cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30131945
title: Nexus between market access and contract farming: a systematic review and meta-regression analysis

description: The impact of market access on contract farming participation and outcomes among smallholder farmers has remained a debatable issue in developing countries. This meta-analysis addresses gaps in the literature by synthesizing evidence on the effect of market access on contract farming among smallholder farmers from 38 peer-reviewed articles published between 1990 and 2024, using data from various databases including Web of Sciences, Dimensions and Scopus. Results show that market access has a moderate and positive effect on contract farming. Subgroup analysis indicates that in developing countries, a relatively high market access significantly affects contract farming by increasing farmers’ income. The analysis further indicates that education and income positively influence participation, while land size has a negative effect. These findings highlight the importance of policies that increase market access for smallholder farmers through investment in infrastructure such as roads, supporting farmer-based organizations, access to technology, access to electricity, building local knowledge-based information centers and addressing physical value-adding activities. In addition, there is a need for policy prioritization for farmer empowerment and regional-level market opportunities for contract farmers. This can be realized through investing in infrastructure and the harmonization of agronomic trade policies across borders.
DOI: 10.6084/m9.figshare.30131945.v1
title: Nexus between market access and contract farming: a systematic review and meta-regression analysis

description: The impact of market access on contract farming participation and outcomes among smallholder farmers has remained a debatable issue in developing countries. This meta-analysis addresses gaps in the literature by synthesizing evidence on the effect of market access on contract farming among smallholder farmers from 38 peer-reviewed articles published between 1990 and 2024, using data from various databases including Web of Sciences, Dimensions and Scopus. Results show that market access has a moderate and positive effect on contract farming. Subgroup analysis indicates that in developing countries, a relatively high market access significantly affects contract farming by increasing farmers’ income. The analysis further indicates that education and income positively influence participation, while land size has a negative effect. These findings highlight the importance of policies that increase market access for smallholder farmers through investment in infrastructure such as roads, supporting farmer-based organizations, access to technology, access to electricity, building local knowledge-based information centers and addressing physical value-adding activities. In addition, there is a need for policy prioritization for farmer empowerment and regional-level market opportunities for contract farmers. This can be realized through investing in infrastructure and the harmonization of agronomic trade policies across borders.
DOI: 10.3535/6jd-6gj-zrg
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mhc-m10-eq8
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qsr-awf-bhg
title: Juglans L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w95-k1m-mak
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4dv-6wd-49a
title: Proboscidea Illiger, 1811

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jxx-s0c-zzm
title: Ursus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.28163332
title: Epigenetic regulation of banana fruit ripening: global and specific DNA methylation profile, and characterization of DNA methylation-related genes

description: Climacteric fruits like bananas often experience significant post-harvest losses due to rapid ripening. This study investigated the molecular processes behind banana ripening, focusing on DNA methylation and its role in regulating gene expression through epigenetics. Physiological changes during ripening included alterations in peel color, fruit firmness, and total soluble solids, with marked increases in starch degradation, brown spot formation, and ethylene production by day 7. Global DNA methylation patterns, analyzed using methylation-sensitive amplification polymorphism, revealed an increase in methylation levels on day 3 of ripening. Key genes involved in DNA methylation and demethylation were identified through <i>in silico</i> gene and protein analysis of <i>Musa acuminata</i>. These include three methyltransferases (<i>MaDRM2-A</i>, <i>MaDRM2-B</i>, and <i>MaDRM2-C</i>) and three demethylation-related genes (<i>MaDML-A</i>, <i>MaDML-B</i>, and <i>MaROS1</i>). Expression levels of <i>MaDRM2-A</i>, <i>MaDRM2-B</i>, <i>MaDML-A</i>, and <i>MaROS1</i> significantly increased by day 3, suggesting their involvement in early ripening processes. Additionally, methylation dynamics were observed on CpG islands of two critical transcription factors, <i>MaMADS1</i> and <i>MaMADS2</i>, though gene regulation was unaffected. The study highlights that DNA methylation regulation precedes visible physiological changes in ripening, offering insights into the molecular mechanisms governing fruit ripening and potential strategies to enhance quality and extend shelf life.
DOI: 10.6084/m9.figshare.28163332.v1
title: Epigenetic regulation of banana fruit ripening: global and specific DNA methylation profile, and characterization of DNA methylation-related genes

description: Climacteric fruits like bananas often experience significant post-harvest losses due to rapid ripening. This study investigated the molecular processes behind banana ripening, focusing on DNA methylation and its role in regulating gene expression through epigenetics. Physiological changes during ripening included alterations in peel color, fruit firmness, and total soluble solids, with marked increases in starch degradation, brown spot formation, and ethylene production by day 7. Global DNA methylation patterns, analyzed using methylation-sensitive amplification polymorphism, revealed an increase in methylation levels on day 3 of ripening. Key genes involved in DNA methylation and demethylation were identified through <i>in silico</i> gene and protein analysis of <i>Musa acuminata</i>. These include three methyltransferases (<i>MaDRM2-A</i>, <i>MaDRM2-B</i>, and <i>MaDRM2-C</i>) and three demethylation-related genes (<i>MaDML-A</i>, <i>MaDML-B</i>, and <i>MaROS1</i>). Expression levels of <i>MaDRM2-A</i>, <i>MaDRM2-B</i>, <i>MaDML-A</i>, and <i>MaROS1</i> significantly increased by day 3, suggesting their involvement in early ripening processes. Additionally, methylation dynamics were observed on CpG islands of two critical transcription factors, <i>MaMADS1</i> and <i>MaMADS2</i>, though gene regulation was unaffected. The study highlights that DNA methylation regulation precedes visible physiological changes in ripening, offering insights into the molecular mechanisms governing fruit ripening and potential strategies to enhance quality and extend shelf life.
DOI: 10.3535/rxk-sjt-je0
title: Equidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cka-4e9-kp5
title: Ursus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cke-fwh-vv1
title: Cervidae Goldfuss, 1820

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c0z-v35-2jp
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fev-gmr-sg1
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sqm-grm-szh
title: †Plegiocidaris Pomel, 1883

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.30152958
title: Changes over time in the genetic parameters of milk production and functional traits in a Holstein population

description: Changes over time in the genetic parameters for milk yield (MY), fat yield (FY), protein yield (PY), fat content (FC), protein content (PC), longevity (LONG), somatic cell score (SCS), calving interval (CI) and age at first calving (AFC) were estimated with information from records of 335,155 pedigreed Chilean Holstein cows with first calvings from 1998 to 2017, using multi-trait linear mixed models within four 5-year periods. Additive genetic variances for MY, FY and PY decreased by 45, 33 and 34% between the first and last periods, increased by 21% for FC and remained constant for PC. Environmental variances for MY, FY, PY, FC and PC increased by 14, 40, 34, 74 and 20%. Heritabilities for MY, FY, PY and FC declined by 43, 44, 44 and 16%. In functional traits, genetic variances and heritabilities remained unchanged, while a decrease over time was observed in environmental variances for SCS, CI and AFC. Genetic and environmental correlations between MY, FY and PY decreased over time, while environmental correlations of FY and LONG with SCS and LONG with CI increased. These findings underscore the importance of changes in genetic and environmental parameters over time for important traits in selected populations of dairy cattle.
DOI: 10.6084/m9.figshare.30152958.v1
title: Changes over time in the genetic parameters of milk production and functional traits in a Holstein population

description: Changes over time in the genetic parameters for milk yield (MY), fat yield (FY), protein yield (PY), fat content (FC), protein content (PC), longevity (LONG), somatic cell score (SCS), calving interval (CI) and age at first calving (AFC) were estimated with information from records of 335,155 pedigreed Chilean Holstein cows with first calvings from 1998 to 2017, using multi-trait linear mixed models within four 5-year periods. Additive genetic variances for MY, FY and PY decreased by 45, 33 and 34% between the first and last periods, increased by 21% for FC and remained constant for PC. Environmental variances for MY, FY, PY, FC and PC increased by 14, 40, 34, 74 and 20%. Heritabilities for MY, FY, PY and FC declined by 43, 44, 44 and 16%. In functional traits, genetic variances and heritabilities remained unchanged, while a decrease over time was observed in environmental variances for SCS, CI and AFC. Genetic and environmental correlations between MY, FY and PY decreased over time, while environmental correlations of FY and LONG with SCS and LONG with CI increased. These findings underscore the importance of changes in genetic and environmental parameters over time for important traits in selected populations of dairy cattle.
DOI: 10.3535/4rr-r5d-nbq
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kex-p6m-wjs
title: Rodentia Bowdich, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29616112
title: Phytogenic and prebiotic feed additives as antibiotic substitutes: effects on broiler meat quality, organ properties, and production efficiency when fed standard and reduced energy and protein diets

description: This study investigated the impact of reduced dietary metabolizable energy (ME) and crude protein (CP) levels on broiler breast meat quality, internal organ yields, feed efficiency (FE), and the European production efficiency factor (EPEF), with or without phytogenic feed additive (PFA) or prebiotic supplementation. Two base diets were used: a reduced-energy and protein diet (−1.5% ME, −5% amino acid density) as the negative control (NC1) and a standard corn–soybean diet as the positive control (PC1). Each was supplemented with PFA (0.15% or 0.25%) or 0.10% prebiotic, resulting in eight treatments. A total of 576 Ross 308 chicks were allocated to these treatments and reared for 35 days. The results showed that reduced ME and CP diets impaired meat quality and performance, with NC1 showing the poorest results. Supplementation with 0.25% PFA in the PC1 diet improved water holding capacity (+6.32%), reduced drip loss (−25.38%) and cooking loss (−27.29%), enhanced tenderness of breast meat, and improved FE (+4.7%) and EPEF (+12.9%). Organ weights improved under NC1 with 0.25% PFA, and prebiotics improved meat color. In conclusion, while ME and CP reduction impaired broiler performance and meat quality, PFA-especially at 0.25% in a standard diet-effectively mitigated these effects. Phytogenic feed additives are an effective supplement for generating high-quality broiler meat, especially at higher inclusion levels, even in low energy and protein diets.Plant-based feed additives showed the potential to enhance feed efficiency and production efficiency, particularly at higher inclusion levels, even under reduced energy and protein diets.The PC1 + 0.25% PFA group showed a 4.7% increase in feed efficiency and a 12.9% increase in European production efficiency over NC1.The immune organs (Bursa) and digestive organs (gizzard and proventriculus) were larger in groups treated with Phytogenic feed additives and particularly NC1 + 0.25% PFA.Phytogenic feed additives are an interesting tool for producing high-grade broiler meat, contributing significantly to several key meat quality characteristics. Phytogenic feed additives are an effective supplement for generating high-quality broiler meat, especially at higher inclusion levels, even in low energy and protein diets. Plant-based feed additives showed the potential to enhance feed efficiency and production efficiency, particularly at higher inclusion levels, even under reduced energy and protein diets. The PC1 + 0.25% PFA group showed a 4.7% increase in feed efficiency and a 12.9% increase in European production efficiency over NC1. The immune organs (Bursa) and digestive organs (gizzard and proventriculus) were larger in groups treated with Phytogenic feed additives and particularly NC1 + 0.25% PFA. Phytogenic feed additives are an interesting tool for producing high-grade broiler meat, contributing significantly to several key meat quality characteristics.
DOI: 10.6084/m9.figshare.30218395
title: Identifying the factors influencing consumption behavior toward organic food: an empirical study in India

description: The present study aims to investigate consumer consumption behavior toward organic food in India with the context of sustainable development goals (SDG) 12 by utilizing the extended Theory of Planned Behavior (TPB) model. The TPB model was extended by incorporating additional variables, such as health, knowledge, availability, price, and motivation. A total of 1,704 responses from various locations in India were collected and analyzed using SmartPLS 4 software to assess the relationships between the constructs. Bootstrapping with 20,000 iterations was used in hypothesis testing. The current work showed a significant correlation between all variables obtained from the TPB. Health and knowledge positively influence consumer attitudes toward organic food. Furthermore, positive consumer motivation has been found to affect subjective norms. This study supported the incorporation of new components into the TPB model to enhance its reliability and precision in understanding consumers’ consumption behavior toward organic food. The price and availability emerged as the significant factors that hinder the consumption of organic food products. The findings will benefit organic food manufacturers, sellers, and policymakers to make decisions by facilitating the advancement of organic food products in the future.
DOI: 10.6084/m9.figshare.30218395.v1
title: Identifying the factors influencing consumption behavior toward organic food: an empirical study in India

description: The present study aims to investigate consumer consumption behavior toward organic food in India with the context of sustainable development goals (SDG) 12 by utilizing the extended Theory of Planned Behavior (TPB) model. The TPB model was extended by incorporating additional variables, such as health, knowledge, availability, price, and motivation. A total of 1,704 responses from various locations in India were collected and analyzed using SmartPLS 4 software to assess the relationships between the constructs. Bootstrapping with 20,000 iterations was used in hypothesis testing. The current work showed a significant correlation between all variables obtained from the TPB. Health and knowledge positively influence consumer attitudes toward organic food. Furthermore, positive consumer motivation has been found to affect subjective norms. This study supported the incorporation of new components into the TPB model to enhance its reliability and precision in understanding consumers’ consumption behavior toward organic food. The price and availability emerged as the significant factors that hinder the consumption of organic food products. The findings will benefit organic food manufacturers, sellers, and policymakers to make decisions by facilitating the advancement of organic food products in the future.
DOI: 10.6084/m9.figshare.30384696
title: Metabolomics analysis of health-care functional substances in Zaohongnuo

description: Zaohongnuo is a folk specialty rice in Dongguan, Guangdong. It is used to boil water for drinking to remove the accumulated moisture in the human body and maintain health. In order to explore the mechanism of removing moisture and maintaining health of Zaohongnuo, the appearance phenotypes of rice and brown rice of two kinds of red glutinous rice were observed, with the common red glutinous rice Hanghongnuo No.1 as the control. The metabolome of rice and brown rice of Hanghongnuo No.1 and Zaohongnuo was determined. The principal component analysis (PCA), sample correlation analysis and metabolite relative content heat map showed that the sequencing results were highly reliable. A total of 1563 metabolites were identified in Zaohongnuo, of which 1178 were successfully classified. The 63 differential metabolites among rice varieties and the 56 differential metabolites among brown rice varieties could be both clustered into three major groups, and the enriched types of differential metabolites were flavonoid glycosides, carbohydrates and their conjugates. The higher content of the medicinal ingredients silibinin, esculin and cholestenone in Zaohongnuo has a targeted therapeutic effect on the clinical manifestations of dampness syndrome such as liver fire inflammation, short urination, chest tightness and irritability. The differential metabolites between rice and brown rice were enriched in three KEGG pathways: ‘galactose metabolism’, ‘neomycin, kanamycin and gentamicin biosynthesis’ and ‘starch and sucrose metabolism’. This study showed that Zaohongnuo contains rich dampness-removing and health-care functional substances, laying a theoretical foundation for the health-care application of Zaohongnuo in industry.
DOI: 10.6084/m9.figshare.30384696.v1
title: Metabolomics analysis of health-care functional substances in Zaohongnuo

description: Zaohongnuo is a folk specialty rice in Dongguan, Guangdong. It is used to boil water for drinking to remove the accumulated moisture in the human body and maintain health. In order to explore the mechanism of removing moisture and maintaining health of Zaohongnuo, the appearance phenotypes of rice and brown rice of two kinds of red glutinous rice were observed, with the common red glutinous rice Hanghongnuo No.1 as the control. The metabolome of rice and brown rice of Hanghongnuo No.1 and Zaohongnuo was determined. The principal component analysis (PCA), sample correlation analysis and metabolite relative content heat map showed that the sequencing results were highly reliable. A total of 1563 metabolites were identified in Zaohongnuo, of which 1178 were successfully classified. The 63 differential metabolites among rice varieties and the 56 differential metabolites among brown rice varieties could be both clustered into three major groups, and the enriched types of differential metabolites were flavonoid glycosides, carbohydrates and their conjugates. The higher content of the medicinal ingredients silibinin, esculin and cholestenone in Zaohongnuo has a targeted therapeutic effect on the clinical manifestations of dampness syndrome such as liver fire inflammation, short urination, chest tightness and irritability. The differential metabolites between rice and brown rice were enriched in three KEGG pathways: ‘galactose metabolism’, ‘neomycin, kanamycin and gentamicin biosynthesis’ and ‘starch and sucrose metabolism’. This study showed that Zaohongnuo contains rich dampness-removing and health-care functional substances, laying a theoretical foundation for the health-care application of Zaohongnuo in industry.
DOI: 10.3535/0jp-bzz-p3l
title: Elephantidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zm3-etj-jx9
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.28631266
title: Comparative analysis of chloroplast genomes in <i>Commiphora gileadensis</i> from Saudi Arabia and Oman reveal evolutionary genetic divergence

description: This study aimed to elucidate chloroplast structure of the wild plant <i>Commiphora gileadensis</i> growing in Saudi Arabia and to compare it with that of the same species grown in Oman. The the two versions exhibited distinct cycles of contraction and expansion, particularly in the small single copy and inverted repeat regions. These variations are attributed to ∼1200 genetic changes, including SNPs and Indels, predominantly occurring in the genic region. Of these mutations, 165 are transitions and 535 are transversions. Nine frameshift mutations were identified in genes encoding DNA-dependent RNA polymerase (e.g. <i>rpoC2</i> and <i>rpoC1</i>), protease (e.g. <i>clpP</i>), and NADH dehydrogenase (e.g. <i>ndhD</i> and <i>ndhA</i>). Mutations in these crucial genes suggest the potential occurrence of heteroplasmy in the chloroplasts from the two origins. Several essential genes were uniquely present in the Saudi chloroplast, while others were unique to the Omani chloroplast. These chloroplast genes are involved in self-replication and photosynthesis. We hypothesize that the genetic divergence between the two chloroplastsresults from exposure to evolutionary forces. These genetic differences are compensatory, as some genes may complement the functions of the missing ones. Elucidating the genomic architecture of chloroplasts provides insights into the interplay of ecological determinants that shape the phylogenetic affinities among plant taxa.