The effect of sainfoin (Onobrychis viciifolia) and carob pods (Ceratonia siliqua) feeding regimes on the control of lamb coccidiosis.

Recent research has suggested that plants containing condensed tannins may offer a promising alternative approach for the control of coccidiosis in lambs and goat kids. The present study aimed to examine the potential effect of condensed tannins in sainfoin (Onobrychis viciifolia) and carob pods (Ceratonia siliqua) incorporated in sheep rations against lamb coccidiosis. The above tannin-rich sources were studied in three independent feeding trials in which the animals (naturally infected by Eimeria spp. ewes and their lambs) were allocated (i) in the control group and received a tannin-free diet (lucerne hay), or (ii) in the treatment groups and received a tannin-rich diet based on sainfoin hay (in trials 1 and 2), or in carob pod meal and a combination of carob pod meal and sainfoin hay (in trial 3). In total, 95 newborn lambs (and their 73 ewes) were enrolled in all trials which started a month before lambing and ended 8-10 weeks after lambs were born (at weaning). The course of coccidial infection was monitored in lambs by faecal oocyst counts and consistencies which were recorded at weekly intervals. Moreover, lambs total weight gain was evaluated at the end of each trial. During all trials, 100 % of the animals got naturally infected by Eimeria species and the infection burden was higher in trials 2 and 3 compared to trial 1 but in all cases, severe signs of diarrhoea were not observed. Tannin-rich diets were well accepted by the animals not affecting their feed intake and body weight gain when compared to the controls. The results suggest that incorporation of both tannin-rich resources (especially sainfoin) in sheep rations can reduce Eimeria oocyst excretion rates by the lambs, which can decrease subsequently the contamination of the farm environment with the parasite. However, the high variability noted on the results is not allowing us to draw any definite conclusions at least until the potential of those plants is further investigated.

Chromatin integrity of ram spermatozoa. Relationships to annual fluctuations of scrotal surface temperature and temperature-humidity index.

The objective of the present study was to explore the potential relationships of ovine sperm chromatin integrity, quantified using the sperm chromatin structure assay (SCSA), to the heat load of the scrotum and the discomfort felt by the animals because of fluctuations of microclimatic factors at different time periods before ejaculation. Ejaculates were collected once per week from five Chios rams and four East Friesian rams for 12 months and stored in liquid nitrogen. Frozen-thawed semen samples were analyzed using the SCSA, to determine the DNA fragmentation index (DFI) and the percentage of cells outside the main sperm population (%DFI) in each one of the samples. Scrotal surface temperature (SST) of each ram was measured using an infrared thermometer on a daily basis. Ambient air temperature and relative humidity were recorded at hourly intervals throughout the experimental period and temperature-humidity index (THI) was used to assess the discomfort felt by the rams. Mean values of SST (SST mean) and THI (THI mean) were computed for eight different time periods (up to 61 days) preceding each ejaculation day (Day 0). A linear mixed-effect model analysis was performed to describe the relation of SCSA parameters to collection month, SST mean, and THI mean of different time periods before ejaculation. The results of the statistical analysis revealed a relation of %DFI to the SST mean of the last 12 days preceding ejaculation, namely the period that resembled the phase of epididymal maturation. On the contrary, the variation of DFI was most adequately described by the linear mixed-effect model applied for Days 54 to 48 before ejaculation, which resembled the phase of spermatogonial mitoses. The effect of collection month was significant for DFI and %DFI, with semen samples collected in September and February exhibiting the lowest DFI values; a less profound seasonal pattern was detected for %DFI. The effect of THI mean on DFI and %DFI was proven nonsignificant in regard to all time periods. In conclusion, a relation of SCSA parameters to SST mean of different periods before ejaculation was shown in the present study, implying an effect of scrotal microenvironment on intratesticular and epididymal sperm population. In contrast, we failed to detect any effect of microclimate-induced discomfort felt by the animals on the chromatin integrity of frozen-thawed ram spermatozoa.

MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

MOTIVATION: PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or productively utilized. The motivation behind this work was the discovery of unanticipated information through the appropriate ranking of MeSH term pairs and, indirectly, documents. Such information can be useful in guiding novel research and following promising trends. METHODS: A web-based tool, called MeSHy, was developed implementing a mainly statistical algorithm. The algorithm takes into account the frequencies of occurrences, concurrences, and the semantic similarities of MeSH terms in retrieved PubMed documents to create MeSH term pairs. These are then scored and ranked, focusing on their unexpectedly frequent or infrequent occurrences. RESULTS: MeSHy presents results through an online interactive interface facilitating further manipulation through filtering and sorting. The results themselves include the MeSH term pairs, along with MeSH categories, the score, and document IDs, all of which are hyperlinked for convenience. To highlight the applicability of the tool, we report the findings of an expert in the pharmacology field on querying the molecularly-targeted drug imatinib and nutrition-related flavonoids. To the best of our knowledge, MeSHy is the first publicly available tool able to directly provide such a different perspective on the complex nature of published work. IMPLEMENTATION AND AVAILABILITY: Implemented in Perl and served by Apache2 at http://bat.ina.certh.gr/tools/meshy/ with all major browsers supported.

PuReD-MCL: a graph-based PubMed document clustering methodology.

MOTIVATION: Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organizing and analyzing such textual knowledge. There are numerous efforts that attempt to exploit this information by using text mining and machine learning techniques. We developed a novel approach, called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL and relevant resources from PubMed. METHODS: PuReD-MCL avoids using natural language processing (NLP) techniques directly; instead, it takes advantage of existing resources, available from PubMed. PuReD-MCL then clusters documents efficiently using the MCL graph clustering algorithm, which is based on graph flow simulation. This process allows users to analyse the results by highlighting important clues, and finally to visualize the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express 3D. RESULTS: The methodology was applied to two different datasets, previously used for the validation of the document clustering tool TextQuest. The first dataset involves the organisms Escherichia coli and yeast, whereas the second is related to Drosophila development. PuReD-MCL successfully reproduces the annotated results obtained from TextQuest, while at the same time provides additional insights into the clusters and the corresponding documents. AVAILABILITY: Source code in perl and R are available from http://tartara.csd.auth.gr/~theodos/

Gene functional annotation by statistical analysis of biomedical articles.

BACKGROUND: Functional annotation of genes is an important task in biology since it facilitates the characterization of genes relationships and the understanding of biochemical pathways. The various gene functions can be described by standardized and structured vocabularies, called bio-ontologies. The assignment of bio-ontology terms to genes is carried out by means of applying certain methods to datasets extracted from biomedical articles. These methods originate from data mining and machine learning and include maximum entropy or support vector machines (SVM). PURPOSE: The aim of this paper is to propose an alternative to the existing methods for functionally annotating genes. The methodology involves building of classification models, validation and graphical representations of the results and reduction of the dimensions of the dataset. METHODS: Classification models are constructed by Linear discriminant analysis (LDA). The validation of the models is based on statistical analysis and interpretation of the results involving techniques like hold-out samples, test datasets and metrics like confusion matrix, accuracy, recall, precision and F-measure. Graphical representations, such as boxplots, Andrew's curves and scatterplots of the variables resulting from the classification models are also used for validating and interpreting the results. RESULTS: The proposed methodology was applied to a dataset extracted from biomedical articles for 12 Gene Ontology terms. The validation of the LDA models and the comparison with the SVM show that LDA (mean F-measure 75.4%) outperforms the SVM (mean F-measure 68.7%) for the specific data. CONCLUSION: The application of certain statistical methods can be beneficial for functional gene annotation from biomedical articles. Apart from the good performance the results can be interpreted and give insight of the bio-text data structure.

Protein sequences of linked genes are highly conserved in two bacterial species.

It has been shown that proteins encoded by linked genes have similar rates of evolution and that clusters of essential genes are found in regions with low recombination rates. We show here that proteins encoded by linked genes in two closely related bacterial species, namely Escherichia coli K12 and Salmonella typhimurium LT2, evolve more slowly when compared with proteins encoded by genes that are not linked as assessed by protein sequence similarity. The proteins encoded by the identified linked genes share an average sequence identity of 82.5% compared with a 46.5% identity of proteins encoded by genes that are not linked.