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176 results for “Ruminant”
A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats
<p>Additional file - A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats </p>
CLRD-GLPS: A Long-term Seasonal Dataset of Ruminant Livestock Distribution in China's Grazing Production Systems (2000-2021) Using Stacking-based Interpretable Machine Learning
<p>Advanced computational methods integrating ensemble learning with interpretable machine learning are essential for precision livestock management under increasing environmental constraints and food security pressures. This study develops a novel stacking-based interpretable machine learning (IML) framework that combines multiple algorithms with SHAP analysis techniques to generate the China's Long-term Ruminant Livestock Distribution in Grazing Livestock Production Systems (CLRD-GLPS) dataset. Our computational approach addresses critical challenges in livestock distribution modelling: livestock segmentation and spatial prediction accuracy. The framework integrates Random Forest, XGBoost, CatBoost, LightGBM, and Extra Trees through a two-layer stacking architecture, enhanced with SHAP (Shapley Additive Explanations) analysis for model interpretability. We also implemented interpretable machine learning for livestock production system segmentation to distinguish grazing from total livestock populations. The stacking ensemble demonstrated superior performance over individual algorithms, achieving R² values of 0.954-0.961 for cattle and 0.896-0.901 for sheep and goats, with improvements of up to 8.3% compared to best performance single-model approaches. Multi-scale validation confirmed computational robustness: livestock segmentation achieved R² = 0.80 at county level, while independent city-level validation of CLRD-GLPS datasets yielded R² = 0.76-0.80. SHAP interpretability analysis revealed distinct environmental drivers, with vegetation indices and topography primarily influencing cattle distribution, while snow conditions and elevation dominated sheep and goat patterns. This computational framework advances livestock distribution modelling through enhanced prediction accuracy, model stability, and interpretability, while the CLRD-GLPS dataset provides essential spatial-temporal information for rangeland sustainability assessments and evidence-based livestock management policies. This dataset is supported by the Second Tibetan Plateau Scientific Expedition and Research Program (STEP, grant no. 2019QZKK0906).</p>
Electronic Identification survey on small ruminants
<p>The results from the survey made in the 7 countries on farmers about the current use of Electronic Identification and main barriers and motivations in October 2018.</p>
Supplementary files - Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk
<p>The dataset is a part of Supplementary file for the manuscript:</p> <p><strong>Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk</strong> by L. Rysova, P. Cejnar, O. Hanus, V. Legarova, J. Havlik, H. Nejeschlebova, I. Nemeckova, R. Jedelska, M. Bozik, submitted to <em>Journal of Dairy Science</em> (Manuscript ID JDS.2021-21396), Received October 8, 2021, Accepted January 31, 2022, Corresponding author: bozik@af.czu.cz, <a href="https://doi.org/10.3168/jds.2021-21396">https://doi.org/10.3168/jds.2021-21396</a></p> <p><strong>File 1:</strong> Detailed MALDI-TOF method description</p> <p><strong>File 2: </strong>Quantification of milk adulteration – calibration of the model Quantification of milk adulteration – calibration of the model</p> <p><strong>Table S1: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of caprine milk<strong> </strong></p> <p><strong>Table S2: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of ovine milk</p> <p><strong>Table S3: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set A as the training set and set B as the test set.</p> <p><strong>Table S4: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using both, set A and set B , as the one training set and set C as the test set.</p> <p><strong>Table S5: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set AB as the training set and set C as the test set.</p> <p>In this version <strong>SD values in Table S2 were corrected</strong>.</p>
Fig. 3 in Exploiting parallels between livestock and wildlife: Predicting the impact of climate change on gastrointestinal nematodes in ruminants
Fig. 3. In marginal grazing systems in Europe sheep often occupy separate summer and winter grazing areas, analogous to the summer and winter ranges of migratory ruminants. In the uplands of Wales, UK, (shown here) sheep are often grazed on extensive areas of land at low stocking densities over the summer period, and sent to lowland dairy farms for winter grazing at higher stocking densities. (Photo: Rose, H.).
Fig. 2 in Exploiting parallels between livestock and wildlife: Predicting the impact of climate change on gastrointestinal nematodes in ruminants
Fig. 2. The relative seasonal incidence of ovine parasitic gastroenteritis (PGE) in the Southwest of England, UK, based on monthly diagnoses of (a) Nematodosis (NOS = species not otherwise specified), (b) Haemonchosis and (c) Nematodirosis (van Dijk et al., 2008).
Fig. 1 in Exploiting parallels between livestock and wildlife: Predicting the impact of climate change on gastrointestinal nematodes in ruminants
Fig. 1. Comparison of the instantaneous daily development rate of Ostertagia ostertagi (grey) and O. gruehneri (black) at a range of constant temperatures. Instantaneous daily development rates were estimated from the time to 50% development of L3, derived from data published in the literature (O. ostertagi: Rose, 1961; Pandey, 1972; Young et al., 1980) and original data (O. gruehneri: Hoar, 2012) as described by Azam et al. (2012).
Fig. 2 in Prevalence and geographical distribution of amphistomes of African wild ruminants: A scoping review
Fig. 2. Map showing geographical distribution of amphistomes in wild ruminants in Africa (1900–2022).
Fig. 2 in Nematode-induced pathological lesions and alterations of mucin pattern identified in abomasa of wild ruminants
Fig. 2. Histochemical staining of fundic tissue for mucin detection. A. Roe deer, sample from gross lesion. Superficially apparent decreasing PAS positivity at the luminal surface (arrow). PAS, magnification ×100. B. Fallow deer, sample from gross lesion. Residual PAS positivity in the upper pits of abomasum (arrow). PAS, magnification ×100. C. Fallow-deer, sample from gross lesion. Residual mucin located from upper abomasal pits (arrow) content to lower parts, including basal glands. Alcian blue, magnification ×200. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1. Abomasal tissue infected predominantly with A. sidemi. A in Nematode-induced pathological lesions and alterations of mucin pattern identified in abomasa of wild ruminants
Fig. 1. Abomasal tissue infected predominantly with A. sidemi. A. Fallow deer, positive for Ashworthius sidemi. Washed abomasal mucosa with apparent extensive areas of hyperemia (arrowheads) and hemorrhagic lesion in the area of the fundus (arrow). B. Red deer, sample from gross lesion. Part of the abomasum with dispersed round-cellular interstitial inflammation at the base of the glands (arrow) and between abomasal pits (arrowheads). Full findings are accompanied by interstitial edema (asterisk). Hematoxylin and eosin (H&E) staining, magnification ×200. C. Fallow deer, sample from gross lesion. Part of the abomasum with hyperemia, consisting of several groups of vital erythrocytes in the interstitial tissue (arrow), including edema (arrowheads). H&E staining, magnification ×200. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in A new genus of tragulid ruminant from the early Miocene of Kenya
Fig. 3. Selected specimens of tragulid ruminant Afrotragulus parvus (Withworth, 1958), Rusinga Island, late early Miocene of Kenya. A. Holotype BMNH M29514, left hemimandible with m1–m3, in occlusal (A1), buccal (A2) and lingual (A3) views. B. Paratype BMNH 485.49, right hemimandibular fragment with m2–m3, in occlusal (B1), buccal (B2) and lingual (B3) views. C. Paratype BMNH 56.51, right hemimandibular fragment with m2–m3, in occlusal (C1), buccal (C2) and lingual (C3) views. D. Paratype BMNH M30201 (BMNH 505.47 in Withworth 1958: table 6), right maxillary fragment with M2–M3, in linguo−occlusal (D1) and buccal (D2) views. E. BMNH M82690, left hemimandibular fragment with m2, in occlusal (E1), lingual (E2) and buccal (E3) views. F. BMNH M82689, left hemimandibular fragment with m1–m2, in occlusal (F1), buccal (F2) and lingual (F3) views. G. BMNH M82688, right astragalus, in dorsal (G1) and plantar (G2) views. H. BMNH M82687, right astragalus, in dorsal (H1) and plantar (H2) views.
Fig. 4 in A new genus of tragulid ruminant from the early Miocene of Kenya
Fig. 4. Afrotragulus moruorotensis (Pickford, 2001) and Dorcatherium naui Kaup and Scholl, 1834, type species of each respective genus, late early Miocene of Kenya and Eppelsheim (Germany), respectively. Also below Moschiola meminna Erxleben, 1777 and Hyemoschus aquaticus Ogilby, 1841 (extant tragulids). A. Drawing of A. moruorotensis, m2 of the holotype CMK Mor 1'2000, showing the main characters discussed in the text. B. Drawing of D. naui, m2 of the right mandible of the specimen BMNH M40432 (Eppelsheim; the holotype is lost, see Hillenbrand et al. 2009), showing the main characters discussed in the text. C. Moschiola meminna, left m2 (private collection Jan van der Made, Madrid). D. Hyemoschus aquaticus, right m1 of the specimen MNCN−CSIC 18947. Note the main morphological features that characterize the lower molars of Afrotragulus in occlusal view (A), differentiating it from Dorcatherium (B) and the extant selenodont (C) and bunoselenodont (D) tragulids: enlarged cristids, main cusps with flat internal walls, enlarged and triangular central valley, separated mesial and distal lobes, presence of interlobular bridge that extends between the post−metacristid and the pre−entocristid (note that the lobes in Moschiola are connected though there is no Tragulus−fold present), incomplete "M"−structure, short Dorcatherium−fold. Note also the clear differences in the mesial closing of the trigonid: whereas in Afrotragulus (A) the pre−metacristid and the pre−protocristid extend forward contacting in a marked angle, Dorcatherium (B) presents a hyper−developed and curved pre−protocristid that contacts with a very short pre−metacristid, forming a well developed mesial platform. Drawings not to scale.
Fig. 2 in A new genus of tragulid ruminant from the early Miocene of Kenya
Fig. 2. Tragulid ruminant Afrotragulus moruorotensis (Pickford, 2001), Moruorot, late early Miocene of Kenya. A. Multi−focus photographs (A1–A3) and SEM (A4–A6) micrographs of the holotype Mor1'2000, left hemimandible with m1–m3, in occlusal (A1, A4), lingual (A2, A5) and buccal (A3, A6) views; B. Multi−focus photographs of the paratype CMK Mor 1'2000, fragment of left maxilla with M2 in occlusal (B1) and buccal (B2) views. C. Multi−focus photograph of the paratype CMK Mor 1'2000, fragment of left maxilla with M3, in occlusal view. D. BMNH M82380, right hemimandibular fragment with m3 in occlusal (D1), buccal (D2) and lingual (D3) views. E. BMNH M82382, left astragalus, in dorsal (E1) and plantar (E2) views.
Fig. 5 in New artiodactyl ruminant mammal from the late Oligocene of Pakistan
Fig. 5. Palaeohypsodontus zinensis sp. nov., late Oligocene (Chattian), Lundo J2, Bugti Hills, Balochistan, Pakistan. A. Left astragalus (ISEM DBJ2−A2) in anterior (A1) and posterior (A2) views. B. Shaft of right metatarsal (ISEM DBJ2−A3) in anterior (B1) and distal (B2) views. All stero−photographs. Scale bars 1 cm.
Fig. 1 in New artiodactyl ruminant mammal from the late Oligocene of Pakistan
Fig. 1. Map of Pakistan with an enlargement of the Bugti area, and the location of Lundo Chur where the described material has been found. Present−day latitudes and longitudes are also shown.
Fig. 2 in New artiodactyl ruminant mammal from the late Oligocene of Pakistan
Fig. 2. Synthetic lithostratigraphic section of the Bugti Member (adapted from Welcomme et al. 2001) with the accurate stratigraphic setting of P. zinensis sp. nov.
Fig. 4 in New artiodactyl ruminant mammal from the late Oligocene of Pakistan
Fig. 4. Palaeohypsodontus zinensis sp. nov., late Oligocene (Chattian), Lundo J2, Bugti Hills, Balochistan, Pakistan. Holotype (ISEM DBJ2−A1). A. S tereophoto of occlusal view. B. Stereophoto of labial view. Scale bars 1 cm.
Fig. 3 in New artiodactyl ruminant mammal from the late Oligocene of Pakistan
Fig. 3. Simplified cladogram illustrating the interrelationships between different families of ruminants (modified from Janis and Scott 1987). The term "Gelocidae" designates a heterogeneous assemblage of extinct hornless pre−pecoran ruminants. The distribution of the characters discussed in the text are indicated by symbols.
FIGURE 4 in Oligocene ruminants from the Kızılırmak Formation, Çankırı-Çorum Basin, Central Anatolia, Turkey
FIGURE 4. Postcranial remains of Iberomeryx parvus and Iberomeryx sp. from the Kızılırmak Formation (early late Oligocene, Central Anatolia). Iberomeryx parvus: 1, Right cubonavicular in anterior view, TP641-16; 2-3, Right astragalus in anterior (2) and posterior (3) views, GK3-39; 4, Right cubonavicular in anterior view, GK2-5; 5-6, Right astragalus in anterior (5) and posterior (6) views, GK3-37; 7, Left calcaneum in medial view, GK3-24. 8, Right calcaneum in medial view, KZ-11; 9-11, Left distal humerus in anterior-cranial (9), lateral (10), and medial (11) views, GK3-22; 12- 13, Proximal part of coalescent metatarsals III and IV in anterior (12), and medial (13) views, GK3-54; 14-16, phalanx proximalis in anterior (14), lateral (15), and proximal views, GK3-13; Iberomeryx sp. 17, Left cubonavicular in anterior view, KZ-2; 18-21, Right astragalus in anterior (18), posterior (19), lateral (20), medial (21) views, TP641-24. Anatomical abbreviations: acf, astragalo-calcaneal facet; ca, capitulum; daf, distal astragalar facet; fbf, fibular facet; imf, internal malleous facet; me, medial epicondyle; of, olecranon fossa; smt2, contact surface of the Mt2; stf, sustentacular facet.
FIGURE 1 in Oligocene ruminants from the Kızılırmak Formation, Çankırı-Çorum Basin, Central Anatolia, Turkey
FIGURE 1. Location map of late Oligocene mammal localities and sections from the Kızılırmak Formation (Çankırı-Çorum Basin, north central Anatolia, Turkey). 1, geotectonic map of Central Anatolia showing the basins including the Çankırı-Çorum Basin, and the main structural features of the area; 2, Geological map of the studied area with the four fossil localities of the Kızılırmak Formation discussed in the text.
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