dataesr/scientific-paragraphs-categorization huggingface dataset:
This parameter ensures that the algorithm does not reconstruct more than k elements non-zero in the solution. The parameter k may be easier to use for two reasons, principally. The user may have an idea of the upper bound of excited fluorophores in each acquisition. If the user thinks the algorithm reconstructs too many fluorophores, he can easily reduce k. In the latter case, the user does not know how to change λ to obtain the wished-for results. The Deep-STORM is a deep learning algorithm. To teach the algorithm, the user needs to create proper simulated images that represent the dataset. This requires an idea of the density, knowledge of the PSF, as well as an estimation of the noise level.
Results of the simulated dataset The first dataset contains simulated acquisitions, which makes it possible to quantitatively evaluate the reconstruction, while the second contains real acquisitions. Figure  1  (a), (b) and (c) show three of the 361 acquisitions of the simulated dataset. We apply the localization algorithms to each image of the acquisition dataset. The sum of the results of the localization of the 361 acquisitions yields the super-resolution image. We use the Jaccard index in order to perform the numerical evaluation of the reconstructions. The Jaccard index evaluates the localization of the reconstructed fluorophores (see  [6] ), and is defined as the ratio between the correctly reconstructed (CR) fluorophores and the sum of CR-, false negatives (FN)-and false positives (FP) fluorophores.
A perfect reconstruction yields an index of 1, and the lower the index, the poorer the reconstruction. Furthermore, the Jaccard index includes an error tolerance in its calculation. The ISBI simulated dataset represents eight tubes of 30 nm diameter. The acquisitions are captured with a 64 × 64 pixels sensor where each pixel is of size 100 × 100 nm 2. The Point Spread Function (PSF) is modeled by a Gaussian function where the Full Width at Half Maximum (FWHM) is 258. 21 nm. In total, there are 81 049 fluorophores on a total of 361 images. We localize the fluorophores on a fine grid of 256 × 256 pixel image, where the size of each pixel is 25nm × 25nm. Mathematically, this is equivalent to reconstruct x ∈ R ML×ML from an acquisition d ∈ R M×M , where M = 64 and L = 4. Note that L could be larger, but this introduces more local minima, and the results might be worse.
Thus, due to the high number of non-zero pixels, the calculation of the Jaccard index is too demanding, but the index would be close to 0. Most of the non-zero pixels have a low intensity, with higher intensity on the tubelins, and that is why we observe in Fig. 2  a good reconstruction. We could fix a threshold, and let all the pixels with an intensity less than the threshold be zero. However, this would not be fair to the other methods as the same operation could be performed on them. Further note that CoBic cannot reconstruct more than 99 non-zero pixels with the given initialization, and there is no value in the case of 142 non-zeros pixels in Table  1. Table  2  shows the average computational time for one image acquisition from the simulated dataset. The Deep-STORM is fast and outperforms the other methods in speed.
Results of the real dataset We compare the algorithms on a high-density dataset of tubulins provided from the 2013 ISBI SMLM challenge. The dataset contains 500 acquisitions of 128 × 128 pixels, and each pixel is of size 100 × 100 nm 2. The FWHM has been estimated to be 351. 8 nm in  [35]  by averaging many fitted PSF on observed single molecules in the given dataset. We localize the fluorophores on a 512 × 512 pixel grid. Each pixel is of size 25 × 25 nm 2. We do not have any beforehand knowledge of the solution, and after trial and error, we set k = 140 for CoBic. We choose the parameters of the other algorithms such that their reconstructions visually looks best. Figure  3.
Even though CoBic reconstruct with high precision in the simulated dataset, we can observe that the constraint is not saturated. This may indicate that the algorithm has converged to a critical point which is not the global minimum. As a perspective, we are interested in how to avoid these non satisfactory critical points that may be saddle points. Furthermore, it seems interesting to further investigate the reformulation of the 0 -norm and to introduce it with other data-fitting terms. The acquisitions from Single-Molecule Localization microscopy has low photon count, and Poisson noise is dominant. The CEL0 penalization cannot be used with a Poisson fitting data term, but this may be possible with the proposed reformulation.
Introduction The Early Jurassic interval witnessed important palaeoceanographic, climate and environmental changes, which were triggered by major tectonic processes leading to palaeogeographic reorganisation, volcanic activity, and associated increases in atmospheric CO 2  (McHone, 1996; Marzoli et al. , 1999; Jourdan et al. , 2008). The supercontinent Pangaea started to break up during the latest Triassic leading to the opening of the Central Atlantic Ocean. As a consequence, numerous epicontinental basins were formed through "Europe", and seaways opened connecting "Europe" to Panthalassa and the Arctic through the Hispanic Corridor (latest Sinemurian-early Pliensbachian)  (Aberhan, 2001; Van de Schootbrugge et al. , 2005; Korte and Hesselbo, 2011)  and Viking Strait (Early Jurassic, less well dated)  (Bjerrum et al.
5. 4. 5. 3. Long-term trend during the upper margaritatus-spinatum Zones. In the Breggia section, the most positive values in the δ 18 O data, which may indicate a cooler temperature, were recorded in sediments corresponding to the top of the margaritatus Z. and the spinatum Z. Low P contents were recorded during this interval concomitant with low continental runoff. In addition, an increase in the illite content at the expense of smectite is recorded in the upper Pliensbachian, which may indicate a shift towards drier conditions (Fig. 5 ). Several studies have suggested that the late Pliensbachian is characterised by cooler seawater and atmospheric temperatures. This is evidenced by oxygen isotope data and Mg/Ca ratios in sections in Algeria  (Baghli et al. , 2020) , Portugal  (Oliveira et al.
(late Pliensbachian;  Berner, 1994; Berner and Kothavala, 2001; Bergman et al. , 2004; Royer, 2006; Price et al. , 2013; Steinthorsdottir and Vajda, 2013)  and may therefore have triggered or amplified this cooling event  (Suan et al. , 2010; Korte and Hesselbo, 2011; Silva et al. , 2011). In addition, lower CO 2 input due to lower volcanic activity an/or changes in current pattern during the break-up of Pangaea might have contributed to climate change  (Schöllhorn et al. , 2020). 5. 4. 5. 4. The negative CIE at the Pliensbachian/Toarcian boundary. At Breggia, the possible negative shift in the δ 13 C data seems to coincide with a decrease in δ 18 O data and a slightly increased P content, suggesting a warmer more humid climate with increased runoff during the Pliensbachian-Toarcian boundary interval.
Implications The Hg data provided from the Breggia and Dorset sections highlight the existence of possibly correlative peaks coinciding with the Sinemurian-Pliensbachian negative CIE and during the davoei and margaritatus Zs. , which partly persist following TOC normalisation. One recent study  (Lena et al. , 2019)  records a Hg spike in Northern America within the margaritatus Z. which could correlate with the Hg spike observed in the Dorset and Breggia sections. However, to date we are not aware of any other report covering the entire Pliensbachian. Therefore, it remains difficult to evaluate the spatial persistence of the Hg enrichments beyond these three sections. This would be necessary in order to interpret the Hg record as possibly influenced by changes in volcanic activity. In the case of a volcanogenic origin, the Hg spikes recorded within the earliest Pliensbachian may coincide with a late phase of the CAMP and/or increased rifting during the opening of the Hispanic corridor.
Conclusions A set of geochemical analyses was performed on Pliensbachian hemipelagic sediments in the Breggia Gorge (southern Switzerland) close to the open Tethys  (Schöllhorn, 2019). Negative carbon isotope excursions are recorded near the Sinemurian/Pliensbachian boundary, in the davoei, margaritatus, and spinatum Zs. , and possibly near the Pliensbachian-Toarcian boundary. These events coincide with environmental conditions characterised by higher temperatures and increased runoff bringing in more nutrients, based on coeval increases in wholerock oxygen isotope data and phosphorus content. This pattern is also observed during the T-OAE in the same section  (Fantasia et al. , 2018a (Fantasia et al. , , 2018b) )  suggesting climate and environmental responses similar for all CIE's. In addition, Hg analyses were performed for the first time on the entire Pliensbachian.
Acknowledgements We would like to acknowledge the logistical and financial support of the  University of Lausanne  which financed the PhD thesis at the origin of this paper (Schöllhorn, 2019). We thank both  Tiffany Monnier  and  Jean-Claude Lavanchy  for their assistance in the laboratories,  Alicia Fantasia  and  Yoann Chevalier  for their help in the field. We thank the  Cantonal Natural Museum of Lugano ,  Rudolf Stockar  and  Marco Antognini  for the sampling permission in the Breggia gorges. Furthermore, we would like to acknowledge the reviewers  Nicolas Thibault  and  Pierre Pellenard  for their constructive advice that improved this study considerably.
Acknowledgments The authors thank the  Ministry of Higher Education and Scientific Research of Benin through the University of Abomey-Calavi (UAC)  and the  Institute of Applied Biomedical Sciences (ISBA)  which sanctioned the contingent grants to  Professor Akadiri Yessoufou  for this work. We also express our sincere thanks to the  Centre d'Etude et de Recherche sur le Paludisme associé à la Grossesse et à l'Enfance  and the  Institute of Research for Development (CERPAGE/UMR216-IRD)  who provided with cytometry platform. We also thank 9  Journal of Immunology Research Professor Anatole Laleye ,  Dr. Marius Adjagba ,  Tatiana Hountohotegbe , and  Odilon Nouatin  for their valuable technical advices. This work was supported by the  University of Abomey-Calavi (UAC)  and the  Institute of Applied Biomedical Sciences (ISBA)  under the  Ministry of Higher Education and Scientific Research of Benin.
Inter-Donor Comparative Analysis between Manual and Reference Protocol Once the LG protocol was developed and validated, six GMP preparations of SVF were performed and retrospectively compared to batches of SVF (n = 33) previously manufactured using the Celution device (Cytori Therapeutics, San Diego, CA, USA); the Celution protocol, used here as the reference protocol, is described in several investigational medical product dossiers for clinical trial authorizations (NCT01813279; NCT02558543; NCT02520843; and NCT02622464). Various biological characteristics of both SVF final products were comparatively assessed and classified as SVF specifications defined for batch release (viability), critical process parameters (recovery yield), and critical quality attributes (cell subset distributions and clonogenic potential) according to the International Conference for Harmonization (ICH; ICH Q5E Harmonized Tripartite Guideline, Comparability of Biotechnological/Biological Products Subject to Changes in their Manufacturing Process; ICH Topic Q 6 B Specifications: Test Procedures and Acceptance Criteria for Biotechnological/Biological Products; and ICH Q8 Harmonized Tripartite Guideline, Pharmaceutical Development).
Then, NucBlue (Thermo Fisher Scientific), which allows the discrimination of viable and dead cells, was added for 5 min prior to flow cytometry analysis on a NAVIOS instrument (Beckman Coulter, Brea, CA, USA). Data files were analyzed using Kaluza software (Beckman Coulter) with a multiparameter gating strategy. Briefly, CD45 -regenerative cells were discriminated as CD34 -CD146 + pericytes and transitional cells, CD34 + CD146 + endothelial cells (ECs), and CD34 + CD146 -CD90 + MSCs. The CD45 + population includes all hematopoietic cells (macrophages, monocytes, lymphocytes, and neutrophils).
Tube Formation Assay SVF samples produced for the intra-donor comparative analysis (n = 2) were loaded at a density of 20,000 cells per well in a µ-slide angiogenesis system (Ibidi, Gräfelfing, Germany) coated with 10 µL of growth factor-reduced Matrigel (6 mg/mL; Corning, Corning, NY, USA) previously polymerized for 30 min; then, they were maintained in endothelial cell growth medium (EGM2-MV; Lonza, Walkersville, MD, USA) at 37 • C and 5% CO 2. Capillary-like structures were recorded during 96 h using a Leica DMI8 video-imaging inverted microscope equipped with an Incubator I8 (Leica Microsystems) at 5× magnification; images were captured using the Leica Application Suite X software (Las X 3. 0. 2. 16120; Leica Microsystems). The network, length of tubes, and nodes were quantified using ImageJ software (Wayne Rasband, National Institutes of Health, Bethesda, MD, USA) with the Angiogenesis Analyzer plug-in http://image.
Following 24 h of culture in EGM2-MV medium, spheroids were fixed for 30 min in 4% paraformaldehyde at room temperature. After washing and permeabilization with PBS containing 0. 1% Triton X-100 and 1% bovine serum albumin (BSA), for 2 h at 4 • C, spheroids were immunolabeled overnight at 4 • C with phalloidin coupled with Alexa-647 (Thermo Fisher Scientific) (1/100), and nuclei were stained with 6-diamidino-2-phenylindole (DAPI) (1/5000) diluted in PBS containing 1% BSA. After washing, we then captured fluorescent optical image stacks along the z-axis at 20× magnification using two lasers in sequential mode under a Leica DMI8 microscope (Leica Microsystems). The Las X software (Leica Microsystems) was used during all image acquisition procedures. Image processing prior to image measurements was performed using Huygens Essential Deconvolution software (Scientific Volume Imaging, Hilversum, The Netherlands) using up to 40 iterations of the classical maximum likelihood estimation algorithm, with a theoretical point spread function and automatic background correction.
Statistical Analyses Statistical analyses were performed using Graph Pad Prism 5 (GraphPad Software, La Jolla, CA, USA). Quantitative variables are reported as the mean ± standard deviation (SD) or the median 25-75 th percentile according to the normality of their distributions; minima and maxima are also provided. Continuous variables were compared using Student's t-test or the nonparametric Mann-Whitney t-test. One-way analysis of variance (ANOVA) was employed to compare more than two groups. For assessment of wound closure in the mouse model, data are reported for each group as the average percentage of wound healing ± SD from the four wounds in each mouse. Two-way ANOVA was used for the in vivo wound healing follow-up. A p-value < 0. 05 was considered to indicate a statistically significant difference.
The biggest drawback of these displacement pumps is the energy loss which is associated with them. However, these losses can be significantly reduced in the presence of load/pressure sensors  [13]. The application of hydraulic systems in itself is a very demanding task. Many researchers have published their results just on the application  [14] , as a simple condition such as cold weather has the potential to decrease the overall efficiency of the hydraulics system  [15]. The discussed articles bring good validity in the proposed work. Another recent work used the same approach for flow control  [16]  but they used it specifically for electric drives. Within  [16] , the process for simulating the controller was similar and MATLAB/Simulink was used for simulation purposes. Additionally, the technique for hardware validation was also similar to our work.
Synoptic View of Control Architecture A synchronous brush-less motor drives the pump. The motor is controlled by a servo-controller and makes the set controller + motor a servomotor, as shown in Figure  5. The controller generates the three-phase currents for the motor, and regulates the current (thus the torque) and the speed. This is a current servo-drive where the minor current loop is embedded into the speed loop. The servo-controller is connected via a digital communication link to a custom controller board and implemented on a Linux computer featuring a PowerPC processor, RAM, an FPGA for GPIOS control, an Ethernet layer (MAC and PHY) and onboard CAN transceivers. The controller board, called the open motion controller, elaborates the control of all the low-level devices on the FURBOT via CAN buses and a CANOpen layer: these include hydraulic motor via a drive manufactured by SEVCON, the traction drives, the steering drive, the signaling of the vehicle and other devices via a CAN-to inputs outputs board (DIO).
Algorithm The whole build system of the OpenMCP, which involves the kernel and the filesystem, the cross-compiler, configuration bash scripts and makefiles was cloned using LINEAR mercurial repository. Within the folders and files, there is the furbot application folder with all the source files (. hpp and. cpp), object dictionary description files (. ods) and the latest binary executable. The architecture of the code is the following: The libcanopen++ API is used to create new can buses handlers and CANOpen "master controllers" which can be linked to a bus. A "master controller" is a CANOpen master node with a specific master object dictionary and which can run several "application controllers" with the use of threads. The software's "application controllers" are linked to a specific hardware-device on the bus.
A Linux kernel and the file system are loaded in the flash by a separate tool. When the device boots, it decompresses the kernel and the file system (SquashFS) on the RAM. The board allows for two kernels and two file systems being available on the flash memory. It automatically loads the latest ones but allows using the old revision if a problem is detected. Particularly if the boot fails with one kernel, it automatically tries the older one after a few attempts. An executable, added to the path, enables one to load a newer revision of the kernel or the file system via the network and the protocols SSH/SCP.
CANOpen Getting the CAN messages from the hardware to a computer requires an adapter (made in silicon with the OpenMCP) and a driver on the computer. An IXXAT "USB to CAN" adapter was used for the early experiments with Linux machine and the drivers from IXXAT. Hardware is shown in Figure  8. On UNIX, several tools are useful for talking to the bus, such as the can-utils tools. Other than that, the SocketCAN stack enable the user to use a network interface to talk to the CAN bus. The tools involved are candump and cansend to filter/see the received messages or send a message on the bus. The application talks with the SocketCan stack via a library. CANFestival CANOpen library is used to interface an application code with the bus working with CANOpen. CANOpen master node was written, with its own object dictionary generated from a python utility given with the CANFestival library, and was able to control the motor in speed regulation and position regulation.
Preliminary Work on the Pressure Sensor The pressure sensor operates from 1 to 160 bars in absolute pressure and operates according to the CANOpen ds404 profile. The pressure sensor was mounted on the hydraulic circuit of the FURBOT and was first directly wired to the personal computer using IXXAT. It was then configured using the cansend tool for Linux and the LSS protocol. CANOpenShell utility provided with the CANFestival libraries was used to take feedback from the sensor, set the state with NMT and get the data via SDO/PDO messages. All the electronic hardware was mounted on the back of the vehicle as shown in Figure  9. A python script was written to get the pressure plot in real time. This ensured that the pressure sensor was working properly.
Pressure Sensor Test and Results for the Pressure Loop The pump was driven at constant speed to verify the results. The plots below are from the python script with which the data were superposed to see "moving curves" in real time. The time basis was 20 ms between samples, and there was a 255 sample-buffer. Figures  13  and 14  are results of the pump driven at constant speed (rpm). The results obtained reveal the hardware's performance at a constant speed, enabling one to judge the robustness of the controller. Blue represents pressure. Red represents set speed from the control loop. Green represents actual speed. Yellow represents torque from the motor, measured from the servomotor. Furthermore, the hardware performance was also validated by running the pump at constant pressure (Figure  15 ).
In silico screening of the I. hospitalis and N. equitans genomes Previously characterized m 5 U RNA methyltransferases were used as BLAST queries  (44)  against open reading frames (ORFs) in I. hospitalis and N. equitans. These included the AdoMet-dependent RlmD (UniProt accession number P55135) and TrmA (P23003) methyltransferases from E. coli K12, the P. abyssi methyltransferases PAB0719 (Q9UZR7) and PAB0760 (Q9UZK1), and the folatedependent enzymes TrmFO (P39815) from Bacillus subtilis, and RlmFO (Q2SS13) from Mycoplasma capricolum  (45). The I. hospitalis and N. equitans genomes were also screened for homologs of TtuA and TtuB that direct thiolation of m 5 U54  (46) , and the Pus10/TrmY combination that produces m 1 54  (47). BLAST queries included the P. abyssi and Pyrococcus furiosus homologs PAB1092 and PF0273 (TtuA), PF1758 (TtuB), PAB2391 and PF1139 (Pus10) and PAB1866 (TrmY).
The N. equitans ORF NEQ283 showed high similarity to PF0273 (TtuA homolog) from P. furiosus, while NEQ523 displayed even closer resemblance to the TtuB homolog PF1758. Genes encoding homologous enzymes are also apparent in the genomes of other Nanoarchaeota. LC/ESI-MS analyses of the N. equitans tRNAs unequivocally showed the presence of m 5 s 2 U (Figure  4 ). Nucleotide m 5 s 2 U at tRNA position 54 has been noted in other hyperthermophiles, where the relative proportions of m 5 U that is thiolated to m 5 s 2 U varies with environmental conditions and in particular the growth temperature  (10, 11, 13, 15). This modified nucleotide is absent in the I. hospitalis tRNAs (Table  1 ). A search for alternative U54 modification pathways in I. hospitalis tRNAs revealed Igni 0342, which is a homolog of the P.
The main exclusion criteria were pregnancy, participation in another clinical study, and the standard contraindications for TAI (intestinal obstruction, inflammatory bowel disease, ischemic colitis, colorectal carcinoma, anal or rectal prolapses or fistulas, anal or colorectal surgery or endoscopic polypectomy in the preceding 3 months, anal or colorectal stenosis, and acute diverticulitis). The study's objectives and procedures were approved by an independent ethics committee (CPP Sud-Est III, Bron, France) on June 21st, 2016, and the study was registered at www. clini caltr ials. gov (NCT02944916). The study protocol was performed in compliance with French and European legislation and the tenets of the Declaration of Helsinki. All included patients received information on the study's objectives and procedures, and gave their written consent prior to participation.