dataesr/scientific-paragraphs-categorization huggingface dataset:
31, 32  This study has limitations. It was a non-comparative randomized trial, therefore precluding direct comparison of the chemotherapy regimen with pazopanib. Baseline tumor biopsies were optional, and only a small number of samples were available for exploratory proteomics analysis, whose results remain hypothesis-generating. There was also no pharmacokinetics (PK) data reported on pazopanib. Such data could help adapt the dosing of pazopanib and improve safety profile. Blood samples collection for PK analysis were planned in the protocol, and results will be reported at a later stage. Performing a randomized clinical trial in very rare diseases such as DT is usually considered as a real challenge. The DESMOPAZ study focused on a very rare condition and completed accrual in expected time.
This paper deals with the performance analysis of both linear (LE) and widely linear (WLE) equalization processes studied in the symbol spaced mode (SSE) as well as in the fractionally spaced one (FSE). This analysis is evaluated -using Matlab software-in terms of bit error rate (BER) and mean square error (MSE) in a system using a rectilinear modulation of type Pulse Amplitude Modulation (PAM) over a frequency selective channel and corrupted by multiple interferences. Moreover, the impact of the number of external interferers on the behavior of the different equalizers is studied. Thus, simulation results show the outstanding performance of the fractionally spaced mode when compared to the symbol spaced one besides the out-performance of the widely linear processing in both modes. Furthermore, results show the performance degradation for the different studied equalizers when the number of interferences increases.
5. SIMULATION RESULTS In this section, the performance evaluation of the linear (LE) (Eq. (  6 )) and widely linear (WLE) (Eq. (  10 )) equalizers for both SSE and FSE mode is studied. Besides, the impact of the number of the external interferences on the equalizers' behavior is analyzed. The different simulation realizations are done using Matlab software. Thus, for these simulations, the different shaping filters (see Figure  1 ) are chosen to be square root raised cosine (SRRC) filters with a roll off factor equal to 1. Regarding the symbol durations, all the interferences have the same symbol duration. Without loss of generality, the interferer symbol duration is chosen to be twice the SOI one (i. e. ,  1 = 2 0 ). The different channel impulse responses of all signals (SOI + interferers) have 60 taps, having each one a Rayleigh modulus and a phase uniformly distributed in [0,2].
Background: As patients on daily hemodialysis (DHD) have heterogeneous profiles, DHD benefit in terms of survival is still debated. The aim of this study was to compare DHD practices in France and in Australia and New Zealand. Methods: This study was based on data from the French Renal Epidemiology and Information Network (REIN) and the Australian and New Zealand Dialysis and Transplant Registry (ANZDATA). All incident patients from both registries who underwent DHD (i. e. , 5-6 sessions/week, including short daily hemodialysis and long nocturnal hemodialysis) at least once during their trajectories were included, and their characteristics and care trajectories were compared. For survival analyses, one French patient was matched to one Australian or New Zealand patient, based on age, sex and year of dialysis start.
Survival was assessed using the Cox proportional hazards model, and access to renal transplantation was evaluated using the Fine & Gray model to take into account death as competing risk. Results: Between 2003 and 2012, 523 patients from the AZNDATA and 753 from the REIN registry started DHD. ANZDATA patients were younger (54. 8 vs 64. 0 years, p < 0. 001) and had comorbidities more frequently than French patients. In both registries, one third of patients were on early DHD (i. e. , DHD started less than one year after dialysis initiation). Long nocturnal hemodialysis was more frequent in the ANZDATA than in the REIN cohort (20. 8 and 3%, respectively). Comparison of the matched subgroups showed comparable survival rates between French and Australian/New Zealand patients (HRadjusted = 1. 08; 95%CI: 0.
Analysis of the REIN data highlighted the clinical feature heterogeneity of patients starting DHD (i. e. , 5 or 6 HD sessions/week)  [15] , and showed that the risk of death is higher in patients on DHD than in matched patients on HD 3 times/week  [16]. This confirmed a previous study by  Suri et al. that included patients undergoing in-center HD  [17]. Conversely, other studies reported that DHD is associated with better survival  [18] [19] [20] [21] [22] [23]. These contradictory results could be explained by differences in the practices associated with DHD between France and other countries  [16, 17]. The Australian and New Zealand Dialysis and Transplant Registry (ANZDATA) has been collecting data on all patients undergoing dialysis and kidney transplantation in Australia and New Zealand for over 40 years.
Analysis of ANZDATA data showed that intensive HD is used in both countries, and that various regimens (long nocturnal, short DHD) have been developed mainly for home dialysis  [24, 25]. Particularly, long nocturnal DHD and home conventional HD have been implemented since 2001  [26, 27]. Since then, several reviews  [25, 26, 28]  described the benefits of nocturnal DHD on biological functions and quality of life. A recent study showed (in some analyses) lower mortality with intensive HD, compared with conventional HD  [24]  in Australia and New Zealand. As the REIN and ANZDATA registries collect similar data, we decided to compare the characteristics, care trajectories, survival and access to renal transplantation of French and Australian/New Zealand patients undergoing DHD to highlight possible differences.
Population The REIN registry was established in 2002, and since 2011 covers the entire French territory. The ANZDATA registry started to collect data on renal dialysis and kidney transplantation in Australia and New Zealand in 1977. REIN and ANZDATA include all patients treated by renal replacement therapy (dialysis or kidney transplantation). After inclusion, REIN collects data annually and when dialysis modalities change, while ANZDATA only collects data annually. The organization of the two registries has been described in detail elsewhere  [14, 29]. This study was a retrospective analysis of prospectively collected REIN and ANZDATA data on all incident patients aged 18 years and over who were treated at least once with DHD during their care trajectories in France or in Australia/New Zealand between January 1, 2003 and December 31, 2012 (inclusion period).
The study endpoint was set at December 31, 2013 to have a minimum of one-year follow-up for the patients included in the study. DHD was defined as 5 or 6 HD sessions/week (short daily or long nocturnal HD). The ANZDATA data did not allow following patients from DHD initiation. Patients were described and followed from the first date of renal replacement therapy registered in the database until death, transplantation, or the study endpoint (December 31, 2013).
Data collection Three categories of variables were included: i) patients' demographic and clinical/laboratory data at DHD initiation: sex, age, hemoglobin rate, body mass index (BMI), smoking status (current, former and never smoker), and comorbidities, such as diabetes, peripheral vascular disease (PVD), cerebrovascular disease (CVD), coronary disease and respiratory insufficiency; ii) DHD modalities: conventional DHD (at least 5 sessions/week) or convective DHD (hemofiltration, hemodiafiltration and biofiltration), number of weekly sessions and duration of each session; iii) patients' care trajectories: date and dialysis modalities at first registration in the database (at dialysis start in REIN, and at the first annual survey in ANZDATA), and clinical outcome at the end of the follow-up: death, kidney transplantation, or endpoint.
Matching procedure To evaluate and compare survival and access to renal transplantation between countries, patients with homogenous DHD modalities in terms of session duration were selected. Consequently, all patients on long nocturnal HD (5-6 sessions/week; ≥5 h/session) were excluded, because this modality is rare in France. Patients on short daily HD (5-6 sessions/week; < 5 h/session) from the ANZDATA registry were randomly matched 1:1 with patients from the REIN registry, based on age (±1 year), sex and year of dialysis initiation.
Outcome analyses The first primary outcome was patient survival. Patients were followed from the first date of dialysis recorded in the database until death, or were censored at renal transplantation or at the endpoint (December 31, 2013). The second primary outcome was access to renal transplantation. For this, patients were followed until transplantation, death, or the endpoint. Cox regression analysis was used to evaluate the association between patients' characteristics and death and renal transplantation in the matched population (the matching structure was taken into account in the survival analyses). Death occurrence during the follow-up was considered as a competing event for renal transplantation. To take into account this competing risk, a Fine & Gray model was applied, and renal transplantation was considered as a time-dependent covariate in survival analyses.
Kaplan-Meier survival curves and Cumulative Incidence Functions were plotted for each group. All variables associated with the event of interest in the univariate model (p-value < 0. 2) were included in the multivariate model. The 95% Confidence Interval (CI) was calculated for all Hazard Ratio (HR) and Subdistribution Hazard Ratio (SHR), and a p-value < 0. 05 was considered as statistically significant. Statistical analyses were performed with the Stata 13. 1 software (College station, TX). The median age at DHD initiation was 55. 5 years (IQR: 45. 7-66. 2) in Australia, 51. 2 (IQR: 41. 3-61. 9) in New Zealand, and 64. 0 years (IQR: 50. 7-76. 3) in France. Patients from New-Zealand were younger and more obese than patients from Australia; however, comorbidity rates were comparable (see Additional file 1: Table  S1  for the details of this comparison).
Patients' outcomes (matched patients on DHD) For the survival analyses, patients on nocturnal DHD were excluded (n = 131). The matching procedure (age, sex, year of dialysis start) allowed matching 226 patients from the French cohort with 226 patients of the Australia/New Zealand cohort. Their mean age was 56. 3 ± 14. 7 years and the male to female ratio 2. 77. After matching, the percentage of patients with comorbidities remained higher in the Australia/New Zealand than in the French cohort (for more details, see Additional file 1: Table  S3 ). By the end of 2013, 106/226 (46. 9%) French patients and 101/226 (44. 7%) Australian/New Zealand patients were dead. The survival of matched patients from inclusion in the database to death is represented in crude Kaplan Meier mortality curves (Fig.
As a consequence, prevalence of chronic diseases, such as CKD, is increasing. In 2013, the overall incidence of renal replacement therapy was 160 per million population (pmp), 110 pmp, and 123 pmp in France  [30] , Australia, and New Zealand  [31] , respectively. The REIN and ANZDATA registries have been established in these countries to monitor the incidence, prevalence and outcomes associated with end-stage renal disease (ESRD). Although the REIN registry is much younger than the ANZDATA registry, they collect similar types of data and have the same objectives. Therefore, their data could be used to study and compare DHD practices in Australia/New Zealand and France. This study shows that patients who started DHD in Australia and New Zealand between 2003 and 2012 were younger, with high BMI, and mainly cardiovascular comorbidities.
The characteristics of patients who underwent kidney transplantation also were comparable, suggesting similar selection criteria in these three countries. We hypothesized that survival rate might be higher among Australian/New Zealand patients than among French patients with ESRD on dialysis. Based on ANZDATA annual report (2013), the mortality rate per 100 patient-years was 13. 1 (95%CI: 12. 5-13. 8) for dialysis-dependent patients in Australia and 13. 7  (12. 3-15. 2) in New Zealand  [37]. In France, the one-year survival was 83. 2% (95%CI: 82. 9-83. 5) for the 2002-2013 incident patients  [38]. We could not compare survival of patients with ESRD in the three countries because in the national annual reports, for survival analyses, transplanted patients were censored in the ANZDATA  [37] , but not in the REIN registry  [38].
Survival rate might not be the best way to highlight the benefits associated with DHD, thus explaining the contradictory results of previous studies  [16] [17] [18] [19] [20] [21] [22] [23]. Alternatively, the analysis of the patients' quality of life could help, but this information is not routinely collected in registries. The major strength of our study is that this is the first comparison of DHD associated practices in France and Australia/New Zealand. Furthermore, thanks to the REIN and ANZDATA registries, we could include a large population-based cohort on DHD between 2003 and 2012 and we could take into account various clinical characteristics. Our study has several limitations. The medical reasons explaining the nephrologist's decisions to start or to switch to DHD were not recorded in the REIN and ANZDATA registries, raising the possibility of selection bias.
Differently from the REIN registry where data are collected at renal replacement therapy initiation, at every dialysis modality change, at death, at renal transplantation and also annually, ANZDATA collects data only annually. Therefore, the dates of dialysis initiation, DHD initiation, death and renal transplantation are registered in ANZDATA at the survey update, and the follow-up times calculated for the Australian/New-Zealand cohort were less consistent. The study design allowed us to analyze the global survival of patients who started DHD between 2003 and 2012 in Australia/New Zealand and France, but not the survival specifically for the period they underwent DHD. Indeed, we could not identify the exact duration of DHD treatment for each included patient. Finally, we could study only the data collected in both registries; for example, we did not have any information on the patients' income or quality of life.
Additional file Additional file 1: Table  S1. Comparison of the characteristics at DHD initiation of incident patients from Australia and New Zealand". This table contains the description and comparison of the characteristics of patients on DHD from Australia and New Zealand. Table  S2. Characteristics of incident patients from the ANZDATA (Australia and New Zealand) and REIN (France) registry according to the starting dialysis modality". This table compares the characteristics of patients according to their starting dialysis modality per registry: left panel, patients from the ANZDATA registry, and right panel, patients from the REIN registry. Table  S3. Characteristics of age-and sex-matched patients by country. To compare access to renal transplantation and survival, one French patient was matched (sex, age and year of dialysis start) to one patient from Australia or New Zealand.
, phenol, and trizol), followed by whole genome amplification (WGA)/WTA amplifications, before Illumina MiSeq sequencing. After trimming and assembly, sequences underwent BLAST (BLASTn and BLASTx). At the end of the first BLAST (n/x), some portions of sequences were uncovered and unassigned. We, then, implemented a novel recursive split-resubmit python program that searched for homologs of > 50 base pairs (bp), uncovering parts for a better exploitation of the datasets. Thirty-eight known viral families were detected in our samples. Circoviridae, Parvoviridae, and Microviridae were found in the majority of the results from easymag V R and Phenol extracted samples, while trizol samples resulted in a majority of Picornaviridae and Coronaviridae. These results show that the viromes are of different composition depending on extraction methods.
Segmentation of the coronary arteries In order to reduce illumination artefacts and homogenise the image contrast, local contrast was normalised by means of the build-in function Normalize Local Contrast in Fiji  [20]. More details about the pre-processing steps are provided in the Supplementary material. The coronary arterial tree was semi-automatically segmented with Carving module from the open-source image analysis software ilastik  [21]. The Carving module uses a seeded watershed algorithm for interactive object carving from image data  [22]. For each object of interest, in our case the coronary vascular tree, the algorithm requires that the user provides 'inside' and 'outside' seeds as input. From these seeds, an initial segmentation is automatically calculated using a biased watershed algorithm that can be refined interactively.
This study was partially supported by the  Spanish Ministry of Economy and Competitiveness  (grant  TIN2014-52923-R  to BB;  Maria de Maeztu Units  of Excellence Programme -MDM-2015-0502);  la Caixa Foundation (Spain) ;  Cerebra Foundation  for the  Brain Injured Child (Carmarthen, Wales, UK) ; the  Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya  ( 2014   SGR  grant nº  928 ,  2016FI_B01184 );  Instituto de Salud Carlos III  ( PI14/00226  to FC,  PI15/00130  to EG and  INT16/ 00168  to FC) as part of the  Plan Nacional de I+D+I  and co-funded by  ISCIII-Subdireccion General de Evaluacion ; the  Fondo Europeo de Desarrollo Regional (FEDER) "Otra manera de hacer Europa" (Spain). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Increased chromatin accessibility at myogenic loci upon small molecule treatment To dissect the mechanism behind S/Da/De/F-mediated myogenic maturation, we investigated the chromatin accessibility landscape using ATAC-seq  (Buenrostro et al. , 2013). Following a 2 day treatment, we detected 62,748 and 80,334 chromatin accessible peaks in DMSO-and S/Da/De/Ftreated cells, respectively (Figure  5A ). Comparison of these two datasets showed an overlap of 20,682 peaks, while 42,066 and 59,652 peaks were specific for DMSO and S/Da/De/F treatments, respectively. To determine whether S/Da/De/F treatment led to significant changes in chromatin accessibility, we next compared the normalized sequencing depth at chromatin accessible peaks identified in all replicates. Principal component analysis (PCA) showed that DMSO-and S/Da/De/Ftreated groups clustered separately (Figure  5 -figure supplement 1A).
Reads were then mapped to the human genome (hg38) using bowtie2 (Langmead and Salzberg, 2012) (parameters -I 25 -X 2000 -local -dovetail -no-mixed -no-discordant) and filtered to remove PCR duplicates. Peaks were identified using MACS2. 1  (Zhang et al. , 2008)  (parametersnomodel -nolambda -keep-dup all -call-subpeaks) and then analyzed using BEDtools  (Quinlan and Hall, 2010)  to identify treatment-specific peaks. For this analysis, we considered peaks detected in 2 of 3 biological replicates. Analysis of differential accessibility was performed by generating a list of peaks representative of all samples using the peak summits identified by MACS2. Each summit was extended 50 bp in both directions and the resulting lists of peaks were combined, sorted and merged to obtain a dataset of unique and non-overlapping loci.
RNA sequencing Myotubes treated with DMSO or S/Da/De/F differentiated for 5 days were used for RNA sequencing in triplicates. RNA was isolated as described above. 500 ng of total RNA was used for generating dual-indexed libraries using the TruSeq stranded mRNA library kit. The libraries were sequenced in NextSeq 550 sequencer using 75 bp paired end run at around 20 million reads per sample. 75 bp FastQ paired-end reads (n = 20. 9 Million per sample) were trimmed using Trimmomatic (v 0. 33). Quality control on raw sequence data was performed with FastQC. Reads were mapped to the human genome (hg38) reference using Hisat2 (v2. 1. 0). Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLC genomics work bench (Qiagen) using raw read counts.
We filtered the generated list based on a minimum 2X Absolute Fold Change and FDR corrected p<0. 05. These filtered genes were then imported into Ingenuity Pathway Analysis Software (Qiagen) for identification of canonical pathways, upstream regulators and their targets. Gene ontology enrichment analysis was performed by uploading the list of differentially expressed genes in the GO database to identify the top enriched cellular components and biological processes. Heatmap of differentially expressed genes was generated using the heatmapper web tool as per the manufacturer's instructions.
Electrical pulses were generated with a cardiac stimulator (Astro-Med Inc, S88 Â Model, 10 ms pulse width) at a frequency of 0. 5 or 20 Hz for 6 s. Contractile forces were recorded using LabView and the data were analyzed using MATLAB (the code is available at GITHUB, https://github. com/weishenumn/contractile-force-analysis. git ; Shen, 2019; copy archived at https://github. com/elifesciences-publications/contractile-force-analysis) (Black et al. , 2009). For each twitch peak or tetanic plateau, the maximum force was used for analysis. The construct was then treated with TRI Reagent (Sigma-Aldrich) for qPCR analysis or immediately frozen in liquid nitrogen for Western blotting. For each differentiation condition, three constructs were quantitatively examined.
Acknowledgements This project was supported by funds from the  NIH , grants  R01 AR055299  and  AR071439  (RCRP) and the  NSF   CAREER DMR-1151529  (WS). RM-G was funded by. We also thank the generous support from  ADVault, Inc and MyDirectives. com(RCRP). The cytogenetic analyses were performed in the  Cytogenomics Shared Resource at the University of Minnesota  with support from the  comprehensive Masonic Cancer Center NIH  Grant # P30 CA077598-09. The monoclonal antibodies to MyHC, Titin, MyHC-neo and MYH1/2 were obtained from the  Developmental Studies Hybridoma Bank developed  under the auspices of the  NICHD  and maintained by the  University of Iowa. We thank  Prof. Robert T Tranquillo ,  Dr. Jeremy Schaefer , and  Dr. Lauren Black  for the use of the contractile force measurement apparatus and for facilitating data analysis.
Statistical analyses Statistical analysis was performed using the STATISTICA software (Version 10, Stat Soft France, 2003). Statistical differences in the concentrations of metabolic serum parameters between the normal and the cystic cows and between follicular and cystic fluid, as well as the comparison of metabolites rate between the vascular compartment and the follicular fluid were carried out using Student's t-test. Correlation coefficients between serum and follicular fluid of normal and cystic cows were performed to compare the metabolites concentrations and to study the balance in these two biological liquids in normal and cystic conditions. Data were expressed as mean ± standard deviation (SD). The results were considered significant when P < 0. 05.