dataesr/scientific-paragraphs-categorization huggingface dataset:
Discussion Our work provides evidence that skin wound healing is improved in female mice during and after pregnancy through enhanced vascular angiogenesis and cell proliferation. This was also observed in a mouse model of SCD in which showing genes, ordered by transcripts per million (TPM) and with TPM >50 expressed in eGFP + fetal microchimeric cells (FMC) harvested from peripheral blood of unwounded post-partum mice. No comparison was performed in order to display the main genes expressed by circulating FMC at steady state. Membrane receptors previously reported to be enriched in blood FMC of wounded pregnant mice  17  are shown. Data are presented as log 2 TPM. (B) Graphical summary obtained upon transcriptional analysis, using ingenuity pathway analysis (IPA) software, of blood FMC harvested from unwounded post-partum mice.
Only transcripts with at least 50 TPM were kept for the analysis. (C) ARCHS4 enrichment analysis of the 500 most expressed genes in FMC in unwounded post-partum mice. (D) Heatmap showing the significantly (adjusted P<0. 05) differentially expressed genes in FMC in post-partum mice with or without wounds. Upregulated membrane receptors are indicated. Data are presented as log 2 fold change. (E) Statistically significant (adjusted P<0. 05) upregulated and downregulated canonical pathways and upstream regulators were determined using IPA software from differentially expressed genes in blood FMC from wounded post-partum mice as compared with unwounded counterparts. Canonical pathways are expressed as a Z score. In (A-E), RNA sequencing was performed in post-partum mice left unwounded (n=3) or 1 day after performing one 6-mm cutaneous wound (n=3 mice).
(B) ARCHS4 enrichment analysis of the 500 most expressed genes in sorted eGFP + FMC of post-partum SAD wounds. (C) Graphical summary obtained upon transcriptional analysis, using ingenuity pathway analysis (IPA) software, of sorted eGFP + FMC from harvested wounds of post-partum SAD mice at day 3 after the injury. (D) Representative images of CD31 + and CD45 + cells co-stained with GFP in wound beds of post-partum SAD mice. White arrowheads show double-stained cells. The quantification of double-stained cells at day 5 is shown. Nuclei were counterstained with DAPI. Data are presented as means ± standard deviations and individual values. Scale bars represent 50 mm. (E) Volcano plot showing differentially expressed genes between wounds of post-partum and virgin SAD mice. Blue dots and red dots represent, respectively, downregulated and upregulated genes in wounds in post-partum mice compared with those in virgin mice.
However, the course and severity of leg ulcers in SCD remain difficult to assess, as retrospective studies have specific biases that may confuse data analysis. We therefore chose to study multiple outcome measurements collected from a single center to reduce variability. As a consequence, we cannot be certain that our cohort is fully representative of the general population of female SCD patients, but it is rather representative of SCD patients with ulcers. Indeed, we confirmed a higher rate of SCD hemolytic complications in our patients as previously published in SCD patients with leg ulcers. 2, 7 Our data indi-cate that the burden related to leg ulcers is reduced in parous SCD female patients, as measured by the age-adjusted total number of ulcers and ulcer episodes. We found no significant difference between nulliparous and parous SCD women in other risk factors for leg ulcers, including venous insufficiency, arteriopathy, diabetes, obesity, smoking, vasculitis, human immunodeficiency virus infection, or   autoimmunity.
(D) Heatmap showing the significantly (adjusted P<0. 05) differentially expressed genes in FMC in post-partum mice with or without wounds. Upregulated membrane receptors are indicated. Data are presented as log 2 fold change. (E) Statistically significant (adjusted P<0. 05) upregulated and downregulated canonical pathways and upstream regulators were determined using IPA software from differentially expressed genes in blood FMC from wounded post-partum mice as compared with unwounded counterparts. Canonical pathways are expressed as a Z score. In (A-E), RNA sequencing was performed in post-partum mice left unwounded (n=3) or 1 day after performing one 6-mm cutaneous wound (n=3 mice).
Acknowledgments We are grateful to all members of the  Cutaneous Biology Laboratory  for helpful discussions. We are grateful to the  Genom'IC platform and animal facility of Institut Cochin , the flow cytometry facilities of  Institut Curie  and the imaging centers of  Institut Cochin and Centre de Recherche St Antoine  for technical support. We particularly thank  Benjamin Saintpierre  and  Lucie Adoux  for their help with RNA-sequencing experiments and analyses.
(C) ARCHS4 enrichment analysis of the 500 most expressed genes in FMC in unwounded post-partum mice. (D) Heatmap showing the significantly (adjusted P<0. 05) differentially expressed genes in FMC in post-partum mice with or without wounds. Upregulated membrane receptors are indicated. Data are presented as log 2 fold change. (E) Statistically significant (adjusted P<0. 05) upregulated and downregulated canonical pathways and upstream regulators were determined using IPA software from differentially expressed genes in blood FMC from wounded post-partum mice as compared with unwounded counterparts. Canonical pathways are expressed as a Z score. In (A-E), RNA sequencing was performed in post-partum mice left unwounded (n=3) or 1 day after performing one 6-mm cutaneous wound (n=3 mice).
Participants We report here six patients with SMA-PME and their genotypes. Clinical information was collected retrospectively. ] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]  Criteria for inclusion were: an isolated neurological presentation, an adequate description of the clinical phenotype, and confirmed pathogenic variants in ASAH1. We excluded reports of cases that lacked clinical data  26  and historical reports of SMA-PME that lacked molecular confirmation. Because several transcripts have been used in the literature when describing variants in ASAH1, we have converted variants to nomenclature corresponding to the NM_177924. 5 transcript. 19.
T. Baker cat#9829-03)/isopropanol (Fisher, cat# A416-4) (5:2; v/v) with 0. 1% formic acid and 10 mmol/L ammonium acetate (solvent B). Gradient elution started with 30% B, ramping to 100% B over 5 min. After 30 min at 100% B, the gradient dropped to 30% B over the course of a minute, where it remained for the time remaining in the run to re-equilibrate the column. Data acquisition was performed in positive ion mode using multiple reaction monitoring (MRM) monitoring the product ion of 264. 3, corresponding to di-dehydrated d18:1 sphingosine backbone. Instrument control and data acquisition were performed with Analyst software (v. 1. 6. 2, AB SCIEX). Processing of quantitative MRM data was performed using MultiQuant software (v. 3. 0. 2, AB SCIEX). Ceramide abundances were expressed as pmol equivalents of Cer(d18:1/16:0-d31) per million cells.
Percent activity, defined as the change in ceramide content at 0, 24, and 48 h following rhAC treatment, was expressed relative to untreated age-and sex-matched controls. Total ceramide content was analyzed statistically using a one-way ANOVA with Holm-Sid ak post-hoc tests. Changes in the abundances of individual ceramide species were determined statistically by multiple t-tests with false discovery rate (FDR) set at 1% using two-stage linear step-up FDR procedure of Benjamini, Krieger and Yekutieli  33  without assuming consistent standard deviation. The change in percent activity was assessed 0-48 h after treatment with rhAC and time needed to correct ceramide levels determined by linear regression. Statistical analyses were performed using GraphPad Prism version 9. 41 (GraphPad Software).
Acknowledgements The authors would like to acknowledge the patients and their families for their participation in this research. Sequencing of ASAH1 for Patient 5 was performed by  Ruobing Zou  and the  Care4Rare Canada Consortium. The authors would like to thank  Dr. Wendy Mears  for sample preparation. Recombinant human acid ceramidase enzyme (rhAC) was provided by Enzyvant under a material transfer agreement, the compound is being further developed for potential clinical use by  Aceragen  as  ACG-801. This work was supported in part by a  Can-Gard Spring Accelerator grant  to DAD and SALB.
Key factor analysis When planning measurements such as those for COVID-19, it is important to analyze the key factors, i. e. , the factors that correlate with changes in, for example, the number of infections. We investigated a method for analyzing the key factors that uses a generalized additive model (GAM)  [10]  in which the response variable depends linearly on the unknown smooth functions of some predictor variables and the focus is on making inferences about the smooth functions. The benefit of GAM is that it takes advantage of the smoothed transforms of the predictor variables using basis functions such as smoothing splines. The distances obtained by the closeness analysis are used as the response variables. The data for the key factor candidates, e. g. , vehicle and public transport increase rates, are used as predictor variables.
COVID-19 sequential data We used reported data for the number of newly infected people n t l for each of the 53 cities on the main island of Japan as reported daily by the Tokyo metropolitan government from April 1, 2020, to May 6, 2021, along with the population N l of each city. Segmentation {P l } l=1,. ,L (described in section 3. 1) was linked to each city in Tokyo (which is a prefecture, not a city). The observed proportion πl t (= n l t /N l ) was quantized into B-states, and B was set to 20.
Then in Section 5 we employ the geometrical models and tools and present a numerical algorithm to compute the distance map for the special case where the Lie group equals the roto-translation group  =  (2). Additionally, we explain how to compute the backtracking of geodesics from end to source point. We present a new version of the anisotropic fast marching algorithm  [37]  that applies to our new data-driven model. In Section 6, we report an extensive experimental evaluation of geodesic tracking in retinal images from the annotated STAR dataset  [38, 39] , and show that our new model allows for adequate geometric tracking of highly complex vasculatures. Finally, in Section 7, we end with a brief discussion of future work and conclude.
Ethics This retrospective cohort study was conducted in accordance with the principles of the Helsinki Declaration. The study was approved by the ethics committee of the French Society of Ophthalmology (IRB 00008855 SocieteFrancaise d'Ophtalmologie IRB#1) and was registered in clinicaltrials. gov (No. NCT03355924). All patients provided informed consent for surgical management. All patients were informed before surgery that their surgery-related data might be used for research purposes. All consented to this possibility. The consent procedure was conducted in accordance with the reference methodology MR-004 of the National Commission for Information Technology and Liberties of France (No. 588909 v1).
Primary and secondary study outcomes The following data were collected retrospectively from the prospectively maintained medical charts: patient age and sex; total operative time; graft donor age and ECD; the time between phacoemulsification and DMEK for the pseudophakic-DMEK patients; preoperative and postoperative (day 8 and 15 and months 3, 6, and 12) BSCVA; preoperative and 12-month refractive data; postoperative (months 3, 6, and 12) ECD; preoperative and 12-month central corneal thickness; 12-month corneal thinning; and postoperative complications, namely, CME, graft detachment that required anterior chamber rebubbling, repeated rebubbling, and graft failure. The primary study outcome was 12-month BSCVA. The secondary study outcomes were BSCVA at earlier postoperative timepoints, endothelial cell loss (ECL) at 3, 6, and 12 months, 12-month central corneal thickness, 12-month refractive outcomes, and complication rates.
The datasets generated during and/or analyzed during the current study are not publicly available according to French Law No. 2018-493 of June 20, 2018 on the protection of personal data (The General Data Protection Regulation (Regulation (EU) 2016/679) (GDPR: article data is subject to daily backups while all archived data is subject to duplicate storage at two different sites. This data processing is compliant with a baseline reference methodology (MR.
Alternative Y maze The alternative Y maze test was used to assess the spatial working memory before and after LD-RT. Rats were placed at the extremity of one arm of the device (50 × 50 × 10 cm) and video-tracked for 5 min. The number of good alternation (success to the test) were automatically measured and analyzed with EthoVision software (Noldus). Rats performing less than four entries during the session were excluded.
Elevated plus maze This test was used to evaluate anxiety-like behaviors. Animals were placed at the center of an apparatus, constituted by 2 open arms (anxiogenic areas; 0 × 50 × 10 cm) and 2 closed arms (50 × 50 × 10 cm), and video-tracked during 5 min. The number of head dipping over the open arms, an index inversely correlated to anxiety, was automatically measured using EthoVision software. Rats performing less than four entries during the session were excluded.
Statistical analysis A sample size analysis with the graphical Douglas Altman's nomogram approach was performed  [30]  and significant data were reported if P ≤ 0. 05 and β < 0. 2. All analyses were performed in blind conditions. Normality of residues was assessed with the Shapiro-Wilk test. One-way ANOVA and Tukey's post hoc test were used to compare plasma samples and western blot results. If data were not normal, Kruskal-Wallis test was used to compare the three independent groups, followed by Dunn's post hoc comparisons. For other results, twoway ANOVA (Group and Hemisphere as between factors) and Tukey's post hoc test were used to compare the groups. Outliers were identified using the ROUT method (Maximal false discovery rate = 1%). All analyses were performed on GraphPad Prism 8. Statistical details are provided in the legend of figures.
1s ). MCP-3 levels decreased in TgAD rats compared to WT rats and were restored after LD-RT (Fig. 1t ). IL-2, IL-12p70, GRO-α and IL-17α, were significantly decreased in TgAD rats compared to WT rats but LD-RT did not restore normal levels (data not shown). Other cytokine levels were unchanged in TgAD rats compared to control animals. Cytokine/chemokine levels were also quantified in the plasma, but no difference was measured between WT and TgAD animals, nor after LD-RT.
933, P = 0. 0599; secreted CLU (sCLU, one-way ANOVA, F (3,19) = 13. 91, P < 0. 0001) and CLUβ chain (Kruskal-Wallis test, P = 0. 1337) in the Triton-soluble fraction of the frontal cortex. Western blot data are normalized to GAPDH. Quantification of genes encoding for pro-inflammatory cytokines (o; Two-way ANOVA: F (3,138) = 9. 788, P < 0. 0001 for group effect; F (3,138) = 6. 043, P < 0. 001 for gene effect; F (9,138) = 3. 748, P < 0. 001, group x gene interaction) and anti-inflammatory cytokines (p; Kruskal-Wallis test) by qPCR in the cortex. q-t Pro-inflammatory cytokines levels quantified by ELISA in the hippocampus. Data are normalized to the weight of tissue of the region of interest. Two-way ANOVA: IL-1α: F (2,24) = 3. 392, P < 0. 05 for group effect; TNFα: F (2,27) = 4. 918, P < 0.
Funding This work was supported by the  Velux foundation  (Grant No  1123 ). PM is funded by the  Swiss National Science Foundation  (project  320030_184713 ). GF is funded by  Association Suisse pour la Recherche sur l' Alzheimer, Genève ;  Fondation Segré , Genève;  Ivan Pictet , Genève;  Fondazione Agusta , Lugano;  Fondation Chmielewski , Genève;  Velux Stiftung ;  Fondation Francis  and  Marie-France Minkoff. VG is funded by the  Swiss National Science Foundation  (projects  320030_169876  and  320030_185028 ), the  Schmidheiny foundation , the Aetas foundation. TZ is funded by the  Swiss National Science Foundation  (project  320030_182366 ). TC, FF, and FC are grateful for financial support provided by the  Regional Council of Normandy, FEDER , the  University of Caen  and  Carnot I2C.
Acknowledgements We are grateful to all physicians, nurses, and health care workers treating Covid-19 patients under very challenging circumstances and still being able to help with providing data for this paper. We are very grateful to the 2648 front-line NHS clinical and research staff and volunteer medical students, who collected these data in challenging circumstances. We thank the generosity of the participants and their families for their individual contributions in these difficult times. We also acknowledge  Lucy Lorris  for extracting clinical information for ISARIC4C patients;  Tovah Klein  for providing samples and clinical information for NorthShore Hospital patients;  Mary Magliocco ,  Michael Stack ,  Elana Shaw ,  Jason Barnett ,  Smilee Samuel  and  Sandhya Xirasagar  for maintaining LabKey database for  NIAID Immune Response  to COVID patients;  Charla Andrews ,  Britta Flach ,  Emily Coates ,  Obrimpong Amoa-Awua ,  Maria Burgos Florez ,  Lasonji Holman ,  Renunda Hicks , for providing samples and clinical information for VRC 200 patients;  Laidlaw Elizabeth  and  Silvia Lage  for providing samples and clinical information for CALYPSO patients.
collection program was initially supported by grants to the  NorthShore Foundation , including a donation from the  Rice Foundation , and support from  NorthShore University HealthSystem Research Institute. Subsequently, NorthShore  received funding from the  Department of Defense  ( W911QY2090012-D. S ). The ISARIC4C is supported by grants from: the  NIHR  (award  CO-CIN-01 ),  MRC  (grant  MC_PC_19059 ),  NIHR Imperial Biomedical Research Centre  (grant  P45058 ), HPRU in Respiratory Infections at  Imperial College London , and  NIHR HPRU in Emerging and Zoonotic Infections at the University of Liverpool , in partnership with  Public Health England  ( NIHR award   200907 ),  Wellcome Trust ,  Department for International Development  ( 215091/Z/18/Z ),  Bill & Melinda Gates Foundation  ( OPP1209135 ),  Liverpool Experimental Cancer Medicine Centre  (grant  C18616/A25153 ),  NIHR Biomedical Research Centre at Imperial College London  ( IS-BRC-1215-20013 ),  EU Platform for European Preparedness Against (Re-) Emerging Epidemics  ( PREPARE ;  FP7  project  602525 ).
[24, 25]  Moreover, this work has also generated a deeper understanding of cervical cancer epidemiology throughout the country. We found that India can be divided into two main groups of 19 and 6 Indian states or groups of states that are characterized by low or high cervical cancer incidence, respectively. As expected, and in line with previously studies, individuals, in particular men, in high-incidence states have more sexual activity with non-regular partners, including commercial partners, than in low-incidence states. [26, 27]  While early sexual debut in women has also previously been suggested to be associated with high cervical cancer incidence and HPV positivity,  [26, 27]  it was associated with lower cervical cancer incidence in the dataset we considered. We hypothesize that, for the Indian context, early sexual debut is common in states with a larger rural population, among whom less sexual activity occurs with non-regular partners, which is the main determining factor for a lower risk of cervical cancer.
Acknowledgments This study was funded by the  Bill & Melinda Gates Foundation  (grant numbers:  OPP48979 ;  INV-039876 ). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the authors identified as personnel of the  International Agency for Research on Cancer or World Health Organization , the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the  International Agency for Research on Cancer or World Health Organization. The designations used and the presentation of the material in this Article do not imply the expression of any opinion whatsoever on the part of  WHO  and the  IARC  about the legal status of any country, territory, city, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries.
Patient Population Pre-treatment tumor blocks were retrieved from 103 consecutive breast cancer patients who underwent neoadjuvant chemotherapy (NACT) between December 2004 and May 2019. All patients who completed NACT and had surgery were eligible for the study. Patients with non-metastatic BC undergoing NACT were included, and their characteristics are described in Table  1. Clinical data included tumor stage, NACT, surgery, date of recurrence, and death date, which were collected retrospectively. All patients were treated with a standard anthracycline regimen and/or taxane-based NACT. HER2-positive patients also received trastuzumab. It is an institutional policy to use NACT for most patients with HER2-positive and TNBC.
Pathological Assessment Immunohistochemical staining was performed for estrogen receptors (ER), progesterone receptors (PR), and HER2 positivity, as well as the Ki-67 proliferative index. Fluorescence in situ hybridization (FISH) was used to confirm HER2 positivity. Patients who completed NACT were eligible (n = 103) for the ISCR analysis. Clinical data were collected from medical records. Pathological complete response (pCR) was defined as the complete disappearance of invasive cancer in the breast and the absence of tumor in the axillary lymph nodes.
QUARTET uses the existing infrastructure at the EORTC to collect all required DICOM and supporting data. The data flow for receiving a case and completing the ICR process can be seen in Fig. 2. Cases are submitted using the EORTC RTQA Uploader (http://www. eortc. be/ Uploader) or AQUILAB OncoPlace (AQUILAB SAS, France) in France where QUARTET submissions have been integrated into their national review programme and their French database PediaRT. ICRs are performed using Velocity (Version 4. 1, Varian Medical Systems Inc. ) via an online Citrix Gateway (Citrix Solutions Inc. ). Ownership of all patient data remains with the trial sponsor, with QUARTET acting as a Data Processor under GDPR  [16].
Conclusions and future work SIOPE is invested in the betterment of paediatric oncology; supporting improvements in access to highquality effective treatments to reduce inequality and provide the best possible control of disease and quality of life after treatment, for children and adolescents across Europe. QUARTET supports this mission through the provision of a centralised, online, interventional RTQA platform which helps to reduce the administrative and logistical burdens of implementing national or individual trial RTQA programmes and equalises access to expertise. Initiatives to improve access to advanced radiotherapy techniques and clinical trials are required to ensure that those countries most in need will benefit. Prospective QA of paediatric radiotherapy treatment planning is highly recommended, particularly within the context of clinical trials where both treatment compliance and dataset uniformity are essential.