dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors wish to thank  Julie Mennetrey  and  Violaine Suchail Drutel  ( Neonatology, Hopital de la Croix-Rousse, Lyon ) for supporting the implementation of the new perfusion system,  Marion Masclef Imbert  ( Neonatology, Hopital de la Croix-Rousse, Lyon ) for help in data collection,  Philip Robinson  ( Hospices Civils de Lyon ) for help in manuscript preparation, and  Philippe Buisson  ( Doran International Toussieu, France ), inventor of the  Edelvaiss Multiline NEO , for providing technological expertise. No compensation was received for their roles.
The nano-topography induced diffusion trap provides a framework for local regulation of supramolecular organization that promote their aggregation through molecular crowding and increased probability for protein interactions  74. We envision the same principle can be applied to diverse 3D cellular and tissue structures in building stable force-resistant nano-domains that regulate protein diffusion, such as cadherin-mediated cell-cell adhesions and neuromuscularjunctions. and Benoît Ladoux for helpful discussions and gift of reagents. We acknowledge financial support from the French Ministry of Research and CNRS, the Human Frontiers Science programme (Grant RGP0009/2017). T. C. is supported by the the French government in the framework of the University of Bordeaux's IdEx "Investments for the Future" program / GPR LIGHT.
C. H. F. E. is supported by the University of Cambridge Career Support Fund. O. R. and G. G. are supported by the France BioImaging national infrastructure ANR-10-INBS-04. for translation in Drosophila, was included just before the methionine initiation codon of mEos3. 2. The CAAX sequence was added into the C-Terminus of mEos3. 2 sequence by PCR amplification using a specific reverse primer that added the CAAX region just before the stop codon amino acid of mEos3. 2. The ubiquitous cytoplasmic actin, encoded by Actin5C, was tagged with mEos3. 2 at the Nterminus as previously described  6. The coding sequence of mEos3. 2 was amplifying by PCR and inserted into a UASp AttP vector, and the amplified Actin5C coding sequence appended to the mEos3. 2 sequence with a GSGS linker sequence.
, San Mateo, CA, USA). The urology community was invited globally to participate via social media (#UroSoMe platforms in Twitter) and the fellow mailing list of international urological associations (Appendix file 2). The link to the online survey (www. surveymonkey. com/MISTKAPSurvey) was provided and respondent could complete the survey online. Internet protocol restriction was implemented, where one internet protocol address could complete the survey once only. All data were only accessible to investigators. In order to facilitate the interpretation on the knowledge, attitude, and practice questions with Likert scale, the investigators decided on the definition of a consensus concerning the respective responses. Consensus was achieved when 70% responses were "agree or strongly agree" and 15% responses were "disagree or strongly disagree" (consensus agree), or when 70% responses were "disagree or strongly disagree" and 15% responses were "agree or strongly agree" (consensus disagree)  [8].
Acknowledgments We thank all the lab members for their involvement in this project and fruitful discussions. This project was founded by the  French National Agency of Research  grants  ANR-CE16- Myochronic  awarded to AM and  ANR-CE16 -Floradoloris  awarded to AR. It was also supported by founding from  CNRS  and  Aix-Marseille University  awarded to IBDM.
Rebreathing At the end of all the experiments, the different BVD were drilled to insert a CO 2 sensor to test rebreathing inside the balloon of the BVD. CO 2 was injected at the patient interface, as shown on Fig. 1. A. BVD was connected to the ASL test lung simulating the mild condition patient profile without PEEP valve. A qualitative assessment was performed using a cut-off value of 3 mmHg after a stabilization time of 30 seconds to determine the presence of CO 2 rebreathing. "Resusci Anne" (Laerdal, Stavange, Norway) and subsequently on the cadaver model. A fixed wall-outlet oxygen flow of 15 L/min supplied the BVD according to clinical usual practice. PEEP was set at zero cmH 2 O and pop-off valves were closed for all BVD. To take into account the increase in volume due to heating and water saturation observed in patients (up to 10%), the data measured on the bench and the cadavers was converted from ATP (Ambient Temperature and Pressure) to BTPS (Body Temperature and Pressure Saturated) as methodologically required.
Statistical analysis Data are summarized as mean (±SD) for continuous variables. For the pre-oxygenation experiments, results of each BVD were averaged over three FeO 2 values. For the CPR manual ventilation experiments, mean values and standard deviations were computed over three ventilation cycles. Normal distribution of the data was assessed with a Shapiro-Wilk test and quantile-quantile plot. Depending on the distribution, comparisons between groups were assessed with ANOVA test or its non-parametric equivalent Kruskal-Wallis test. Comparisons between two groups were computed using a student t test or its non-parametric equivalent Mann-Whitney. Results with p < 0. 05 were considered statistically significant. Bonferroni correction was applied for multiple comparisons. Statistical analysis was performed on Python software (Python version 3.
ACKNOWLEDGEMENTS 5 We would like to thank the technical assistance of  Adrián Kószó  in the laboratory of G. T. and that of the  Microscopy Rennes Imaging Center (BIOSIT, Université Rennes 1). The work in the Timinszky laboratory was supported by the  National Research Development and Innovation Office  ( K143248 ). A. G. K. was supported by the  National Academy of Scientist Education.
Program  of the  National Biomedical Foundation  under the sponsorship of the  Hungarian Ministry of Culture and Innovation  and the  New National Excellence Program of the Hungarian Ministry of Culture and Innovation  ( UNKP-22-3-SZTE-264 ). For this work, S. H. 's group received financial support from the  Agence Nationale de la Recherche  ( AROSE ,  ANR-22-CE12-0039 ), the  Institut National du Cancer  ( PLBIO-2019 ) and the  Institut Universitaire de France. Research in the Haracska laboratory was supported by the  National Research, Development and Innovation Office (PharmaLab ,  RRF-2. 3. 1-21-2022-00015  and  TKP-31-8/PALY-2021 ). The models in Figure 6 were created with BioRender. AUTHORS CONTRIBUTIONS G. T. conceived the project. H. M. , R. F. B. and G. T. planned the research. H.
Phylogenetics The phylogenetic tree of the ompA gene is based on a 923 bp muscle alignment (except MIK308348/19_Great tit [898 bp]) with ClustalW sequence weighting scheme and was finally constructed in Geneious prime version 8. 1. 9. with the Neighbour-Joining method using the Tamura-Nei genetic distance model. Bootstrapping was performed by a random seed of 500. 000 and 1000 replicates. Sequences of C. psittaci reference strains (genotypes A-E/ F) were included. The seven housekeeping genes of the MLST method  [4, 5]  were amplified and sequenced using primers and conditions described on the Chlamydiales MLST website (http://pubmlst. org/ chlamydiales/http://mlst. ucc. ie/, accessed on 1 February 2020). Sequencing of both DNA strands was performed by Eurofins Genomics (Ebersberg, Germany) and numbers for alleles and sequence types (STs) were assigned in accordance with the Chlamydiales MLST Database.
DNA sequences of the seven MLST alleles were assembled. We then performed multiple alignments of these concatenated gene fragments with a panel of C. psittaci reference strains using MEGA7 software, as previously described  [14]. Phylogenetic trees were constructed by using the Maximum Likelihood method based on the Tamura 3-parameter-model and Gamma distribution  [15]. The new ST was deposited to the Chlamydiales MLST Database.
At least two patients required intensive care, one of them suffered a stroke in the aftermaths of the infection. No fatalities were recorded (data missing from six cases). A majority (25/42, 60 %) of the cases reported domestic bird feeding. Nine cases reported outdoor exposure to birds and five reported other temporary exposure to birds or bird droppings. Professional or recreational contact with poultry, pigeons or caged birds was reported in three, one and two cases, respectively. Four cases reported no known exposure to birds or bird droppings, despite thorough interviews. Case S-1427/19, exhibiting a pigeon type according to ompA analysis and PCR-HRM, had extensive contact with pigeons, establishing a clear link to the source of infection. Similarly, case G-2650/18, identified as having a psittacine type by MLST and PCR-HRM, had multiple pet birds at home, including lovebirds.
The use of the ompA sequence alone for typing leads to imprecise genotype clustering, in particular inside this group of closely related strains subjected to high recombination events. The SNP-Mat116 genotype has been relatively uncommon thus far, with only a limited number of specimens identified  [6]. Among these specimens are the 99DC05 strain, which was isolated from a horse in Germany, and another strain from a French patient with unknown transmission source. Our study also analysed bird samples collected from various regions of Sweden, and the typing data showed a strong correlation between the genotype obtained and the suggested source of bird exposure for human cases. Indeed, the Mat116 genotype was associated with cases exposed to wild birds, mainly passerines visiting feeders, while the pigeon and psittacine genotypes were found in cases exposed to domestic/pet birds.
Acknowledgements Collaborators: The Chlamydia psittaci study group represents four other participating regions in Sweden ( Leif Dotevall ,  Ann-Cathrine Petersson ,  Malin Bengn er ,  Ulf Ryding ), the  Public Health Agency of Sweden  ( Pontus Jur een ) and the  Swedish National Veterinary Institute  ( Tomas Jinnerot ). Tomas Cumlin  is acknowledged for submission of sequences to GenBank.
Objective: To analyze outcomes and complications of cytoreductive prostatectomy (CRP) for oligometastatic prostate cancer (PCa) in order to elucidate its role in this space. Methods: We performed a systematic literature search using three databases (Medline, Scopus, and Web of Science). The primary endpoints were oncologic outcomes. The secondary endpoints were complication rates and functional results. Results: In all studies, overall survival was better or at least comparable variable in the groups with CRP compared to no local treatment. The greatest benefit from CRP in 5-year overall survival in one study was 67. 4% for CRP versus 22. 5% for no local treatment. Cancer-specific survival (CSS) showed the same trend. Several authors found significant benefits from CSS in the CRP group: from 79% vs.
Search strategy and inclusion criteria This systematic review was carried out in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines (Fig. 1 ). The detailed search strategy and review protocol have been published in PROSPERO (ID CRD42020192328). The scope of the review according to the Patient, Intervention, Comparison, Outcomes (PICO) process is as follows: (P) patients with oligometastatic PCa; (I) cytoreductive prostatectomy; (C) conventional therapy (RT, hormonal therapy, chemotherapy, or any combination of these); (O) oncological outcomes (CSS, progression-free survival [PFS], and OS), functional outcomes (urinary incontinence and erectile function rates), and complications. We have performed a systematic literature search using three databases (PubMed, Scopus, and Web of Science) based on the following search query: "prostate cancer" AND ("pligo metast * " OR "bone metast "prostatectomy" OR "surgery" OR "cytoreductive prostatectomy").
Once the titles and abstracts were reviewed, Chuvalov L removed any duplicates. In the final stage, Chuvalov L and Morozov A performed independently a full-text review of the relevant texts. They excluded articles focusing on the procedure technique, in which the authors did not provide any data on outcomes. Any articles with procedures other than CRP or without CRP for metastatic PCa were excluded. All types of original articles were included: both prospective and retrospective, with different groups of comparison and without them. If only one reviewer approved an article, the final decision of whether it should be included in the analysis was made by Enikeev D.
0 ng/mL resulted in 78% biochemical relapse-free survival, while higher PSA (!8 ng/mL) led to 32% biochemical relapse-free survival. A number of trials related to local treatment in oligometastatic disease are ongoing. Ranasinghe et al. [43]  in 2020 conducted a review of this topic and identified nine randomized trials. Among them, the most promising are LoMP II (a randomized trial comparing RT and CRP), NCT03456843 (a randomization between CRP and NLT), and IP2-ATLANTA (the first arm: standard of care; the second arm: standard þ ablative therapy; the third arm: standard þ RT or CRP). We believe that the trial designed with randomization or comparison of different local treatment modalities will allow us to understand better the role of these interventions. Besides, several reviews on this topic have been published recently.
9  Nonetheless, these findings are mixed with those of other studies that reported no benefit from cyclosporine. 7, 14, 15  No randomized prospective data are available regarding the optimal choice of CNI after LT, specifically for PSC. The limitations of existing observational studies include single-center designs, potential selection bias, calendar effects, variations in the length of follow-up, residual and incomplete confounding assessments, and insufficient statistical power to reliably disentangle the independent effects of various immunosuppressants (CNI type, steroid use, antimetabolite use, and type). To the best of our knowledge, no existing studies have applied propensity score matching to balance the differences in baseline characteristics. Furthermore, the definition of recurrent PSC varies, and competing risks are usually not considered in analyses of disease recurrence.
Material and methods Anonymized data were retrieved from the European Liver Transplant Registry (ELTR) and the Scientific Registry of Transplant Recipients (SRTR). The coordinating committees of both registries reviewed and approved this study. This study was approved by the Institutional Review Board of the Helsinki University Hospital, Abdominal Center (HUS/155/2021). The ELTR prospectively collected LT-related data from 174 centers in 32 European countries using standardized forms. Data quality and validity were ensured by audit visits to randomly selected contributing centers. This study also used SRTR data. The SRTR data system includes data on all donors, wait-listed candidates, and transplant recipients in the US submitted by members of the OPTN (Organ Procurement and Transplantation Network).
Estimation of the propensity scores The propensity scores were derived by regressing the CNI type on the covariates using logistic regression (R-package 'logistf,' version 1. 24. 1)  16  and then using the regression coefficients and covariate values to estimate the probability of being cyclosporine-treated ("propensity score"; a higher score indicated a higher probability of cyclosporine treatment). The median propensity scores were 0. 091 (range, 0. 0202-0. 439; IQR, 0. 0605-0. 129) and 0. 170 (range, 0. 022-0. 432; IQR, 0. 108-0. 238) in patients treated with tacrolimus and cyclosporine, respectively. Propensity scores were restricted to the shared domain between tacrolimus-and cyclosporine-treated patients (propensity scores between 0. 022 and 0. 432), and patients with propensity scores outside this interval were excluded before matching.
secondary), HCV antibody status, azathioprine and mycophenolate levels, and steroid use during the first post-LT month. The proportional hazard assumption was visually confirmed using covariate-specific Schoenfeld residual plots (data not shown). We tested the interaction terms between CNI type and age, sex, register, LT year, and MELD score for death and the composite outcome of death or graft loss using Cox regression in the entire matched cohort. Competing-risk analysis was performed using Aalen-Johansen estimates stratified by CNI type. To confirm the robustness of the results, we conducted a sensitivity analysis using 1:1 propensity score matching instead of 1:3 matching. The data were analyzed using R software version 4. 1. 3. 18 Only existing data were used, with no imputation of missing values.
90, 95% CI 0. 55-0. 96, p = 0. 001), donor age (HR/10 years 1. 14, 95% CI 1. 08-1. 19, p <0. 001), donor/recipient sex mismatch (HR 1. 23, 95% CI 1. 05-1. 44, p = 0. 010), and mycophenolate use during the first month (HR 0. 82, 95% CI 0. 69-0. 98, p = 0. 029) (Fig. 4 ). Steroid use during the first month was not statistically significant. The interaction terms between CNI type and age, sex, register, LT year, and MELD score were all non-significant (data not shown).
In addition, data on CNI trough levels were missing, and target levels probably decreased over time; this was partly accounted for by the exact matching of calendar times. Regarding missing data, we did not perform imputation. Tacrolimus is generally associated with slightly improved survival in LT. 10  The rationale for considering cyclosporine after LT in patients with PSC is based on the perception of a reduced risk of recurrent PSC in some studies,  2, 8, 9  improved control of frequently coexisting IBD,  19  and the association between IBD activity and increased PSC recurrence risk. 15, 20  Although our study does not exclude such potential benefits of cyclosporine over tacrolimus, any differences in this regard between cyclosporine and tacrolimus are likely small, and the fact remains that both patient and graft survival were better with tacrolimus therapy in our study.
Therefore, tacrolimus should be the standard CNI used after LT for patients with PSC. Affiliations 1 Helsinki University Hospital and University of Helsinki, Transplantation and Liver Surgery Unit, Finland; 2 Medaffcon Oy, Espoo, Finland; 3 European Liver Transplant Registry, APHP Hôpital Paul Brousse, Université, Paris-Sud, Inserm U 935, Villejuif, France;  4  The Queen Elizabeth Hospital, Queen Elizabeth Medical Center, Birmingham, UK; 5 King's College Hospital, Institute of Liver Studies, London, UK;  6  Rikshospitalet, Department of Transplantation Medicine, Oslo, Norway;  7  Institute for Clinical Medicine, University of Oslo, Oslo, Norway; 8 Sahlgrenska University Hospital, Transplant Institute, Gothenburg, Sweden; 9 Karolinska Institutet, CLINTEC, Division of Transplantation Surgery, Stockholm, Sweden; 10 Medical University of Warsaw, Department of General, Transplant and Liver Surgery, Warsaw, Poland;  11  St James & Seacroft University Hospital, Leeds, UK;  12  University Hospital Copenhagen, Department for Surgery and Transplantation, Copenhagen, Denmark;  13  Hannover Medical School, Department of General, Visceral and Transplant Surgery, Hannover, Germany;  14  Royal Free Hospital, Liver Transplantation, London, UK;  15  Hospital Universitario La Paz, General and Digestive Surgery, Madrid, Spain reporting of these data are the responsibility of the author(s) and in no way should be seen as an official policy of or interpretation by the SRTR or the US Government.
Acknowledgments The European data have been supplied by the ELTR. The ELTR is supported by a grant from  Astellas ,  Novartis ,  Institut Georges Lopez ,  Sandoz ,  Chiesi  and logistic support from the  Paul Brousse Hospital (Assistance Publique -Hôpitaux de Paris). The Organ Sharing Organizations: the  French ABM  ( Sami Djabbour ), the  Dutch NTS (Maaike de Wolf) , the  Eurotransplant Foundation  ( Marieke Van Meel ), the  Spanish RETH/ONT (Gloria de la Rosa) , the  UK-Ireland NHSBT  ( Malcolm   Fox)  and the Scandiatransplatnt ( Ilse Duus Weinreich ) are acknowledged for the data cross-check and sharing with the ELTR. The USA data reported here have been supplied by the  Hennepin Healthcare Research Institute (HHRI)  as the contractor for the Scientific Registry of Transplant Recipients (SRTR).
Acknowledgements: We thank the expert and novice meditators for their participation in our study. The authors would like to thank the  Neuropain laboratory (Lyon) ,  Sofie Valk ,  Romain Quentin , and  Josua T. Vogelstein  for their valuable inputs in theoretical and statistical discussions. Gratitude is also extended to  Clara Benson ,  Liliana Garcia Mondragon ,  Oussama Abdoun ,  Kristien Aarts  and  Eléa Perraud  for their assistance during data collection, and the recruitment of experts. Appreciation is also expressed to  Franck Lamberton  and  Camille Fauchon  for their help with the technical aspects of the protocol. Their contributions have greatly enhanced the quality of this research.
Acknowledgements The authors thank the zebrafish platform and the cell-imaging platform, for technical assistance in confocal imaging acquisition and analysis;  Etienne Morel ,  Perrine Renard , for insightful discussions. Lentiviruses were produced by the platform Structure  Fédérative de Recherche Necker Vecteurs  viraux et transfert de genes ( Structure Féderative de Recherche Nêcker-Université Paris Descartes ,  S Fabrega ). This work was supported by grants from  Fondation Lejeune 2017 to PdL ,  Agence Nationale de la Recherche  to PdL and  PvE  ( ANR -AAPG 2018 CE17 MetabInf ), the  Association Française contre les Myopathies  to PdL, SM, HdC and EK ( AFM 2016 -2018 n°19773 ;  AFM 2022 -2025 n°24269 ),  Tango2 Research Foundation   2020  to PdL,.
RT-PCR Total mRNA was extracted from cultured MFs resuspended in TRI-ZOL. cDNA was obtained in a final volume of 100 μL by reverse transcription via a random hexamer priming kit used in accordance with manufacturer recommendations (Thermo Fisher Scientific, Applied Bioscience). Specific pre-developed TaqMan probes (Thermo Fisher Scientific) were then used for PCR amplification of GUSB, IL1B, IL6, IL12A, IL12B, IL18, IL23A (details in supplemental Table  2 ). Fluorescence was detected with a CFX96 Dx Real-Time PCR and results analyzed with CFX ManagerTM software v 3. 1 (Bio-Rad). Gene expression was normalized to the expression of the endogenous control GUSB using the comparative ΔCt method (relative expression = 100*2 -ΔCt ).
Flow cytometry PBMCs were incubated with antibodies or control isotypes for 30 min at 4 • C in phosphate-buffered saline (PBS) supplemented with 0. 5 % bovine serum albumin (BSA). Cells were then fixed and permeabilized using an intracellular fixation and permeabilization buffer set (Thermo Fisher Scientific, eBioscience) and incubated for 30 min at 4 • C with antibodies or isotypes (details in supplemental Table  3 ). A BD FACS Canto™ flow cytometer and FlowJo v10 software were used for analyses.
Along this line, it was previously shown that tofacitinib, a Janus kinase (JAK) inhibitor targeting JAK3 and JAK1, was able to suppress innate and adaptive immunity in the vessel wall and thus decrease vasculitis  [26]. In addition, baricitinib, which specifically blocks JAK1 and JAK2, was suggested to be effective in a recent phase 2 trial  [34] , and more comprehensive data will be provided by the results of a phase 3 trial (SELECT-GCA: NCT03725202) investigating the efficacy of upadacitinib in GCA, which has just completed recruitment.
Contributorship statement MS and HG were the principal investigators and take primary responsibility for the paper. MS, BB, AR, SA, SO, TG and HG recruited the patients. AR, CGen, CGer, CC, MC, LM, GT, CCG, LA and HG performed the laboratory work. HG did the statistical analyses. MS and BB coordinated the research. MS, BB, MCB, RAR, MCC and HG contributed to data interpretation. MS, BB and HG drafted the manuscript. All authors revised and approved the manuscript.