dataesr/scientific-paragraphs-categorization huggingface dataset:
Conversely, the baseline hardly distinguishes the bimodal and regimes. In particular, both AIC and BIC are biased towards ZINB predictions, and thus poorly suited for zero-inflation analysis of real data. Robustness for lowly-expressed genes An important consideration is the robustness of AutoZI's performance for lowly expressed genes. Using Poisson-log-normal datasets with average expressions spanning from 10 -4 to 10 2 , we found that AutoZI's decisions became biased towards ZINB for genes with low average expression or, equivalently, average predicted negative binomial mean: notably, 92. 7 (resp. 2. 4%) of NB genes with average expressions above (resp. below) 1 were correctly retrieved. Such results suggest that the statistical problem of detecting zeroinflation becomes harder for low values of the negative binomial mean.
Application to detecting zero-inflation in real datasets A significant application is investigate how zero-inflation affects real datasets and whether the decisions taken by AutoZI have a biological meaning. Negative control (ERCC spike-in and RNA) We apply AutoZI to four droplet-based negative control datasets, spanning a wide range of experimental protocols (10x Chromium v1  [14] , inDrops  [15]  and GemCode  [16] ) and based on ERCC spike-ins and control RNAs. Such datasets do not capture any biological process and the ERCCs were shown not to be zero inflated in  [7]. To investigate whether AutoZI decision-making mechanism can reproduce similar results, we selected ERCC spike-ins and added the 100 most expressed control RNAs in each dataset for joint analysis. 32. 4% of ERCC spike-ins and 100% of control RNAs had sufficient average expression.
Hence we analyze between 24 and 44 spike-ins per dataset. We report decisions from AutoZI in Table  1. AutoZI has a perfectly symmetric prior and is therefore not biased towards any specific decision. However, 98. 3% of ERCC spike-ins and 94% of the control RNA under study are retrieved as NB. These results corroborates the hypothesis from  [7]  that droplet-based ERCC spike-ins measurements are not zero-inflated and even may extend it to the control RNAs part of these datasets. A collection of 10X biological datasets We now check whether the fraction of ZINB genes in PBMC datasets sequenced using 10X Chromium is higher than in previous control RNA data and whether it decreases with the version of the protocol, as technical improvements may suggest. We focus on pbmc3k (10X v1. 1. 0), pbmc8k (10X v2.
1. 0) and pbmc10k (10X v3. 0. 0, with protein expressions). Their cell types were estimated using clustering techniques and marker genes or proteins. We focus on B cells, CD14+ monocytes, CD4 T cells and CD8 T cells. For training, we select genes both among the 1,000 most variable and expressed across all cell types in all datasets. For analysis, in each cell type, we select genes with sufficient average expression in all datasets, yielding between 203 and 228 genes per cell type. We report the percentages of ZINB genes predicted for each cell type by a gene-cell-type extension of AutoZI in Table  2. We note a higher general fraction of zero-inflated biological gene-cell-types (29. 3%) than control RNAs (6%), indicating potential biological phenomena. However, for all cell types, we find that the fraction of predicted ZINB genes decreases with the version of 10X Chromium, potentially showing additional technical factors in zero-inflation.
This may lead to a less straightforward conclusion than in  [7]  where droplet-based zero-inflation is stated as only biological. Transcriptional burst kinetics of embryonic stem-cells We previously explored the ability of AutoZI to capture bimodal genes from simulated Beta-Poisson models. Such model was fitted to an allele-specific scRNA-seq dataset of mESCs for characterizing transcriptional bursting  [3]  through estimates of the kinetic parameters k on , k off and s for each gene. We investigated whether the decisions made by AutoZI could recapitulate the different regimes for the Beta-Poisson distribution (Bimodal, UZ, UNZ) in this dataset. Given the limited number of cells (188), we applied AutoZI to a larger mouse hybrid ESC dataset  [17]  (704 cells, one common allele), which was not used for the inference of the kinetic parameters, but should be biologically similar.
After intersecting the gene lists in the two datasets, we further randomly filtered the genes and kept 52 bimodal, 52 UNZ and 29 UZ genes. Only one of the UNZ genes did not have sufficient expression for analysis. We report the decisions from AutoZI with respect to the kinetic parameters k on and k off in Figure  3. AutoZI predicts that 38 out of the 52 bimodal genes are zero-inflated and that 37 out of 51 UNZ genes are not zero-inflated. Taken together, our results suggest that AutoZI's predictions of zero-inflation can be used not only to account for technical factors (which are evident by the decrease in ZI with progress in technology in Table  2 ) but may also reflect biological factors such as transcriptional bursting. Figure  3 : Genes from the ESC dataset from  [17]  plotted in the space of (k on , k off ) kinetic parameters, with their NB/ZINB labels from AutoZI.
Acknowledgements We thank  Valentine Svensson  whose work on zero-inflation in droplet scRNA-seq inspired the project,  Chenling Xu  for her help on ESC and 10X Genomics data and  Pierre Boyeau  for the cooperation on Poisson log-normal datasets. We also thank  Matthew Jones  and  Zoë Steier  for insightful biological discussions. Nir Yosef  is a Chan Zuckerberg Biohub investigator.
Additionally, the combination of images acquired at different focus to perform a phase image reconstruction needs sophisticated algorithms including several corrections of misalignment and distortion  (Koch, 2014)  as well as a non-trivial adjustment of parameters, limiting the use of phase image reconstruction. To fully appreciate the benefits of phase image reconstruction the development of a user-friendly method able to retrieve a phase image from a limited number of phase-contrast images is needed. Based on a method requiring two defocused images and a simple numerical treatment  (Donnadieu et al. , 2008) , we have implemented a plugin able to perform a quantitative phase-contrast reconstruction in the widely used image processing software ImageJ  (Schneider et al. , 2012). Moreover, we have adapted this approach to compute a qualitative phase image reconstruction enhancing borders and structures by using only oneimage.
The processing will involve the experimental defocused images (either one or two if the one-image or two-images treatment is chosen, respectively) and two images build by the operator, i. e. the constant intensity image that will stand for the zero-focus image and an image in reciprocal space representing the Tikhonov function T(q). In the present case, as described in the next section, it was chosen to write a plugin for the software ImageJ  (Schneider et al. , 2012). Because of the image subtraction involved in the processing, the images I(+ Δz) and I(-Δz) have to be properly aligned. Shift correction can be done using a plugin already available for ImageJ  (Schneider et al. , 2012)  such as TomoJ software  (Messaoudi, 2011). Also because of the focus difference, the images I(+ Δz) and I(-Δz) may have slightly different magnification.
This can occur for high focus, in such case a re-scaling should be done directly with ImageJ software. When nedded, image alignment and re-scaling should be done as a pretreatment before retrieving the phase image. Finally, it is worth noting that the output of the calculation is in radian, that providing the reciprocal scaling factor has been taken into account. For a N pixel ROI and a pixel size p in direct space, the pixel size in the reciprocal space is 1/Np. Therefore, a multiplication by a factor N 2 p 2 arises when the numerical calculation of the Tikhonov regularization function is done in reciprocal space pixel. In this section we describe the implementation of the ImageJ plugin and its evaluation with gold nano-particle, trypanosome resin embedded and frozen hydrated bacteria as examples for material science and biological applications.
From that point of view, the one-image treatment is clearly advantageous on the two-images one. First with the one-image treatment, image alignment is not necessary. Therefore, there is no risk of artifact on the object size due to too ill corrected misalignment. This is particularly important for biological samples as they require high defocus inducing specific image distortion preventing from good alignment of the two images focal series. Also even if the two-images SPCI treatment is chosen in view of quantitative results, the one-image SPCI treatment is always worth doing in order to detect artifact due to incorrect image alignment. This is a preliminary step required for shape descriptors and dimension studies, which can be directly performed in the ImageJ software where SPCI plugin has been implemented.
Acknowledgment We are grateful to  Prof. G. A. Botton  from  CCEM-Canadian Center for Electron Microscopy  for the nano-particle imaging facilities and to  Sylvain Trépout  for the T. brucei grid and the critical reading of the manuscript. We acknowledge the  PICT-IBISA  for providing access to their image equipment. A. Verguet is recipient of a CIFRE grant and is supported by  JEOL (Europe) SAS.
Intervention and resuscitation scenario On the day of participation after random allocation, each participating paramedic will: (1) complete a survey collecting data regarding their demographics, care training, and simulation and computer experience; (2) receive a standardized 5-min training session on how to use PedAMINES; as well as (3) a presentation of the simulation manikin characteristics. The paramedics will then be asked to perform a 20-min highly realistic pediatric CPR scenario on a high-fidelity WiFi manikin (Laerdal SimBaby, Laerdal Medical, Stavanger, Norway). The procedure will be standardized across all sites to follow the same chronological progression and range of difficulty in order to ensure that each participant is exposed to exactly the same case, with similar challenges in decision-making and treatment preparation provided on the same manikin.
Methods of measurement and data collection Research using simulation as a valid and reliable investigative methodology to study factors affecting human and systems performance in health care has been reviewed  [30]. In this study, all actions (i. e. , outcomes) performed by the paramedics during the scenario will be automatically recorded and stored by the responsive simulator detectors (Laerdal SimBaby, Laerdal Medical, Stavanger, Norway) and the three GoPro video cameras. The set-up of the three cameras will be standardized to record at a resolution of 1080p at 90 frames per second, a wide field of view, and a 16:9 aspect ratio. Similarly, the position of the cameras will be standardized. The first camera will be mounted on a head strap placed on the paramedic's head with a 45°downward inclination to allow to capture footage of the front scene.
The stress level (HR) of each participant will be recorded during the entire resuscitation scenario with the HR monitor on a Polar A360 watch (Polar Electro Oy, Kempele, Finland). Data will be stored on the wristwatch itself with further analysis performed offline. The investigators will double-check on-site that the questionnaires are fully and accurately completed. Data collection will be carried out using the REDCap database (REDCap, Vanderbilt University, Nashville, TN, USA). This study offers the major advantage to observe a unique 60-min period per paramedic. Therefore, neither follow-up nor retention plans will be necessary. The intervention protocol is highly standardized and paramedic deviation from the protocol in terms of drug preparation is a parameter that is of interest in our study (i.
Blinding Blinding to the direct IV drugs and doses intended for use will be maintained during recruitment to minimize preparation bias. Allocation concealment will be ensured with the allocation software and will not be released until the paramedics start the scenario. Study team members will be revealed to the participants just before the scenario starts. Although the intervention could not be masked, all investigators will remain unaware of the outcomes until all data are unlocked for analysis at the end of the trial. All scenarios will be video-recorded for later analysis. A post-scenario video review will be done without blinding by two reviewers, but undertaken independently with each blinded to the other's reviews. In the case of disagreement, a third independent evaluator will help reach a consensus.
The limits of agreement will be assessed by the interval of ± 1. 96 standard deviations (SD) of the measurement difference either side of the mean difference. The null hypothesis that there is no difference on average between both reviewers will be tested using a t test. The mean difference will be reported with its 95% CI. Additionally, the intraclass correlation coefficients for volumes of drugs drawn, time to drug preparation, and time to drug delivery will be assessed, assuming that raters are a sample from a larger population of possible raters. The agreement will be investigated for the data of each study period. Finally, means and SDs will be determined for perceived stress and satisfaction scores of individuals for each questionnaire item, as well as for the UTAUT questionnaire, and reported with descriptive statistics.
Trial status The protocol version is 1. 0 (29 March 2018). The trial is registered at ClinicalTrials. gov, ID: NCT03921346, 18 April 2019, https://clinicaltrials. gov/ct2/show/ NCT03921346. The recruitment of subjects is expected to start mid-2019. We anticipate that the intervention will be completed in early 2020 and study results will be available in late 2020 (publication expected in early 2021). multicenter studies that are being conducted in several cantons/trial centers in Switzerland should not have to be reviewed in full by every cantonal ethics committee, but only from the lead ethics committee which is responsible at the site of activity of the project coordinator. This trial protocol version 1. 0 received a declaration of no objection by the Geneva Cantonal Ethics Committee on 29 March 2018, as the purpose of the study will be to examine the effect of the intervention on health care providers.
This provides information on lightning closely linked with the microphysical structure of the cloud in which the discharges propagate. In the frame of the HyMeX program  (Ducrocq et al. , 2014) , which aims at documenting the water cycle in the Mediterranean basin that is considered as a climatic hot spot  (Giorgi, 2006) , we plan to monitor the convection for addressing the question about the evolution of highly precipitating events and deep convection in response to the climatic change. For this purpose, the Collectivité Territoriale de Corse -via the PCOA (CORSiCA Atmospheric Observations Platform, https://corsica. obsmip. fr/) -gave us the opportunity to equip the Corsica Island with a LMA instrument that is considered as a reference for the accurate detection of total lightning activity.
, 2004). As a matter of fact, a minimum of 6 stations is required in the data processing although only 4 unknowns (x, y, z, t) are to be determined for each VHF source. This consideration of redundant measurements is useful for checking the solution's validity. The primary advantage of a 12-station network is that more VHF sources can be located during a given discharges because 2 different sets of 6 stations can detect sources in the same time window. Nevertheless, during high flash rate period or during spread and very active events each lightning is logically less well sampled since sources emitted by numerous different lightings compete to be detected by the 2 sets of 6 stations in the same time windows. A comprehensive description of the operation of LMA stations is available in Appendix A of  Thomas et al.
(2004). As in all LMA systems, each SAETTA station is configured to record on internal disk the amplitude and the arrival time of the strongest radiation event -above an adjusted detection threshold -which it detects and digitizes in each time window of 80 μs. The accurate time of arrival is obtained thanks to a GPS receiver device, with an accuracy of about 40 ns. The data is collected on site at each station by changing the internal disks, which are brought back to the Laboratoire d'Aérologie in Toulouse (France) to implement the calculation of the 3D position of the VHF sources. In addition, each station is connected by wireless communication links via a modem and a GSM antenna in order to (i) monitor and control the station operation by displaying a large amount of information (e. g. the detection threshold, the filling rate of the internal disk, the batter y voltage, the load current from the solar panel.
In July the most frequent lightning activity concentrates over the northern half of the island, with a main maximum close to the crossroads of the 3 main valleys over a secondary relief south west of Compoli station, and a secondary maximum in the north-east quarter of the domain in the Gulf of Genoa. In August,  To complete these geographical observations, one can also look at the overall observations reported as a histogram in Fig. 9. This figure shows the number of stormy days on the domain of better detection accuracy for each month and each year, together with the monthly average number of stormy days. The whole available data set is here enriched with 2017 data (easy to extract). The graph exhibits 2 maxima in July and in September, and a minimum in August (winter is disregarded). From May to August the number of stormy days seems to follow the elevation of the Sun in the sky, i.
A more comprehensive assessment of SAETTA's performance could undoubtedly benefit from comparisons with the trajectories of airliners that are detected by the network. We plan to perform this kind of comparison with GPS data of commercial flights. Combining observations from the years 2004 to 2006, we have elaborated a short of climatology of total lightning activity on Corsica, which has never been done so far, in a 240 km × 240 km domain. The number of lightning days per square kilometer is dominated by daytime convection over the relief from June to July, with a local maximum at the north center of the island produced in July between 11:00 UT and 14:00 UT. Tidiga et al. (2018)  showed -via a numerical study using the cloud resolving model Meso-NH at high resolution -that in absence of synoptic forcing this local maximum is likely due to the low-level convergence of moist air fluxes originated from sea breezes channeled through three main valleys that converge towards each other at this place.
Subsequent studies envisaged should analyze the fine-scale impact of synoptic forcing on this scenario. Besides, the monthly number of lightning days undergoes two maxima: (i) one in June due to daytime convection in phase with the maximum of solar flux at the summer solstice; (ii), and one in September associated with numerous small storms over the sea or with some high precipitation events. Those last events may be associated with high precipitation and flash floods  (Scheffknecht et al, 2016)  and are the focus of the HyMeX program  (Ducrocq et al. , 2014). The present paper also reports unusual lightning events that occurred in a mesoscale convective system on June 8, 2015. Produced during convective surges, the first type of lightning events was constituted of numerous VHF sources concentrated on a small perimeter (5 km by 5 km) and protruding from the top of the cloud located at about 11.
Acknowledgments Acknowledgements are addressed to SAETTA main sponsors:  Collectivité Territoriale de Corse  through the  Fonds Européen de Développement Régional  of the European Operational Program 2007-2013 and the  Contrat de Plan Etat Région  that funded the  CORSiCA  project;  Collectivité de Corse  through the CORSiCA 2017-2019 project;  CNRS-INSU  through the  HyMeX/MISTRALS program ;  ANR IODA-MED ;  CNES  through the  SOLID  project;  UPS/Observatoire Midi-Pyrénées ; and Laboratoire d'Aérologie. We also strongly thank the many individuals and regional institutions in Corsica (including the  Conservatoire du Littoral ,  Qualitair Corse , and  INRA San Giuliano)  who host the 12 stations of the network, who helped us to find sites, or who bring us assistance for the logistics during missions in the field.
A modification of these coefficients strongly affect the solar production as demonstrated by Hellstrom et al. [4] , who analyzed the impact of the modification of a solar collector on its steady-state performance and its annual production, and Rehman et al. [5]  in their study of the influence of failures on a solar heating system. There are only few works about analysing the influence of a solar collector fault on the efficiency of this component whereas it is more common in other areas such as the work of Bun  [6]  who compared the influence of different dysfunctions on the I-V curve of PV panels. The purpose of this paper is therefore to assess the relationship between faults and the efficiency curve of a solar collector. 2 Data to analyse the impact of a fault on the behaviour of a system can be produced either by experimental or simulation means.
However obtaining experimental data of a faulty system is in general not possible or limited to one specific fault and one specific system. On the other hand, a numerical model is flexible and allows a deep understanding of the system both in faulty and normal modes. In this paper, a numerical study on the impact of three solar collector faults on the efficiency coefficients is developed: • the « transparent cover failure » fault which gathers two main failures : a broken glass cover and the tearing of the FEP foil if any ; • the « opacification » fault related to the opacification of the glass cover ; • the « insulation degradation » fault linked to a decrease of the thermal insulation ability of the back insulation. To achieve this goal, a model of a flat-plate solar thermal collector is developed.
Versions of this model are derived to reproduce the behavior of a collector affected by the three presented faults. Experimental data enable a validation of these models for some cases. They are then used to simulate the three faults with different severity and to obtain the corresponding steady-state efficiency coefficients. The organization of this paper is as follows: section 2 presents a state of the art about solar collector faults and their impact on its efficiency. The models of the solar collector in normal and faulty operation are then detailed in section 3. Section 4 presents the experimental validation of the different models. Finally section 5 provides an analysis of the faults impact on the efficiency coefficients, completed by a comparison with the literature. Section 6 concludes this paper.
The authors model the faults by a 1-node lumped capacity model based on the equation  (1). The faults are reproduced by a modification of efficiency coefficients however they cannot always easily be linked to physical phenomena, in particular the thermal losses coefficients 1 and. Several authors developed models with more nodes, which enable a parameterization with physical features and are more accurate. Matuska et al. [14]  developed a small software called Kollektor 2. 2, which allows the design of flat plate thermal solar collectors. The tool does a detailed calculation the steady-state heat transfers between the different elements of the collector and deduces the normative efficiency curves. The model comprises seven thermal nodes and is experimentally validated. Zima and Dziewa  [15]  proposed a 5xN-nodes model and a special care was taken in the choice of the number of nodes along the fluid.