dataesr/scientific-paragraphs-categorization huggingface dataset:
Retrieval of deleted and non-predicted loci The mapping of C. neoformans H99 protein sequences in the C. deneoformans JEC21 genome and JEC21 protein sequences in the H99 genome by Exonerate v2. 2. 0 program (https://www. ebi. ac. uk/about/vertebrate-genomics/software/exonerate) with the following parameters (protein2genome -percent 30-bestn 1 -minintron 30-maxintron 4000 -showalignment false -showvulgar false -showtargetgff true -refine region -subopt false) was performed to recover sequences deleted in the previous filtering step with conserved orthology in Cryptococcus. For this purpose, the mapped gene coordinates matching previously predicted sequences (GFFCompare program) were used to add these deleted genes to the annotation with an in-house AWK script. The addition of non-predicted genes was performed by comparing the mapped protein sequence coordinates and the genomic regions without predicted genes.
Automatization of the C3Q pipeline The C3Q pipeline, an automatic gene predictor, was built with Python3 code (C3Q_gene-predictor. py) and is available in Github (https://github. com/UBTEC/C3Q) The C3Q pipeline includes all established parameters for Cryptococcus genome annotation (C3Q6 protocol): • The Cufflinks assembly of transcripts for each RNA-seq library. • The merging of the generated GTF files by Cuffmerge. • The GTF conversion to GFF format (needed for CodingQuarry). • The training and genome prediction by CodingQuarry, using the merged GFF file and the reference genome. • The sequence filtering: deletion of small transcripts up to 150 nt and intronless transcripts up to 300 nt; deletion of genome-predicted sequences without supporting reads and deletion of alternative transcripts from multi-transcript loci.
Gene prediction in C. deuterogattii R265 Gene prediction in C. deuterogattii R265 was performed with the C3Q pipeline (C3Q6 protocol) using the C3Q_gene-predictor. py script. For this, the five RNA-seq triplicate libraries from C. deuterogattii R265 (Exponential phase at 30 C, Exponential phase at 37 C, Stationary phase at 30 C, Stationary phase at 37 C and Mating) were subsampled to 7. 5 million reads each, and input into the script in addition to the C. neoformans H99 and C. deneoformans JEC21 protein sequences for the Exonerate step. Concomitantly, manual correction of genes from chromosomes 9 and 14 was performed with the software Artemis  (Carver et al. 2012) , the R265 genome (NCBI assembly GCA_002954075. 1), and the stranded paired-end RNA-seq data from C. deuterogattii R265 in the five growth conditions.
The predicted annotation was evaluated by comparing it to the manually corrected genes from chromosomes 9 and 14, as well as the C. deuterogattii R265 annotations from Broad (NCBI assembly GCA_000149475. 3) and  Ferrareze et al. (2017). CDS gene coordinates from old annotations were also identified in the new sequenced genome with Exonerate aligner (coding2genome). The predicted novel genes were named with CNBG ID numbers above 10000. The statistics of the gene annotations ware generated by AGAT script agat_sp_statistics. pl (https:// github. com/NBISweden/AGAT). The final annotation is available in file S1.
Antisense transcription analysis To evaluate the antisense transcription in the genomes analyzed, we first generated a reversed annotation, which consisted of a GFF file with genes assigned to the opposite strand of their actual annotation. With the annotation and the reverse annotation, we analyzed the percentage of antisense transcription for each protein-coding gene using the software HTseq-count using the following attributes (-f bam -r pos-s yes -t CDS -i ID -m intersectionnonempty -nonunique none (. bam) (. gff)) and the distinct RNA-seq libraries. Sense/antisense counts ratios for each gene for each condition were plotted. The script used for generation of a reverse GFF is available (reverse_gff. py).
Data Availability Raw and summarized sequencing data are available at SRA with the accession number: PRJNA660459. The C3Q pipeline is available in Github (https://github. com/UBTEC/C3Q); Supplementary files are available at FigShare (https://doi. org/10. 25387/g3. 12901307). The final annotation of C. deuterogattii genome was submitted to NCBI and is available on accessions CP025759. 1 to CP025772. 1.
neoformans H99 genome were input into the BRAKER1 and Cufflink-CodingQuarry pipelines  (Wallace et al. 2020). For the Cufflink-CodingQuarry-based analyses, we used two alternative protocols. In the first case, we first merged the BAM files from each of the three replicates (CUFF-CQ protocol). In the second case, each replicate BAM file was used to generate a unique GTF prediction file, these files were then merged using Cuffmerge and used by CodingQuarry as a single transcript source (C3Q1 protocol) (Figure  1 ). To compare the quality of these pipelines for identification of coding genes, we calculated their sensitivity (percentage of coding genes present in the reference annotation overlapping with one coding gene in the de novo annotation) and their specificity (percentage of predicted coding genes overlapping with one coding gene in the reference annotation).
Thus, replicate samples with 1, 5, 7. 5, 10, 15, 20, 30, and 40 million reads were used for de novo annotation of the C. neoformans H99 genome, and the quality of the gene predictions were compared. We performed this analysis using the same strategy for C. deneoformans. As shown in Figure  3 , the quality of the gene structure prediction was highly dependent on the size of the RNA-seq initial data set in both species and strongly anti-correlated with the number of Cufflinks-assembled transcripts (Supplementary Table  S1 ). The highest-quality predictions were obtained with replicate samples with only 5-10 million reads. Using this adjusted read depth, the prediction showed improvement in nearly all parameters, including for missed genes, missed exons, and missed introns (Supplementary Table  S1 ).
Accordingly, we found that the number of predicted transcripts decreased when too much data was used. Second, we found a nearly linear relationship between the number of introns predicted and the quality of the annotation. However, this correlation did not hold when two of the pipelines were compared; the BRAKER pipeline predicted more introns than the C3Q pipeline, along with predicting many more genes. Nevertheless, the correlation between intron number and annotation quality provided a facile way to evaluate the reliability of a de novo annotation, which might be affected, for instance, by the quality of the RNA-seq data. Third, we found the final step of comparative genomics did not always improve the quality of the annotation. In our assay, the Exonerate-based analysis step using the whole proteome of a reference species primarily introduced errors into the annotation.
Acknowledgments PAGF was supported by a  CAPES   exchange grant  ( Advanced Network of Computational Biology-RABICO ´-Grant  no. 23038. 010041/2013-13 ). This work was supported by a  CAPES COFECUB  grant n  39712ZK  to GJ, by a  CNPq grant  ( 309897/2017-3 ) to CCS, and by a  NIH/NIAID   R37   MERIT  Award  AI39115-23  and a  NIH/NIAID   R01  Award  AI50113-16  to JH. JH is co-director and fellow of CIFAR program Fungal Kingdom: Threats & Opportunities. SJP was supported by the  NIH/NIAID   F31  Fellowship  1F31AI143136-02. Members of the  Heitman laboratory  are acknowledged for valuable discussion.
The weak form of governing equations is obtained by means of the standard Galerkin procedure and is then discretized in space by means of the finite element method. Integration in the time domain is carried out with the generalized mid-point rule where a Crank-Nicolson scheme is used. The fix point method is used to account for the nonlinear nature of the system of equations. A mixed finite element space is adopted where quadratic elements (triangular with six nodes and quadrangular with eight nodes) are used for u s , while linear elements (triangular with three nodes and quadrangular with four nodes) are used for p l and p b. The described model has been implemented in the code CAST3M (http://www-cast3m. cea. fr) of the French Atomic Energy Commission.
If any seizure activities were recorded during video-EEG monitoring, the FDG-PET/MRI investigation was postponed to the following day. The PET/ MRI scan was started 60 min after the FDG administration. For the prevention of movement artifacts, we informed the patients that they should avoid voluntary movements in the scanner. After the scanning procedure the patients were further supervised for two half-lives of the radioisotope decay (ca. 240 min). To ensure complete simultaneous PET coverage, a 20 min and a 35 min list mode PET acquisition were applied. For PET attenuation correction purposes vendor-provided T2 ultrashort echo time (UTE) sequence was used, μMaps were Fig. 1  An algorithm describing the steps of presurgical evaluation at our centers generated automatically. From the PET RAW DATA a 20 min and a 35 min static image dataset were produced.
Acknowledgements This article was supported by the  Hungarian Brain Research Program  ( 2017-1. 2. 1-NKP-2017-00002 ),  NKFIH   EFOP-3. 6. 2-16-2017-00008 , and  GINOP-2. 3. 3-15-2016-00032government -based funds. Our research was financed by  Dr. József Baka Diagnostic ,  Radiation Oncology ,  Research and Teaching Center, University of Kaposvár and MEDICOPUS Healthcare Provider and Public Nonprofit Ltd. , Kaposvár, PET Center, University of Kaposvár.
Background: The incidence of cholecystectomy is increasing as the result of the aging worldwide. Our aim was to determine the influence of heart failure on in-hospital outcomes in patients undergoing cholecystectomy in the Spanish National Health System (SNHS). Methods: We conducted a retrospective study using the Spanish National Hospital Discharge Database. Patients older than 17 years undergoing cholecystectomy in the period 2007-2015 were included. Demographic and administrative variables related to patients' diseases as well as procedures were collected. Results: 478,111 episodes of cholecystectomy were identified according to the data from SNHS hospitals in the period evaluated. From all the episodes, 3357 (0. 7%) were excluded, as the result the sample was represented by 474,754 episodes.
Study Design, Data Source and Patient Population A retrospective observational study of admissions undergoing cholecystectomy was performed. The analysis of our data was obtained from the Minimum Basic Data Set (MBDS) belonging to the National Health System (NHS). Data extraction is carried out through a request to the Ministry of Health and Consumption of the Spanish National Health System. All hospitals in our country are urged to provide with the medical activity data of each patient admitted. For each patient, clinical data such as age, sex, main and secondary diagnosis, procedures performed during hospitalization, discharge destination (including exitus) and early readmission, as well as the average length of stay are collected. In the case of this research we have used the ICD 9 classification for disease codes and procedures.
Discussion We have analyzed a large clinical-administrative database with more than 470,000 cholecystectomies in all hospitals in Spain over a period of 9 years in order to identify heart failure (HF) and its impact on patients undergoing this surgical procedure. Among the patients with HF, we found more women, in accordance with the population of patients undergoing surgical procedure at an older age  [12]. The low incidence of HF in our series is surprising, something that may be related to the low coding in discharge reports, a problem already reported when working with large clinical-administrative databases  [6, 13]. The mean age of the series is slightly higher compared to others found in the literature  [7, 14]. Patients with HF are significantly older for several reasons. Age is one major risk factor in the development of HF  [12].
This study, based on data obtained from a clinical-administrative database, has some limitations related to insufficient information such as: (1) lack of data about the moment in which HF appears, if the patient developed HF during admission or if it was a comorbid condition and at what point in the postoperative period HF appeared; (2) if re-admission occurred after the surgical procedure; (3) pharmacological treatment; (4) analytical data. Another limitation is undoubtedly dependent on a discharge report made by physicians who may or may not code all of the patients' diagnoses and procedures. The undercoding of HF that possibly exists in our study may reflect a defect in the diagnosis, a problem in the coding, or a truly low prevalence. The relative absence of the phenotype in these large databases due to under-coding could limit the usefulness of predictive models based on this type of information.
J Am Coll Cardiol 2019;73:e285e350. 133. Bonaca MP, Nault P, Giugliano RP, et al. Low-density lipoprotein cholesterol lowering with evolocumab and outcomes in patients with peripheral artery disease: insights from the FOURIER trial (further cardiovascular outcomes research with PCSK9 inhibition in subjects with elevated risk). Circulation 2018;137:338e50. 134. Sabatine MS, Giugliano RP, Keech AC, et al. Evolocumab and clinical outcomes in patients with cardiovascular disease. N Engl J Med 2017;376:1713e22. 135. Wang D, Liu B, Tao W, et al. Fibrates for secondary prevention of cardiovascular disease and stroke. Cochrane Database Syst Rev 2015;10:CD009580. 136. Bhatt DL, Steg PG, Miller M, et al. Cardiovascular risk reduction with icosapent ethyl for hypertriglyceridemia. N Engl J Med 2019;380:11e22.
Circulation 2006;114: 1549e53. 142. Ciszewski A, Bilinska ZT, Brydak LB, et al. Influenza vaccination in secondary prevention from coronary ischaemic events in coronary artery disease: FLUCAD study. Eur Heart J 2008;29:1350e8. 143. Gurfinkel EP, Leon de la Fuente R, Mendiz O, et al. Flu vaccination in acute coronary syndromes and planned percutaneous coronary interventions (FLUVACS) Study. Eur Heart J 2004;25:25e31. 144. Watson L, Ellis B, Leng GC. Exercise for intermittent claudication. Cochrane Database Syst Rev 2008;4:CD000990. 145. INSERM. Activit e physique e Pr evention et traitement des maladies chroniques. Editions EDP Sciences. Collection Expertise collective. Montrouge : EDP Sciences, 2019, XVI-805 p, 2019, http://hdl. handle. net/10608/9690; 2019. 146. Gardner AW, Montgomery PS, Flinn WR, et al.
Circulation 2012;125: 130e9. 155. Lane R, Ellis B, Watson L, et al. Exercise for intermittent claudication. Cochrane Database Syst Rev 2014;7: CD000990. 156. Stewart KJ, Hiatt WR, Regensteiner JG, et al. Exercise training for claudication. N Engl J Med 2002;347:1941e51. 157. Bronas UG, Treat-Jacobson D, Leon AS. Comparison of the effect of upper body-ergometry aerobic training vs treadmill training on central cardiorespiratory improvement and walking distance in patients with claudication. J Vasc Surg 2011;53:1557e64. 158. Tew G, Nawaz S, Zwierska I, et al. Limb-specific and crosstransfer effects of arm-crank exercise training in patients with symptomatic peripheral arterial disease. Clin Sci (Lond) 2009;117:405e13. 159. Zwierska I, Walker RD, Choksy SA, et al. Upper-vs lowerlimb aerobic exercise rehabilitation in patients with symptomatic peripheral arterial disease: a randomized controlled trial.
Introduction: Atopic dermatitis (AD) can have a profound negative impact on the quality of life (QoL) of patients. We analyzed the longterm changes in AD symptoms, QoL, and patient assessment of treatment effect in adults with moderate-to-severe AD treated for 2 years with dupilumab. Methods: LIBERTY AD OLE (NCT01949311) is a multicenter, open-label extension (OLE) study in adults with moderate-to-severe AD who previously participated in dupilumab clinical trials (parent studies). Patients received dupilumab 300 mg weekly. Patient-Oriented Eczema Measure (POEM), Dermatology Life Quality Index (DLQI), EQ-5D-3L, and the Patient Global Assessment of Treatment Effect (PGATE) were assessed at weeks 48 and 100. Results: A total of 2677 patients were included in the OLE, and 1028 completed week 100.
In an ongoing, open-label extension (OLE) study in adults with moderate-to-severe AD (LIBERTY AD OLE; NCT01949311), dupilumab has also demonstrated sustained efficacy with an acceptable safety profile for up to 3 years  [11]. In this study we report the long-term changes in symptoms and QoL as well as patient assessment of treatment effect in adults with moderate-to-severe AD treated for 2 years with dupilumab in an OLE study (LIBERTY AD OLE). A short author video summarizing the key findings of this study can be found in the online version of the manuscript.
Study Design LIBERTY AD OLE (NCT01949311) is an ongoing phase 3, multicenter, OLE clinical trial in adults with moderate-to-severe AD who previously participated in phase 1-3 clinical trials of dupilumab. The study design has been previously reported  [11]. Briefly, patients with moderate-to-severe AD were eligible for inclusion if they had adequately completed the required assessments of the parent phase 1-3 dupilumab studies. Patients treated with dupilumab in the parent studies (prior dupilumab treated) as well as patients who received placebo in the parent studies (dupilumab treatment-naı ¨ve) were included. Patients were excluded if they had experienced dupilumab-related adverse events (AEs) or serious AEs (SAEs) leading to discontinuation from the parent studies. Treatment consisted initially (October 2013) of subcutaneous dupilumab 200 mg weekly (qw), which was revised following a protocol amendment (December 2013) to 300 mg qw.
Patients A total of 2677 patients were included in LIB-ERTY AD OLE and received study treatment. At the time of the interim database lock, 82. 4% of patients (2207/2677) had completed up to week 52, 1028 (38. 4%) up to week 100, and 347 (13. 0%) up to week 148  [11]. Of the 1325 (49. 5%) patients who withdrew from the study, most (807 [30. 1%]) did so because of per-protocol study termination by the sponsor upon regulatory approval/commercial availability of the drug and 57 (4. 3%) because of lack of efficacy  [11]. The patient disposition, baseline demographics, and disease characteristics for this patient population in LIBERTY AD OLE have been previously reported, along with efficacy, and overall safety outcomes up to 3 years  [11]. At the parent study and OLE baselines, patients had a mean age of approximately 39 years (Table  1 ).
Individual anonymized participant data will be considered for sharing once the product and indication has been approved by major health authorities (e. g. , FDA, EMA, PMDA), if there is legal authority to share the data and there is not a reasonable likelihood of participant re-identification. Submit requests to https://vivli. org/. Medical Writing and Assistance. Medical writing/editorial assistance was provided by Carolyn Ellenberger, PhD, of Excerpta Medica, funded by Sanofi Genzyme and Regeneron Pharmaceuticals, Inc. , according to the Good Publication Practice guideline. Open Access. This article is licensed under a Creative Commons Attribution-NonCommercial 4. 0 International License, which permits any non-commercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
Demographic data and clinical characteristics were collected from the participants and recorded in an electronic medical record (e-CRF). The ethics committee Comité de Protection des Personnes Sud Mediterranee III (University Hospital Center of Nîmes, Nîmes, France) approved the study protocol. Written informed consent was obtained from all patients. The study was done in accordance with the principles of the Declaration of Helsinki and the International Conference on Harmonization-Good Clinical Practice guidelines.
Quantification of Viral Load RNA extraction was performed by the laboratories of the National Reference Center for Respiratory Viruses, France, using the NucliSens easyMAG instrument (bioMérieux, Marcy-l'Etoile, France) following the manufacturer's instructions. RdRp-IP2 and RdRp-IP4 quantitative RT-PCR was used to detect SARS-CoV-2. Primer and probe sequences (Eurofins, Genomics, Germany), described in the Table  1 , correspond to the RdRp-IP2 and the RdRp-IP4 assays designed at The Institut Pasteur to target a section of the RdRp gene (nt 12621-12727 and 14010-14116 positions) based on the sequences of SARS-CoV-2 (NC_004718) made available on the Global Initiative on Sharing All Influenza Data database on 11 January 2020.
Acknowledgments: We thank and acknowledge the contribution of all the patients and trial team members. More particularly,  Sophie Lengagne ,  Eva Geraud , and  Anthea Loiez  from the  Emile Roux Hospital Center (le Puy-en-Velay, France). We also thank all the technicians from the  CNR  for their work. We also extend our thanks to  Eric Bomel ,  EZUS, University Lyon1 , who provided central administrative support to the project;  Ursula Sutter  from  Greiner Bio-One GmbH (St. Gallen, Switzerland ); and  Dr. Eric Gonzalez Garcia , from  Greiner Bio-One GmbH (Kremsmuenster, Austria ), who provided kindly technical support.
Study Sample and Available Data The population was initially composed of a sample of 35,841 highly connected Withings customers, those who had purchased at least three Withings-connected devices: a pulse activity tracker  [23, 24] , a body weighing scale  [25] , and a BP-800 blood pressure monitor  [26]  (Withings SA). Customer data, including sex, age, number of steps per day, body weight, heart rate, and blood pressure, were provided by Withings and were collected between October 2009 and April 2016. Data were preprocessed before analysis, as we excluded some outliers from daily data on weight and steps with unlikely values as follows: (1) a lower threshold of 500 steps per day was used to denote valid days with daily step count data  [27, 28] , but the application of this criterion did not result in any deletion of data as the minimum daily step value was 501 steps per day; (2) daily step values exceeding the 99 th percentile of the steps per day distribution were removed (99th percentile=22,414 steps/day; 151,937 measurements removed); and (3) weight values lower than 45 kg and above 200 kg were excluded (12,403 measurements removed).
In addition, individuals were excluded if they did not (1) have at least two step measurements within the first and sixth 30-day period of activity tracker use (n=4733) and (  2 ) have at least one weight measurement within the first 30-day period of activity tracker use and 6 months after (n=4173). Figure  1  shows the inclusion criteria of this study. The final study sample comprised 26,935 individuals (23,580 males and 3355 females). Consent for participation in this study was obtained electronically when users created their Withings account and accepted the treatment of personal data anonymously by Withings for research purposes.
Monitoring of PA The Withings Pulse activity tracker is a commercially available device that can be worn on the wrist or clipped onto a belt or clothing. This activity tracker monitors physical behaviors including the total number of steps taken per day. In addition, it provides the user with real-time feedback on their health metrics through the tracker itself or via an app on the user's smartphone or tablet with internet access. The wearable device and the app are synchronized, which allows the data recorded by the activity tracker to be instantly transferred from the device to the app via Bluetooth, thus enabling long-term data tracking by users themselves or, for instance, by researchers or health professionals. Wearable activity trackers are considered to be an accurate and objective assessment method that permits PA monitoring  [29].