dataesr/scientific-paragraphs-categorization huggingface dataset:
All types of dietary data are measured with some error, including from individual-level surveys as well as national food availability estimates. Additionally, the standardisation of available global data required certain decisions and assumptions about serving sizes, food group definitions, energy adjustment, and the disaggregation of householdlevel data when standard ising the dietary surveys. However, we utilised rigorous methods developed over 14 years of work and carefully documented and detailed each survey's methods and standardisation process to maximise transparency in our methods. This iteration of the GDD did not collect information on poultry, an important ASF in many countries globally. Last, our analysis was limited to the consumption of ASF and does not describe trends in ASF production.
Data sharing The modelled estimates of animal-source food intakes by population subgroup, country, region, and globe in 1990 and 2018 are available for download from the Global Dietary Database. Survey-level information and original data download weblinks are also provided for all public surveys; and survey-level microdata or stratum-level aggregate data are provided for direct download for all non-public surveys granted consent for public sharing by the data owner. Editorial note: the Lancet Group takes a neutral position with respect to territorial claims in published maps and institutional affiliations.
PURPOSE Pembrolizumab demonstrated durable antitumor activity in patients with previously treated, advanced microsatellite instability-high or mismatch repair-deficient (MSI-H/dMMR) tumors, including endometrial cancer, in the nonrandomized, open-label, multicohort, phase II KEYNOTE-158 study (NCT02628067). We report efficacy and safety outcomes for patients with MSI-H/dMMR endometrial cancer enrolled in KEYNOTE-158. METHODS Eligible patients from cohorts D (endometrial cancer, regardless of MSI-H/dMMR status) and K (any MSI-H/dMMR solid tumor, except colorectal) with previously treated, advanced MSI-H/dMMR endometrial cancer received pembrolizumab 200 mg once every 3 weeks for 35 cycles. The primary end point was objective response rate per RECIST version 1. 1 by independent central radiologic review.
13 In a prospective analysis from the KEYNOTE-016 study, pembrolizumab resulted in an objective response in eight of 15 (53%) patients with dMMR endometrial cancer,  14  providing early evidence of antitumor activity in this setting. In the nonrandomized, open-label, multicohort, phase II KEYNOTE-158 (ClinicalTrials. gov identifier: NCT02628067) study of pembrolizumab in multiple types of advanced (unresectable and/or metastatic) rare cancers, pembrolizumab demonstrated an ORR of 34. 3% among 233 patients with previously treated unresectable or metastatic MSI-H/dMMR noncolorectal cancers. 15  an initial analysis of outcomes among the first 49 patients with MSI-H/dMMR endometrial cancer enrolled in KEYNOTE-158, the ORR was 57%. 16 Here, we report efficacy and safety data in a larger number of patients with longer follow-up in patients with previously treated advanced MSI-H/dMMR endometrial cancer from KEYNOTE-158.
Statistical Analyses Efficacy was assessed in patients who received $ 1 dose of pembrolizumab and had been enrolled $ 26 weeks before data cutoff (to allow sufficient time for responses to occur and be assessed). Safety was assessed in all patients who received $ 1 dose of pembrolizumab. The point estimate and exact Clopper-Pearson 95% CIs were provided for ORR. The Kaplan-Meier method was used to estimate duration of response, PFS, and OS.
Patients A total of 90 patients with MSI-H/dMMR endometrial cancer were enrolled in cohorts D (11 patients) or K (79 patients) of KEYNOTE-158 between February 1, 2016, and September 23, 2020, from 38 sites in 15 countries. As of the data cutoff date (October 5, 2020), 79 patients had received $ 1 dose of pembrolizumab, were enrolled $ 26 weeks before data cutoff, and were therefore included in the efficacy analysis population. All 90 patients were included in the safety analysis population. The median age was 64 years (range, 42-86 years), and 61% of patients had an Eastern Cooperative Oncology Group performance status of 1; 48% had received $ 2 lines of prior therapy, and the majority of patients (68%) had received prior radiation therapy (Table  1 ). The median duration of treatment was 8.
DATA SHARING STATEMENT Merck Sharp & Dohme Corp, a subsidiary of Merck & Co, Inc, Kenilworth, NJ, USA (MSD) is committed to providing qualified scientific researchers access to anonymized data and clinical study reports from the company's clinical trials for the purpose of conducting legitimate scientific research. MSD is also obligated to protect the rights and privacy of trial participants and, as such, has a procedure in place for evaluating and fulfilling requests for sharing company clinical trial data with qualified external scientific researchers. The MSD data sharing website (available at http:// engagezone. msd. com/ds_documentation. php) outlines the process and requirements for submitting a data request. Applications will be promptly assessed for completeness and policy compliance.
Feasible requests will be reviewed by a committee of MSD subject matter experts to assess the scientific validity of the request and the qualifications of the requestors. In line with data privacy legislation, submitters of approved requests must enter into a standard data-sharing agreement with MSD before data access is granted. Data will be made available for request after product approval in the United States and European Union or after product development is discontinued. There are circumstances that may prevent MSD from sharing requested data, including country-or region-specific regulations. If the request is declined, it will be communicated to the investigator. Access to genetic or exploratory biomarker data requires a detailed, hypothesis-driven statistical analysis plan that is collaboratively developed by the requestor and MSD subject matter experts; after approval of the statistical analysis plan and execution of a data-sharing agreement, MSD will either perform the proposed analyses and share the results with the requestor or will construct biomarker covariates and add them to a file with clinical data that is uploaded to an analysis portal so that the requestor can perform the proposed analyses.
This study explored cases of sustainable food production in urban and non-urban areas, including the development of urban gardens, and particularly the social relations involved in these community projects. A qualitative approach was used to compare four case studies in Chile and France: shared gardens in Lyon, family and workers' gardens in Santiago in Chile, an indigenous agricultural project in Lonquimay in the southern Andes, and the work of the NGO Cultivos Urbanos. The data was collected through surveys, participant observation and semi-structured in-depth interviews. The results show that tending gardens in these settings (worker, family, collective, or shared gardens) promotes social values that can lead to more sustainable forms of community living. As opposed to intensive agriculture, small-scale gardening practices, specifically in urban and peri-urban gardens, encourage human/nonhuman relationships, and the transmission of caring for nature and for others, which promotes ecological citizenship.
Methods The study was based on comparative problematization  (Hibou, 2014)  in a multi-site approach  (Marcus, 1995). The data was collected from ethnographic research and interviews and involved observing, describing and analyzing the interactions between the different agri-food systems and social processes. We sought to identify the differences and similarities in these varied contexts through a comparative method, understanding this as an exercise for organizing different elements to create a general representation, and unifying multiple techniques for collecting data in order to offer a different understanding of ecological citizenship  (Denecheau et al. , 2021). In terms of describing and characterizing different approaches to ecological citizenship, we develop a comparative case study with a logic of "tracing across" proposed by  Bartlett and Vavrus (2017) , where we select different cases seeking to understand how from different places, scales, and organizations, have tried to build citizenship.
Data collection included conducting surveys in Lyon in a process of co-construction and co-comprehension of local issues through working with various stakeholders  (Guber, 2011). We sought to collect information from a range of stakeholders working to develop sustainable food in their local area (e. g. , farmers, gardeners, social and solidarity economy organizations, project leaders, elected local officials, etc. ). This long-term investigation involved participant observation in situ (e. g. , at meetings or events) and participatory investigation methods (e. g. , guided walks, photo elicitation). The case studies in Chile involved different methodology, based on conducting in-depth ethnographic interviews with stakeholders. In Santiago, we conducted three non-structured interviews (from September 2021 to March 2022) with key stakeholders in the NGO Cultivos Urbanos.
The interviews sought information about the objectives, barriers, aspirations, and evaluation of a project led by the Ministry of Environment to create family gardens. The Mapuche participants were also asked about their response to and evaluation of this government action and their expectation of its effects on their lives. We also observed the performance of officials in the field (in offices, community meetings and Mapuche homes) and their interaction with community members. In La Pintana (a working class municipality on the southern outskirts of Santiago), we collected data on a workers' garden, primarily through participant observation with Alberto, who has lived for almost 60 years on a 5,000-sq-m plot that is part of a family vegetable garden cooperative. These observations and interviews were part of more extensive research in Santiago on environmental activism in the city.
Frontiers in To further test this relationship, it is necessary to look into the plastome of Microschizaea, which produces chlorophyllous gametophytes instead. In addition, the losses of some tRNA genes and structural changes in Schizaeaceae plastomes warrant further investigations with a more comprehensive species sampling. In this study, we first inferred a Schizaeaceae phylogeny using a three-plastid-region dataset. Our sampling is the most comprehensive to date at the species level, and included all previously recognized genera and species groups (Table  1 ). Based on this phylogeny, representatives from every clade were then selected for a phyloplastomic reconstruction together with species from the other two Schizaeales families. This plastomebased approach resulted in better resolved inter-generic relationships within Schizaeaceae, allowing us to trace the evolutionary changes of plastome structures.
Sampling and Sequencing for Phylogenetic Analyses A total of 47 Schizaeaceae specimens from 27 species (~ 77% of the species diversity of the family; PPG I, 2016) were sampled, including seven Microschizaea spp. , seven Actinostachys spp. , and 13 Schizaea spp. (Supplementary Table  1 ). This sampling covered all bioregions in each genus/clade (Table  1 ). For outgroups, we sampled the other two Schizaeales families: Anemia phylliditis from Anemiaceae and Lygodium japonicum from Lygodiaceae  (PPG I, 2016). A modified CTAB protocol was used for DNA extractions  (Kuo, 2015). The rpoC2, rbcL, and trnL-L-F (trnL gene + trnL-F intergenic spacer) were sequenced for our three-plastid-region dataset. PCRs were performed in 15 μl reactions each with 20 ng of genomic DNA, 0. 5 μM of each primer, and 1 × SuperRed PCR Master Mix RED (TOOLS, New Taipei City, Taiwan).
NOVOplasty  (Dierckxsens et al. , 2017)  was used to assemble the plastomes with the setting of "Kmer = 39, " and conspecific rbcL sequences were used as the input seeds. These plastome assemblies were annotated using Geneious  (Kearse et al. , 2012)  with the published Schizaeaceae plastomes (GenBank accessions: KU764518, KX258660-61) as references. We manually inspected every protein-coding gene annotation, and adjusted the coordinates if necessary. Details about the PCR primers are provided in Supplementary Table  2. Details about the voucher information, GenBank accessions, and NCBI Sequence Read Archive accessions can be found in Supplementary Table  1.
Phylogenetic Analyses For the three-plastid-region dataset (i. e. , "rpoC2 + rbcL + trnL-L-F"), the nucleotide sequences were first aligned with MUSCLE  (Edgar, 2004) , as implemented in AliView  (Larsson, 2014) , and then concatenated into a single matrix. This three-plastidregion matrix was partitioned by gene, by intergenic spacer (IGS), and by codon position in order to find the best partition scheme and substitution models using ModelFinder  (Kalyaanamoorthy et al. , 2017)  with the Bayesian information criterion (BIC;  Schwarz, 1978). Based on the inferred partition scheme and the substitution models, IQtree 1. 6. 8 (Nguyen et al. , 2015)  was used to construct the maximum likelihood (ML) phylogeny with 1,000 ultrafast bootstrap replicates (UFBS). The Bayesian phylogeny was inferred using MrBayes 3.
2. 7  (Ronquist et al. , 2012). Two simultaneous runs were carried out with four chains (10 million generations each). Each chain was sampled every 1,000 generations. Log likelihoods of MCMC runs were inspected in Tracer 1. 6  (Rambaut and Drummond, 2013)  and RWTY  (Warren et al. , 2017)  to confirm their convergence. The first 25% of the sample was discarded as burn-in, and the remaining was used to calculate the maximum clade credibility consensus tree with TreeAnnotator  (Rambaut and Drummond, 2013). For the phyloplastomic datasets, we only included coding sequences, introns, and intergenic spacers (IGS) that were consistently located in the large single copy (LSC) region of the Schizaeaceae plastomes. The restriction to LSC genes aimed to reduce phylogenetic artifacts resulting from substitution rate  heterotachy, because the movement of genes between the inverted repeat (IR) and single copy (SC) regions would lead to changes in their substitution rates  (Li et al.
Confirming the Existence of ndh and Missing Plastid Genes in Transcriptomes and Genomes To confirm whether the nuclear-encoded ndh complex related genes was present or not in the Schizaeales, we downloaded their homologue sequences from the well-annotated case of Apostasia odorata (detailed in the Supplementary Material S2 of  Lin et al. , 2017) , and blast-searched them against six Schizaeales transcriptomes  (Qi et al. , 2018; Shen et al. , 2018 ; One Thousand Plant Transcriptomes (OTPT) Initiative, 2019) and two fern whole genomes  (Li et al. , 2018). For PnsB1, the homologue sequence from Marchantia polymorpha  (Ueda et al. , 2012)  was used instead, because the annotated sequence from A. odorata (GenBank accession: KX156894) appeared to be misidentified. We also included the ndhV from Zostera marina  (Ma et al.
After obtaining the fern homologous sequences from these genomes, we then added these sequences into the tBLASTx searches against the transcriptomic assemblies using blast-2. 10. 0 +  (Camacho et al. , 2009). Only the transcripts having > 60% sequence identity and consistent hits to all query homologues (i. e. , those from the two ferns, A. odorata, Z. marina, and M. polymorpha) were kept. To examine the possibility that the missing protein-coding genes in the plastome have been transferred to and are now transcribed in the nuclear genome, we also conducted local tBLASTx searches for these genes as mentioned above. The query sequences were derived from plastomes of the closest relatives that still retain those genes (e. g. , using Anemiaceae's rps16 sequence to blast against the Schizaeaceae's transcriptomes).
Phylogeny of Schizaeaceae From our three-plastid-region and plastome datasets (Figures  2, 3 ) four well-supported clades were recovered (UFBS = 100, Bayesian inference = 1. 00) within Schizaeaceae-Schizaea, S. pusilla, Actinostachys, and Microschizaea (Figure  3 ). These clades closely matched their generic definition by  Reed (1947) , except for S. pusilla which formed a rather distinct clade from other Microschizaea spp. However, the inferred inter-clade relationships differed among our phylogenetic analyses (Table  2 ). Generally, topology I received the highest branch supports, and another two were rejected by most of our topological tests (Table  2 ). Only the "codon3" matrix with a gene-partitioned GTR + F + R10 model highly supported topology II (Table  2 ), but this support was declined or nearly unchanged when applying the degeneratecoded matrices with analyses (Supplementary Table  4 ).
Presence of ndh and chl Genes in Transcriptomes and Genomes We detected the nuclear-encoded ndh-related genes in the transcriptomes of other Schizaeales (Anemiaceae and Lygodiaceae) and the genomes of Salvinia and Azolla, except for pnsL1-4, psnB2, ndhV, CRR2-4, and CRR21 (Figure  4 ). For CRR41, we identified it in Salvinia but not in Azolla. This gene likely existed in other Schizaeales (Anemiaceae and Lygodiaceae), whose CRR41-matched transcripts showed consistent blast-hits to the homologous queries of CRR41 although relatively low in the identity ranging from 40-54%. In contrast, all plastid and most nuclear-encoded ndh-related genes were missing in the Schizaeaceae transcriptomes (Figure  4 ). We were also unable to detect any chl genes in the transcriptome of Actinostachys, whose plastomes also lack these genes.
A New Generic Classification of Schizaeaceae Our phylogenetic analyses based on different datasets, models, and partitions resulted in three general topologies (Figure  2 ). While data from plastome structure and gene content failed to provide additional evidence, we have more confidence in topology I (Table  2 ). This topology received, on average, higher branch supports (i. e. , nodes A and B), and was not rejected in most of the topology tests (Table  2 ). On the other hand, although topology II also received high branch supports in some analyses, it was mostly derived from matrices comprised of the third codon positions. It is likely that the support for topology II is a result of high homoplasy at the third codon position (Supplementary Table  4 ), which is known to have higher substitution rates and therefore be more likely to reach saturation (e.
ACKNOWLEDGMENTS We thank  Leon Perrie ,  Claudine Mynssen ,  Joel Nitta ,  Carl Rothfels ,  Tian-Chuan Hsu ,  Michael Kessler  and  Kathleen Pryer's lab  for providing their DNA collections of this study;  Taiwan Pteridophyte Research Group (TPG)  for maintaining DNA collections of this study; the staff in herbaria MEL, MO, NSW, P, PE, SEL, TAIF, UC, and WELT for making their collections available for this study; the two reviewers for their comments on the manuscript;  Chih-Yun Sun  for preparing the line drawing;  Technology Common  ( College of Life Science, National Taiwan University, Taiwan ) for the assistance with DNA library constructions; Genomics Corp. ( New Taipei City, Taiwan ) for Hiseq sequencing; and  Mr. Shann-Jye Moore Memorial Scholarship  for providing financial support for herbarium collection surveys.
Environmental Engel curves describe how households' income relates to the pollution associated with the services and goods consumed. This paper estimates these curves with neural networks using the novel dataset constructed in Levinson and O'Brien. We provide further statistical rigor to the empirical analysis by constructing prediction intervals obtained from novel neural network methods such as extra-neural nets and MC dropout. The application of these techniques for five different pollutants allow us to confirm statistically that Environmental Engel curves are upward sloping, have income elasticities smaller than one and shift down, becoming more concave, over time. Importantly, for the last year of the sample, we find an inverted U shape that suggests the existence of a maximum in pollution for medium-to-high levels of household income beyond which pollution flattens or decreases for top income earners.
The EN nets approach implemented in this paper extends the extra-trees algorithm introduced by  Geurts et al. (2006)  by estimating T different sub-networks with randomised architectures (each network will have different layer-specific widths) that are independently trained on the same dataset. By constructing prediction intervals, we are able to attach statistical measures of uncertainty to the pointwise predictions of the model and, hence, add statistical rigor to the empirical findings of  Levinson and O'Brien (2019)  on the relationship between pollution and income. We construct intervals for the predictions of household pollution along the EEC curve for the reduced model that only considers household income and also for the extended model that incorporates eighteen households' characteristics.
EN network The EN network approach can be interpreted as an ensemble predictor for NN models. This methodology, formally introduced in Mancini et al. (  2021 ), is based on the extremely randomised trees approach proposed by  Geurts et al. (2006)  for random forests. For notation purposes, we will identify the fixed Bernoulli mask as r ⋆ as opposed to r ⋆ usually employed for dropout training. In this setting, T sets of vectors {r ⋆(t) } T t=1 are sampled from a Bernoulli distribution prior to training and are kept constant during both train and test phases. This approach reduces to train and independently fit T random sub-networks on the same dataset. In this setting, generating the predictive distribution is similar, in spirit, to an ensemble approach that trains different sub-neural networks on the same dataset.
8  Following  Levinson and O'Brien (2019)  we report results for the years 1984 and 2012 and consider five different pollutants: particulates smaller than 10 microns (PM10), VOCs, NO x , SO 2 , and CO. 9 Table  1  in  Levinson and O'Brien (2019)  presents the relevant summary statistics for the different variables observed for the year 1984 and 2012. The table reports the average values and the standard errors (when possible) of the variables comprising the dataset. The number of observations adopted for the study is 3184 for the year 1984 and 3538 for the year 2012. These authors construct two types of EECs: one using income and squared income as only covariates and an extended version of the model in which the set of covariates is expanded to incorporate other available households' characteristics.
Late Holocene hydroclimate evolution of the central Sahara The sediment record of Lake Yoa at Ounianga Kebir  (10, 14)  revealed hydrological and vegetation responses in the central Sahara to the marked decline in climatic moisture balance over the last 6000 years  (1, 3) , thereby reinvigorating the long-standing debate about whether Mid-Holocene drying of the Sahara was gradual or abrupt  (22, (30) (31) (32). The data now extracted from Lake Teli at Ounianga Serir provide detailed information, heretofore lacking, on Saharan climate evolution within the last four millennia, i. e. , most of the interval since the end of the AHP. Our data indicate that, immediately before ca 4200 years ago, the central basin floor of Ounianga Serir must have been completely desiccated, implying that open-water aquatic habitat, if present, only remained in areas of spring discharge along the basin's periphery.