dataesr/scientific-paragraphs-categorization huggingface dataset:
Validation of Species-Specific Primers Using Barcode DNA The assembled DNA was searched for species-specific primers. As a result of BLAST, nine chloroplast DNA loci were selected among 279 nucleotides and annotated genes matched in Scutellaria species. All the transcripts containing detected nucleotides and chloroplast DNA were subjected to primer design with Primer3. Among the resulting large number of primer pairs, 4 primers that specifically amplified DNA in 3 species were selected (Table  7 ). As shown in Figure  6A    3. 9. Validation of Species-Specific Primers Using Barcode DNA The assembled DNA was searched for species-specific primers. As a result of BLAST, nine chloroplast DNA loci were selected among 279 nucleotides and annotated genes matched in Scutellaria species. All the transcripts containing detected nucleotides and chloroplast DNA were subjected to primer design with Primer3.
indica L. were actually S. indica var. tsusimensis (H. Hara) Ohwi  [2]. In the NCBI GenBank database, about 17 species in the genus Scutellaria L. have reported the complete chloroplast genomes. However, among the five species of Scutellaria L. selected for this study, only S. baicalensis Georgi has been reported as a complete chloroplast genome. A specific primer developed using the reference genome was tested but classification failed because it did not show specific amplification. For this reason, we performed whole-genome de novo assembly to obtain the genome of the subspecies S. indica var. tsusimensis (H. Hara) Ohwi. Most of the genes did not have hits and 279 genes matched the genus Scutellaria. Primers were prepared by screening these 279 genes and nine annotated chloroplast barcoded DNA loci.
Since the primers prepared with each sequence registered in GenBank did not show specific amplification, we aimed to design primers that were specific to each species by using the gene matched with the genus Scutellaria via BLAST. As a result, four specifically amplifying primers were designed and three species could be classified. The SP primer was specific to S. pekinensis var. transitra (Makino) H. Hara (S. pekinensis var. transitra (Makino) H. Hara voucher KUS:2006-1082 trnH-PsbA intergenic spacer, partial sequence; and PsbA (psbA) gene, partial CDS). It was prepared using the base sequence of the chloroplast (KX060016. 1). Primers (ST1 and ST2 primers) specific to S. indica var. tsusimensis (H. Hara) Ohwi were prepared using the annotated chloroplast barcode DNA AtpI_0 and rbCL_3 nucleotide sequences.
The sequences of these two barcode DNAs were registered in the NCBI GenBank database and given accession numbers MZ714561 and MZ714562, respectively. For S. baicalensis Georgi, the complete chloroplast genome sequence (S. baicalensis Georgi isolate BOP028266 chloroplast, complete genome (MF521633. 1)) was deposited in GenBank, so it was possible to obtain the specific SB primer. The SL primer was produced using the nucleotide sequence of the S. indica L. TCP transcription factor (CYC2B) gene, partial CDS (KM526800. 1), but amplified DNA in two species, S. indica L. and S. indica var. tsusimensis (H. Hara) Ohwi. However, when this primer was used with the ST1 or ST2 primer, S. indica L. could be discerned. The SD1 primer amplifies DNA in the Scutellaria insignis chloroplast, the complete genome (KT750009.
Acknowledgments The authors thank  Prof. Jean-Marc Allain  for access to the OCT imager. The authors also acknowledge all members of the  Barakat group  for their constructive input during the project and the preparation of the manuscript. This work was funded in part by an endowment in Cardiovascular Bioengineering from the  AXA Research Fund  (to AIB) and an  AMX doctoral fellowship  from  Ecole Polytechnique  (to CAD).
Data Collection Kyphosis is a sagittal disorder of the spine, and its diagnosis is based clinically on the arrow of kyphosis measured with plumb lines measured using the half sum of the high thoracic arrow measured at C7 and the lumbar lordosis arrow at L2 (Figure  1 ). We defined kyphosis as an arrow >40 mm. SPA can be corrected actively or passively, although kyphosis is a definite deformation (Figure  2 ). For clarity, we use the term "kyphosis" here as a generic term that includes all types of SPA. The following risk factors were studied: neonatal characteristics; sex; prematurity (<37 weeks of amenorrhea); intrauterine growth retardation (defined as a neonate of size and/or weight <10th percentile for gestational age); associated Abbreviations: EA, Esophageal atresia; SPA, Sagittal posture abnormalities.
We examined the performance of the selected models in terms of calibration using the Hosmer-Lemeshow goodness-of-fit test and discrimination by calculating the c-statistics  (11). Statistical testing was performed at the two-tailed α level of 0. 05. Data were analyzed using SAS software (version 9. 4, SAS Institute Inc. , Cary, NC, USA). Values are expressed as the number/total number of patients (%).
In the second step, the wave vectors are analyzed independently according to the different schemes. If the wave vector data exceeds the capacity of the available memory, both algorithms split the job into several groups at the price of recalculating the image FFTs several times (see "Appendix C" for more details). The program is written in C++11 and CUDA v. 10. 2 with graphical support of the OpenCV 3. 0 library. We tested the program with the Fourier transform libraries CUFFT (version provided in CUDA v. 10. 2) for GPU execution and FFTW 3. 3. 3 [33]  for the CPU implementations. The code was compiled with MS compiler v120 and the compiler of CUDA v. 10. 2 in Visual Studio 2019. The program was executed on a machine with the following specifications: -CPU: Intel Core TM i9-9880H, -32 GB DDR4 RAM, -Graphic card: NVIDIA Quadro RTX 4000 with 8GB of dedicated G-RAM memory, Test images of 512 × 512 pixels were taken from the experiment described in Sect.
Therefore, at processing images composed of many pixels, both the WITH_FT and WITHOUT_FT algorithm must spend a large fraction of time preparing the time sequences before their analysis. Considering for example the WITH_FT at processing 16384 images, the first step and memory IO operations occupy 44% of the execution time with images composed of 1024 × 1024 pixels, and they occupy 62% of the execution time for the images composed of 2048 × 2048 pixels. The performance loss caused by large datasets can be partially mitigated by adopting larger memory areas to store the image FFTs. As a final test, we processed 16384 images of 512 × 512 pixels with the CPU-WITH_FT algorithm releasing to the program 23 GB of RAM. In this configuration, we obtained a speedup of a factor of 2 compared to the previous tests in which the RAM was limited to 8 GB, thanks to the larger available memory area.
3  [34]  and is freely available for download at  [35]. The program can readily be used for calculating the structure function from an arbitrary set of images. A more efficient version of the code (about 10 times faster on GPU) is currently under development and will be commercially available in the next future. We split the calculation on the time sequence in two parts d (m) = da (m) + dc (m) where: da (m) = 1 N -m N -1 n=m | Ĩn-m| 2 + | Ĩn| 2 , (B. 1) dc (m) = 2 N -m N -1 n=m Re Ĩ * n-m Ĩn. (B. 2) The term da (m), i. e. , the average of the 2D spatial power spectra of the images with a computational complexity of O (N ), is calculated by using the following iterative formula: da (N -n -1) = n n + 1 da (N -n) + |In| 2 + |IN-n-1| 2 n + 1 , (B. 3) where the index n is in the range [0, N -1].
The vertical line marks the crossing point in which the algorithm divides the execution from one into two groups. The labels "Step 1" and "Step 2" refer to the steps of the algorithm described in the main text and the label "Disk" refers to the memory I/O operations WITH_FT algorithm, instead, operates sequentially on different groups of wave vectors for all the d (m) and saves the partial results of each group on the hard drive. The partial results are merged at the final stage of the program. In practice, in both algorithms, the images are loaded and Fourier transformed one time for each group because only a part of the FFTs data can be saved on the local memory. The impact of repeating these operations over the entire execution time is presented in Fig. 6 , in which we present the execution time as a function of the number of images to process.
Acknowledgements We thank  R. Cerbino  for valuable comments on the manuscript and  J. Braun  for proofreading the manuscript. This research was partially carried out under the framework of the  E2S UPPA Hub Newpores and Industrial Chair CO2ES  supported by the " Investissements d'Avenir" French program  managed by  ANR  ( ANR-16-IDEX-0002 ). This work received funding from the  French space agency CNES  and the  European Space Agency (ESA)  within the  ESA MAP   Technes  project. It also benefit from the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sk lodowska-Curie Grant  Agreement No 801110 and the  Austrian Federal Ministry of Education, Science and Research (BMBWF). It reflects only the author's view, the  EU Agency  is not responsible for any use that may be made of the information it contains.
Hypotheses are tested with data from two consecutive waves of a sociometric panel study among 148 employees of three units in a Dutch childcare organization. Stochastic actor-oriented models (SAOMs; Snijders 2017;  Snijders, van de Bunt, and Steglich 2010)  are employed to measure the association between the gossip exchanged in wave one and the evolution of the friendship networks between waves one and two. Results reveal positive gossip favors the creation and maintenance of receiver-target friendships, whereas negative gossip inhibits them. We also find evidence supporting that, for damaging relationships, negative gossip needs to originate in more than a single sender. Positive gossip about a high number of targets seems to discourage friendships with colleagues in general, while negative gossip about many targets produces diverging trends across the units investigated.
Data Data come from a sociometric panel dataset of the relationships between 148 employees in three units of a Dutch childcare organization. The dataset spans three years and contains six waves. Our analyses, however, are restricted to the first two waves  (March 2008 and September-October 2008) , when complete gossip data (sender, receiver, target, and valence) are collected. The organization is a major independent, subsidized, regional child protection institution. The three units (hereafter units A, B, and C) are medium-sized daycare units focusing on children with special needs. Professions comprised behavioral scientists, medical doctors, (physio) therapists, pediatricians, social workers, and administrative and household staff. All units are formally subdivided into work teams, each team responsible for a group of children.
The data were collected using self-administered computer-based questionnaires, interviews, and secondary data. We gathered information covering individual attributes, employment data, the formal team structure of each unit, relational data, and gossip between employees (a complete list with all the information available in the dataset can be found in Table  S1  in the Supplementary Material). Rosters of names  (Hlebec 1993)  were used to collect sociometric information and gossip (cued recall  ; Marsden 1990 ) to reduce biases due to memory effects.
Discussion and conclusion The present study introduced simple and complex contagion processes into the study of workplace gossip and its impact on friendship relations. It argued that hearing gossip from multiple senders or about multiple targets impacts receivers' friendship relations with gossip targets. The related hypotheses were tested with longitudinal sociometric field data on gossip and friendships between colleagues in three units of a Dutch childcare organization. Stochastic Actororiented Models yielded at least partial support for three of the nine hypothesized effects and contradicting evidence for two others. Simple contagion processes are reflected in two of the three significant findings. This is in line with the core prediction of reputation scholars, according to which positive gossip favors positive interactions between receiver and target, whereas negative gossip discourages them  (Costello and   and adjusted with Benjamini's and Hochberg's method.
Funding Open access funding provided by  Linköping University. Financial support was received from  "la Caixa" Foundation  ( ID 100010434  [fellowship code  LCF/BQ/EU17/11590070 ]) for  José Luis Estévez  and from the  Dutch Organization for Scientific Research  ( NWO 2017 Gravitation Program  [grant number  024. 003. 025 ]) for Rafael Wittek. Partial financial support was also received from the  European Research Council  (the  European Union 's  Horizon 2020 research and innovation program  [grant agreement number  648693 , PI: Károly Takács]).
coli). The visualization of bacteria captured on the surface was performed using an Olympus IX71 fluorescence microscope equipped with a xenon lamp emitting at 470 and 490 nm. The microscope was connected to a DP71 digital camera and fluorescence images of the samples were taken by using Qcapture imaging software (QImaging Corporation, Surrey, BC, Canada). Six to eight images were collected per sample at different sites of the membranes with a 20× magnification. The fluorescence images were analyzed with ImageJ software  [39]  in order to estimate the corresponding bacterial surface coverage.
We analyzed the data collected from the interviews by first identifying the food chain where the actor interviewed was involved. Second, we searched who was at the origin of the introduction of the Blockchain in the food chain. The results are given Section 5. 1. In total, 12 food chains were identified. Of these, four were subjected to further data analysis, as we felt they were of different types (blockchain introduced by different types of actors and provided by different technical providers), and we had contacts to investigate further if necessary. In addition, we selected these four cases because the first survey provided us with enough data to be sure to obtain interesting results.
For the chicken chain, the corpus of data consists of one interview with the retailer, one interview with the organization for the defense of the appellation and origin, one interview with the initial blockchain supplier, one interview with the new technical supplier, one interview with a technical supplier who was particularly familiar with the case in question, and one press release. For the minced steak chain, the corpus of data consists of one article published in a French trade journal, two interviews conducted with the technical supplier, and one press article on the introducing actor for the food chain. For the milk chain, the corpus of data consists of one interview with the blockchain provider, one interview with the cooperative group to which the farmers belong, one press release from the cooperative, and one press release from a food industry federation.
all the information contained in the blockchain is not always accessible in a uniform manner to all the players in the chain; 14. the implementation of such a system can generate fears and mistrust on the part of agricultural producers. Subsequently, these themes formed the basis for the analysis of the data related to the four cases studied. These themes were used to code the material from the second study using NVivo. To interpret our results, we reuse the coding made by  [81]  de Moya and Pallud (2020) of  [79]   Foucault's (1977)  work on the panopticon. They constructed this reading grid in order to interpret the experiences of users of "quantified-self" technologies  [81]. Our work will consist of revealing the elaboration of a panopticon by the implementation of blockchain in food chains, based on the material obtained from the actors at work in the construction of this panopticon.
The 12 Food Chains Introducing Blockchain The data collected from the first range of interviews allowed us to identify 12 food chains having recently introduced blockchain in French agri-food chains. These 12 chains are: • a corn chain where the "pivotal" or central actor appears to be a corn trader and producer; • a vegetable chain where a large part of the production is labeled "organic" and where the central actor is also a producer and trader; • a chain of poultry from a specific geographical area whose central actor is the retailer; • a honey chain where the cooperative collects honey from all over France and the retailer is the initiator of the blockchain; • a tomato chain with less than 10 producers in a specific geographical area, where the central actor is the retailer; • an egg chain protected by a geographical indication and where the blockchain was introduced by the retailer; • a milk chain where the blockchain project was initiated by the agricultural cooperative; • a wheat chain with very few producers and where the project was initiated by the agricultural cooperative; • a duck meat chain whose project was also initiated by the agricultural cooperative; • a milk chain whose project was carried out by a food brand initiated by the agricultural producers themselves; • a meat chain in which the actor introducing blockchain is a small food company; • a chain in the process of being created, where a few producers want to get together to use blockchain to enhance the value of their cereal production without having to rely on labelling or the creation of specifications for an appellation.
Analyses of Discourses Thanks to an Inductive Coding We analyzed the data from these four study cases from the codes identified during the open coding carried out following the first exploratory study. We kept only the codes for which we had enough data (so, we eliminated the codes 2. blockchain has an impact on the continuity of relationships between chain actors; 3. blockchain has an impact on the price of the product; 6. blockchain does not replace physical meetings producers/consumers; 14. blockchain can generate fears and mistrust on the part of agricultural producers). The results are summarized in Tables  3  and 4. The Table  3  gathers the verbatims relevant to the main results relating to the management of information to be entered into the blockchain, while Table  4  looks more specifically at the consequences of blockchain introduction for farmers.
The dwell volumes and extra-column volumes were respectively 170 μL and 22 μL in 1 D, and 80 μL and 8. 5 μL in 2 D (loop volume excluded). For the make-up flow strategy, an additional high-pressure binary pump from an Acquity UPLC I-Class liquid chromatography system from Waters (Milford, MA, USA) was used. The schematic representations of the four different setups used in this work are given in Fig. 1. The 2D-LC system was hyphenated to an Agilent Q-TOF mass spectrometer (model G6545B) equipped with a Jet Stream electrospray ionization (ESI) source. The 2D-LC-UV system and the additional high-pressure pump were controlled using Agilent Open-Lab software and Waters MassLynx software, respectively. The mass spectrometer was controlled using Agilent MassHunter software. HRMS data were processed using Agilent MassHunter qual-itative analysis software.
PFSS Modelling To estimate where open flux is rooted in the photosphere, potential field source surface (PFSS,  Altschuler and Newkirk, 1969; Schatten, Wilcox, and Ness, 1969)  modelling was carried out using the pfsspy software package  (Stansby, Yeates, and Badman, 2020). Several observatories provide synoptic magnetic field maps, using different observing equipment, techniques, and data processing pipelines (see e. g. Riley et al. , 2014, Table   1  for a list). In this study synoptic maps from the Kitt Peak Vacuum Telescope (KPVT,  Livingston et al. , 1976 ), Michelson Doppler Interferometer (MDI, Scherrer et al. , 1995) , Synoptic Optical Longterm Investigations of the Sun (SOLIS,  Keller and NSO Staff, 1998) , and Global Oscillations Network Group (GONG,  Harvey et al. , 1996)  were used.
The resulting dataset is available at https://doi. org/10. 5281/zenodo. 4783720, and the code used to generate it at https://doi. org/10. 5281/zenodo. 4787880. Two examples of this methodology are shown in Figure  1 , one during solar minimum (left hand panels) and one during solar maximum (right hand panels). The top two panels show the photospheric maps used as input to the PFSS modelling, and the middle two panels show the photospheric footpoints of open field lines, coloured by B r,. The bottom panels show the partitioning of open field lines into active region and coronal hole regions; for more details see Section 2. 2.
Contribution of Active Regions to the Solar Wind The total open flux in each PFSS extrapolation was calculated by summing all radial magnetic field values on the source surface, and multiplying by the constant solid angle area element of each cell shown in different coloured lines. Where they overlap, the results from each observatory agree well, even on monthly timescales within individual solar cycles. The fraction of open solar flux contained within active regions follows the solar cycle; for comparison, the middle panel shows the rotation averaged sunspot number (SILSO World Data Center, 2021). Larger amplitude sunspot cycles result in a larger fraction of open flux originating in active regions. This is a non-trivial result, depending on the details of how open flux is distributed between coronal holes (both equatorial and polar) and active regions, and how this varies with cycle amplitude.
g. in 2003, 2011, 2016)   As well as investigating variations over time, our dataset allows investigation of the angular extent of active region open flux in the heliosphere. Figure  6  shows the fraction of all source surface longitudes connected to active region open flux, as a function of source surface latitude and time. This reveals substantial variation between different solar cycles. During Cycles 21 -23 active regions were connected to heliospheric latitudes ±60 • , with their extent decreasing as the solar cycle declined. In contrast, during the Cycle 24 their heliospheric connections were typically limited to ±30 • , with no obvious reduction in this extent as the cycle progressed. The gaps during solar minima were also highly variable: between both Cycles 21, 22 and the current minima there were extended ∼ 5 year periods with hardly any active region contributions to the solar wind, with.
Acknowledgments D. S. is supported by  STFC  grant  ST/S000240/1. L. v. D. G. is partially funded under under  STFC  consolidated grant number  ST/S000240/1  and acknowledges the  Hungarian National Research, Development and Innovation Office  grant  OTKA K-131508. L. M. G. is grateful to the  Royal Society  for support through a  University Research Fellowship. T. S. H. is supported by  STFC  grant  ST/S000364/1. The authors thank the referee for constructive comments that improved the paper. This research used the following software packages: pfsspy (Stansby, Yeates, and Badman, 2020), sunpy (The SunPy Community et al. , SOLA: ar_sources_final_arxiv. tex; 11 August 2021; 0:46; p. 13 D. Stansby et al. 2020), astropy (The Astropy Collaboration et al. , 2018), Matplotlib (Hunter, 2007). This work utilises SOLIS data obtained by the  NSO   Integrated Synoptic Program (NISP) , managed by the  National Solar Observatory , which is operated by the  Association of Universities for Research in Astronomy (AURA), Inc.