dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We are grateful to  Jim Mitchell  for general advice. This work was supported by the National key research and development Ó 2019 The Authors New Phytologist Ó 2019  New Phytologist Trust New Phytologist  (2020) 225:  234-249  www. newphytologist. comprogram of China ( 2018YFD0900703 ,  2018YFD0901503-8 ,  2016YFC1402102 ),  National Natural Science Foundation of China (41676145) ;  Shandong key Research and Development Plan  ( 2018GHY115010 );  Qingdao Municipal Science and Technology plan project  ( 17-1-1-96-jch );  Special Scientific Research Funds for Central Non-Profit Institutes ,  Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences  ( 20603022019006 ,  20603022016001 );  Youth Talent Program Supported by Laboratory for Marine Fisheries Science and Food Production Processes ,  Pilot National Laboratory for Marine Science and Technology (Qingdao)  ( 2018-MFS-01 );  China Agriculture Research System  ( CARS-50 );  Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)  (no.
S1-S9 and their source Illumina clean data for methylome have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession no. GSE117191 (https://www. ncbi. nlm. nih. gov/geo/query/acc. c gi?acc=GSE117191). The Illumina raw data for transcriptomes have been deposited at the NCBI database (the SRA accession numbers are SRR5860561-SRR5860568). The Illumina data of the MeDIP-seq experiments and the WGS data were deposited at CNGB Nucleotide Sequence Archive (https:// db. cngb. org/cnsa/, with project accession no. CNP0000364), as were the reassembled genome and genomic loci for TEs, CGIs, genes, circRNAs, lncRNAs, tRNAs and the detailed methylation data for genome-wide visualization (visualization data is also deposited in GEO Series accession no. GSE117191).
Organic food consumption was obtained by attributing the respective percentages, 0, 25, 50, 75, and 100, to the aforementioned modalities. Fuller details regarding the Org-FFQ and sensitivity analyses as regards the weighting have been published elsewhere  (23). The different food and beverage items were aggregated into 16 food groups. Values for nutrients were derived from a published ad hoc food composition database  (34). Of note, the production system (organic compared with conventional) of the products was not taken into account when evaluating nutritional profiles.
Environmental impact assessment The description of the environmental impact assessment in NutriNet-Santé has been detailed elsewhere  (37). The environmental dimension was assessed per day at the farm level (i. e. , conditioning, transport, processing, storage, and recycling were excluded from the analysis) by computing 3 indicators pertaining to the production of a given quantity of food product: the GHGEs measured as kg of CO 2 equivalents (CO 2-eq), the cumulative energy demand (CED) in MJ, and the land occupation expressed in m 2. Data were collected using the tool DIALECTE  (38). Diet-related GHGEs, CED, and land occupation were obtained by multiplying the reported intake of each food item by its respective environmental indicator and conversion factor values, and summing over all food items consumed by the participant, while accounting for the production system (Supplemental Material 2).
Economic-related data assessment Data on places of food purchase were collected in July 2014 through a complementary questionnaire, available during 6 months on the NutriNet-Santé platform, focusing on attitudes, intentions, and practices toward organic food. Food prices for each of the 264 food-frequency questionnaire items for every place of purchase proposed in the aforementioned questionnaire were based on mean price values obtained using the 2012 Kantar Worldpanel purchase database  (39). This home-scan data set is based on records of a French representative consumer panel of 20,000 households. Purchased quantities and expenditures were used to calculate mean prices of each of the 264 items depending on the product type (organic compared with conventional) and the site of purchase (superstores, supermarkets, specialized stores).
Pesticide exposure assessment The dimension of diet sustainability related to toxicology aspects was evaluated through the dietary exposure via plant food intakes-by far the most contaminated food groups (40)to 15 available pesticides considering both their frequency of detection above the maximum residue levels when sufficient data were available and their acceptable daily intake. Contamination data were derived from the Chemisches und Veterinäruntersuchungsamt (CVUA) Stuttgart database (41). One hundred and eighty plant ingredients that were both important constituents of the 264 food items and available in the CVUA database were attributed a contamination value in organic and conventional modes. For each pesticide, the estimated daily intake (EDI) (in μg/kg bw/d) under lower-and upper-bound scenarios was calculated using methods described by Nougadère et al.
Energy adjustment was conducted using the residual method for nutrient intake. Concerning dietary exposure to pesticides, the main model was further adjusted for the coverage of the diet. P values were estimated via linear contrast tests (corrected for multiple comparisons using a Bonferroni procedure). Two-sided tests were used, and a P value of <0. 05 was considered significant. Data management and statistical analyses were performed using SAS (version 9. 4; SAS Institute, Inc. ).
Second, food-consumption data were self-reported. The use of a 5-point ordinal scale has probably led to an overestimation of the actual organic food consumption. However, data collection regarding overall food consumption was derived from a validated food-frequency questionnaire that had shown relative validity and reproducibility  (32). Third, the production system was not taken into account when evaluating nutritional values of foods. This may have led to an underestimation of some nutrient intakes in the case of organic food consumers  (9). Fourth, owing to a paucity of studies on postfarm impacts in both conventional and organic agriculture, the life cycle assessment analyses were limited to the prefarm and on-farm activities. Transportation, distribution of waste, and losses through the supply chain were not included in the evaluation of the environmental impacts.
We especially thank  Younes Esseddik ,  Paul Flanzy , and  Thi Hong Van Duong  (computer scientists);  Veronique Gourlet ,  Fabien Szabo ,  Nathalie Arnault ,  Laurent Bourhis , and  Stephen Besseau  (statisticians); and  Cédric Agaësse  and  Claudia Chahine  (dieticians). We warmly thank all of the dedicated and conscientious volunteers involved in the NutriNet-Santé cohort. We also thank  Bioconsom' acteurs' members for price collection, the  CVUA Stuttgart  for the pesticide residue database, and  Noémie Soton  for her contribution to the data management of the CVUA database. The authors' responsibilities were as follows-PG, SH, DL, and EK-G: conducted the study. JB, PP, RV, BT-L, BL, PG, SH, CB-S, OH, L-GS, DL, and EK-G: conducted the research and implemented databases. JB and EK-G: performed statistical analyses and provided preliminary interpretation of findings.
The  NutriNet-Santé cohort study  is funded by the following public institutions:  French Ministry of Health, Santé Publique France, National Institute for Health and Medical Research, National Institute for Agricultural Research, National Conservatory of Arts and Crafts, and University of Paris 13. The  BioNutriNet  project was supported by the  French National Research Agency (Agence Nationale de la Recherche)  in the context of the 2013  Programme de Recherche Systèmes Alimentaires Durables  ( ANR-13-ALID-0001 ). The funders had no role in the study design, data collection, analysis, interpretation of data, preparation of the manuscript, and decision to submit it for publication.
conventional) and further allocations of edibility and cooking factors to obtain impacts at the consumer level Division of the diet monetary cost by the household income reported by the participants. Because incomes were declared in categories, the mean of each class was used, whereas arbitrary incomes were determined for extreme classes Assessment of the plant-based exposure based on 180 plant ingredients, differentiating the food production systems (organic vs. conventional), and further allocations of edibility and cooking factors to obtain impacts at the consumer level Aim/definition Measure of the absolute and relative intakes of main relevant food and nutrients Measure of the consumption of a wide variety of foods and of the overall nutritional diet quality (including adequacy to French nutritional guidelines and reference values) Measure of underweight or different levels of overweight Measure of climate change Partial reflection of natural resource depletion Reflection of resource depletion and biodiversity Assessment of the budget devoted to diet Assessment of the importance placed on diet in the total budget Measure of the exposure from plant-derived products to 15 pesticides Data sources NutriNet-Santé composition database (2014) NutriNet-Santé composition database (2014) NutriNet-Santé anthropometric questionnaire (2014) Mostly DIALECTE database (2000-2015 with 50% of data collected after 2010) completed by data available in the literature Mostly DIALECTE database (2000-2015 with 50% of data collected after 2010) completed by data available in the literature Mostly DIALECTE database (2000-2015 with 50% of data collected after 2010) completed by data available in the literature Kantar-World panel purchase database (2012) completed by ∼2000 prices collected from short supply chains by Bioconsom'acteurs' members (fall 2014 and spring 2015) NutriNet-Santé socio-economic questionnaire and computed diet monetary costs Chemisches und Veterinäruntersuchungsamt (European reference laboratory for the development of methods for the analysis of residues on plant products) Stuttgart database (2012-2015) Sustainability dimension measured by the indicator Nutrition-related dimension Nutrition-related dimension Nutritional anthropometry dimension Environment-related dimension Environment-related dimension Environment-related dimension Economic-related dimension Economic-related dimension Toxicology-related dimension Indicator Dietary intakes Dietary scores BMI Greenhouse-gas emission Cumulative energy demand Land occupation Diet monetary costs Percentage of the total budget allocated to food Dietary pesticide exposure Downloaded from https://academic.
Ecol Econ 26:189-209 Bolt J, Inklaar R, de Jong H, van Zanden JL (2018) Maddison Project Database 2018. https ://www. rug. nl/ggdc/histo rical devel opmen t/ maddi son/relea ses/maddi son-proje ct-datab ase-2018. Accessed 12 Apr 2018 Brandt AR, Dale M, Barnhart CJ (2013) Calculating systems-scale energy efficiency and net energy returns: a bottom-up matrixbased approach. Energy 62:235-247 Broberg T, Berg C, Samakovlis E (2015) The economy-wide rebound effect from improved energy efficiency in Swedish industries-A general equilibrium analysis. Energy Policy 83:26-37 Brockway P, Saunders H, Heun M, Foxon T, Steinberger J, Barrett J, Sorrell S (2017) Energy rebound as a potential threat to a Energy and exergy efficiency of primary-to-final conversion processes By definition, the different 1 are the inverse of the primary ( Φ P ) or final ( Φ F ) exergy factors of Table 1.
| Animals The case records of client-owned cats, diagnosed with RCM based on conventional echocardiographic and Doppler examination at the Alfort Cardiology Unit (UCA, National Veterinary School of Alfort, France) between October 2001 and December 2015 were retrospectively reviewed. The main epidemiological (age, body weight, sex, and breed) and clinical characteristics of the included animals were extracted from computerized databases. The presence of concurrent systemic disease and treatment at diagnosis were recorded. Cats with hyperthyroidism and those with systemic arterial hypertension (systolic arterial blood pressure measured in awake cats by the standard Doppler method [811-BL; Parks Medical Electronics, Inc, Aloha, Oregon] >160 mm Hg in unstressed animals)  11, 12  were not included in the study, nor were cats with systolic cranial motion of the mitral valve or focal hypertrophy of the IVS.
| Conventional echocardiography and Doppler examination Standard transthoracic M-mode, 2-dimensional (2D), and Doppler examinations with concomitant ECG tracings were performed by trained observers (Dipl. ECVIM-CA Cardiology, last year resident, clinician with at least 3 years of experience at our unit) in awake cats by the use of ultrasound units (Vingmed System 5, Vivid 5, Vivid 7, Vivid E9; General Electric Medical System, Waukesha, Wisconsin) equipped with phased-array transducers, as previously described and validated. 14 Data from the original echocardiographic reports were collected. All images additionally were reviewed by 2 board-certified specialists (V. Chetboul and V. Gouni).
2 (upper cutoff obtained from a population of 100 prospectively recruited healthy cats). 18 The right end-diastolic atrial diameter also was measured at the level of the tricuspid annulus from the 2D right parasternal 4-chamber view. The right atrium (RA) was judged as dilated if its diameter was wider than the upper reference limit (>15 mm) obtained from a population of 120 healthy adult (≥12 months) cats recruited at the UCA and determined as previously described by applying the statistical procedures recommended by the Clinical and Laboratory Standards Institute guidelines,  20, 21  and by using the Tukey method for identifying outliers and the Anderson-Darling test for evaluating normality of the distribution (Xlstat-Biomed, Version 2016, Addinsoft, Data Analysis and Statistical Solution for Microsoft Excel, Paris, France).
| Follow-up Follow-up data were collected by reviewing the paper and electronic records of cats diagnosed with RCM as defined above. At the time of diagnosis, cats were classified as either clinically or subclinically affected, that is, with or without clinical signs attributed to RCM, respectively (eg, dyspnea, ascites, syncope, aortic thromboembolism [ATE]). Owners of cats for which the outcome could not be found in the database at the time of writing were contacted by telephone or e-mail to determine the current status of their animals: alive (clinically or subclinically affected) or dead (date and cause of death, defined as cardiac or noncardiac). Cases of animals dying suddenly, euthanized for cardiac reasons or dying from nonresponsive CHF or ATE, were considered as CD. Sudden deaths included sudden witnessed deaths and suspected sudden deaths (cats found dead at home without an obvious cause and completely asymptomatic during the previous 24 hours).
| Statistical analysis Commercially available software (Addinsoft (2019). XLSTAT statistical and data analysis solution. Long Island, NY, USA) was used for the statistical analyses. Data were expressed as proportions (%), medians, and interquartile ranges (IQR). Median survival times to all-cause death and to cardiac death both were estimated using the Kaplan-Meier method and compared by applying a log rank test. Regarding CD, adjusted hazard ratios (HR) were estimated using multivariate Cox proportional hazard models. We hypothesized that the following variables were risk factors for CD: end-diastolic LA : Ao ratio (as quantitative variable and binary After exclusion of the 39 cats initially recruited for the study, all cats finally included (n = 92) had normal 2D and M-mode LV variables (ie, IVSd, IVSs, LVFWd, LVFWs, SA-IVSd, LVDd, LVDs, and SF% within normal ranges)  18, 19    In 54 of 92 cats (59%), RCM was associated with a concomitant systemic disease, of which 19 (35%) were infectious diseases (eg, feline immunodeficiency virus infection, pyometra, urinary infection, bronchitis, feline infectious peritonitis, pyothorax).
Search strategy and inclusion criteria for systematic reviews To identify the systematic reviews of interest, search strategies in the following databases were launched on December 2016: Cochrane Database of Systematic Reviews, PubMed, EMBASE and CINHAL. The search strategy included the following terms: systematic review, meta-analysis, underweight, weight loss, underfeed, protein energy malnutrition, undernourished, undernutrition (search strategies for each database are detailed in Appendix A). Montori's search strategy  (Montori et al. , 2005)  was used in PubMed. After extracting the references from the literature databases and after eliminating duplicates, title and abstract screening was Subsequently, full-texts of all relevant abstracts were obtained and screened to identify SRs of interest based on: a) the use of at least two medical literature databases; b) used a systematic search strategy; c) quality of primary studies reported; c) the inclusion of at least one comparative primary study; e) the use of at least one non-pharmacological intervention for malnutrition; and f) the inclusion of at least one study with older persons (mean age of participants >65 years old) at risk of malnutrition or malnourished (see definitions above).
Data extraction and management All the primary studies identified according to the inclusion/exclusion criteria were reviewed, data were extracted directly from the studies, not from the systematic reviews. Characteristics of the included primary studies were described based on the study design (randomised controlled trial  [RCT]  or controlled clinical trial  [CCT] ), population, setting, intervention, outcomes, and funding (Table  1 ). Data extraction was also performed A C C E P T E D M A N U S C R I P T by two independent reviewers. Disagreement was resolved by discussion and, when needed, by a third senior reviewer.
Data synthesis and analysis Following a PICO (Patient Intervention Comparator Outcome) process (O'Connor D, Green S, 2011), studies were pooled together for meta-analysis if they used the same intervention, outcome measure and study design. When a meta-analysis was feasible with at least two studies, data synthesis was carried out using Review Manager Software 5. 3 according to the Cochrane Collaboration Statistical Guidelines. A random effects model was chosen to perform the meta-analysis due to the heterogeneity of the study designs. Unless otherwise stated, data are presented as mean ± SD. Results are presented in a narrative way when no meta-analysis could be performed. Participants were treated as the unit of analysis in all primary studies included in this review.
FUNDING The preparation of this paper was supported by the MalNutrition in the ELderly (MaNuEL) knowledge hub. MaNuEL is supported by the  Joint Programming Initiative 'Healthy Diet for a Healthy Life '. The MaNuEL funding agencies supporting this paper are (in alphabetical order of participating Member State): France:  Ecole Supérieure d'Agricultires (ESA) ; Germany:  Federal Ministry of Food and Agriculture (BMEL)  represented by  Federal Office for Agriculture and Food (BLE) ; The Netherlands: The  Netherlands Organisation for Health Research and Development (ZonMw). This work was also supported by the SENATOR trial ( FP7-HEALTH-2012-305930 ).
Using the longwavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as $12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that remeasured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.
, 1976). However, many important anomalous scatterers do not have their K and L absorption edges within the wavelength ranges of standard synchrotron beamlines for macromolecular crystallography, resulting in weak anomalous signals. Recently, a novel beamline, I23, at Diamond Light Source was introduced to collect anomalous data at substantially longer wavelengths than was previously possible. The I23 beamline operates in an in-vacuum sample environment and features a number of other innovations that make it optimal for anomalous data collection  (Wagner et al. , 2016). Here, we present an optimized data-collection strategy for the identification of iodine anomalous scattering positions that greatly improves our ability to detect weak and partially occupied states in crystals. Co-crystals of the chaperone Spy with its disordered client Im7 were used to collect anomalous data for three iodinecontaining Im7 mutants.
, 2016). 2. 1. 1. Crystal harvesting. The crystals were cryoprotected by increasing the PEG 3000 concentration to 35% and were flash-cooled in liquid nitrogen. The crystals were harvested using LithoLoop sample mounts (Molecular Dimensions, Newmarket, England) matched to the size of the crystal and glued to copper pins as part of the dedicated I23 sampleholder assembly, which is optimized for cryogenic sample transfer and storage in the beamline vacuum environment. 2. 1. 2. Data collection. Data were collected on beamline I23 at Diamond Light Source at X-ray energies of 5. 2 and 4. 5 keV, which are above and below the iodine L absorption edges [E(L I ) = 5. 188 keV, E(L II ) = 4. 852 keV, E(L III ) = 4. 557 keV], using the semi-cylindrical PILATUS 12M area detector. For each data set, 360 of data were collected with an exposure time of 0.
1 s per 0. 1 rotation in an inverse-beam setting of 20 wedges. Taking advantage of the multi-axis goniometer, data were collected at 5. 2 keV at different and ' goniometer angles (Table  1 ). To identify the remaining anomalously scattering ligands, zinc and chloride ions, two additional sets of data were collected for the Spy-Im7 L19pI-Phe complex at 2. 87 and 2. 75 keV. 2. 1. 3. Model building and refinement. Data integration and scaling were performed with XDS  (Kabsch, 2010)  and with AIMLESS  (Evans & Murshudov, 2013) , respectively. Phased anomalous difference Fourier maps were calculated using ANODE  (Thorn & Sheldrick, 2011). Molecular replacement was performed using the known structure of the Spy-Im7 complex (PDB entry 5wnw;  Horowitz et al. , 2016)  as the search model in Phenix  (Adams et al.
m. s. d. ) of 0. 41 A ˚. Refinement statistics are given in  Table 2. 2. 1. 4. Dose estimation. The absorbed dose was estimated for each crystal using RADDOSE-3D  (Bury et al. , 2018). strategy (number of images, oscillation range and exposure time). The cumulative dose was estimated for those crystals submitted to multiple and sequential data collections.
READ ensemble selection The previously described READ selection procedure was used to select an ensemble of structures to fit the weak residual density and the iodine anomalous signals  (Salmon et al. , 2018; Horowitz et al. , 2016). In order to obtain sufficient experimental information, we combined previous crystallographic data sets of Spy and Im7 6-45 (data set 1), both the residual electron density and the iodine signals, with the data presented here (data set 2). All selections include the electron density from data set 1, the iodine anomalous signals from data set 1, except for those arising from L19pI-Phe, and a variable combination of iodine anomalous signals arising from L18pI-Phe (data set 2), L19pI-Phe (data set 1 or 2) or K20pI-Phe (data set 2). To test the predictive power of the ensemble and the coherence of the data set, some iodine anomalous signals not used in the fit were back-predicted from the final ensemble.