dataesr/scientific-paragraphs-categorization huggingface dataset:
Article https://doi. org/10. 1038/s43587-023-00401-5 Experimental fish were obtained by crossing tert +/-fish with tert +/-; fabp2: loxP-dsRed-loxP-tert-T2A-CFP. Their embryos were microinjected with 1. 4 nl of either 25 ng µl -1 Cre mRNA diluted in RNase-free water (Cre-induced fish) or RNase-free water alone (mock-injected fish). This experimental setup provided sibling fish that were either tert -/-; fabp2: loxP-dsRed-loxP-tert-T2A-CFP (mock-injected tert -/-, referred to as tert -/-no Cre), tert -/-; fabp2: tert-T2A-CFP (Cre-induced tert -/-, referred to as tert -/-+ Cre) or tert +/+ ; fabp2: loxP-dsRed-loxP-tert-T2A-CFP (mockinjected WT, referred to as WT). Overall characterization of these three genotypes was performed in F1 siblings at 9 months of age. Due to a male sex bias in our crosses, primarily observed in the tert -/-progeny, we were unable to obtain significant numbers of females for analysis; thus, all but our survival data are restricted to males.
Acknowledgements We thank members from the telomeres and genome stability and the telomere shortening and cancer laboratories for fruitful discussions. We thank  F. Graslin  for processing the metabolomics samples. We thank  E. Lazzerini Denchi  ( National Institutes of Health/National Cancer Institute ),  L. Saúde  ( Instituto de Medicina Molecula ),  D. Vallenzano  ( Friedrich-Loeffler-Institute ) and  A. R. Araújo  ( Institut de Pharmacologie Moléculaire et Cellulaire ) for critically reading our manuscript. This work was supported by the  Fondation ARC pour la Recherche sur le Cancer  ( PJA20161205137 ) and the  Fondation pour la Recherche Médicale  ( EQU201903007804 ). M. E. M. was supported by a postdoctoral fellowship from the  Ville de Nice. This work was also supported by the  Université Côte d'Azur-Académie 4  (installation grant:  Action 2-2019 ) and the  Howard Hughes Medical Institute   International Early Career Scientist grant  awarded to M.
Data availability Data generated or analyzed during this study are included in this published article, its Supplementary Information and Source Data files. The raw RNA-seq reads generated in this study have been deposited to the Sequence Read Archive database under accession no. PRJNA937311. Data used for the GSEA can be found online at https://github. com/ maliabird17/El-Mai-GSEA-Analysis. All other data pertaining to this study are available from the corresponding author upon reasonable request.
Background: Individuals who have recently acquired HIV represent a unique population because the time frame since HIV acquisition is relatively short and identification of missed HIV prevention opportunities is, therefore, closer to real time and less subject to recall bias. Identifying prevention measures used and missed opportunities for using them, can help stop further HIV transmission. Objectives: This systematic review aims to synthesise current global evidence on uptake of HIV prevention methods among people with recently acquired HIV from 2007, the year that the concept of ART as a prevention method was first introduced. Methods and analysis: MEDLINE/PubMed, EMBASE, PsycINFO, Cochrane and Web of Science databases, will be searched for articles published January 2007 -July 2023. Eligible studies will be those that reported on HIV prevention methods among people with recently acquired HIV.
We propose undertaking a systematic review to synthesise current global evidence on prior access to and uptake of HIV prevention interventions among people with recently acquired HIV. To prevent duplication of reviews, a preliminary search of similar protocols and reviews was conducted in July 2023 using the Cochrane Library, MEDLINE, Embase, PubMed, Web of Science, PsycINFO and The International Prospective Register of Systematic Reviews (PROSPERO) databases. No review protocol or systematic review on this topic was identified. Rather, systematic reviews on recently acquired HIV, identified through searches of these databases, examined the diagnostic, clinical and public health implications of identifying and treating people with recently acquired HIV  [10] [11] [12] [13] [14] [15] [16] [17] [18].
Searches We will search peer reviewed articles on the access and use of HIV prevention interventions among people with recent HIV infection, published in English, from 1 January 2007 to 17 July 2023 (2007 being the year that the concept of ART as a prevention method was introduced  [22] ). From our search, we will identify studies that assessed at least one of: HIV prevention, condom use, uptake of HIV testing, PrEP, post exposure prophylaxis (PEP), harm reduction (i. e. , needle exchange, opioid substitution therapy (OSP), etc. ), counselling. The search will be performed in the following databases:  CINAHL Plus  MEDLINE  PubMed  PsycINFO  Web of Science  EMBASE The following search strategy will be adapted for all databases. Searches will combine key terms relating to HIV/AIDS (HIV, AIDS, human immunodeficiency virus, etc.
Study selection Potential articles will be collected in the systematic review software Covidence  [23]. Duplicates will be removed by AK using Covidence software. Based on the pre-specified eligibility criteria, studies will be selected using a two-staged approach; titles and abstracts will be examined first and then the full-text of all potential eligible studies will be retrieved and screened. AK and ER-B will independently screen a sample of 100 citations to pre-test and refine coding guidance based on the inclusion criteria and until at least 90% agreement is achieved. Disagreements about eligibility will be resolved through discussion. AK will then screen the remaining citations for inclusion in the review using the pre-tested coding guidance. Full-text of all potentially eligible studies will be retrieved and AK and ER-B will assess all full text articles to determine final study selection.
5,6 Search strategy 10 Present draft of search strategy to be used for at least one electronic database, including planned limits, such that it could be repeated 5, Appendix 2 Study records: Data management 11a Describe the mechanism(s) that will be used to manage records and data throughout the review 6,7 Selection process 11b State the process that will be used for selecting studies (such as two independent reviewers) through each phase of the review (that is, screening, eligibility and inclusion in meta-analysis) 6,7.
Conflicts of interest The funders did not participate in the study design and will not intervene in its process, analysis or publication of the findings. ST has received speaker honoraria and consultancy fees from  Gilead Sciences. CC has received speaker/moderator honoraria and advisory board fees from  Gilead Sciences ,  GSK/ViiV  and MSD as well as an unrestricted  Gilead Sciences Nordic Fellowship Research Grant. CS has received funding from  Gilead Sciences ,  ViiV Healthcare  and  Janssen-Cilag  for participation in Advisory Boards, speaker panels and for preparation of educational materials. MVdV has received consultancies fees for participation in advisory boards and research grants from  Gilead ,  MSD  and  ViiV  all paid to his institution. FB has received funding from  Gilead Sciences Ltd  for preparation and delivery of educational materials.
Annotation of the analyzed compounds was carried out using MSDial ver. 4. 9. 221218. A nuclear magnetic resonance (NMR) spectrometer with a frequency of 600 MHz was employed. The 1 H and 13 C frequencies were 600 MHz and 150 MHz, respectively. The spectra were produced by dissolving the sample in the hydrogen-free solvent. The peak signals were corrected using a solvent signal of acetone-d6 (δH 2. 05 ppm and δC 29. 84 ppm) or methanol-d4 (δH 3. 31 ppm and δC 49. 00 ppm) as the reference. The 1D NMR spectra of 1 H and 13 C and 2D NMR spectra of COSY (correlated spectroscopy), HMQC (heteronuclear multiple quantum coherence), and HMBC (heteronuclear multiple bond correlation) were examined using NMR data processing tools (JEOL Delta version 6. 0, JEOL, USA). Direct correlations between 1 H and 13 C were determined by HMQC spectra.
Acknowledgments The authors acknowledge the  Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia  for funding this research through the  Pendidikan Magister Menuju Doktor untuk Sarjana Unggul (PMDSU) Program  (Grant Number:  3703/IT3. L1/PT. 01. 03/P/B/2022 ) and the  Enhancing International Publication Program 2022   for PMDSU scholars.
, 2019). Additional autologous cell sources are thus under investigations. In particular, ProtheraCytes ® , an advanced therapeutic medicinal product (ATMP) derived from autologous expanded CD34+ cells can represent a novel source for the treatment of OA cartilage lesion. ProtheraCytes ® have regenerative properties and have shown to improve global cardiac function in post-acute myocardial infarction  (Saucourt et al. , 2019). In a pilot clinical study, we showed that intramyocardial delivery of human CD34+ cells in post-acute myocardial infarction (AMI) patients is safe and leads to long term improvement  (Pasquet et al. , 2009). Even patients who were initially recommended for a heart transplant, no longer required it several years after the cell injection. Based on these promising clinical results, we are now conducting a multicenter, randomized, controlled Phase 2 clinical trial in severe AMI to investigate the safety and efficacy of Protheracytes ® (ClinicalTrials.
gov Identifier: NCT02669810). Protheracytes ® are manufactured using the StemXpand ® system, which is a closed, automated, ISO13485: 2016 certified device for GMP manufacturing that we developed. In this study, we decided to investigate the therapeutic potential of ProtheraCytes ® in an in vitro OA cartilage model. In this in vitro OA model, we cocultured ProtheraCytes ® with human OA chondrocytes in medium containing pro-inflammatory cytokines  (Acevedo Rua et al. , 2021)  to investigate their survival and capacity to modulate their inflammatory/degrading state. We also evaluated the survival and engraftment of ProtheraCytes ® after intra-articular (IA) injection in the murine model of collagenase-induced osteoarthritis (CIOA) to determine the best timing of cell injection for future therapeutic efficacy studies in this animal model.
Coculture of ProtheraCytes ® with OA synovial fluid ProtheraCytes ® resuspended in 2% HSA/PBS were incubated with four different concentrations (0, 10, 20 and 50%) of synovial fluid from six OA patients (donor 1: female, 73 years; donor 2, male, 70 years; donor 3, male, 79 years; donor 4, male, 67 years; donor 5, female, 70 years; donor 6, male, 69 years) and for five different timepoints  (1, 3, 6, 24, and 96 h). The synovial fluid samples were provided by Dr. S. Lefebvre, MD from the Mulhouse Institute of the Musculoskeletal System after signed informed consent. Cell number and viability were assessed with the Stem Cell Enumeration kit (BD) via flow cytometry with FACS Canto II and FACSDiva software (BD Biosciences).
2. 9 In vitro assessment of ProtheraCytes ® after delivery with a needle for intra-articular injection We evaluated the viability, purity, and number of ProtheraCytes ® before and after delivery with a needle for knee injection in humans (21G, 2″BD301155) and mice (20G, 25 mm BD304827). These parameters were evaluated with the Stem Cell Enumeration kit (BD) via flow cytometry with FACS Canto II and FACSDiva software (BD Biosciences).
Acknowledgments We would like to thank  Dr. S. Lefebvre, MD , who provided the OA synovial fluid samples. We gratefully acknowledge the platform ECELLFrance on non-clinical models in Montpellier supported by the  PIA ANR program  ( PIA-ANR-11-INBS-005 ) for the in vivo experiments. We acknowledge the  "Réseau d'Histologie Expérimentale de Montpellier"-RHEM  facility for histology technics and expertise.
The purpose of this study was to assess the effect of orthokeratology treatment with DRL lenses on the control of myopia progression compared with single vision glasses users (monofocal glasses). It was also possible to analyze the clinical efficacy of orthokeratology treatment with DRL lenses for myopia correction in children and adolescents in a 2 year retrospective, multicenter study, performed in eight different ophthalmology centers in France. A total of 360 data records of children and adolescents with myopia between -0. 50 D and -7. 00 D at baseline visit, who completed treatment and had a centered outcome, were selected for the study from a database of 1271. The final sample included subjects undergoing orthokeratology treatment with DRL lenses (n = 211 eyes) and spectacle wearers (n = 149 eyes).
Subjects We retrospectively collected data from subjects undergoing orthokeratology treatment with the DRL lens (n = 590 eyes with DRL) in 8 ophthalmology clinical centers in France, and in 3 of these centers data from patients wearing glasses were also collected (n = 684 eyes with glasses). Only complete patient files that met the study objectives were considered for data collection. Specifically, refraction and visual acuity data, as well as records of reported adverse events (0-4 on the CCLRU scale). The protocol and study procedures were reviewed and approved by Study, published on the Health Data Hub n • F20220113001828, France. This study followed the principles of the Declaration of Helsinki. All parents of the participants provided informed consent after they received an explanation of the nature, procedures, and consequences of the study.
Statistical Analysis The statistical package SPSS v. 21 (SPSS Inc. , Chicago, IL, USA) was used to conduct the statistical analysis. The Kolmogorov-Smirnov Test was applied to evaluate the normality of data distribution. The chi-squared test was used to analyze the variables between the groups. The Mann-Whitney U-test or Kruskal-Wallis test were used for the analysis of differences in refraction variables before and after treatment at one and two years. Comparison between the three visits was made with the repeated measures ANOVA test with Bonferroni adjustment. A p-value < 0. 05 was accepted as statistically significant.
35 D (p < 0. 001 Mann-Whitney U-test, Table  3 ) less in the first year and M = -0. 60 D (p < 0. 001 Mann-Whitney U-test, Table  4 ) less in the second year of treatment for the DRL lens wearers. This is in agreement with the studies that show us that a decrease of 0. 30 D SER per year plays an important role in the long-term control of myopia  [14, 40, 41]. This report describes the clinical study conducted in eight ophthalmology clinics in France during the years 2016 to 2020. This study was based on the clinical data of children and adolescents between 5 and 17 years old. In a retrospective way, we analyzed files of patients who used glasses (Single-vision-SV) and orthokeratology contact lenses (DRL Orthokeratology) with a consultation record of at least 1 or 2 years performed by the same ophthalmologist during that period.
After data collection, refraction variables were studied and their evolution over two years was analyzed. A total of 360 clinical files were studied, of which 211 were orthokeratology contact lens wearers and 149 were spectacle wearers, which in this study served as the control group. The clinical refraction of both groups is described in Table  2. In the last two decades, there have been several longitudinal studies with orthokeratology contact lenses. Known by the orthokeratology technique for night use, they are associated with a decrease in central refraction and an increase in corneal power in the periphery, making the peripheral blur initially hypermetropic become myopic. From the first study with Pauline Cho until today, the values found vary from 30 to 60% when compared to other types of contact lenses or even glasses  [15, 19, 34, [42] [43] [44].
2023a (Dovciak et al. , 2023b)). Level 2 data were downloaded from the IXPE archive at the HEASARC  59  and analyzed with both IXPEOBSSIM version 30. 6. 2  (Baldini et al. 2022)  and HEASOFT/XSPEC version 12. 13. 1d  (Arnaud 1996). IXPE observations of Swift J1727. 8-1613 were carried out placing a "gray" filter in front of the detector  (Ferrazzoli et al. 2020; Soffitta et al. 2021). The filter was used to reduce (by a factor of ∼10) the incident flux from a very bright source, especially at low energies, to a level compatible with the dead time of the detector units and with the need to transmit all data within the allocated telemetry. Now different response matrices have to be used for data analysis, which are available both in the IXPEOBSSIM package and in the HEASARC CALDB. Comparing the polarization obtained by the PCUBE algorithm in IXPEOBSSIM and the one from XSPEC, we found that the latter provides more consistent results as it fully takes into account the energy response of the instrument.
Acknowledgments The Imaging X-ray Polarimetry Explorer (IXPE) is a joint US and Italian mission. The US contribution is supported by the  National Aeronautics and Space Administration (NASA)  and led and managed by its  Marshall Space Flight Center (MSFC) , with industry partner  Ball Aerospace  (contract  NNM15AA18C ). The Italian contribution is supported by the  Italian Space Agency (Agenzia Spaziale Italiana, ASI)  through contract  ASI-OHBI-2022-13-I. 0 , agreements  ASI-INAF-2022-19-HH. 0  and  ASI-INFN-2017. 13-H0 , and its  Space Science Data Center (SSDC)  with agreements  ASI-INAF-2022-14-HH. 0  and  ASI-INFN 2021-43-HH. 0 , and by the  Istituto Nazionale di Astrofisica (INAF)  and the  Istituto Nazionale di Fisica Nucleare (INFN) in Italy. This research used data products provided by the  IXPE Team (MSFC ,  SSDC ,  INAF , and  INFN)  and distributed with additional software tools by the  High-Energy Astrophysics Science Archive Research Center (HEASARC) , at  NASA Goddard Space Flight Center (GSFC).
Data collection Data were recorded on five central plants of each ridge making a total of ten plants per plot except for D50F where the data were collected considering the total plant per plot. Collected data were on traits such as days to 50% flowering (D50F), thousand-seed weight (TSW) and seed yield (SY). To get the thousand-seed weight values, the coefficient of variation of 8-10 samples of 100 seeds were calculated. Thousand-seed weight value was approved when the coefficient was less than 5%. The value obtained was multiplied by 10 to obtain the thousandseed weight  [1]. The seed yield was calculated using the following formula (Eq. 1) by Nadeem et al. [26].
Multi-trait stability index The multi-trait stability index (MTSI) was determined following the formula (Eq. 6) used by Olivoto et al. [29]  to select the stable accessions for the studied traits. The accessions with lowest MTSI were considered as superior accessions  [25]. MTSI i = [ ∑ f j=1 ( F ij -F j ) 2 ] 0. 5 6 MTSIi = multi-trait stability index for the i-th genotype, F ij = j-th score of the i-th genotype, F j = j-th score of ideal genotypes. The different analysis were performed with package "metan" in software R 4. 0. 5 RCore Team  [30].
As a community, we expect that individualised HCC risk will be the cornerstone of personalised surveillance, directly influencing what surveillance regimen the patient receives. [3] [4] [5]  As such, the development and validation of HCC risk models has become an active area of research with numerous models now available to clinicians. [8] [9] [10] [11]  In our view however, there are several barriers to using these models in an individualised screening context which are not widely recognised. J o u r n a l P r e -p r o o f 1. Low model quality and applicability HCC risk models aim to improve patient care, yet they could equally cause harm if their predictions are biased. A key concern is overfitting, where the model is fitted to the noise in a dataset rather than the true signal. Overfitted models generate predictions that are too extreme -i.
e. too low for lower risk patients and too high for higher risk patients  [12]. The best defence against overfitting is to develop models from large longitudinal datasets with many incident HCC cases occurring over a sufficient long follow-up. Despite some exceptions however, most HCC risk models have been produced from small datasets, including several with <5 events per prognostic parameter (Figure  2 ). For these models, we should not expect their predictions to be reliable, even for a set of patients who closely resemble the dataset used to train the model. Second, virtually all models to-date have been developed using Cox regression  [8] [9] [10] [11] , which does not account for competing risk events which are particularly numerous in patients affected by CLDs and include non-HCC liver-related and extra-hepatic mortality.
Convenience external validation: HCC risk models are normally developed from a just tiny fraction of the "at-risk" population. External validation (EV) means assessing model performance on "new" patients who are eligible to use the model but were not part of the development dataset. It can be a critical step towards clinical implementation providing EV cohorts are selected thoughtfully and strategically. However, in our experience, EV cohorts tend to be chosen more for reasons of convenience than with a clear implementation strategy in mind. A crucial distinction is the difference between a model's reproducibility and its transportability. [15]  A model is reproducible if its performance can be replicated in cohorts which closely resemble the development cohort. Conversely, a model is transportable if the performance can be replicated in patients that deviate in some way from the patients on which the model was developed (e.
Funding: HI is supported by a  Viral Hepatitis Fellowship  from the  Medical Research Foundation  (grant ID:  C0825 ). PN has received research grants from  AstraZeneca ,  AbbVie ,  Bristol-Myers Squibb and Eisai. Pierre Nahon 's research is funded in part by the  European Union  (GENIAL, Grant agreement ID:  101096312 ) and  French Agence Nationale de la Recherche  ( France 2030  DELIVER  ANR-21-RHUS-0001 ) Author contributions: PN and HI have contributed equally in terms of the concept of the article and the writing and editing of the manuscript.
, 2015) , recommended in GATK best practices (Van der  Auwera et al. , 2013). We created mpileup files of the 224 individuals using samtools v1. 9  (Danecek et al. , 2021)  and converted them into pro files using sam2pro v0. 8. We detected bi-allelic SNPs using the Bayesian genotype caller (BGC) described in  (Maruki & Lynch, 2017). We created a file summarizing nucleotide read quartets for the 224 individuals from the pro files using a genotype-frequency estimator (GFE)  (Maruki & Lynch, 2015)  and called genotypes with the BGC software. We discarded SNPs with a minor allele frequency (MAF) lower than 10%, with more than 5% of missing calls and located in regions annotated as transposable elements in the Q. robur reference genome. These filters were achieved with a combination of awk command lines and PLINK v1.
Population genomics analysis of sessile oak populations We estimated linkage disequilibrium (LD) decay along the oak genome using the r² function available in PLINK v1. 9 with window size of 50kb. To study the genetic structure of Q. petraea populations we pruned the SNPs according to LD previously estimated and removed highly correlated markers (r² > 0. 2) using the "--indep-pairwise" function of PLINK v1. 9  (Chang et al. , 2015)  with a window size of 2 kb and a stepsize of 1. We computed an average Hudson FST  (Bhatia et al. , 2013)  index between pairs of populations, estimated across all SNPs in the pruned dataset using the "--fst" PLINK v2. 0  (Chang et al. , 2015)  with default parameters. We computed FST  (Weir & Cockerham, 1984)  across populations using the "--fst" function in PLINK v2.