dataesr/scientific-paragraphs-categorization huggingface dataset:
The cells were then treated with 2 µg/mL of mitomycin for 2 h to arrest cell proliferation, afterward a "scratch" was made in the cell monolayer using a 200 µL pipette tip to create a wound. The detached cells were washed out using phosphate-buffered saline (PBS). Excepted for the control made up of the same number of cells and equal concentration of DMSO (0. 1%) used for drug dissolution, all wells were treated with five different concentrations of I. cylindrica root extract chosen below its 24h IC 50 value, i. e. 15, 30, 40, 50, and 60 µg/mL. In the same field, the wound distance was measured before and after incubation (16h), under IX 73 Olympus inverted fluorescence microscope at 4X magnification (Cairn, Kent, UK) to evaluate wound closure. Wound healing was analysed using ImageJ software (National Institute of Health, USA).
After permeabilization, the cells were again washed twice with PBS and stained with 0. 2% crystal violet, incubated for 15 min at RT and washed with PBS. The non-migratory cells were removed from the top aspect of the membrane using cotton buds. For their quantification, cells were imaged under a Nikon Inverted Microscope ECLIPSE TE2000-S and counted using ImageJ software. All assays were performed at least three times.
After permeabilization, the cells were again washed twice with PBS and stained with 0. 2% crystal violet, incubated for 15 min at RT and washed with PBS. The non-invasive cells were removed from the top aspect of the membrane using cotton buds. For their quantification, cells were imaged under a Nikon Inverted Microscope ECLIPSE TE2000-S and counted using ImageJ software. All assays were performed at least three times. CaSki cells were seeded in 6-well plates at 3×10 5 cells per well followed by overnight incubation. After 24 h of treatment with concentrations of the plant extract, cells were washed with PBS, trypsinized and incubated with lysis buffer for 20 min at -80 o C. The lysate was then centrifuged at 14,000 rpm for 20 min at 4 o C. Protein quantification was performed using the Bradford protein assay kit.
The primary antibodies used for the in vivo assay were anti-MMP2 (Cell Signaling Technology USA,87809), anti-MMP9 (Cell Signaling Technology USA,13667), anti-MT1-MMP (Cell Signaling Technology USA, 13130) and anti-GAPDH (Santa Cruz USA, SC-47724) at appropriate dilutions as recommended by the manufacturer. GAPDH was used as a loading control. After overnight incubation at 4 o C, the blots were washed in Tris buffered saline containing 0. 1% Tween 20 three times for 15 min each. Afterward, the blots were then incubated with anti-rabbit HRP secondary conjugated antibody (Santa Cruz USA, 7074) for 1h at room temperature. Following this, all membranes were washed and developed with an ELC chemiluminescence kit. ImageJ software was used to estimate the band intensities on scanned images.
Quantitative reverse transcription PCR (RT-qPCR) In order to investigate the expression of certain matrix metalloproteinase (MMP) genes involved in CaSki cell metastasis, the quantitative reverse transcription was performed on synthesised cDNAs. Total RNA was extracted from CaSki cells that were treated (24 h) with methanolic root extract of I. cylindrica  (30, 40, 50 , and 60 g/mL) or vehicule (0. 1%DMSO) using Trizol reagent according to the manufacturer's protocol. RNA samples were resuspended in 20 µl DEPC treated water, properly dissolved by incubating at 55 °C for 10 min and quantified using a Nano-Drop spectrophotometer (ThermoFischer Scientific). The First strand cDNA synthesis was done using SuperScript III cDNA synthesis kit from 2 μg of the purified RNA. The cDNA obtained was used to perform real-time PCR using the QuantStudio Flex 6 RT-PCR machine (Applied biosystem, Foster City, USA) with respect to SYBR Green (Invitrogen) method.
Data analysis All the in vitro experiments were performed three times, on independent cell passages. In the cell proliferation assay, IC 50 values were calculated from the concentration-inhibition curve by nonlinear regression analysis. Migration, invasion, RTqPCR and western blot data were plotted as mean  SD. Statistical analysis was done using GraphPad Prism Version 8. 1. 0 (GraphPad Software, CA, USA). Differences between the means of treated and untreated cells or groups were evaluated using one-way analysis of variance (one-way ANOVA).
Acknowledgements The  World Academy of Science (TWAS)  and  Department of Biotechnology (DBT) of India  for the award of  DBT-TWAS  fellowship. The animal work in the  NCBS/inStem Animal Care and Resource Centre , partially supported by the  National Mouse Research Resource (NaMoR)  grant#  BT/PR5981/MED/31/2012 ; 2013-2016 & 102/IFD/SAN5003/2017-2018  from the  Indian Department of Biotechnology. Swati Choudhary ,  Shefta E moula  and  Bhagyashree S. for their assistance in some experiments.
Background: In low-and middle-income countries (LMICs), data related to antimicrobial resistance (AMR) are often inconsistently collected. Humanitarian, private and non-governmental medical organizations (NGOs), working with or in parallel to public medical systems, are sometimes present in these contexts. Yet, what is the role of NGOs in the fight against AMR, and how can they contribute to AMR data collection in contexts where reporting is scarce? How can context-adapted, high-quality clinical bacteriology be implemented in remote, challenging and underserved areas of the world? Objectives: The aim was to provide an overview of AMR data collection challenges in LMICs and describe one initiative, the Mini-Lab project developed by M edecins Sans Fronti eres (MSF), that attempts to partially address them.
Sources: We conducted a literature review using PubMed and Google scholar databases to identify peerreviewed research and grey literature from publicly available reports and websites. Content: We address the necessity of and difficulties related to obtaining AMR data in LMICs, as well as the role that actors outside of public medical systems can play in the collection of this information. We then describe how the Mini-Lab can provide simplified bacteriological diagnosis and AMR surveillance in challenging settings. Implications: NGOs are responsible for a large amount of healthcare provision in some very lowresourced contexts. As a result, they also have a role in AMR control, including bacteriological diagnosis and the collection of AMR-related data. Actors outside the public medical system can actively contribute to implementing and adapting clinical bacteriology in LMICs and can help improve AMR surveillance and data collection.
Introduction Representative and comparable data for drug-resistant bacterial infections are essential to developing evidence-based treatment guidelines and to measuring the impact of antimicrobial resistance (AMR) control efforts  [1]. Yet, these data have proven extremely challenging to obtain in low-and middle-income countries (LMICs), despite the increasing evidence that AMR is rapidly increasing in these contexts  [2e5]. AMR poses a uniquely dangerous threat to low-resource settings, with the potential to reverse recent progress towards infectious disease control and to damage healthcare provision generally and threaten the safety of essential services (like surgery) among some of the world's most vulnerable and underserved populations  [2, 3, 6]. We present an overview of current AMR data collection challenges in LMICs and describe an initiative developed by the humanitarian medical organization M edecins Sans Fronti eres (MSF) that may contribute to this endeavour.
Material and methods We searched PubMed and Google Scholar for human research and articles in English published from 1 January 2000 to 15 December 2020 using the terms 'Antimicrobial resistance', 'Surveillance', 'Lowand Middle-Income Countries', 'Non-governmental organization' and 'Non-state actors'. All available study types were included, as were 'grey literature' publications (including reports, working papers, evaluations or government documents). We then used this literature to inform our description of MSF's Mini-Lab project, which we illustrate using implementation data from the first 8 months of its use in Haiti.
The MSF AMR response focuses on antibiotic and diagnostic stewardship, surveillance and infection prevention and control (IPC) and prioritizes sites that have high-risk patients (burns, neonatology, paediatric and trauma wards) or are in high-risk AMR regions (especially the Middle East and North Africa)  [5]. Though resource and time intensive, MSF prioritizes building the capacity of a host country's workforce for both quality and sustainability reasons (establishing a microbiology laboratory with scarce skilled human resources generally takes 1e2 years depending on the sample types they will analyse)  [5]. The Mini-Lab: leapfrogging to close the LMIC surveillance gap MSF has a standardized approach to surveillance and data in its own stand-alone laboratories or when working in partnership with another laboratory.
Rigorous laboratory testing then occurred  [29, 30]  with validation from experts in academia, including a prototype fieldtest in an MSF burn hospital in Haiti in 2019e2020 (Fig. 2 ). The Mini-Lab is built around a Quality Management System (QMS) that ensures that all components meet quality requirements and provide accurate results, even in the absence of an on-site microbiologist, and follow the WHO SLIPTA (Stepwise Laboratory Improvement Process Towards Accreditation) and other recommendations [31e34]. The Mini-Lab will soon be used in the Central African Republic (CAR), a conflict affected country with critical health system needs where MSF has 12 medical sites. In CAR, there is not a single CBL outside of the capitol Bangui, and very few national AMR data overall  [35]. In 2021, MSF will evaluate its Mini-Lab there as a test of its ability to sustainably establish a CBL in remote hospital facilities, to improve patient care and to bolster AMR surveillance  [12].
Special attention is given to commonly used antibiotics, antibiotics of last resort and proxy indicators of resistance mechanisms per GLASS requirements  [50]  and AWaRe classifications  [51]. Mini-LIMS will support AST interpretation by incorporating WHONET expert system functionalities in a tabledriven approach. AMR data will then feed into high-level surveillance systems with connection to WHONET  [52]  or DHIS2 platforms for direct data uploading to a country GLASS representative when available. The Mini-Lab's AST system will help clinicians select the correct antimicrobial agent, will support the adaptation of local antimicrobial guidelines and will provide epidemiological surveillance data. These characteristics ensure that the Mini-Lab is able to (a) correctly diagnose bloodstream infections and improve case management, (b) provide the information required for antimicrobial stewardship and (c) capture data from decentralized, rural areas for AMR surveillance.
Conclusion Effective and comprehensive surveillance systems are critical to a better understanding of the global AMR problem, to adapting therapeutic guidelines, to designing and implementing interventions and to assessing the effectiveness of the response. Actors across the public, private, governmental and civil society spheres must all contribute to capturing actionable data. Extending AMR surveillance networks to primary care and utilizing all existing data sources is a key piece of AMR control, yet largely missing in most LMICs. The Mini-Lab may fill gaps in AMR surveillance in remote settings. When deployed, it will generate standardized, representative, high-quality data on pathogens and drug susceptibility from target populations and improve patients' clinical management in sentinelle site.
Acknowledgements The authors acknowledge all the team who have contributed to the  Mini-Lab  development:  Albane Mazoyer ,  Bernard Baillet ,  Alice Rochard ,  Julie Hubert ,  Baptiste Boillot ,  Baptiste Le Corre ,  Delphine Berger ,  Saoussen Oueslati ,  Florica Ratiu ,  L ea Courtier  and many others; the scientific committee members who are ensuring scientific robustness of this concept:  Antoine Andremont ,  Stijn Deborggraeve ,  David Dolinger ,  Wael Elamin ,  Jan Jacobs ,  Rupa Kanapathipillai ,  Thomas Kesteman ,  C eline Langendorf ,  Tjalling Leenstra ,  Justine Michel ,  Thierry Naas ,  Maurice Page ,  John Stelling ,  Elsa Tran ,  Olivier Vandenberg ,  Timothy Walsh ; Virginie S eguineau who helped in designing figure 1; finally  Janet Ousley  for editing support provided to this manuscript.
Study Design and Participants LATTE-2 is a phase 2b, randomized, multicenter, parallel-group, open-label study using an induction-maintenance design conducted at 50 sites in Canada, France, Germany, Spain, and the United States (NCT02120352). Eligible participants were adults aged ≥18 years with HIV-1 RNA ≥1000 copies/mL, CD4 + count ≥200 cells/µL, and ≤10 days of previous ART. Key exclusion criteria were presence of any major resistance-associated mutation, moderate/severe hepatic impairment, clinically relevant hepatitis, chronic hepatitis B infection, history of liver cirrhosis, creatinine clearance <50 mL/minute, laboratory values or electrocardiographic findings of clinical concern, long-term anticoagulation, and presence of HLA-B*5701 plus inability to use an abacavircontaining nucleoside reverse transcriptase inhibitor backbone.
d Optimized loading doses were cabotegravir 600 mg (one 3-mL injection) + rilpivirine 900 mg (one 3-mL injection) LA. e Reasons for discontinuation have been previously reported  [9]. Abbreviations: AE, adverse event; ART, antiretroviral therapy; c/mL, copies per milliliter; HIV-1, human immunodeficiency virus type 1; IM, intramuscular; LA, long acting; NNRTI, nonnucleoside reverse transcriptase inhibitor; Q4W, every 4 weeks; Q8W, every 8 weeks; QD, once daily; RAM, resistance-associated mutation. participants randomized to oral therapy during the maintenance period who switched to and received ≥1 dose of the optimized LA regimen in the extension period. Data are reported from the maintenance plus extension periods for the randomized Q8W/Q4W groups and from the extension period only for the extension-switch groups.
Financial support. This work was supported by  ViiV Healthcare and Janssen Research and Development. Potential conflicts of interest. G. H. R. S. conducts clinical trials funded by  Merck ,  Gilead Sciences , and  GlaxoSmithKline/ViiV Healthcare. W. K. H. conducts clinical trials funded by  Merck ,  Janssen Pharmaceutica ,  Gilead Sciences , and  GlaxoSmithKline/ViiV Healthcare , with funds going to his institution. D. P. has received research grants and/or honoraria for advisory board and/or conference participation from  ViiV Healthcare ,  Gilead Sciences ,  Janssen Pharmaceutica , and  Merck Sharp & Dohme  (MSD). M. D. M. M. has received personal fees and nonfinancial support from  ViiV Healthcare ,  Janssen , and  MSD. H. J. has received honoraria for presentations and scientific consulting from  Gilead Sciences, MSD ,  Janssen-Cilag ,  ViiV Healthcare , and Theratechnologies.
Inhibition of NO synthesis in vivo induces up-regulation and ectopic expression of RA pathway genes The differential RNA-seq analysis revealed the up-regulation of 392 genes and the down-regulation of 50 genes upon TRIM treatment (Figure  1C , and Figure  1 -figure supplement 3). Interestingly, several differentially up-regulated genes are implicated in RA metabolism and signaling pathways (synthesis and storage, catabolism and known direct RA target genes): Adh3,  Rdh11/12. 18, Aldh1a. 2, Crabp, Cyp26. 1, Cyp26. 2, Cyp26. 3, RAR, Hox1, Hox3,. In order to confirm this finding, we additionally validated RNA-seq data by quantitative RT-PCR (qRT-PCR) analyses of up-regulated, down-regulated, and unaffected genes. The results showed a consistent expression trend with the RNA-seq data (Figure  1 -figure supplement 5A-C').
Imaging Control and TRIM-treated larvae at 72 hpf were stained with DAPI. A high-resolution Z-stack was acquired using a Zeiss confocal microscopy LSM 800, and a medium speed fast interactive deconvolution was applied. The 3D reconstruction was made employing Imaris 9. 3. 1 software; different larval body structures have been stained using the following five color blindness-friendly colors: #A6D854 green; #E78AC3 violet; #FFD92F yellow; #8DA0CB blue; #FC8D62 orange. Pharynx and body length measurements were performed on 72 hpf larvae captured with Axio Imager. Z2 microscope using a 10Â objective, and employing the Ruler tool in Photoshop CS5 with a digital zoom of 50%. The pharynx was measured from the most anterior part of the pre-oral pit to the most posterior part of the first pharyngeal slit.
The raw sequence files generated (fastq files) underwent quality control analysis using FastQC. Transcriptome sequences were deposited in the NCBI Sequence Read Archive (SRA) database with the accession number: PRJNA630453. Reads were mapped on the B. lanceolatum transcriptome  (Oulion et al. , 2012)  using the aligner Bowtie2 with default parameters  (Langmead and Salzberg, 2012). The read counts were obtained using IdxStats  (Li et al. , 2009; Cock et al. , 2013)  and the differential expression analysis between treated and wild-type embryos was performed using the R package DESeq2  (Love et al. , 2014). Mapping and read counting were performed on the Roscoff ABiMS Galaxy platform.
Gene expression analysis by qRT-PCR Total RNA was extracted from embryos at different developmental stages: 30, 36, 42, 48, and 72 hpf using the RNeasy Plus Mini Kit (Qiagen); 350-1000 ng of total RNA were retrotranscribed in cDNA which was used undiluted (only for Nos genes) or diluted 1:10 for the qRT-PCR. Each reaction contained a final concentration of 0. 7 mM of each primer and Fast SYBR Green Master mix with ROX (Applied Biosystems) in 10 ml total volume. qRT-PCR were run in a ViiA 7 Real-Time PCR System (Applied Biosystems). The cycling conditions were: 95˚C for 20 s, 40 cycles with 95˚C for 1 s, 60˚C for 20 s, 95˚C for 15 s, 60˚C 1 min, followed by a dissociation curve analysis using a gradient from 60˚C to 95˚C with a continuous detection at 0. 015˚C/s increment for 15 min. The results were analyzed using the ViiA 7 Software and exported into Microsoft Excel for further analysis.
Each sample was processed in biological triplicates. The 2 ÀDDCt Rpl32 method was used to calculate the relative gene expression. Ribosomal protein L32 (Rpl32), expressed at a constant level during development, was used as a reference gene for the normalization of each gene expression level  (Annona et al. , 2017). Primers used are listed in Supplementary file 1. For the statistical analysis, we used the GraphPad Prism software employing the paired t-test. Statistical significance cut-off criteria was set at p < 0. 05.
Acknowledgements The authors thank  Rebecca Adikes  and  Hannah Rosenblatt , course assistants at the  MBL Embryology Course 2019 in Woods Hole (USA) , and  Periklis Paganos  for their help with imaging. We are also grateful to  Enrico D'Aniello ,  Ricard Albalat ,  Marion Picard , and  Haley Flom  for their critical reading of the manuscript. We thank  A ´ngel R de Lera  for providing the RA antagonist BMS009, and  Carola Murano  and  Anna Palumbo  for their help with the NO quantification (DAN assay). We are grateful to the  Institut Francais de Bioinformatique  and the  Roscoff Bioinformatics platform ABiMS  for providing computing and storage resources for the RNA-seq analysis, and the  BIO2MAR platform (EMBRC-France)  supported by  ANR  grant no. ANR-10-INBS-02  for giving us access to analytical material.
Funding Funder Grant reference number Author European Commission  BA010618  and  360BA0619 Salvatore D'Aniello Company of Biologists DEVTF-170211 Filomena Caccavale Agence Nationale de la Recherche   ANR-16-CE12-0008-01  and  ANR-19-CE13-0011 Hector Escriva European Commission H2020-INFRAIA-1-2016-2017  n. 730984 Hector Escriva The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Each mouse was weighed every day to assess the toxicity. Mice were sacri ced on the 30th day. The tumors were isolated and incubated with 1 mg/ml collagenase I at 37°C for 1 hour. Then the tumor single-cell suspension was prepared by ltering through a 40 µ m cell stainer. The tumor-draining lymph nodes were collected, ground and ltered. The single-cell suspension was rst blocked with anti-CD16/32, and then classi ed and labeled with the following ow cytometry antibodies: CD3ε, CD4, CD8, Foxp3, Gr-1, CD11b, CD11c, and CD86. Finally, the proportion of all kinds of cells was analyzed by ow cytometry, and the data were processed by Flow Jo software.
A global gold standard framework for primary immunodeficiency (PID) care, structured around six principles, was published in 2014. To measure the implementation status of these principles IPOPI developed the PID Life Index in 2020, an interactive tool aggregating national PID data. This development was combined with a revision of the principles to consider advances in the field of health and science as well as political developments since 2014. The revision resulted in the following six principles: PID diagnosis, treatments, universal health coverage, specialised centres, national patient organisations and registries for PIDs. A questionnaire corresponding to these principles was sent out to IPOPI's national member organisations and to countries in which IPOPI had medical contacts, and data was gathered from 60 countries.
This particular procedure has been performed in patients with PIDs as a potential cure for the longest period of time, and this is reflected in the number of countries that provide them within their health benefits to their nationals. Nearly half of the countries (24 out of 53) offer the procedure within their coverage and 8 countries cover from 70% to 90% of the price. Although a larger dataset would offer further insight, the scope of this study did not allow for more in-depth investigation of the number of patients who needed BMT/HSCT and effectively received it without financial hardship. The available data instead provides a general coverage overview for BMT/HSCT, allowing for more focused research in future publications to offer more detailed insight on this principle. Gene therapy is a procedure that is still relatively novel and has only received its first marketing authorisation for one type of PID in 2016.
Through this process the patients should be empowered to selfmanage, supported by their multidisciplinary team. The age to start preparing the patient and the family for transition varies, in some countries it is recommended at a specific age, and in some it depends on the maturity of the patient. Many AYA PID patients are followed by the same health care team for many years and both the patient and their close contacts may fear the transition to adult care where the patient needs to learn to become autonomous and aware of adult risks. It is thus important for the multidisciplinary team to cooperate to make this experience positive and efficient for the patient and bridge the gap between paediatric and adult care. Based on data from the PID Life Index, there is still a vast amount of work needed to ensure that AYAs receive appropriate support and guidance during their transition.