/, which currently is only available for Zebrafish, not for Medaka.
b), we present the error rates that were calculated for each expert as compared to the final consensus based on Dataset 2. Expert 1, who processed the 3,192 videos (Dataset 1), has a similarity rate of 98. 5% with respect to the consensus data. Consequently, the experts' observations can be considered sufficiently reliable to analyze the results of the entire program. The results of this analysis (program vs. expert 1) are described below. Out of the initial 3,192 Dataset 1 videos, the program correctly flagged 655 as unusable and incorrectly flagged another 5 as unusable due to some error within the program itself. If we consider the entire set, 3,187 videos were correctly.
summarizes the establishment of ground truth datasets. Our first Dataset 0 Dataset 1 Dataset 2 Screening method Microscope Videos Videos Dataset size 3192 3192 200 Experts in charge Expert 0 Expert 1 Experts 1, 2 of the analysis* and 3 Classification "Alive" or "Dead" "Unusable", "Alive" or "Dead" labels used "Alive" or "Dead" * Each expert screened the entire dataset.
Acknowledgements. Special thanks are due to  Aldo Benites-Palomino ,  Rafael Varas-Malca , and  Walter Aguirre  ( Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos ) for their most valuable and friendly assistance and fruitful discussion on several aspects of the cetacean assemblage of the Pisco Formation. We are also grateful to  Elena Cioppi  and  Stefano Dominici  ( Museo di Storia Naturale, Sezione di Geologia e Paleontologia, Università degli Studi di Firenze ),  Giuseppe Manganelli  ( Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università di Siena ),  Fabrizio Cancelli  ( Museo di Storia Naturale dell'Accademia dei Fisiocritici ),  Gianni Insacco  ( Museo Civico di Storia Naturale di Comiso ),  Daniel Robineau  and  Christine Lefèvre  ( Muséum National d'Histoire Naturelle ),  James G.
Mead  and  Charles W. Potter  ( National Museum of Natural History, Smithsonian Institution ),  Lawrence G. Barnes  and  Vanessa R. Rhue  ( Natural History Museum of Los Angeles County ), and  Adri Rol  ( Zoological Museum Amsterdam ) for providing access to specimens under their care. This research was supported by a grant of the  Italian Ministero dell'Istruzione dell'Università e della Ricerca  ( PRIN  Project  2012YJSBMK ) to  Giovanni Bianucci. Alberto Collareta received support from the  SYNTHESYS  Project http://www. synthesys. info/(Project Number  FR-TAF-6129 ), which is financed by  European Community Research Infrastructure Action  under the  FP7 "Capacities" Program. This paper greatly benefited from constructive comments and thoughtful suggestions by  Mark D. Uhen  ( George Mason University ) and  Stephen J.
Statistical analysis Data analyses were performed in R version 2. 10. 1 (R Foundation for Statistical Computing (http://www. r-project. org), and p 0. 05 denoted statistical significance. The mosquito community structure at the different study sites and transects was analyzed using the following approaches: diversity using a Shannon equitability index (H 0 ), and similarity of mosquito fauna using the Jaccard Index of similarity (J), based on the presence/absence of data only. We used the number of mosquito adults caught as the numeric surrogate for analyzing the effect of the types of trap, months, localities, and biotopes with a multi-way ANOVA (analysis of variance). We used Tukey's honest significant difference (HSD) to determine which pairs of means were significantly different.