Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Breed classification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
PubMed1994

Evolution of a computer program for classifying protein segments as transmembrane domains using genetic programming.

The recently-developed genetic programming paradigm is used to evolve a computer program to classify a given protein segment as being a transmembrane domain or non-transmembrane area of the protein. Genetic programming starts with a primordial ooze of randomly generated computer programs composed of available programmatic ingredients and then genetically breeds the population of programs using the Darwinian principle of survival of the fittest and an analog of the naturally occurring genetic operation of crossover (sexual recombination). Automatic function definition enables genetic programming to dynamically create subroutines dynamically during the run. Genetic programming is given a training set of differently-sized protein segments and their correct classification (but no biochemical knowledge, such as hydrophobicity values). Correlation is used as the fitness measure to drive the evolutionary process. The best genetically-evolved program achieves an out-of-sample correlation of 0.968 and an out-of-sample error rate of 1.6%. This error rate is better than that reported for four other algorithms reported at the First International Conference on Intelligent Systems for Molecular Biology. Our genetically evolved program is an instance of an algorithm discovered by an automated learning paradigm that is superior to that written by human investigators.

Amino Acid Sequence↗
PubMed2005

The proportion of beef bulls in Sweden with mature spermiograms at 11-13 months of age.

Semen samples collected postmortem from 142 yearling beef bulls (11-13 months old) of three different breeds (Charolais, Hereford and Simmental) were examined to evaluate the proportion of bulls with mature spermiograms. Before slaughter, testes and epididymides were clinically examined and scrotal circumferences were measured. Aliquots of the cauda epididymal contents taken postmortem were used for sperm morphology examination. Sperm head morphology was studied in dry smears stained with carbol-fuchsine. For each preparation, 500 spermatozoa were counted in each smear under light microscope (x 1000). The presence of proximal cytoplasmic droplets, abnormal acrosomes, detached heads and abnormalities of the midpiece and tail were recorded in wet preparations of formol-saline-fixed spermatozoa. For each preparation, 200 spermatozoa were counted in each preparation under a phase-contrast microscope (x 1000). The abnormalities were classified according to a classification system developed by Bane (1961). Morphological abnormalities were recorded as a percentage of the total number of counted spermatozoa. Criteria for a spermiogram to be considered mature included <15% abnormal heads and <15% proximal droplets. According to this definition approximately 48% (68 of 142) of the examined bulls were considered mature. The bulls in this study represent approximately one-fifth of the total amount of performance-tested beef bulls in Sweden during 5 years. Our results indicate that only less than half of the Swedish yearling beef bulls at the testing station appear to have a mature spermiogram at the time they are offered for breeding purposes.

Age Factors↗
PubMed2002

Breeding soundness evaluations of 3,648 yearling beef bulls using the 1993 Society for Theriogenology guidelines.

Our objective was to perform a retrospective analysis of breeding soundness evaluations (BSEs) as classified by the 1993 Society for Theriogenology (SFT) guidelines [Chenoweth et al., Guidelines for using the bull breeding soundness evaluation form, in: Theriogenology Handbook, 1993, pp. B-10]. Data included BSE information obtained from five performance-testing stations in South Carolina (SC1, SC2, SC3) and Tennessee (TN1, TN2) from 1986 through 1999 on 3648 Angus, Brangus, Charolais, Chianina, Gelbvieh, Limousin, Polled Hereford, Santa Gertrudis, Simbrah, and Simmental bulls. Analyses were simplified by classifying all bulls as either satisfactory or unsatisfactory potential breeders. Of the 3648 bulls evaluated, 76.2% were classified as satisfactory potential breeders. Of all bulls evaluated, 4.0% were unsatisfactory due to inadequate spermatozoal motility, 7.0% due to inadequate spermatozoal morphology and 2.6% due to a combination of inadequate motility and morphology. Unsatisfactory classifications due to non-spermatozoal parameters out of all bulls were 10.2%, with 7.1% for inadequate scrotal circumference and 3.1% for physical abnormalities. For satisfactory and unsatisfactory bulls, respectively, means and standard deviations were 35.8 +/- 2.7 and 33.0 +/- 4.1 cm (P < 0.001) for scrotal circumference, 63 +/- 18 and 35 +/- 24% (P < 0.001) for percent motility, and 86 +/- 7 and 63 +/- 21% (P < 0.001) for percent normal morphology.

Animals↗
PubMed2002

Risk factors for stillbirths in two swine farms in the south of Brazil.

We evaluated stillbirth risk factors in two commercial swine farms of the Rio Grande do Sul State (south of Brazil). The study was conducted during 1 month in Farm A and during 2 months in Farm B, both during 1999. Data for all farrowings that occurred during the study period were recorded (101 for Farm A and 373 for Farm B), without interference in the farm management. In Farm A, 39% of all litters born during the period of interest had stillborn piglets and the stillborn risk for piglets was 12%. In Farm B, 25% of all litters had stillborn piglets whereas the stillborn risk was 2%. Variables considered as potential risk factors for stillbirths were: parity (1, 2-3, 4+); breed (purebred or crossbred); sow body-condition (normal or fat); use of oxytocin during parturition (yes or no); obstetric intervention through vaginal palpation (yes or no); farrowing duration (<4 or > or =4h); mummified fetuses (yes or no); total litter size (<12 or > or =12 piglets); and litter birth weight (<11 or > or =11kg). All stillborn piglets had their classification validated by necropsy. In multivariable logistic-regressions, the cases were the litters having at least one stillborn piglet. In Farm A, litters having at least 12 pigs and in which oxytocin was used during the parturition had 20.8-times-higher odds of stillborn occurrence. In Farm B, litters from sows having parity > or =4 had 2.2-times-higher odds of stillborn occurrence than litters from parity 2 to 3 females, litters having > or =12 pigs had 2.0-times-higher odds of a stillborn piglet than smaller litters and farrowings in which vaginal palpation was performed had 8.0-times-higher odds. Farrowing room management to minimize stillborn risk should target higher-parity females, large litters and optimization of practices of obstetric interventions.

Animal Husbandry↗
PubMedDate not supplied

[Joint research on the precise determination of the energy and protein requirements of fattening pigs. 6. The effect of various energy and protein levels on the performance and feed expenditure of fattening pigs].

Scientific feeding experiments with hybrid pigs of the type Hungahib in the fattening period between 30 and 100 kg were carried out with one repetition as part of a joint international experiment. Feed, nutrient and energy expenditure were tested on 3 levels of energy supply (100 : 85 : 70%) and 3 levels of protein supply (18 : 16 : 14%) in the fattening period between 30 and 60 kg and 16 : 14 : 12% in the fattening period between 60 and 100 kg). In addition to this, parallel metabolism experiments were carried out to determine the digestibility and the N-balance of the feed mixtures used. The cost of feeding was also taken into consideration. The best results with regard to the fattening performance and the minimising of feed cost were achieved with the following ration type: (Table: see text). The fattening performance with this ration type was 712 g average daily live weight gain in the range between 30 and 60 kg live weight in the 1st fattening experiment and 601 g in the 2nd fattening experiment. A classification of the expenditure values has been attempted in the 10th contribution to this series of publications dealing with the total results of the joint international experiment.

Animal Feed↗
PubMedDate not supplied

Canine transitional cell carcinoma.

Transitional cell carcinoma (TCC) of the urinary bladder, the most common malignancy of the urinary tract in dogs, is challenging to both diagnose and treat effectively. The prevalence of this disease may be increasing. The etiology of canine TCC is likely multifactorial. Epidemiological studies of TCC in the dog have revealed a number of risk factors, including breed and female gender, as well as environmental factors, such as insecticide exposure. This tumor is difficult to remove surgically and responds poorly to chemotherapy. The efficacy of radiotherapy and other treatment modalities needs further investigation. Cyclooxygenase-inhibiting drugs have some activity against TCC, and studies to further define these effects are ongoing. Use of the tumor/node/ metastasis (TNM) classification scheme for bladder cancer has allowed for the identification of prognostic factors. Urinary tract obstruction and metastatic disease remain challenges to treat. Work with canine TCC has demonstrated how closely this disease resembles human invasive urinary bladder cancer. Therefore, future research has the potential to benefit both dogs and humans with TCC.

Animals↗
PubMed1984

Real-time ultrasonic scanning in the diagnosis of pregnancy and the determination of fetal numbers in sheep.

Two trials were conducted on a total of 1120 ewes of four breeds to evaluate the use of real-time ultrasonic scanning as a means of diagnosing pregnancy, differentiating barren, single- and multiple-bearing ewes and determining actual fetal numbers in pregnant ewes. In trial 1 (566 ewes) the accuracy of an inexperienced operator, as judged against assessments of an experienced operator, improved from 81 to 100 per cent for the classification of ewes as carrying no, one or more than one fetus, and from 69 to 100 per cent for the determination of actual fetal numbers more than one. In trial 2 the accuracies of the same operator, judged against the lambing performance of 267 ewes, ranged from 90 to 97 per cent for both types of assessment, and for an experienced operator from 95 to 100 per cent (554 ewes). In both trials pregnancy was diagnosed with an accuracy of 100 per cent. It is concluded that real-time ultrasonic scanning of sheep between days 50 and 100 of gestation offers a safe and practicable means of diagnosing pregnancy and of determining fetal numbers. Accuracies of diagnosis of pregnancy of more than 99 per cent, of differentiation of barren, single- and multiple-bearing ewes of 98 per cent, and of determination of actual fetal numbers of 97 per cent can be achieved in practice at scanning rates of at least one ewe per minute. Some of the benefits to flock management and performance likely to result from the use of the technique are considered.

Animals↗
PubMed2001

Genetic analysis of body condition score of lactating Dutch Holstein and Red-and-White heifers.

The aim of this study was to estimate phenotypic and genetic parameters for body condition scores (BCS) from the Dutch type classification system. Data included 108,809 Holstein (H) and 26,208 Red-and-White (R) heifers from 9701 herds that were scored once during lactation on a 1 to 9 scale (1 = emaciated and 9 = obese). Mean BCS for H and R data were 4.50 and 4.94, respectively. The BCS decreased as the percentage of Holstein genes increased. For both breeds, BCS after calving was about 5.6 and BCS was lowest around wk 11. For H heifers, mean BCS at drying off was about 0.8 lower than BCS at calving, whereas for R heifers BCS was at about the same level as at calving. Variance components were estimated using an animal model including the effects of herd x visit, classifier, age at calving, DIM, and genetic group. The random herd x visit effect explained about 10 to 15% of the phenotypic variation. Heritabilities ranged from 0.24 to 0.38, depending on breed and lactation period. Genetic correlations between BCS observations in bimonthly lactation periods were close to unity, especially for H. It was concluded that BCS data collected by type classifiers can well be used for genetic evaluation and that genetic variation between animals for BCS-change patterns is a small component of the overall variation in BCS.

Analysis of Variance↗
PubMed2002

A probabilistic methodology to assess the risk of groundwater quality degradation.

An approach to assess the risk of groundwater quality degradation with regard to fixed standards. based on Disjunctive Kriging (DK) is presented. The DK allows one to evaluate the Conditional Probability (CP) of overriding a given threshold of concentration of a pollutant at a given time, and at a generic point in a considered groundwater system. The result of such investigation over the considered area can be plotted in form of maps of spatial risk. By repeating this analysis at different times, several spatial risk maps will be produced, one for each considered time. By means of non-parametric statistics, the temporal trend of the CPs can be evaluated at every point of the considered area. The trend index, assessed by means of a sort of classification of the trend values obtained as described above, can be superimposed on the most recent values of the spatial risk (i.e.: the most recent values of probability). Consequently a classification of the risk of groundwater quality degradation results with which to weigh both the spatial distribution and the temporal behaviour of the probability to exceed a given standard threshold. The methodology has been applied to values of nitrate concentration sampled in the monitoring well network of the Modena plain, northern Italy. This area is characterised by intensive agricultural exploitation and hog breeding along with industrial and civil developments. The influence of agriculture on groundwater results in a high nitrate pollution that limits its use for potable purposes.

Agriculture↗
PubMed2001

Inheritance of the black hackle of the Indian Game bantam.

1. An investigation was conducted among the progeny from crosses between pea-combed Indian Game and single combed double-laced Barnevelder bantams in an effort to determine the inheritance of the black hackle phenotype of the former. 2. The double-laced feather pattern phenotype of both breeds has been shown to depend upon homozygosity of both the linked eumelanin extension melanotic ML*M and the feather pattern arranging gene PG*P. However the hackles of the Indian Game are black, whilst those of the Barnevelder are partially striped, which suggests the presence of an extra eumelaniser in the genome of the Indian Game. This could not be due to variation at the extended black-E*-locus since the Indian Game and the Barnevelder have been shown respectively to depend upon the wheaten E*WH and brown E*B alleles; the former normally less heavily eumelanised. 3. A mating of a Barnevelder male with an Indian Game female produced 11 chicks, all of which were black in hackle. The mating of 2 F1 males with 5 Barnevelder females produced 35 chicks in the backcross to the double recessive, all of which were of parental phenotype. These comprised 18 peacomb, black in hackle and 17 single comb, partially striped hackle; classification being clear injuvenile plumage. 4. The absence of crossovers in the backcross suggest allelism or extremely close linkage between the loci of peacomb and the dominant eumelanin extension which causes the black in hackles. 5. The eumelanin extension isolated in this work appears therefore to be allelic to, if not a further manifestation of the well-established charcoal CHA*C gene.

Alleles↗
PubMed1976

Prenancy diagnosis in dairy cattle by progesterone concentration in milk.

Concentration of progesterone in whole milk was used to diagnose pregnancy in lactating dairy cows. Milk samples were taken 21 to 22 days postbreeding and analyzed for progesterone by radioimmunoassay. Progesterone in milk greater than 11 ng/ml, 8 to 11 ng/ml, and less than 8 ng/ml was used classify animals as pregnant, questionable, and not pregnant. In this classification for 123 cows, 67 were classified pregnant, 7 questionable, and 49 not pregnant. A comparison of progesterone diagnosis with actual calving results showed agreement of 73 and 98% for the cows classified as pregnant and not pregnant. Thirteen of 19 animals, in which there were discrepancies between diagnoses by milk progesterone and calving results, were not detected in estrus within 30 days after breeding. One animal classified not pregnant by milk progesterone was pregnant.

Animals↗
PubMed1999

The Tpv2 family of retrotransposons of Phaseolus vulgaris: structure, integration characteristics, and use for genotype classification.

The Tpv2 family of transposable elements of common bean, Phaseolus vulgaris, belongs to the Ty1/copia group of long terminal repeat (LTR) containing retrotransposons. By reverse transcriptase (RT)-PCR and by analysis of genomic clones, we characterized four of the approximately 40 copies present in the Phaseolus genome, and the genomic environment of their integration sites. Tpv2 integrated preferentially into actively transcribed regions. While none of the isolated elements had all the functional domains necessary for transposition, analysis of bean cultivars suggested that some members of the Tpv2 family transposed in recent breeding history. Probes derived from Tpv2, as well as flanking genomic sequences, may be useful for classifying Phaseolus cultivars.

Amino Acid Sequence↗
PubMed2002

Characterization of porcine endogenous retrovirus gamma pro-pol nucleotide sequences.

Endogenous retroviral sequences in the pig genome (PERV) represent a potential infectious risk in xenotransplantation. All known infectious PERV have been asssigned to the PERV gamma1 family, consisting of the subfamilies A, B, and C. The aim of the study was the concise examination of PERV gamma by the analysis of the retroviral pro-pol sequences. The analysis of 52 pro-pol clones amplified in this study revealed eight PERV gamma families. In addition to four already-described families (gamma1, gamma4, gamma5, gamma6), four novel families (gamma7, gamma8, gamma9, gamma10) were identified. Quantitative analysis of the novel PERV gamma sequences in selected breeds revealed variations in the endogenous retroviral load. Open reading frames (ORF) in the amplified proviral fragment were only found for PERV gamma1. In addition, novel ORF-containing PERV gamma1 clones consisting of hybrid sequences were revealed. Sequence comparison from published full-length PERV gamma1 clones of the PERV subfamilies A, B, and C resulted in a lack of strict correlation of the classification of pro-pol and env. The results indicated the occurrence of causative recombination events between retroviral genomes. Thus, our study on PERV gamma provides new data for the evaluation and selection of pigs intended to be used in xenotransplantation.

Animals↗
PubMed2004

Heritability and correlations for body condition score and dairy form within and across lactation and age.

The objectives of the current study were to investigate the relationship between body condition score (BCS) and dairy form and changes in genetic parameters for BCS and dairy form within and across lactations and age. Body condition score and dairy form were obtained from the Holstein Association USA, Inc. Records were edited to include those cows classified between 24 and 60 mo of age and between 0 and 335 d in milk (DIM). A minimum of 20 daughters per sire and 15 cows per herd-classification visit were required. The dataset consisted of 135,178 records from 119,215 cows. Repeatability, multiple trait, and random regression models were used to analyze the data. All models included fixed effects for herd-classification visit, age within lactations 1, 2, and 3 or higher, and 5th-order polynomials for DIM. Random effects included sire and permanent environment for all models. Random regression models included age at classification nested within sire or DIM and lactation number nested within sire. Genetic variance for both BCS and dairy form was lowest in early lactation and highest in midlactation. Genetic correlations within and across lactations were high. The genetic correlation between DIM 0 in lactation 1 and DIM 305 in lactation 3 was estimated to be 0.77 for BCS and 0.60 for dairy form. The genetic correlation estimate between 30 mo of age at classification and 50 mo of age at classification was 0.94 for both dairy form and BCS. The repeatability models appeared to generate accurate evaluations for BCS or dairy form at all ages and stages of lactation.

Aging↗
PubMed2005

Use of a remote sensing-based geographic information system in the characterizing spatial patterns for Anopheles minimus A and C breeding habitats in western Thailand.

A remote sensing (RS)-based Geographic Information System (GIS) was used to characterize the breeding habitats of Anopheles minimus species A and C in five different districts of Kanchanaburi Province in western Thailand. The GIS and RS were used to monitor the area for the presence and absence of An. minimus A and C in five major land areas, forest, agriculture, urban, water and bare land. The results show that An. minimus A survives both in dense canopy forest and in open fields where agriculture is dominant. A scatter plot of land-use/land-cover for An. minimus, considering proximities to the forest and proximities to agriculture, suggests that An. minimus A has a wider habitat preference, ranging from dense canopy forest to open agricultural fields. A scatter plot for An. minimus C, on the other hand, showed a narrow habitat preference. A scatter plot for proximities performed on separate populations of An. minimus species A, one in the north and the other in the south, showed that there was an association in the northern population with the forest and in the southern population with agricultural areas. There were no statistically significant differences in the scatter plot of proximities to urban areas and water bodies with the An. minimus A north, south, and An. minimus C. LANDSAT TM satellite data classification was used to identify larval habitats that produce An. minimus A and C and analyze proximities between land-use/land-cover classes and locations of larval habitats. An. minimus A has a wide habitat preference, from dense canopy forest to open agricultural fields, while An. minimus C has a narrow habitat preference.

Animals↗
PubMed2005

[The use of unsupervised classification of Landsat-5 TM images in analysing the types of vegetation in the areas of "breaking dikes or opening sluice for water store"].

OBJECTIVE: To clarify the change of vegetation types and its relationship between the density of alive-snails in the areas of "breaking dikes or opening sluice for water store" in Jicheng. METHODS: Synthesized false color images of Jicheng before and after 1998 (1994 and 2003) were classified without supervision and results were compared. Vegetation types were identified on the spot. RESULTS: Normalized difference vegetation index (NDVI) of snail habitats before 1998 were between 126 and 183 in Jicheng, whose vegetation types were mainly paddy, cotton and cabbage. NDVI of snail habitats in Jicheng after 1998 were between 152 and 193 whose vegetation types were mainly poplar forest, bulrush and grass. Areas of snail habitats increased from 64.64% to 66.47%. Snail habitats were mostly composed of mixed vegetation types and mono-typed vegetation was hardly found. According to the density of alive-snails orders from high to low were poplar forest and bulrush, poplar forest and grass, bulrush. CONCLUSION: Vegetation types would not be identified by unsupervised classification only. Poplar forest, bulrush and grass were closedly related to the density of alive-snails.

Animals↗
PubMed1995

[Possibilities of epidemiological studies via automated veterinary practice administration].

This study of the occurrence of tumours in dogs was carried out in order to see whether veterinary medical records can be used for epidemiological research. The relationship between tumour occurrence and breed, sex, and age was investigated by using the electronic tumourcards for 16049 dogs from three veterinary practices. Striking results include the difference in tumour occurrence between sprayed bitches (11.31%) and intact bitches (6.58%), and the high percentage of mongrels with a tumour (78.15%). Such unexpected results may be the result of selection processes underlying the composition of the population. Because these registers do not use a standard diagnostic classification system, it is difficult to identify all dogs with a specific diagnosis. This means that registers cannot be used for aetiological epidemiological research. However, they do contain valuable information for veterinary health care research and can be used as a source of cases for case-control studies, provided that a suitable mans of standardization is used.

Animals↗
PubMed2000

A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1.

Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more. The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice, which derives from the Indian cultivar FR13A. Submergence screening of 8-day-old plants of F3 families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes. Bulked segregant analysis was used to identify AFLP markers linked to Sub1. A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus, 2.4 and 4.9 cM away. Submergence tolerance was measured in the recombinant plants, and AFLP markers closely linked to Sub1 were mapped. Two AFLP markers cosegregated with Sub1 in this large population, and other markers were localized within 0.2 cM of Sub1. The high-resolution map should serve as the basis for map-based cloning of this important locus, as it will permit the identification of BAC clones spanning the region.

Chromosome Mapping↗