dataesr/scientific-paragraphs-categorization huggingface dataset:
(2) The integration of an automatic hyperparameter optimization based on a TPE optimization algorithm and a k-fold crossvalidation technique within the LSTM models. A case study based on real time-series datasets acquired from NPPs is carried out to validate the proposed modeling framework. To the authors' knowledge, this is the first study using a hybrid framework combining EEMD and LSTM for addressing the multi-step ahead prediction problem of NPP signals. The rest of the paper is organized as follows. Section 2 introduces the EEMD decomposition technique, the LSTM neural network and the TPE hyperparameter optimization. Section 3 focuses on describing the proposed method for multi-step ahead prediction. The details of the practical case study are presented in Section 4 and the obtained results are discussed in Section 5.
Access to data Newly described bla KPC genes were submitted to GenBank under Submission ID: 2410531. Accession numbers are KPC_E7: MW440444; KPC_E11: MW440445; KPC_A1: MW440446; KPC_A6: MW440447; KPC_A8: MW440448; KPC_E10: MW440449; KPC_A10: MW440450; KPC_A9: MW440451; KPC_B2: MW440452; KPC_B5: MW440453; KPC_D4: MW440454.
Sampling frame The sampling frame was the Fideli (Demographic files on dwellings and individuals) (13), a comprehensive database obtained by merging several administrative files, an approach tested several years previously for the French Labor Force Survey  (14). These files are updated yearly from annual tax returns, and are curated by the National Institute of Economics and Statistics (Insee), to eliminate duplicates and to identify community housing structures (nursing homes, prisons, military barracks, etc. ) and residential hotels for separate treatment. This file covers 96. 4% of the population and their dwellings, according to French census data. The Fideli datafile compiled in 2018 was used for EpiCov. All the dwellings included in Fideli are associated with a mailing address, which can be used to contact the individuals sampled.
Participation rate (flow chart in figure 1) No contact was established for 222,151 of the individuals selected. For the others, a specific assessment was performed to check that the respondent was indeed the selected individual, by comparing the sex and birth date recorded on the questionnaire with those available from the Fideli sampling frame. This assessment led to the exclusion of 2,348 individuals who were not the selected individual. Another 5,487 individuals were considered to be outside the sampling frame (deceased, living in a communal institution for the elderly, no longer living in France, or living in French Guiana or Mayotte), and 6,623 completed too few items for retention in the final database. There were 134,391 respondents in total (Fig. 3 ): 120,154 completed the short form of the questionnaire and 14,237 completed the long questionnaire.
The Fideli administrative database as a sampling frame had many advantages. It provides a very high coverage of the target population, with postal addresses for all, and additional e-mail addresses or telephone numbers for most, and a rich set of auxiliary information useful for non-response correction. A mixed-mode web/telephone data collection approach was decided early in the project, to limit selection bias which should have occurred with a single collection mode, because internet and telephone access are not uniformly distributed between age groups, areas of residence and educational levels. This decision was consistent with the general guidelines for social surveys  (17, 18). A recent meta-analysis on a corpus of 45 mixed-mode and 51 single-mode surveys  (23)  showed that mixed-mode surveys were of better quality, in terms of representativeness, than singlemode surveys.
To a certain extent, the transition to mixed-mode surveys  (20) , including online data collection, was already underway worldwide, but has been accelerated by the pandemic  (24). We selected directly individuals from the sampling frame, rather using first-stage household units. Both options were possible with Fideli, but the former, though more complex to implement, had the advantage of avoiding overrepresentation of the households' tax registrants. Tax registrants are inconsistent in the provision of e-mail addresses or phone numbers for the other members of their households, and are likely to be the member of the household with the highest income or social position. Some individuals tried to respond in place of the selected person, as observed for 2348 contacts. We then anticipated a larger proportion of non-responses than with household sampling, because the first person contacted may refuse or forget to transmit the announce letter or email to the eligible one, particularly if not at home during the survey.
Acknowledgements The authors first sincerely thank all the participants to the EpiCoV study. We thank greatly the  INSERM  staff, and especially  Karim Ammour ,  Jean-Marc Boivent ,  Sophie Circosta ,  Jean-Marie Gagliolo ,  Michael Hisbergues ,  Frédérique Le Saulnier , and  Frédéric Robergeau ,. whoparticipated with an exceptional engagement to make it possible to develop, in a particularly short period of time, and to maintain all regulatory, budgetary, technical, and logistical aspects of the EpiCov study. We thank greatly the staff of  Santé Publique France , and especially  Lucy Duchesne , who played a major role in the organization and quality of the seroprevalence component of the EpiCov study. We thank greatly the  CRB biobank staff (Centre Hospitalier Universitaire Pellegrin, Bordeaux, France) , and especially her head,  Dr Isabelle Pellegrin , for the quality of the management process of DBS samples, implemented in such a short period fort the first-round of the EpiCov study.
A questionnaire comprised of both closed and open choice questions was used to collect information in a manner that promoted flexibility between known topics of interest and topics that emerged during discussion (see Supplementary Materials). The questionnaire was informed by critical work on cross-cultural survey design  (Harkness et al. , 2003) , developed in consultation with regional and thematic experts, and piloted with mountain residents in Nepal and Peru prior to data collection. Participants were asked to recall hydrological conditions over the last decade, a temporal scope short enough to enable coherent recollection of past events while long enough to provide insights into the effects of recent, rapid climatic changes in the mountains of Peru and Nepal. Forty household interviews were conducted in each study community (total n = 160) with individuals 18 and older following a stratified random participant selection protocol that prioritized the equal inclusion of men and women and age groups  (18-35, 36-55, 56 and older).
Interviews focused on individuals within households, although other family members were sometimes present. Summary statistics were calculated for quantitative data from the household interviews. Qualitative content from interviews was examined using manifest (explicitly stated) and latent (implicit) content analysis  (Bengtsson, 2016; Payne & Payne, 2004) , where responses were grouped and analyzed according to their relationship to exposure, sensitivity, adaptation, and vulnerability. Key informant interviews were conducted with government officials, community leaders, resource managers, researchers, and members of the private sector. The majority of key informants were from or working in the study regions, although several interviews were also completed with relevant experts in Kathmandu and Huaraz (large cites near the study sites).
RT-qPCR analysis Total RNA and ribosome bound RNA were isolated using TRIzol reagent (Invitrogen). 0. 05 micrograms of RNA were used to synthesize complementary DNA with reverse transcription kit (Vazyme). Realtime PCR was performed using SYBR Premix ExTaq(TaKaRa) on ABI 7500 real time PCR system. For the normalization of gene expression, rice ACTIN was used as an internal standard. Triplicate reactions were performed for each sample. The 2 -CT method was used for quantification of relative expression  (34). Primers used in RT-qPCR are listed in Supplementary Dataset S7.
Rice HDA714 KO results in defects in plant growth and development Previous studies indicated that plant HDACs are localized in different cellular compartments  (22, 42, 43). In rice, there are 13 RPD3-like HDAC genes that fall into the 3 classes of human HDAC proteins: class 1, class II and class IV  (27, 30)  (Supplementary Figure  S1A ). The nomenclature of the plant HDACs ('7' for rice proteins) was based the ChromDB database  (44). To study subcellular localization of rice HDACs, we fused GFP to seven of the rice RPD3like HDAC proteins and tested their subcellular localization by transient expression in protoplasts. We found that HDA702, HDA704 and HDA711 were exclusively localized in the nucleus; HDA705 and HDA706 were detected in both the nucleus and cytoplasm, while HDA713 and HDA714 appeared to be only in the cytoplasm (Supplementary Figure  S1B ).
Identification of a comprehensive protein acetylome in rice To study whether the mutations affected the overall protein Kac levels in rice cells, we performed MS-based quantitative acetylproteomic studies of hda705, hda706 and hda714 (two independent KO lines per gene were combined) and wild type 14-day-old seedling green tissues (Supplementary Figure  S3A ). The data obtained from the two biological replicates were highly correlated, indicating a good reproducibility of the assays (Supplementary Figure  S3B, C ). In total, we detected 4868 acetylated lysine residues in 1952 proteins in wild type rice, among which 4091 Kac sites in 1729 proteins were quantifiable (Table  1 , Supplemental Dataset S1). Calibration of the acetylomic data with the proteomes (Supplemental Dataset S1) revealed 3413 normalized Kac sites in 1333 proteins (Table  1 ).
Furthermore, we found that 76 chromatin and transcription factors were acetylated (Supplemental Dataset S2), of which 18 have been functionally studied (Supplementary Table  S1 ). Analysis of amino acid sequences flanking the 4868 Kac sites revealed an enrichment of phenylalanine (F), lysine (K) or histidine (H) at the +1 position, and aspartic acid (D), glutamic acid (E) or phenylalanine (F) at the -1 position (Supplementary Figure  S4E ), consistent with previous data  (45, 47, 48). Acetylated proteins were found to be enriched for 20 of the 35 Map-Man bins or functions  (49) , and especially for metabolic pathways such as photosynthesis, TCA cycle, and glycolysis (Supplementary Figure  S4F ). Together, our data identified a comprehensive protein acetylome in rice.
Effect of the hda705, hda706 and hda714 mutations on proteome and protein acetylome Proteome analysis revealed that the hda705, hda706 and hda714 mutations had no drastic effect on overall protein    S5A-C ). The Kac changes in the mutants relative to wild type were correlated (r > 0. 78) between the biological replicates (Figure  2A , Supplementary Figure  S3B ). The hda714 and hda706, but not hda705, mutations led to clear increases of Kac levels in many proteins (Figure  2A -D, Supplemental Dataset S4). In total, 227 (9. 6%) Kac sites in 172 proteins and 616 (26. 2%) Kac sites in 312 proteins showed higher (>1. 5-fold) acetylation levels respectively in hda706 and hda714, while very few sites displayed lower Kac levels in the mutants (Figure  2E ). In addition, a large number of Kac sites (1467 in hda714 and 1884 in hda706) showed <1.
HDA714 regulates lysine acetylation of ribosomal proteins Analysis of published acetylomes in other organisms  (22, (50) (51) (52)  revealed that Kac of r-proteins was a general phenomenon in eukaryotes (Supplementary Figure  S6 ). At least105 annotated r-proteins (or isoforms) and 21 translational initiation and 12 elongation factors were largely acetylated in rice (Supplemental Dataset S5). Most of the acetylated ribosomal proteins and translational factors showed multiple Kac sites. In particular, 12 and 24 Kac sites were respectively found in r-protein RPS6 and elongation factor EF2, most of which showed higher acetylation in hda714 (Supplementary Figure  S4B , Figure  3A , B, Supplemental Dataset S5). The HAD714 mutations led to increases (>1. 5-fold) of Kac at 113 sites in 49 ribosomal proteins and 25 sites in four translational initiation and elongation factors (Figure  3A, B ).
Moreover, we performed coimmunoprecipitation assays with rice protein extracts using anti-HDA714 and analyzed the precipitated proteins by Western blots using anti-RPS3 and anti-RPS6. Results showed interaction between HDA714 and RPS3 and RPS6 in vivo in rice plants (Figure  4C ). Collectively, the data indicate that HDA714 targets r-proteins for deacetylation.
The RNA-seq revealed > 96% of the mapped reads in both wild type and mutant samples (Supplementary Table  S2 ). There were a number of differentially expressed genes (Supplementary Figure  S9C , Supplemental Dataset S6) in the mutant versus wild type. Among the highly repressed genes were Os11g0101200 (RNase P subunit p30) and Os01g0777400 (NB-ARC domain containing protein) (Supplemental Dataset S6). The lengths of Ribo-seq reads were about 26-29 nucleotides (nt) (Supplementary Figure  S10A ), consistent with the sizes protected by 80S ribosomes  (55). However, the reads peak in hda714 appeared at 27-nt compared to 28-nt in the wild type (Supplementary Figure  S10A ). About 83% of the mapped reads were localized to annotated exons or coding DNA sequences (CDS) (Supplementary Figure  S10B, C ).
This is consistent with previous results indicating that the assembly of the initiation complex is a relatively slow process, resulting in a pronounced accumulation of signal around the start codon  (56) (57) (58). Ribosome accumulation at the last codon is caused by the slow kinetics of translation termination and peptide release  (59). A similar profile of ribosome binding was found in hda714 (Figure  6A ). In hda714 plants, 983 mRNA species showed significantly  higher (>2-fold, P < 0. 05) and 167 mRNA showed lower (>2-fold, P < 0. 05) ribosomal binding compared with wild type (Figure  6B , Supplemental Dataset S6). Normalization of ribosome binding (Ribo-seq) with mRNA abundance (RNA-seq) identified 759 mRNA species with significantly higher (>2-fold, P < 0. 05) and 491 with lower (>2-fold, P < 0.
05) (Figure  6C , Supplemental Dataset S6) ribosomal binding efficiency (RBE). Among the RBE upregulated genes were Os06g0488200 (Similar to myosin heavy chain), Os08g0461600 (CCHC-type zinc finger domain containing protein), and Os04g0437500 (tetratricopeptide-like helical domain protein). Among the RBE downregulated genes were Os01g0586800 (WRKY5), Os07g0565100 (ribosomal RPS11) and Os03g0785900 (glutathione-S-transferase) (Supplemental Dataset S6). The transcripts that displayed higher RBE corresponded to most lowly expressed genes in the genome (Figure  6D ). These genes are larger (longer transcripts (CDS) were more significantly downregulated for RBE, i. e. with lower P values) (Figure  6E ), while their 5 -UTR (untranslated regions) are shorter than the genomic average (Figure  6F ) and contained a cytidine (C)-rich sequence (Figure  6G ).
Whether the protein Kac and the TORC1 pathways crosstalk to regulate translational activity remains to be studied. Protein Kac affects metabolic enzyme activity such as inhibition of glycolytic enzymes  (20, (82) (83) (84). It was shown that Kac can also act as a feedback response to high acetyl-CoA levels in the cell, as the acetylation of an active site lysine residue inhibits the activity of acetyl-CoA synthetase  (85). The inhibitory effect of Kac on glycolytic enzyme activities  (20, (82) (83) (84)  may also be a feedback response to high acetyl-CoA levels in cells under stress. Glycolysis is a predominant energy metabolic pathway during rice seed germination under submergence  (86). The hda714 mutations also resulted in hyper Kac of glycolytic enzymes (Supplemental Dataset S4). Due to their sessile life style, plants have to cope with rapidly changing environmental conditions by fine-tuning cellular activities for optimal growth and development.
ACKNOWLEDGEMENTS We thank  Dr W. D. Liu  for help in acetylome characterization,  H. Z. Song  for help in confocal experiments and  Dr Z. Y. Cheng  in proteomic and acetylomic analysis. Q. X. performed most of the experiments and analyzed the data. Q. L. analyzed the Ribo-seq and RNA-seq data, Z. C. , Y. Y. , Y. L. and Y. Z. contributed to the experimentation. D. X. Z. supervised the project, analyzed the data and wrote the paper with inputs from Q. X. All authors read and approved the final manuscript.
IAU Often Avant-Garde During this time, and thus just prior to the full implementation of the ERASMUS program in Europe and its commitment to easing the recognition of credits, as well as the Council of Europe and UNESCO Lisbon Recognition Convention, the IAU was spearheading an international project-TRACE-designed to make information about higher education institutions and credentials worldwide available to all. The project, in part supported by UNESCO, proposed a technology-based, decentralized data entry system which, by using a standardized and agreed-upon structure, would make the data comparable. The goals of this project were to facilitate information sharing for recognition purposes, to ensure that only bona fide information was included and to promote collaboration on a level playing field among the world's universities.
These were indeed the central themes that IAU addressed with policy statements, conferences, research projects based on data that IAU gathered from its membership and through partnerships and collaborations with other groups. In all of this, IAU remained and is today still deeply rooted in its initial values. Though at times this has brought criticism of a lack of pragmatism, too much idealism, and even naivete, it is also the reason why IAU inspires loyalty-from Board members, from the staff of the secretariat and from all institutional representatives who get directly involved in the work of the association. Despite all of this, the value and purpose of the IAU are not obvious to everyone. Those who represent the IAU are often asked why a university should join the IAU. This is not, and never will be, an easy question to answer.
Although the value of singular biomarkers so far remains limited in UCB, it has previously been suggested that a panel of biomarkers can significantly improve outcome prognosis  [7, [27] [28] [29]. We, therefore, hypothesized that a panel of readily available blood-based SIR biomarkers could improve outcome prediction in patients treated with RC for UCB. Using a machine-learning-based variable selection approach, we analysed a large, well-established, international multicentre database to determine the most effective predictors and create the most informative, yet parsimonious model with respect to several clinically important outcome variables. To fully determine the discriminative ability of the finally included SIR biomarkers, their additional predictive and prognostic value was separately assessed in a comprehensive model performance evaluation.
Subjects/Patients This retrospective study included patients who underwent RC for treatment of clinically non-metastatic UCB from 12 participating international medical institutions between 1979 and 2012. All cases were histologically confirmed UCB with only a minor secondary variant component, if any. The preoperative serum levels of AGR, neutrophil-lymphocyte ratio (NLR), mGPS, MLR and the De Ritis ratio were measured in 4199 patients within 4 weeks of RC. The biomarkers and the respective thresholds have previously been described in detail  [23] [24] [25] [26]. The study was approved by the local ethics committee. No patient received NAC or radiotherapy. The extent of lymph node dissection and the choice of urinary diversion were at the surgeon's discretion. Patients with known autoimmune, chronic inflammatory or haematological disorders, as well as patients with any concomitant second malignancy other than UCB, concomitant upper urinary tract carcinoma, or missing data were excluded.
The weight of k that minimizes deviation in the cross-validation is given by k min ; however, the weight of k that empirically has been shown to create the most parsimonious yet informative model is k 1. se , defined as the value of k within one standard deviation of the minimum mean cross-validated error  [33]. Variables whose LASSO coefficient were not equal to zero at k 1. se were extracted and used during fitting of the prognostic models. This cross-validation process minimizes risk of overfitting and is a way of assessing how a model will perform in an independent dataset. In summary, the LASSO procedure allows a machine-learning-based variable selection for the fitting of prognostic and predictive models. It has been suggested to be particularly well suited for variables that show high levels of multicollinearity, as would be expected for SIR biomarkers  [34, 35].
Results Overall, 4199 patients were included in the analysis. With the exception of a higher rate of administration of adjuvant chemotherapy in the testing cohort (23% vs 19%; P < 0. 001), patient characteristics as well as the distribution of SIR biomarkers were similar in both cohorts (Table  S1 ). There was no statistically significant correlation between the assessed SIR biomarkers (P > 0. 05 for all). The median (interquartile range) follow-up of all surviving patients was 41. 9 (18. 1-84. 3) months. The 5-year RFS, CSS and OS were 61. 2% (95% CI 59. 5-62. 9), 67. 3% (95% CI 65. 6-69) and 56. 3% (95% CI 54. 6-58), respectively. Overall, our database included 1527 patients (36. 3%) who were staged to have non-muscle-invasive disease before RC; upstaging to MIBC occurred in 43. 7% of these cases.
Trial design and data acquisition Patients were studied in supine position with the head of the bed elevated 30° from horizontal position. They were ventilated with the Servo-i ventilator (Maquet, Sweden) using Fisher and Paykel (Auckland, New Zealand) breathing circuit (RT380) and heated humidifier (MR850). The compensation algorithm for circuit compliance was checked before use and running in all patients. After enrollment, arterial blood from an indwelling catheter was withdrawn and ventilator settings remained as set by treating clinicians. Vei was measured using three different techniques, which were applied in the following nonrandomized order: 1) Reference standard (Vei reference ): during an endinspiratory occlusion the endotracheal tube was briefly occluded with dedicated Kocher scissors (Additional file 1: Figure  S1 ).
Third, patients had a severe airway obstruction, as indicated by a long time constant, but P plateau was below 25 cmH 2 O in all patients and Vei measured with the reference standard above 1400 mL in only four patients. This may due to the fact that data were obtained in an ICU with expertise in mechanical ventilation and quantification of Vei using Vei formula is part of the clinical protocol. Indeed, none of the patients developed complications associated with dynamic pulmonary hyperinflation. Also, it should be noted that there is increased attention for lung protective ventilation in the last decade as compared to 30 years ago, thereby limiting minute ventilation and especially tidal volumes (i. e. , both were almost halved in our study as compared to Williams et al. [5] ). However, it should be acknowledged that severe complications resulting from dynamic pulmonary hyperinflation are still reported, highlighting the need for bedside monitoring tools to quantify dynamic pulmonary hyperinflation  [1, 6, 7].