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Yang X, Arroyo Cerezo A, Berzaghi P, Magrin L. Comparative near Infrared (NIR) spectroscopy calibrations performance of dried and undried forage on dry and wet matter bases. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124287. [PMID: 38701573 DOI: 10.1016/j.saa.2024.124287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024]
Abstract
The application of Near Infrared (NIR) spectroscopy for analyzing wet feed directly on farms is increasingly recognized for its role in supporting harvest-time decisions and refining the precision of animal feeding practices. This study aims to evaluate the accuracy of NIR spectroscopy calibrations for both undried, unprocessed samples and dried, ground samples. Additionally, it investigates the influence of the bases of reference data (wet vs. dry basis) on the predictive capabilities of the NIR analysis. The study utilized 492 Corn Whole Plant (CWP) and 405 High Moisture Corn (HMC) samples, sourced from various farms across Italy. Spectral data were acquired from both undried, unground and dried, ground samples using laboratory bench NIR instruments, covering a spectral range of 1100 to 2498 nm. The reference chemical composition of these samples was analyzed and presented in two formats: on a wet matter basis and on a dry matter basis. The study revealed that calibrations based on undried samples generally exhibited lower predictive accuracy for most traits, with the exception of Dry Matter (DM). Notably, the decline in predictive performance was more pronounced in highly moist products like CWP, where the average error increased by 60-70%. Conversely, this reduction in accuracy was relatively contained (10-15%) in drier samples such as HMC. The Standard Error of Cross-Validation (SECV) values for DMres, Ash, CP, and EE were notably low, at 0.39, 0.30, 0.29, 0.21% for CWP and 0.49, 0.14, 0.25, 0.14% for HMC, respectively. These results align with previous studies, indicating the reliability of NIR spectroscopy in diverse moisture contexts. The study attributes this variance to the interference caused by water in 'as is' samples, where the spectral features predominantly reflect water content, thereby obscuring the spectral signatures of other nutrients. In terms of calibration development strategies, the study concludes that there is no significant difference in predictive performance between undried calibrations based on either 'dry matter' or 'as is' basis. This finding emphasizes the potential of NIR spectroscopy in diverse moisture contexts, although with varying degrees of accuracy contingent upon the moisture content of the analyzed samples. Overall, this research provides valuable insights into the calibration strategies of NIR spectroscopy and its practical applications in agricultural settings, particularly for on-farm forage analysis.
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Affiliation(s)
- Xueping Yang
- College of Grassland Science and Technology, China Agricultural University, 100193 Beijing, China; Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy.
| | - Alejandra Arroyo Cerezo
- Department of Analytical Chemistry, University of Granada, C/ Fuentenueva s/n, 18071 Granada, Spain
| | - Paolo Berzaghi
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy; GraiNit s.r.l., 35020 Padova, Italy.
| | - Luisa Magrin
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy
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De Zutter A, Landschoot S, Vermeir P, Van Waes C, Muylle H, Roldán-Ruiz I, Douidah L, De Boever J, Haesaert G. Variation in potential feeding value of triticale forage among plant fraction, maturity stage, growing season and genotype. Heliyon 2022; 9:e12760. [PMID: 36685447 PMCID: PMC9849984 DOI: 10.1016/j.heliyon.2022.e12760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/25/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Cereal forages, such as triticale forage, progressively gain interest as alternative crop for maize. The main study objective was to investigate the variation in potential feeding value of triticale forage among maturity stage, growing season and genotype, using total plant and stem fractions. Therefore, near infrared spectroscopy (NIRS) was evaluated as fast screening tool. The prediction ability was good (ratio of prediction to deviation, RPD ≥3.0) for total plant residual moisture, starch, sugars and for stem crude ash (CAsh) and neutral detergent fibre (aNDFom); suitable for screening (2.0 ≤ RPD <3.0) for total plant CAsh, acid detergent fibre (ADFom), in vitro digestibility of organic matter (IVOMD), in vitro digestibility of neutral detergent fibre (IVNDFD) and for stem total lignin (TL) and IVNDFD; poor (1.5 ≤ RPD <2.0) for total plant crude protein, crude fat, aNDFom, lignin (sa) and for stem Klason lignin (KL); unreliable (RPD <1.5) for stem residual moisture and acid soluble lignin (ASL). The evolution in potential feeding value of 36 genotypes harvested at the medium and late milk to the early, soft and hard dough stage was followed. The most important changes occurred between the late milk and early dough stage, with little variation in quality after the soft dough stage. During 2 growing seasons, variation in feeding value of 120 genotypes harvested at the soft dough stage was demonstrated. Interestingly, variation in stem IVNDFD is almost twice as high as for the total plant (CV 12.4% versus 6.6%). Furthermore, Spearman correlations show no link between dry matter yield and digestibility of genotypes harvested at the soft dough stage. Based on linear regression models ADFom appears as main predictor of both plant IVOMD and plant IVNDFD. Stem IVNDFD is particularly determined by KL.
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Key Words
- 1-VR, determination coefficient of cross-validation
- ADFom, acid detergent fibre expressed exclusive of residual ash
- CAsh, crude ash
- CELL, cellulose
- CFat, crude fat
- CP, crude protein
- CV, coefficient of variation
- DM, dry matter
- DMY, dry matter yield
- DOMY, digestible organic matter yield
- Digestibility
- Feeding value
- Forage
- GDD, growing degree days
- HCELL, hemicellulose
- IVNDFD, in vitro digestibilty of neutral detergent fibre
- IVOMD, in vitro digestibility of organic matter
- KL, Klason lignin
- Lignin (sa), lignin determined by solubilisation of cellulose with sulphuric acid
- MS, maturity stage
- MSE, mean squared error
- NIRS
- NIRS, near infrared spectroscopy
- RPD, ratio of prediction to deviation
- SECV, standard error of cross-validation
- STA, starch
- SUG, sugars
- Stem
- TL, total lignin
- Triticale
- aNDFom, neutral detergent fibre assayed with a heat stable amylase and expressed exclusive of residual ash
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Affiliation(s)
- Anneleen De Zutter
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Diepestraat 1, 9820 Bottelare, Belgium
- Corresponding author.
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Diepestraat 1, 9820 Bottelare, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Chris Van Waes
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark Zwijnaarde 71, 9052 Zwijnaarde, Belgium
| | - Laid Douidah
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Animal Sciences Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Johan De Boever
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Animal Sciences Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Diepestraat 1, 9820 Bottelare, Belgium
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Campbell M, Ortuño J, Koidis A, Theodoridou K. The use of near-infrared and mid-infrared spectroscopy to rapidly measure the nutrient composition and the in vitro rumen dry matter digestibility of brown seaweeds. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Review: Synergy between mechanistic modelling and data-driven models for modern animal production systems in the era of big data. Animal 2020; 14:s223-s237. [PMID: 32141423 DOI: 10.1017/s1751731120000312] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mechanistic models (MMs) have served as causal pathway analysis and 'decision-support' tools within animal production systems for decades. Such models quantitatively define how a biological system works based on causal relationships and use that cumulative biological knowledge to generate predictions and recommendations (in practice) and generate/evaluate hypotheses (in research). Their limitations revolve around obtaining sufficiently accurate inputs, user training and accuracy/precision of predictions on-farm. The new wave in digitalization technologies may negate some of these challenges. New data-driven (DD) modelling methods such as machine learning (ML) and deep learning (DL) examine patterns in data to produce accurate predictions (forecasting, classification of animals, etc.). The deluge of sensor data and new self-learning modelling techniques may address some of the limitations of traditional MM approaches - access to input data (e.g. sensors) and on-farm calibration. However, most of these new methods lack transparency in the reasoning behind predictions, in contrast to MM that have historically been used to translate knowledge into wisdom. The objective of this paper is to propose means to hybridize these two seemingly divergent methodologies to advance the models we use in animal production systems and support movement towards truly knowledge-based precision agriculture. In order to identify potential niches for models in animal production of the future, a cross-species (dairy, swine and poultry) examination of the current state of the art in MM and new DD methodologies (ML, DL analytics) is undertaken. We hypothesize that there are several ways via which synergy may be achieved to advance both our predictive capabilities and system understanding, being: (1) building and utilizing data streams (e.g. intake, rumination behaviour, rumen sensors, activity sensors, environmental sensors, cameras and near IR) to apply MM in real-time and/or with new resolution and capabilities; (2) hybridization of MM and DD approaches where, for example, a ML framework is augmented by MM-generated parameters or predicted outcomes and (3) hybridization of the MM and DD approaches, where biological bounds are placed on parameters within a MM framework, and the DD system parameterizes the MM for individual animals, farms or other such clusters of data. As animal systems modellers, we should expand our toolbox to explore new DD approaches and big data to find opportunities to increase understanding of biological systems, find new patterns in data and move the field towards intelligent, knowledge-based precision agriculture systems.
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The Effect of Time and Method of Storage on the Chemical Composition, Pepsin-Cellulase Digestibility, and Near-Infrared Spectra of Whole-Maize Forage. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9245390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study examined the effects of long-term storage conditions on the chemical composition, pepsin-cellulase dry matter digestibility (PCDMD), and visible (VIS)/near infrared spectra (NIR) of forage. Eighteen samples of different whole-crop maize varieties originally harvested in 1987 were used. After drying, these samples were analyzed in the laboratory for ash, crude protein (CP), structural carbohydrates, total soluble carbohydrates (TSC), starch and PCDMD, and the remaining samples were stored frozen (at −20°C) or at barn temperature (ambient temperatures ranged from −8.5 °C to 27.1 °C). In 2016, the samples were analyzed for ash, CP, structural carbohydrates, TSC, starch and PCDMD. The visible/NIR spectra of both storage methods were obtained. Chemical composition and PCDMD analyses revealed significant differences (p < 0.05) between the storage methods for TSC but not for the other parameters (p > 0.05). After sample harvesting in 1987, the analyses were compared with those in 2016. It was found that the post-harvest TSC and ash content were higher (p < 0.05) and lower (p < 0.05), respectively, during 2016. No significant differences were found for starch and PCDMD. Important differences between the VIS/NIR spectra of both storage methods were obtained in the VIS segment, particularly in the area between 630 and 760 nm. We concluded that storing dry forage samples at ambient temperature for a very long time (29 years) did not change their nutritive value compared to the values obtained before storage.
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Krieg J, Koenzen E, Seifried N, Steingass H, Schenkel H, Rodehutscord M. Prediction of CP and starch concentrations in ruminal in situ studies and ruminal degradation of cereal grains using NIRS. Animal 2018; 12:472-480. [PMID: 28770698 DOI: 10.1017/s1751731117001926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ruminal in situ incubations are widely used to assess the nutritional value of feedstuffs for ruminants. In in situ methods, feed samples are ruminally incubated in indigestible bags over a predefined timespan and the disappearance of nutrients from the bags is recorded. To describe the degradation of specific nutrients, information on the concentration of feed samples and undegraded feed after in situ incubation ('bag residues') is needed. For cereal and pea grains, CP and starch (ST) analyses are of interest. The numerous analyses of residues following ruminal incubation contribute greatly to the substantial investments in labour and money, and faster methods would be beneficial. Therefore, calibrations were developed to estimate CP and ST concentrations in grains and bag residues following in situ incubations by using their near-infrared spectra recorded from 680 to 2500 nm. The samples comprised rye, triticale, barley, wheat, and maize grains (20 genotypes each), and 15 durum wheat and 13 pea grains. In addition, residues after ruminal incubation were included (at least from four samples per species for various incubation times). To establish CP and ST calibrations, 620 and 610 samples (grains and bag residues after incubation, respectively) were chemically analysed for their CP and ST concentration. Calibrations using wavelengths from 1250 to 2450 nm and the first derivative of the spectra produced the best results (R 2 Validation=0.99 for CP and ST; standard error of prediction=0.47 and 2.10% DM for CP and ST, respectively). Hence, CP and ST concentration in cereal grains and peas and their bag residues could be predicted with high precision by NIRS for use in in situ studies. No differences were found between the effective ruminal degradation calculated from NIRS estimations and those calculated from chemical analyses (P>0.70). Calibrations were also calculated to predict ruminal degradation kinetics of cereal grains from the spectra of ground grains. Estimation of the effective ruminal degradation of CP and ST from the near-infrared spectra of cereal grains showed promising results (R 2>0.90), but the database needs to be extended to obtain more stable calibrations for routine use.
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Affiliation(s)
- J Krieg
- 1Institut für Nutztierwissenschaften,Universität Hohenheim,Emil-Wolff-Straße 10,70599 Stuttgart,Deutschland
| | - E Koenzen
- 2Core Facility Hohenheim,Universität Hohenheim,Emil-Wolff-Straße 12,70599 Stuttgart,Deutschland
| | - N Seifried
- 1Institut für Nutztierwissenschaften,Universität Hohenheim,Emil-Wolff-Straße 10,70599 Stuttgart,Deutschland
| | - H Steingass
- 1Institut für Nutztierwissenschaften,Universität Hohenheim,Emil-Wolff-Straße 10,70599 Stuttgart,Deutschland
| | - H Schenkel
- 1Institut für Nutztierwissenschaften,Universität Hohenheim,Emil-Wolff-Straße 10,70599 Stuttgart,Deutschland
| | - M Rodehutscord
- 1Institut für Nutztierwissenschaften,Universität Hohenheim,Emil-Wolff-Straße 10,70599 Stuttgart,Deutschland
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Villamuelas M, Serrano E, Espunyes J, Fernández N, López-Olvera JR, Garel M, Santos J, Parra-Aguado MÁ, Ramanzin M, Fernández-Aguilar X, Colom-Cadena A, Marco I, Lavín S, Bartolomé J, Albanell E. Predicting herbivore faecal nitrogen using a multispecies near-infrared reflectance spectroscopy calibration. PLoS One 2017; 12:e0176635. [PMID: 28453544 PMCID: PMC5409079 DOI: 10.1371/journal.pone.0176635] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/13/2017] [Indexed: 11/25/2022] Open
Abstract
Optimal management of free-ranging herbivores requires the accurate assessment of an animal’s nutritional status. For this purpose ‘near-infrared reflectance spectroscopy’ (NIRS) is very useful, especially when nutritional assessment is done through faecal indicators such as faecal nitrogen (FN). In order to perform an NIRS calibration, the default protocol recommends starting by generating an initial equation based on at least 50–75 samples from the given species. Although this protocol optimises prediction accuracy, it limits the use of NIRS with rare or endangered species where sample sizes are often small. To overcome this limitation we tested a single NIRS equation (i.e., multispecies calibration) to predict FN in herbivores. Firstly, we used five herbivore species with highly contrasting digestive physiologies to build monospecies and multispecies calibrations, namely horse, sheep, Pyrenean chamois, red deer and European rabbit. Secondly, the equation accuracy was evaluated by two procedures using: (1) an external validation with samples from the same species, which were not used in the calibration process; and (2) samples from different ungulate species, specifically Alpine ibex, domestic goat, European mouflon, roe deer and cattle. The multispecies equation was highly accurate in terms of the coefficient of determination for calibration R2 = 0.98, standard error of validation SECV = 0.10, standard error of external validation SEP = 0.12, ratio of performance to deviation RPD = 5.3, and range error of prediction RER = 28.4. The accuracy of the multispecies equation to predict other herbivore species was also satisfactory (R2 > 0.86, SEP < 0.27, RPD > 2.6, and RER > 8.1). Lastly, the agreement between multi- and monospecies calibrations was also confirmed by the Bland-Altman method. In conclusion, our single multispecies equation can be used as a reliable, cost-effective, easy and powerful analytical method to assess FN in a wide range of herbivore species.
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Affiliation(s)
- Miriam Villamuelas
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (UNIPD), Agripolis, Legnaro, Italy
| | - Emmanuel Serrano
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro (UA), Aveiro, Portugal
- * E-mail: (EA); (ES)
| | - Johan Espunyes
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Néstor Fernández
- Department of Conservation Biology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas EBD-CSIC, Sevilla, Spain
| | - Jorge R. López-Olvera
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage (ONCFS - Unité Faune de Montagne), Gières, France
| | - João Santos
- Departamento de Biologia & CESAM, Universidade de Aveiro (UA), Aveiro, Portugal
- Sanidad y Biotecnología (SaBio), Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - María Ángeles Parra-Aguado
- Sanidad y Biotecnología (SaBio), Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Maurizio Ramanzin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (UNIPD), Agripolis, Legnaro, Italy
| | - Xavier Fernández-Aguilar
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Andreu Colom-Cadena
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Ignasi Marco
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Santiago Lavín
- Servei d’Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Facultat de Veterinária, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Jordi Bartolomé
- Ruminant Research Group, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Elena Albanell
- Ruminant Research Group, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- * E-mail: (EA); (ES)
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Lyons G, Sharma S, Aubry A, Carmichael E, Annett R. A preliminary evaluation of the use of mid infrared spectroscopy to develop calibration equations for determining faecal composition, intake and digestibility in sheep. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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