TUT DIGITAL OPEN REPOSITORY

Recent Submissions

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    A method to enhance web service clustering by integrating label-enhanced functional semantics and service collaboration.
    (IEEE, 2024-05-06) Liu, Qingxue; Wang, Lifang; Du, Shengzhi; Van Wyk, Barend Jacobus
    In Web service clustering, the service function vector (SFV) directly determines the quality of service (QoS) clustering. To improve service clustering performance, a method is proposed in this paper by integrating label-enhanced functional semantics and service collaboration. It improves the SFV from three aspects: generation model, corpus, and structural auxiliary information. At the generation model level, a Sentence-BERT is constructed based on singular value decomposition (SVD), to alleviate the anisotropy problem of BERT in vectorizing service descriptions. For corpus, the semantic features of SFV are supplemented by extracting specific named entities from service descriptions. Meanwhile, the service collaboration graph is established according to the collaboration relationship among Web services, which is conducive to the variational graph auto-encoders (VGAE) to realize service collaboration feature aggregation and further improve the SFV. Experiments show that the improved model, corpus and structural auxiliary information effectively enhance the SFV clustering. The proposed Web service clustering method is superior to the state-of-the-art methods.
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    Genetic diversity of South African indigenous goat population from four provinces using genome-wide SNP Data.
    (MDPI, 2020-11-27) Chokoe, Tlou Caswell; Mdladla-Hadebe, Khanyisile; Muchadeyi, Farai; Dzomba, Edgar; Matelele, Tlou; Mphahlele, Tumudi; Mpofu, Takalani J.; Nephawe, Khathutshelo; Mtileni, Bohani
    Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p < 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.
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    Effect of agro-ecological zone, season of birth and sex on pre-weaning performance of Nguni calves in Limpopo Province, South Africa.
    (Springer, 2016-11-04) Mpofu, T. J.; Ginindza, M. M.; Siwendu, N. A.; Nephawe, K. A.; Mtileni, B. J.
    The study was conducted to determine the effect of agro-ecological zone, season of birth and sex on Nguni calves’ pre-weaning performance. Production indices such as birth weight (BW), weaning weight (WW), pre-weaning average daily gain (P-ADG) and pre-weaning gain (P-WG) were assessed in the different agro-ecological zones. Herd records on performance of 826 Nguni calves’ from nine Nguni herds representing different agro-ecological zones: arid zone (n = 217); semi-arid zone (n = 296); dry sub-humid zone (n = 118) and humid zone (n = 195) were used for the analysis of pre-weaning calf performance. General linear model (GLM) procedure of SAS (2013) was used to analyse data, whereas mean separation was conducted using Tukey’s HSD test. Agro-ecological zone had a great influence (P < 0.01) on performance levels arising from pasture conditions which were dependent on rain, temperature, topography and soil type. Fluctuations in WW, P-ADG and P-WG performance across agro-ecological zones depicted the sensitivity of Nguni calves’ to postnatal stress. Calves’ in humid zone had higher performance with 121.21 kg for WW, 96.83 kg for PWG and 0.477 kg/day for P-ADG. The lowest WW (114.51 kg), P-WG (89.98 kg) and P-ADG (0.438 kg/day) were observed in arid zone. Male calves were heavier at weaning (128.18 kg), P-ADG (0.503 kg/day) and total gain (103.03 kg); however, similar BW of 25 kg was observed for both male and female calves. Season had a significant (P < 0.05) effect on BW, P-ADG and P-WG. The P-ADG was 0.461 kg/day for calves born in summer and 0.449 kg/day for calves born in winter season. Calves born in summer gained 94.69 kg and calves born in winter gained 92.10 kg. Summer calves gained 2.59 kg more than winter calves. Summer heifer calves performed poorly whilst summer male calves outperformed heifer calves in terms of WW, P-WG and P-ADG. Pre-weaned calves in humid zone outperformed all calves in other agro-ecological zones. It was concluded that acceptable levels of growth are achievable from Nguni cattle under the different agro-ecological zones of Limpopo province, South Africa.
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    Influence of male–male competition on reproductive performance and mortality of broiler breeders following intra-spiking.
    (Elsevier, 2019-05-02) Mphepya, Lesiba C.; Van Rensburg, Willie J.; Mpofu, Takalani J.; Mtileni, Bohani J.; Nephawe, Khathutshelo A.
    The study was conducted to determine the influence of male–male competition on reproductive performance and male mortality of Cobb 500 broiler breeder flocks following double intra-spiking. Broiler breeders were housed in 3 open-sided houses each accommodating 8,200 females and 820 males. Males of the same age on the same farm were exchanged between the houses (intra-spiking) to stimulate competition thereby changing the social hierarchy of each house. Intra-spiking was performed by replacing 25, 35, and 45% of males between the houses at 40 and 48 weeks of age (WOA), respectively. Eggs were collected from 36 to 55 WOA, when egg fertility and male mortality were recorded. Data was analyzed using repeated measures techniques of SAS 9.4, modeling the covariance structure of the observed data. Male–male competition (intra-spiking), age and their interaction significantly (P < 0.05) influenced egg fertility, hatchability, and male mortality. Average fertility and hatchability were increased in the 45% intra-spiked flocks (P < 0.05) (95.89 and 85.83%) compared with the 35% (95.13 and 86.30%) and 25% (94.42 and 0.23%) intra-spiked flocks. Fertility and hatchability with the 45% double intra-spiked flocks was consistently higher (P < 0.05) over time than the other double intra-spiked flocks. Male mortality was lower (P < 0.05) in the 45% intra-spiked flock (0.23%) than in the 35% (0.40%) and 25% (0.44%) intra-spiked flocks. After double intra-spiking, the male mortality in the 25 and 35% double intra-spiked flocks significantly increased (P < 0.05), whereas that of 45% intra-spiked flocks remained relatively low. Male mortality in the 45% intra-spiked flocks was consistently low over time than other double intra-spike levels from 45 WOA until the end of the trial. Noteworthy, egg fertility and hatchability gradually decreased, and mortality increased with increasing flock age toward the end of the productive life cycle. High level of male–male competition (45%) showed great promise as a tool to slow down the decrease in egg fertility and hatchability, and reduce male mortality in aging broiler breeder flocks.
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    Pedigree-based genetic diversity in the South African boerboel dog breed.
    (MDPI, 2024-03-14) Mabunda, Ripfumelo Success; Nephawe, Khathutshelo Agree; Mtileni, Bohani; Makgahlela, Mahlako Linah
    The Boerboel dog breed (BBD) is indigenous to South Africa (SA) and plays an important role in safeguarding homes and farms. The Department of Agriculture, Land Reform, and Rural Development (DALRRD) classifies the BBD as a protected species, and it is valued for its intelligence, boldness, and strength, as well as for continually ensuring the safety of its owners. The aim of this study was to investigate genetic diversity within the BBD population using pedigree information. The original BBD data, which contained 87,808 records, were obtained from the Integrated Registration and Genetic Information System (INTERGIS). After editing, the pedigree data included 87,755 records of animals born between 1971 and 2019. Pedigree analyses were performed using PEDIG (Fortran 77 software) to determine the completeness, inbreeding coefficients, and genetic diversity as defined by the genetic contributions of the most important ancestors of the current animals. This study identified 91.2% inbred animals in the BBD population, with an average and maximum inbreeding of 7.5% and 50% of inbred animals, respectively. The estimated inbreeding rate per year was 0.20% with an effective population size of 83.1. The most influential ancestors explained 82.63% and 80.92% of the total genetic variation for males and females in the studied populations, respectively. Only 10 important ancestors explained more than 50% of the entire population’s genetic diversity. The numbers of founders (f) were 348 and 356, and the effective numbers of founders (fe) were 57.4 and 60.1, respectively, for males and females. The numbers of founders were higher than the effective numbers of founders, implying a loss of genetic diversity due to unequal founder contributions. The BBD population was not critically endangered based on the inbreeding rates and effective population size; however, the population experienced a significant loss of genetic variability, unequal genetic contributions by founders, and a genetic bottleneck. Future breeding strategies could benefit from using equal proportions of parent stock and including new genetically distant breeds.