dataesr/scientific-paragraphs-categorization huggingface dataset:
7%) Failed attention check (study 2b) 1,195 (30. 8%) 1,367 (25. 6%) 5,528 (30. 2%) 8,090 (29. 4%) Final sample Study 1a 381 622 566 1,569 Study 1b 327 553 546 1,426 Study 2a 323 690 2,971 3,984 Study 2b 277 576 2,660 3,513 Note. Study 1b and study 2b refer to the speedboat dilemmas. Recall that all of our subjects responded to one trolley and one speedboat dilemma. NaturE HumaN BEHaviour | www. nature. com/nathumbehav 2. Our knowledge on the cultural universality of the effect of personal force and intention in moral judgements is scarce. 3. The resulting database (with many types of trolley problems and additional measures) could assist and guide future research and applications on moral thinking.
Using RNA extracted from the serum of patient samples, we find that the combined PLUM reader and paper-based Zika sensor provide analytical sensitivity and specificity for the Zika virus equivalent to RT-qPCR, with a diagnostic accuracy of 98. 5%. We further show that the combination of molecular, hardware and software tools can be used as an adaptive system for the point of need. In a second proof-of-concept effort, we demonstrate that by simply changing the molecular components that confer specificity to the assay (in particular, NASBA primers and toehold switch), we can detect the chikungunya virus (98. 5% accuracy), which is another arbovirus with worldwide distribution that causes significant morbidity  [26] [27] [28].
All of the data were collected and analysed using the in-house PLUM reader. RT-qPCR was performed in parallel for all experiments for comparison. Using the same method, validation was followed by a patient trial using RNA extracted from patient serum samples. concentrations as low as 1. 24 molecules per µl (equivalent to ~2 aM) (Fig. 2a ,b and Supplementary Method 1). This is an increase in analytical sensitivity of three orders of magnitude over our previously published results, which was achieved by optimizing primer concentration (500 nM to 12. 5 uM)  15  , and, ultimately, we found that reducing the primer concentration (to 500 nM) provided the best sensitivity. Before transferring the assay to the teams in Latin America, we wanted to confirm that the workflow would accommodate the detection of virus-encapsulated target sequences.
2 , bottom). Optical measurements. Optical absorbance measurements are a routine and key functionality for plate readers and are central to measurement of the LacZ reporter output for the Zika virus diagnostic (570 nm). To measure absorbance, conventional plate readers directly monitor the intensity of the wavelength of interest and create an absorbance value by inverting the quantified decrease in transmitted light signal (Supplementary Fig. 3a )  32. However, without the sophisticated components of conventional plate readers, such as monochromators and optical slits, we needed an alternative approach. Our solution was to use computer-vision-based software to compensate for the simplicity of the PLUM reader's components (for example, camera-based measurement; Supplementary Fig. 3b ). Here, rather than measuring absorbance directly, we use all the light reaching the RGB channels of the camera to measure the spectral colour shift caused by optical changes in the sample (Supplementary Fig.
2 , left column). Using the colour additive theory, the resulting algorithm calculates absorbance-equivalent values by taking a ratio of the increasing colour channel over the decreasing colour channel value  33, 34. During each experiment, an image of the plate is collected at each capture interval (for example, 5 minute periods), and the RGB channel values for all well regions of interest are stored in a data file (for example, CSV). To quantify the purple reporter signal of Zika-positive samples, onboard software calculates the ratio of blue channel values over green channel values, providing similar absorbance-equivalent outputs (Supplementary Fig. 2 ). Once done, using well-assignment data from the plate map, data can then be automatically analysed, graphed (Fig. 2g ), uploaded via the Internet to the cloud storage (Amazon Web Services S3) and shared worldwide with collaborators.
2e ). In PLUM, a low-cost camera and a credit-card-sized computer are used to collect and analyse the data from the entire multiwell plate in a single image capture. This strategy substantially reduces the complexity and cost of the device and moves much of the data collection burden to the software. Device configuration. The PLUM reader was assembled (Fig. 2e ) using a Raspberry Pi computer, off-the-shelf electronics and rapid prototyping techniques such as three-dimensional (3D) printing and a laser-cut acrylic housing. Much like a conventional plate reader, users interact with a user-friendly graphical user interface (GUI) (Fig. 2f  and Supplementary Fig. 1 ) that coordinates all functions of the PLUM reader. An LCD touch screen is integrated into the device for a simple and compact system that can be easily brought, as we did for this project, to multiple sites of use.
This toaster-size device (20 cm × 20 cm × 20 cm) weighs only 2 kg, which compares well to conventional devices that are considerably bulkier and can weigh as much as 35 kg (for example, BioTek Neo2). The device is capable, with the correct adaptor, of operating on global power supplies or can run for 8-9 h using a standard lithium-ion brick battery (100 Wh). PLUM software controls the 3D-printed plate reader tray, powered by a servomotor, for automated operation and dependable control over tray position (Fig. 2e ). Through the GUI, the user can setup the plate map (for example, control and samples wells) for onboard data analysis and plotting at the end of each experiment (Fig. 2f ,g and Supplementary Fig. 1b-d ). Once the plate is loaded, the position of the plate is identified through a validation algorithm that automatically finds reusable yellow acrylic markers that sit in the four corner wells of the plate for image alignment (Supplementary Fig.
1a ). Upon recognition of these markers, a digital template of the multiwell plate is used to assign the red, green and blue (RGB) channel pixel values for each well into regions of interest, which are used to create absorbance-equivalent data for all 384 wells. Collateral benefits of this approach are that PLUM's computer vision-enabled software can be easily configured to collect optical data from any plate format, and periodic calibration of device alignment is not necessary. Light path. Another challenge to operationalizing the camera-based approach was the collection of high-quality, high-sensitivity data with such a simple hardware configuration. The light box, which is located at the top of the device, sits above the multiwell plate, with the camera looking up at the colour-based paper reactions in the plate much like an illuminated-stained glass window (Fig.
3c ). This threshold (0. 1603 arbitrary units (a. u. ) above background) was then applied to the analysis of data from double-blinded, paper-based testing of extracted RNA from patient serum samples. The resulting PLUM-based analysis allowed for the differentiation of positive from negative samples as early as 130 min (Supplementary Fig. 4c ). A total of 268 patient samples were analysed using our diagnostic system in parallel with RT-qPCR (Fig. 3d  and Table  1 ). In comparison with the RT-qPCR assay  25  , we detected four false-negative and zero false-positive samples, which translates to a calculated  35  diagnostic accuracy and specificity of 98. 51% (95% confidence interval (CI), 96. 22-99. 59 %) and 100%, respectively. Datasets from the field trial diagnostic (0. 1603 a. u) and RT-qPCR (Ct ≤ 38) were plotted to show the similar accuracy of the respective thresholds in correctly segregating positive and negative patient samples (Fig.
Accordingly, it is not possible to directly correlate the results from synthetic RNA (Fig. 2b ) to the lentiviral data (Fig. 2c, d ) or viral stock (Fig. 3b ). PLUM (a. u. )   3  | Performance of the diagnostic system for the Zika virus in Latin America. a, Specificity was determined for ZIKV Am against a panel of off-target viruses (at 10 6 PFU ml -1 ) that included ZIKV Af, CHIKV, YFV and DENV-1-4. b, Analytical sensitivity experiment using cultured Zika virus as well as the mean Ct value obtained in the parallel RT-qPCR (Supplementary Fig. 4b ). NA, not applicable. Visual outputs at final time point of 235 min are shown below the graphs in a and b (yellow, negative; purple, positive). The graphs in a and b represent the mean ± s. d. of technical replicates from a single representative experiment (three independent biological triplicates were performed) at 130 min of the cell-free experiments (preceded by 70 min NASBA reaction).
2e ). The combined hardware and software of the unit provides a self-contained, automated and easy-to-use system and includes onboard data collection and analysis, incubation and cloud-based data storage. These combined purpose-built molecular and hardware technologies come together to help move a proof-of-concept, lab-based assay towards providing low-cost, clinical-grade diagnostics at the point of need. Using 268 patient samples, we found that the paper-based Zika diagnostic could provide analytical specificity and sensitivity equivalent to RT-qPCR, with a diagnostic accuracy of 98. 5% (Table  1 ). Similar performance for the chikungunya sensors shows promise for a path towards a generalizable diagnostic approach. The PLUM reader adds considerably to the molecular diagnostic assay by providing the option for portable use and, via signal thresholding, the automated discrimination of positive and negative samples.
Discussion This report provides the results of validation studies, onsite in Latin America, of paper-based synthetic gene networks  22, 42  as diagnostic systems for the Zika and chikungunya viruses (Figs. 3  and 4 ). This work also extends the concept of low-cost and portable companion hardware by describing the development of the PLUM reader. For both ZIKV and CHIKV viruses, the diagnostic trial was performed using RNA extracted from patient serum. All data were collected and quantified using the PLUM reader. The patient trial data were collected over the course of 235 min. The segregation of positive and negative samples was performed at the 130 min time point for the ZIKV diagnostic using the set ZIKV threshold (Fig. 3c  and Supplementary Fig. 4c ) and at the 75 min time point for the CHIKV diagnostic using the set CHIKV threshold (Fig.
DNA encoding the target chikungunya sequence was ordered through IDT as dsDNA with a T7 RNAP promoter. The primers used to amplify the target DNA are listed in Supplementary Table  1. After amplification, in vitro T7 RNAP-based transcription was performed as described above and then purified. Virus strains, virus culture and purification. All arboviruses used in this study were provided by the Laboratory of Virology and Experimental Therapy, Oswaldo Cruz Foundation (FIOCRUZ), in Recife, Brazil. Zika virus, American strain PE243 (GenBank accession no. KX197192), was isolated from an infected patient in Pernambuco State, Brazil. Zika virus, African strain MR766 (GenBank accession no. AY632535), was isolated from infected mouse brain suspension. All four Dengue virus (DENV (1-4)) serotypes used were isolated from patient samples in Pernambuco State, Brazil: DENV-1, strain PE/97-42735 (GenBank accession no.
EU259529), DENV-2, strain PE/95-3808 (GenBank accession no. EU259569), DENV-3, strain PE/02-95016 (GenBank accession no. KC425219) and DENV-4, strain PE/10-0081 (unpublished). Yellow fever virus, strain 17DD (GenBank accession no. DQ100292) is used as a vaccine strain. Chikungunya virus, strain PE2016-480 (unpublished), was isolated from a patient serum in Pernambuco State, Brazil, and chikungunya strain PB302 (unpublished) was isolated from serum of patient in Paraiba State, Brazil. Mayaro virus, strain BR/Sinop/H307/2015 (GenBank accession no. MH513597. 1) was provided by the Federal University of Mato Grosso in Sinop, Brazil. Arbovirus cultures and titration. All viruses used in this study were propagated in Vero cells using DMEM (Gibco) supplemented with 2% of inactivated FBS (Gibco), 2 mM ʟ-glutamine (Gibco), 100 units per ml of streptomycin and 100 μg ml -1 of penicillin (Gibco) at 37 °C under 5% CO 2.
For results analysis, the QuantStudio Design and Analysis Software version 1. 5 was used with automatic threshold and baseline. Samples were considered positive with Ct ≤ 38. 0. PLUM hardware. The PLUM reader consists of two chambers housed within a laser-cut acrylic box fastened together with metal screws and mounting brackets (Fig. 2 ; McMaster-Carr, 8505K14 and 98164A061; Digi-Key, 36-621-ND). The light box is designed with 54 LEDs (YJ-VTC-5730-G01-65, YUJI LED) for illumination. The motorized tray is designed to hold a standard multiwell plate and positions the plate at the correct focal length for the camera (US$35, Raspberry Pi V2, 8-megapixel). This configuration allows for clear visualization of the plate from below for capture of the image data (Supplementary Fig. 3 ). On the side panels, the detection chamber houses a fan-based air incubator (Incubator Warehouse, IncuKit MINI) for heating, DS18B20 temperature sensor for recording (RobotShop, RB-Dfr-270), two tray rail guides, a Hitec HSR-1425CR continuous servomotor with 12T Metal Servo Gear (RobotShop, RB-Hit-78, RB-Sct-458) for controlling the tray and a microswitch (RobotShop, RB-Tam-71) for homing the tray.
The servomotor gears engage with 3D-printed tray teeth to open and close the tray. The electronic components of PLUM are controlled by a Raspberry Pi 3B. The camera (Raspberry Pi Camera Module V2) in the detection compartment and the LCD display unit (Raspberry Pi Touch Display 7 inch) mounted on the front panel of the PLUM are connected directly to the Raspberry Pi unit with flex cables (Flex Cable for Camera-24 inch/610 mm). The Raspberry Pi controls the detection unit components, with the exception of the incubator, via a 40-pin header ribbon cable connected to the custom-made motherboard PCB (printed circuit board) (Supplementary Information, vendor). The motherboard PCB facilitates connections of the servos, temperature probe, required resistors, microswitch, power to the LCD display and light box operation with mating connectors.
Acknowledgements We thank all of the  Pardee laboratory  members as well as  T. Narahari ,  J. Dahmer ,  A. Sklavounos ,  T. Kim ,  M. Satkauskas ,  I. Clotea ,  S. M. Ho ,  J. Lamannna ,  C. Dixon  and  A. R. Wheeler  (all at the  University of Toronto ) for fruitful discussions about experimental design and analysis methodology and help with assembling the PLUM readers. We also thank  F. Federici  and  A. Arce  ( Pontificia Universidad Catolica de Chile ) for discussion on the use of locally manufactured cell-free reagents. M. K. is supported by the  Precision Medicine Initiative (PRiME) at the University of Toronto , internal fellowship number  PRMF2019-002. S. J. R. d. S. is supported by a doctoral fellowship sponsored by the  Foundation for Science and Technology of Pernambuco-Brazil  ( IBPG-1321-2.
23  Still, 15 genomes as of 27/02/2022 being hybrids of these two variants and highly similar between each other were reported since February 2022 (https://github. com/covlineages/pango-designation/issues/444). We herein report three infections by a recombinant SARS-CoV-2 Delta 21K/AY. 4-Omicron 21K/BA. 1 whose genome is highly similar to the 15 previously reported genomes and the isolation of the recombinant virus from one of the patients.
Materials and methods Nasopharyngeal samples were collected from two patients in our university hospital institute (Méditerranée Infection; https://www. mediterranee-infection. com/) and tested for SARS-CoV-2 infection by real-time reverse transcription-PCR (qPCR) as previously described. 3, 28, 29 The third patient was sampled in a private medical biology laboratory in southern France (Inovie Labosud, Montpellier, France). qPCR assays that screen for SARS-CoV-2 variants were performed as recommended by French public health authorities (https://www. data. gouv. fr/fr/datasets/donnees-de-laboratoires-pour-le-depistage-indicateurssur-les-mutations/). In our center this included the detection of spike mutation among which K417N (Thermo Fisher Scientific, Waltham, USA), combined with testing with the TaqPath COVID-19 kit (Thermo Fisher Scientific) that target viral genes ORF1, N (nucleocapsid) and S (spike), as previously reported.
Then, sequence read processing and genome analysis were performed as previously described. 3, 28 Briefly, for Illumina NovaSeq reads, base calling was performed with the Dragen Bcl Convert pipeline [v3. 9. 3; https://emea. support. illumina. com/sequencing/sequencing_software/bcl-convert. html (Illumina Inc. )], mapping was performed with the bwa-mem2 tool (v. 2. 2. 1; https://github. com/bwa-mem2/bwa-mem2) on the Wuhan-Hu-1 isolate genome (GenBank accession no. NC_045512. 2) then cleaned with Samtools (v. 1. 13; https://www. htslib. org/), variant calling was carried out with freebayes (v. 1. 3. 5; https://github. com/freebayes/freebayes) and consensus genomes were built using Bcftools (v. 1. 13; https://samtools. github. io/bcftools/bcftools. html). ONT reads were processed with the ARTIC-nCoV-bioinformaticsSOP pipeline v1.
1. 0 (https://github. com/articnetwork/fieldbioinformatics). Nucleotide and amino acid changes relatively to the Wuhan-Hu-1 isolate genome were obtained using the Nextclade tool (https://clades. nextstrain. org/). 25, 26 Nextstrain clades and Pangolin lineages were determined using the Nextclade web application (https://clades. nextstrain. org/)  25, 26 and the Pangolin tool (https://cov-lineages. org/pangolin. html),  27 respectively. Genome sequences described here were deposited in the GenBank sequence database (https://www. ncbi. nlm. nih. gov/genbank/)  30 990851, OM990852, OM991095, OM991295), and on the IHU Méditerranée Infection website (https://www. mediterranee-infection. com/sars-cov-2-recombinant/). The Simplot software (https://sray. med. som. jhmi. edu/SCRoftware/SimPlot/) 31  was used for recombination.
4 and Omicron 21K/BA. 1 variants in the sequence database of our institute that contains approximately 50,000 SARS-CoV-2 genomes; then, they were incorporated in the phylogeny together with the genome of the Wuhan-Hu-1 isolate. As a matter of fact, it should not be acceptable to make a phylogenetic tree based on concatenation of sequences from different origin. SARS-CoV-2 culture isolation was performed by inoculating 200 µL of respiratory sample on Vero E6 cells as previously described. 36  Cytopathic effect was observed by inverted microscopy. Viral particles were visualized in the culture supernatant by scanning electron microscopy with a SU5000 microscope (Hitachi High-Technologies Corporation, Tokyo, Japan), as previously described. 38, 39  Briefly, amino acid changes were introduced in the framework of a complete This study was approved by the ethics committee of University Hospital Institute Méditerranée Infection (No.
The three viral genomes [GenBank Accession no. OM990851, OM990852, OM991095 (https://www. ncbi. nlm. nih. gov/genbank/)  30 ; available on the IHU Méditerranée Infection website (https://www. mediterranee-infection. com/sars-cov-2-recombinant/)] were hybrids of Delta 21J/AY. 4 and Omicron 21K/BA. 1 variant genomes (Figures  1a, b, c ; Table  1 ). At positions harboring mutations compared to the genome of the Wuhan-Hu-1 isolate, mean sequencing depth was between 1,163-1,421 reads and mean prevalence of the majoritary nucleotide was between 99. 4-99. 9% (with minimum values between 80. 3-98. 7%), ruling out the concurrent presence of two variants in the samples either due to co-infection or to contamination. In this SARS-CoV-2 recombinant, most of the spike gene was replaced in a Delta 21J/AY.
4 variant genomes identified in our institute, while the region spanning a large part of their spike gene was most closely related to Omicron 21K/BA. 1 variant genomes identified in our institute. The respiratory sample from which the first recombinant genome was obtained was inoculated on Vero E6 cells the day following recombinant identification, and cytopathic effect was observed after 4 days (Figures  2a, b ; collection of strains of IHU Méditerranée Infection, no. IHUMI-6070VR). The same day, supernatant was collected and next-generation genome sequencing was performed using Nanopore technology on a GridION instrument after PCR amplification with Artic primers, which allowed obtaining the genome sequence of the viral isolate 8 h later [GenBank Accession no. OM991295 (https://www. ncbi.
nlm. nih. gov/genbank/)  30 ; available on the IHU Méditerranée Infection website (https://www. mediterranee-infection. com/sars-cov-2-recombinant/)]. At mutated positions compared to the Wuhan-Hu-1 isolate genome, mean sequencing depth was 2,771 reads and mean prevalence of the majoritary nucleotide was 99. 1% (minimum, 95. 1%), and the consensus genome was identical to that obtained from the respiratory sample, showing unambiguously that the virus isolated was the Delta 21J/AY. 4-Omicron 21K/BA. 1 recombinant. Finally, viral particles were observed in the culture supernatant by scanning electron microscopy with a SU5000 microscope within minutes after supernatant collection (Figure  2c ). The overall structure of the recombinant spike protein was predicted (Figures  3a-c ). When superimposed with the spike of the Omicron 21K/BA.
Ethics This study has been approved by the ethics committee of the University Hospital Institute Méditerranée Infection (No. 2022-001). Access to the patients' biological and registry data issued from the hospital information system was approved by the data protection committee of Assistance Publique-Hôpitaux de Marseille (APHM) and was recorded in the European General Data Protection Regulation registry under number RGPD/APHM 2019-73. from screenshots of the nextclade web application output (https://clades. nextstrain. org). 25, 26 or codes for nucleotide mutations and are marked regions as follows: Green: U; yellow: G; blue: C; red: A; grey: deletions or uncovered regions. Genomes are labelled with the identifiers of the IHU Méditerranée Infection and the GenBank (https://www. ncbi. nlm.
nih. gov/genbank/)  30  genomes the most similar genetically to these regions of the recombinant genomes obtained here were selected from the sequence database of our institute through a BLAST  35  search, then were incorporated in the phylogeny together with the genome of the Wuhan-Hu-1 isolate. Sequences are labelled with the identifiers of the IHU Méditerranée Infection and the GenBank (https://www. ncbi. nlm. nih. gov/genbank/) 30 sequence databases.
Data availability The dataset generated during the current study is available from the GenBank database (https://www. ncbi. nlm. nih. gov/genbank/)  30 (GenBank Accession no. OM990851, OM990852, OM991095, OM991295) and from the IHU Méditerranée Infection website (https://www. mediterranee-infection. com/sars-cov-2-recombinant/).
Study design We performed a prospective, randomized, single-blind, multicentre study in 7 centres in France (Institut de Cancérologie de Lorraine (Nancy), Centre Paul Strauss (Strasbourg), Groupe hospitalier Pellegrin (Bordeaux), Hôpital de la Timone (Marseille), Centre Léon Bérard (Lyon), the University Hospital of Brest and the University Hospital of Bastia). The study was registered with ClinicalTrials. gov under the number NCT02867644, and was approved by the Ethics Committee CPP (Comité de Protection des Personnes) Est III on 3 May 2016 under the number ID-RCB: 2016-A00232-49, and by the French Agency for Health Products Safety (ANSM) on 22 April 2016 under the number 160225B-31. All patients were informed about the study and all provided written informed consent. The study was financed by the national hospital nurse & paramedical research programme (Programme Hospitalier de Recherche Infirmière et Paramédicale-PHRIP; grant obtained in 2015).