dataesr/scientific-paragraphs-categorization huggingface dataset:
In a previous study,  Malkov et al. found no signs of DNA staining in response to 33 mM SNAC in Caco-2  [54]. It seems that very high SNAC concentrations are required to permit even a weak detergent action based on a non-specific mechanism of action. Even though SNAC caused a reduction in the PMP in Caco-2 cells, this effect might still not be enough to permit either IC efflux or flux of FD4. With HCA, CN is also used to monitor cell proliferation. The MTS assay gave a good correlation for cell viability, which was matched to reductions in CN. Conflicting reports are found in the literature regarding the comparison of CN with data from the MTT assay. One group suggested high concordance between the two methods  [65]. Since the MTS assay indirectly measures mitochondrial activity, comparing the HCA mitochondrial parameter is imperative.
Drugs and ex vivo assay The drug susceptibility assays were performed using the HRP2 ELISA-based assay Malaria Ag Celisa kit (ref KM2159, Cellabs PTY LDT, Brookvale, Australia) as previously described  [32]. Each batch of plates was validated using the CQresistant W2 strain (isolated from Indochina; MRA-157 obtained from MR4, VA, USA) in four independent experiments. The mean 50% inhibitory concentration (IC 50 ) values for all the batches used over 2 years were 495 ± 45 nM for CQ, 401 ± 36 nM for QN, 93 ± 17 nM for DQ, 23. 9 ± 3. 4 nM for MQ, 57. 1 ± 5. 6 nM for PPQ, 18. 6 ± 3. 1 nM for PND, 2. 4 ± 0. 4 nM for DHA and 1. 6 ± 0. 4 nM for AS. A comparison of the W2 anti-malarial susceptibility data between the different batches of plates indicated that there was no significant difference in the responses to anti-malarial drugs over the 2 years (0.
Data management and statistical analysis IC 50 values were calculated with the inhibitory sigmoid E max model, with estimation of the IC 50 through nonlinear regression using a standard function of the R software ICEstimator version 1. 2 (http://www. antim alari al-icest imato r. net/). IC 50 s estimates values and sequences analysis were collected and analyzed on excel sheets and GraphPad Prism (V7. 0a). Samples were grouped by regions for analysis to reflect parasites population structure sharing the same genetic background. The median of the IC 50 values was calculated for parasites with identical genotypes. Comparison between groups was implemented with Mann-Whitney test. Proportions were compared by Chi square test or Fisher exact test depending on sample size at significance level of 0.
Data analysis Statistical analyses were also performed using GraphPad Prism 7. 04 (GraphPad Software, La Jolla CA, USA) and SAS 9. 4 (SAS Institute Inc. , Cary, NC, USA). Pharmacokinetic calculations were performed using the noncompartmental approach. Chlorophacinone concentrations in milk were used to estimate the elimination rate constant and half-life from daily samples collected between 48 and 168 h post-exposure, except for one animal having a concentration below the LOQ for the 168-h time point. The half-life of elimination (t 1/2(el) ) was calculated using a linear regression. For residues in milk (< 50% of samples under the LOQ), the Kaplan-Meier method was used to estimate the extremes of the mean in the whole flock  (Helsel, 2005). Lowest bound was calculated replacing values under the LOQ by 0.
Acknowledgements The authors would like to thank  Dr Anne-Marie JACQUES , pharmacokinetics expert at the  Anses-ANMV , and  Dr Thierry GODARD , toxicological expert at the  Anses-ANMV , for their mindful review of this publication. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Any use of trade, product or firm names is for descriptive purposes only and does not imply endorsement by the  U. S. Government. The contribution of  Barnett Rattner  to this study was supported by the  Contaminant Biology Program  of the  U. S. Geological Survey Environmental Health Mission Area.
[18]  Scheme 1. Mechanism proposed for the IspH/LytB catalysed reaction. The above reduction/water elimination steps were investigated by EPR/ENDOR spectroscopy using E. coli and A. aeolicus IspH  [16, 17, 19]  reduced with dithionite, or by crystallography. [11, 14]  An alternative conformation of the substrate with the OH group rotated and not oriented towards the Fe/S center was observed in some mutants of IspH ([3Fe-4S] form) in complex with the substrate. [14]  A similar alternative conformation of (E)-4amino-3-methylbut-2-en-1-yl diphosphate (AMBPP), a HMBPP analogue in which the OH group was replaced by an amino group, was also reported in a IspH:AMBPP complex structure (PDB ID: 4H4D). [20] However this conformation could not be observed in another independently reported structure of this complex (PDB ID: 3ZGL) in which the occupancy of the [4Fe-4S] was verified to be 100%.
Scheme 2. Synthesis of (S)-[4-2H1]HMBPP 4 and (R)-[4-2H1]HMBPP 5. (i) SOCl2, NEt3, CH2Cl2, 0°C to RT, (ii) DIBAL-D, THF, -78°C to RT, (iii) Dess Martin periodinane, CH2Cl2, 0°C to RT, (iv) (R)-Alpine borane, THF, (iv') (S)-Alpine borane, THF, (v) (n-Bu4N)3HP2O7, CH3CN. E. coli IspH was produced, purified under anaerobic conditions and characterized as described previously. [21, 29]  The UV/visible spectrum, the iron and sulfur content and the activity (750 nmol min-1. mg-1) were in agreement with previously reported data  [8, 21, 29]  confirming that the [4Fe-4S] cluster was intact. To further explore the rotation step in the IspH mechanism, the fate of the deuterium on C-4 of stereospecific labeled HMBPP was monitored using an IspH assay performed under anaerobic conditions in the presence of the biological reduction system.
Acknowledgements We are grateful to  Prof. A. Boronat  ( University of Barcelona, Spain ) and his group for providing us with the E. coli strain overexpressing LytB. This work was supported by the  'Agence Nationale de la Recherche ' ( ANR-2011-BSV5-028 ), by the  "Centre International de Recherche aux Frontières de la Chimie " and  COST Action 1201  to M. S. Keywords: • [4Fe-4S] cluster • Enzyme catalysis  • IspH/LytB • Metalloenzyme • Methylerythritol  phosphate pathway.
Ex Vivo Microscopy for Quantification of EEF in Mice Liver The livers of Mdr2 -/-and WT mice were removed 4, 12, 24 and 40 h respectively after being injected with 50,000 GFP-expressing PbANKA SPZ. Livers were placed in PBS in a 35 mm imaging dish with Polymer Coverslip Bottom (Ibidi GmbH, Gräfelfing, Bayern, Germany) and observed using a Zeiss Axiovert (Zeiss, Oberkochen, Germany) equipped with phase-contrast and epifluorescence microscopy. EEF were counted on 20 fields (objective × 10) and normalized by 10 mm 2. Parasite size was determined on microscopy pictures using the ImageJ software.
All antibodies were purchased from BD Biosciences, San Jose, CA, USA. Cells were washed and resuspended in FACS buffer before analysis. A total of 5 × 10 5 living or fixed cells were analyzed using a Cytoflex cytometer (Beckman Coulter Life Sciences, Villepinte, France) and the software FlowJo (FlowJo LLC, Ashland, OR, USA).
These data prompted us to quantitatively assess the parasite load in the liver. Female WT and Mdr2 -/-mice were inoculated intravenously (iv) with 10 4 SPZ and liver samples collected at 4, 12, 24, and 48 h post-infection (p. i) were subjected to qRT-PCR analysis of parasite 18S rRNA. While in WT mice the presence of the parasite was detected at 4 h and then progressed afterwards through 48 h p. i, the parasite was just present at the limit of detection throughout the entire pre-erythrocytic phase in Mdr2 -/-mice (Figure  1E ). In parallel, we examined the abundance of exoerythrocytic forms (EEFs) in the liver of WT and Mdr2 -/-mice inoculated with 5 × 10 4 PbANKA SPZ by fluorescence microscopy at the same time points as in Figure  1E. As shown in Figure  1F , EEFs were readily observed at 4h p.
Efficacy of neutrophil depletion was assessed in the blood of treated mice by flow cytometry and showed a complete absence of neutrophils as compared to untreated mice (Figure  4E ). These data provide evidence that neutrophils are key players in blocking EEF development in vivo in infected Mdr2 -/-mice. Reversal of Mdr2 -/-Associated Infection Phenotype in IL-6-Deficient Mice At this point, it is tempting to postulate from the combined data obtained in Figures  3  and 4  that neutrophils may act in concert with IL-6 to ensure parasite clearance in the liver of Mdr2 -/-mice. We first assessed IL-6 expression in the liver before and 40h after SPZ inoculation. As shown in Figure  5A , basal levels tend to be higher in total liver tissue of Mdr2 -/-mice and while IL-6 was significantly down-regulated in infected WT FVB mice, there was a dramatic upregulation of IL-6 in the liver of infected Mdr2 -/-mice.
Counts of CD69 + CD62L -KLRG1 -cells analyzed by flow cytometry expressed in percentage (e, o) and absolute number (j, t) of cells of CD3 + CD8 + CD44 hi (C) or CD3 + CD4 + CD44 hi cells (D). The asterisks indicate significant differences using the Mann-Whitney test (*p < 0. 05; **p < 0. 01). Shown data are representative of three independent experiments. put forward establishing the inter-relationship between liver inflammation and host resistance to Plasmodium infection. Neutrophils and IL-6 were found to be among the most discriminative components between WT and Mdr2 -/-mice that are critical in controlling the parasite development. Neutrophils are essential for maintaining immune surveillance in homeostatic conditions and can be rapidly recruited in inflamed tissue under the control of several signals including CXCR2 and CXCL5.
ACKNOWLEDGMENTS We thank the  CEPIA (Centre d'eĺevage, de production et d'infection des anopheles, Institut Pasteur, Paris)  for providing infected Anopheles mosquitoes, and the cytometry platform ( CB-UtechS facility) at the Institut Pasteur  for providing technical assistance. We also thank  Dr. Olivier Silvie  ( Sorbonne Universite , Inserm  U1135 ,  CNRS ERL 8255 , Paris) and  Dr. Nicolas Blanchard  ( INSERM UMR1043-CNRS UMR5282 -UniversiteT oulouse III)  for their constructive discussions regarding the manuscript.
They made the following observations  (Hladìková et al. 2013)  The authors conclude that "environmental factors play an important role in breast cancer development". Instead of mysterious "environmental factors" such outcomes can also result from a random dispersion of manufacturing outputs. Next, we consider this problem in a more general way. The starting point is a dataset for a sample comprising M monozygotic (MZ) twins and D dizygotic (DZ) twins. Secondly, one focuses on the frequency of a specific congenital malformation. This leads to define and compute the following variables. • Concordant pairs, i. e. pairs in which both twins have the malformation; we denote their number by c m and c d respectively for MZ and DZ twins. • "Discordant" pairs, i. e. pairs in which one child has the malformation but not the other; we denote their number by d m and d d respectively for MZ and DZ twins.
Numerical simulation FEM was used for numerical modelling. All simulations were performed using the software Abaqus® (Abaqus® Standard 6. 13, Dassault Systèmes, Vélizy-Villacoublay, (1) France). To represent the compaction process, the die and punches were modelled as analytical rigid surfaces and the tablet was defined as a continuous deformable solid. For symmetry reasons, axysymmetrical simulations were performed. A friction coefficient dependent of the speed was used to represent the friction between the tooling and the tablet during compression. Its value was taken from a previous publication  (Desbois et al. , 2019). Linear elastic and viscoelastic laws with Prony series were used.
Thus, for each product, two sets of data will be presented: one for the tablets obtained under 100 MPa and one for the tablets obtained under 200 MPa. After this first compression (either at 100MPa or at 200MPa), two more compressions with extended dwell times were performed at a pressure lower than the first one in order to complete as much as possible the plastic and viscoplastic deformations. Finally, the viscoelastic properties were measured during the fourth compaction. The displacement during this compaction was set between 50 and 100 µm (depending on the product) which corresponds to a global strain between 1. 75% and 3. 5%. These values were chosen as a trade-off between a displacement value sufficiently high to ensure the precision of the measurements and overpass the initial non-linear elasticity  (Brewin et al.
Finite element method integration As mentioned previously, all the simulations were performed using the software Abaqus®. Viscoelasticity based on prony series is already implemented in the code. Nevertheless, in Abaqus®, Prony series formulation is slightly different from the expression presented above. In equation 5 and 6, gi and ki correspond to moduli normalized with respect to the infinite moduli (G∞,K∞). In Abaqus, the parameters correspond to moduli normalized with respect to the initial moduli. The parameters calculated above had thus to be transformed in order to be implanted in the code. Nevertheless, for clarity reasons, in the following text, we will still express the parameters of the Prony series based on infinite moduli as formulated in equation 5 and 6. The simulations carried out represent compressions with the experimental loading times (30ms, 300ms, 3000ms).
As shown in this article, the apparent elastic moduli of a pharmaceutical tablet might be influenced by the strain rate. This is important to consider when comparing results of elastic moduli found in different studies as tableting conditions might differ greatly from one study to the other. Finally, Prony series could be used in numerical simulation to represent the viscoelastic behavior of a powder during compression. Nevertheless, some code limitation may arise. For example, in the current version of Abaqus ® (6. 13), it is not possible to use simultaneously viscoelasticity and plasticity. The use of this model might thus require the development of user defined mechanical behavior in FEM codes.
Introduction Hydroxychloroquine was recently promoted in patients infected with COVID-19 infection. A recent experimental study has suggested an increased toxicity of hydroxychloroquine in association with metformin in mice. Objective The present study was undertaken to investigate the reality of this putative drug-drug interaction between hydroxychloroquine and metformin using pharmacovigilance data. Methods Using VigiBase ® , the WHO pharmacovigilance database, we performed a disproportionality analysis (case/noncase study). Cases were reports of fatal outcomes with the drugs of interest and non-cases were all other reports for these drugs registered between 1 January 2000 and 31 December 2019. Data with hydroxychloroquine (or metformin) alone were compared with the association hydroxychloroquine + metformin.
Methods The study was performed in VigiBase ® , the WHO pharmacovigilance database, which registers all Individual Case Safety Reports (ICSRs) from more than 130 countries around the world. ICSRs are entered into VigiBase ® after rigorous quality checks and deduplication  [7]. We extracted all ICSRs registered between 1 January 2000 and 31 December 2019 as 'fatal outcomes' [High Level Group Term (HLGT) in the System Organ Class (SOC) group 'General Disorders and Administration Site Conditions' according to the Medical Dictionary for Regulatory Activities (MedDRA ® )] in patients aged between 18 and 64 years. We excluded ICSRs from patients with sex unknown as well as those < 18 years and > 64 years because in a preliminary analysis of VigiBase ® we failed to find any fatal outcome with the drug association (hydroxychloroquine + metformin) in patients aged < 18 and > 64 years.
Following current protocols to detect a pharmacovigilance signal in large pharmacovigilance databases  [8] , we performed a disproportionality analysis (case/non-case analysis)  [8] , with cases being occurrence of 'fatal outcomes' with hydroxychloroquine (or chloroquine) (P01BA according to ATC classification of drugs) and non-cases all other ICSRs with hydroxychloroquine (or chloroquine) alone. Data with hydroxychloroquine (or chloroquine) alone were compared with the association hydroxychloroquine (or chloroquine) + metformin (A10BA). We also performed such analyses including other drugs used in diabetes mellitus; that is, sulfonylureas (A10BB), alpha glucosidase inhibitors (A10BF), thiazolidinediones (A10BG), dipeptidyl peptidase 4 (DPP-4) inhibitors (A10BH), glucagon like peptide-1 (GLP-1) analogues (A10BJ) and sodium glucose cotransporter 2 (SGLT2) inhibitors (A10BK).
Key Points Following a recent non-peer-reviewed publication describing fatal toxicity of hydroxychloroquine in association with metformin in mice, the present study was undertaken to investigate this putative drug-drug interaction between hydroxychloroquine and metformin using pharmacovigilance data. Using VigiBase ® , the WHO pharmacovigilance database, we found an increased risk of fatal outcomes with the association in comparison with each of the two drugs when used alone. This study suggests a pharmacovigilance signal of fatal outcome with the association hydroxychloroquine + metformin that should be confirmed by further studies. For chloroquine, 15 deaths were registered (60. 0% in women, 73. 3% aged 18-44 years, including eight completed suicides. No fatal outcome was registered for the association chloroquine + metformin (or other drugs used in diabetes).
Of course, it is important to underline that ROR investigates the risk of ADR reporting rather than a true risk. Our study was not performed in COVID-19 patients but in those receiving hydroxychloroquine for rheumatic or dermatologic diseases. However, there is no reason to believe that the described drug-drug interaction could depend on the underlying disease(s). It was not possible to perform direct adjustments due to the characteristics of VigiBase ®. However, Seabroke's group found that in large pharmacovigilance databases, subgroup analyses (as performed in this study) improve both sensitivity and precision and are clearly beneficial over crude analyses  [12, 13]. The fact that the completed suicide/non-suicidal ratio is higher for the association than with the drugs alone could suggest an additional toxicity of hydroxychloroquine and metformin taken together.
Since hydroxychloroquine doses are higher for COVID-19 than for lupus or rheumatoid arthritis, this might increase the significance of the signal. In contrast, the results of the present study have several important strengths. They are reflective of clinical conditions and cases were retrieved from the world's largest pharmacovigilance database. It used a validated method for the first detection of pharmacovigilance signals  [7] [8] [9]. We found high significant values of ROR suggesting a true association between the investigated factors. Our results extend the conclusions obtained in animals by Rajeshkumar et al. [5]  and should be considered as a meaningful pharmacovigilance signal of a drug-drug interaction between hydroxychloroquine and metformin. In fact, metformin is a widely used drug, particularly in aged and/or obese patients that are found to be particularly at risk for COVID-19 pandemic infection  [14].
Statistical analysis All values are expressed as the mean ± SD. The normality of distributions was examined with the Shapiro-Wilk test. Since the studied variables displayed a normal distribution and a similar variance among groups, the effects were analyzed with a two-way ANOVA. In the case of a significant interaction effect, Fisher's LSD post hoc tests were performed. Otherwise, the data were analyzed by the nonparametric Kruskal-Wallis and Dunn's multiple comparisons tests. Analyses were performed on GraphPad Prism software (Prism 8, GraphPad software, La Jolla, CA, USA). The level of statistical significance was set at p < 0. 05.
Acknowledgements The authors would like to thank  Dr. Martin Sandvoss  and  Viktor Pfeifer  for analytical support. M. Valero ,  D. Bouzouita ,  A. Palazzolo  are grateful to the  EU ISOTOPICS  iTN project from the  European Unions Horizon 2020  research and innovation programme under the  Marie Sklodowska-Curie  grant agreement No. 675071.
Methods The French pharmacovigilance database (FPVD)  [18]  centralizes all spontaneous reports of ADR  [19] , respecting anonymity of both patients and notifiers, in order to accrue the European database EudraVigilance. Such reporting of ADR is deemed mandatory in France for every health professional. The RCPV of Nice-Alpes-Côte d'Azur (RCPV of Nice) was appointed by the French Drug Agency (Agence nationale de sécurité des medicaments et des produits de santé [ANSM]) on March 27th, 2020, to investigate all reports of cardiotoxicity reported to any of the 31 RCPVs, associated with HCQ, CQ, AZI, or LOPI used empirically against COVID-19. Reports were analyzed for causality assessment, validated and a score was associated with each case  [20]. Reports were excluded from analysis by each RCPV if chronological and semiological data ruled out the role of the designated drug in the notified effect (i.
e. the effect was preexisting before the drug administration). After a first expertise by the RCPV receiver, all notified reports of cardiac ADRs associated with any of the drugs involved were sent consecutively to the RCPV of Nice to be included in this study, since the scope of expertise of that RCPV is precisely drug-induced long QT syndrome. To assess the completeness of the case-series, an extraction of the FPVD was also done backwards to January 1st, 2020. This extraction involved a research by the treatment indication ''coronavirus infection'' or ''COVID-19'' and a research by drugs HCQ, CQ, AZI, LOPI. Reports related to another indication than COVID-19 for these drugs were excluded. Each transmitted ADR case was reviewed by pharmacovigilants first, to assess for missing data required for expertise, in particular the electrocardiograms (ECGs) before, during and after treatment when necessary.
Data on clinical symptoms, patient' characteristics such as sex, age and comorbidities were gathered, as well as drug titrations, prescription dates, ADR time to onset and outcomes, concomitant drugs (and especially those known to induce potential QTc prolongation), kalemia, magnesemia, renal function and any other reported risk factors. Potential automedication and/or overdosage were noted as well. Missing data were requested by pharmacovigilants to the reporting initial health professional. All ECGs were examined by two residents in clinical pharmacology specializing in pharmacovigilance under the tutelage of a trained cardiologist in the field. All digitized ECGs parameters were measured with help of a digital caliper (Iconico ® , CardioCalipers ® , http://www. iconico. com/), by classical standard methods  [21].
ADRs not matching the abovementioned were classified as ''other cardiac ADRs''. Categories may occur more than once for patient with conduction disorders. Because of uncertainties in exhaustive reporting or prescription, we aimed to roughly evaluate the incidence of cardiac ADRs associated with HCQ only, because of its frequent use. This drug is marketed in boxes of two blisters containing each 15 tablets impossible to isolate. Standard operating procedures of hospital pharmacies imply that one blister minimum (15 tablets) and 2 blisters (30 tablets) maximum are to be delivered for a complete treatment against COVID-19 infection taking into consideration the various therapeutic regimens proposed. The number of patients treated for COVID-19 in hospitals in March 2020 (outside of a clinical trial) was estimated based on national HCQ consumption data and these considerations.