The Effect of Dietary Supplementation with Spent Cider Yeast on the Swine Distal Gut Microbiome

peer-reviewedBackground: There is an increasing need for alternatives to antibiotics for promoting animal health, given the increasing problems associated with antibiotic resistance. In this regard, we evaluated spent cider yeast as a potential probiotic for modifying the gut microbiota in weanling pigs using pyrosequencing of 16S rRNA gene libraries. Methodology and Principal Findings: Piglets aged 24–26 days were assigned to one of two study groups; control (n = 12) and treatment (n = 12). The control animals were fed with a basal diet and the treatment animals were fed with basal diet in combination with cider yeast supplement (500 ml cider yeast containing ,7.6 log CFU/ml) for 21 days. Faecal samples were collected for 16s rRNA gene compositional analysis. 16S rRNA compositional sequencing analysis of the faecal samples collected from day 0 and day 21 revealed marked differences in microbial diversity at both the phylum and genus levels between the control and treatment groups. This analysis confirmed that levels of Salmonella and Escherichia were significantly decreased in the treatment group, compared with the control (P,0.001). This data suggest a positive influence of dietary supplementation with live cider yeast on the microbial diversity of the pig distal gut. Conclusions/Significance: The effect of dietary cider yeast on porcine gut microbial communities was characterized for the first time using 16S rRNA gene compositional sequencing. Dietary cider yeast can potentially alter the gut microbiota, however such changes depend on their endogenous microbiota that causes a divergence in relative response to that given diet.This work was funded by Enterprise Ireland, under the Commercialisation Fund (Contract No: CFTD/05/117), the Irish Government under the National Development Plan, 2000–2006, the European Research and Development Fund and Science Foundation Ireland (SFI).European Research and Development Fun

Transportation and Marketing Efficiency in the California Processing Tomato Industry

Agribusiness, Marketing,

Intelligent phishing detection parameter framework for E-banking transactions based on Neuro-fuzzy

Phishing attacks have become more sophisticated in web-based transactions. As a result, various solutions have been developed to tackle the problem. Such solutions including feature-based and blacklist-based approaches applying machine learning algorithms. However, there is still a lack of accuracy and real-time solution. Most machine learning algorithms are parameter driven, but the parameters are difficult to tune to a desirable output. In line with Jiang and Ma’s findings, this study presents a parameter tuning framework, using Neuron-fuzzy system with comprehensive features in order to maximize systems performance. The neuron-fuzzy system was chosen because it has ability to generate fuzzy rules by given features and to learn new features. Extensive experiments were conducted, using different feature-sets, two cross-validation methods, a hybrid method and different parameters and achieved 98.4% accuracy. Our results demonstrated a high performance compared to other results in the field. As a contribution, we introduced a novel parameter tuning framework based on a neuron-fuzzy with six feature-sets and identified different numbers of membership functions different number of epochs, different sizes of feature-sets on a single platform. Parameter tuning based on neuron-fuzzy system with comprehensive features can enhance system performance in real-time. The outcome will provide guidance to the researchers who are using similar techniques in the field. It will decrease difficulties and increase confidence in the process of tuning parameters on a given problem

Evaluating a transfer gradient assumption in a fomite-mediated microbial transmission model using an experimental and Bayesian approach

Current microbial exposure models assume that microbial exchange follows a concentration gradient during hand-to-surface contacts. Our objectives were to evaluate this assumption using transfer efficiency experiments and to evaluate a model's ability to explain concentration changes using approximate Bayesian computation (ABC) on these experimental data. Experiments were conducted with two phages (MS2,; Φ; X174) simultaneously to study bidirectional transfer. Concentrations on the fingertip and surface were quantified before and after fingertip-to-surface contacts. Prior distributions for surface and fingertip swabbing efficiencies and transfer efficiency were used to estimate concentrations on the fingertip and surface post contact. To inform posterior distributions, Euclidean distances were calculated for predicted detectable concentrations (log; 10; PFU cm; -2; ) on the fingertip and surface post contact in comparison with experimental values. To demonstrate the usefulness of posterior distributions in calibrated model applications, posterior transfer efficiencies were used to estimate rotavirus infection risks for a fingertip-to-surface and subsequent fingertip-to-mouth contact. Experimental findings supported the transfer gradient assumption. Through ABC, the model explained concentration changes more consistently when concentrations on the fingertip and surface were similar. Future studies evaluating microbial transfer should consider accounting for differing fingertip-to-surface and surface-to-fingertip transfer efficiencies and extend this work for other microbial types

Reduced Kidney Function is Associated with Poorer Domain‐Specific Cognitive Performance in Community‐Dwelling Older Adults

OBJECTIVES: Whilst chronic kidney disease has been associated with cognitive impairment, the association between reduced estimated Glomerular Filtration Rate (eGFR) and domain‐specific cognitive performance is less clear and may represent an important target for the promotion of optimal brain health in older adults. METHODS: Participants aged >60 years from the Trinity‐Ulster‐Department of Agriculture study underwent detailed cognitive assessment using the Mini‐Mental State Examination (Mini‐Mental State Examination (MMSE)), Frontal Assessment Battery (FAB) and Repeatable Battery for Assessment of Neuropsychological Status (RBANS). Poisson and linear regression models assessed the relationship between eGFR strata and cognitive performance. RESULTS: In 4887 older adults (73.9 ± 8.3 years; 67.7% female), declining eGFR strata was associated with greater likelihood of error on the MMSE/FAB and poorer overall performance on the RBANS. Following robust covariate adjustment, findings were greatest for GFR 80 years. CONCLUSIONS: Reduced kidney function was associated with poorer global and domain‐specific neuropsychological performance. Associations were strongest with eGFR <45 ml/min/1.73 m(2) and in those aged 60–70 years, suggesting that this population may potentially benefit from potential multi‐domain interventions aimed at promoting optimal brain health in older adults

Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms

Background: Organoids are 3-dimensional experimental models that summarize the anatomical and functional structure of an organ. Although a promising experimental model for precision medicine, patient-derived tumor organoids (PDTOs) have currently been developed only for a fraction of tumor types. Results: We have generated the first multi-omic dataset (whole-genome sequencing [WGS] and RNA-sequencing [RNA-seq]) of PDTOs from the rare and understudied pulmonary neuroendocrine tumors (n = 12; 6 grade 1, 6 grade 2) and provide data from other rare neuroendocrine neoplasms: small intestine (ileal) neuroendocrine tumors (n = 6; 2 grade 1 and 4 grade 2) and large-cell neuroendocrine carcinoma (n = 5; 1 pancreatic and 4 pulmonary). This dataset includes a matched sample from the parental sample (primary tumor or metastasis) for a majority of samples (21/23) and longitudinal sampling of the PDTOs (1 to 2 time points), for a total of n = 47 RNA-seq and n = 33 WGS. We here provide quality control for each technique and the raw and processed data as well as all scripts for genomic analyses to ensure an optimal reuse of the data. In addition, we report gene expression data and somatic small variant calls and describe how they were generated, in particular how we used WGS somatic calls to train a random forest classifier to detect variants in tumor-only RNA-seq. We also report all histopathological images used for medical diagnosis: hematoxylin and eosin–stained slides, brightfield images, and immunohistochemistry images of protein markers of clinical relevance. Conclusions: This dataset will be critical to future studies relying on this PDTO biobank, such as drug screens for novel therapies and experiments investigating the mechanisms of carcinogenesis in these understudied diseases

Methicillin-resistant Staphylococcus aureus carriage in a long-term care facility: hypothesis about selection and transmission

Background: many studies have identified long-term care facilities (LTCFs) as reservoirs of patients carrying methicillin-resistant Staphylococcus aureus (MRSA). However, few data about the mechanisms of MRSA diffusion in these settings are available.Objectives: the purpose of our study was to suggest hypothesis on the possible ways of MRSA transmission to residents in or outside a LTCF. Methods: data concerning patients on the day of the survey and within the preceding year were collected. Multivariate analysis was performed by logistic regression to identify characteristics associated with MRSA carriage. MRSA strains were analysed by pulsed-field gel electrophoresis (PFGE) and the relatedness between DNA patterns was studied with Gel Compar software. Results: the prevalence of MRSA carriage was 37.6%. Treatment with fluoroquinolones or third-generation cephalosporins [odds ratio (OR) = 12.07; 95% confidence interval (CI) = 5.90–24.7], treatment with other antimicrobial agents (OR = 4.40; 95% CI = 2.43–7.97), at least one medical imaging session (OR = 5.08; 95% CI = 2.66–9.69) within the 12 preceding months, and the presence of a subcutaneous catheter on the day of the survey (OR = 3.09; 95% CI = 1.87–5.10) were independently associated with MRSA carriage. Twenty-eight of the 38 strains tested were clustered in two major groups. In each of these groups, strains had at least a 90% relatedness. These strains were isolated in patients hospitalised in different areas of the LTCF. Conclusion: we identified that both molecular and epidemiological arguments support the hypothesis of the possibility of MRSA cross-transmission inside the LTCF. Further studies are needed to confirm and explain the association identified between MRSA carriage and medical imaging

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t