Potts model for haplotype associations

Bayesian spatial modeling has become important in disease mapping and has also been suggested as a useful tool in genetic fine mapping. We have implemented the Potts model and applied it to the Genetic Analysis Workshop 14 (GAW14) simulated data. Because the "answers" were known we have analyzed latent phenotype P1-related observed phenotypes affection status (genetically determined) and i (random) in the Danacaa population replicate 2. Analysis of the microsatellite/single-nucleotide polymorphism-based haplotypes at chromosomes 1 and 3 failed to identify multiple clusters of haplotype effects. However, the analysis of separately simulated data with postulated differences in the effects of the two clusters has yielded clear estimated division into the two clusters, demonstrating the correctness of the algorithm. Although we could not clearly identify the disease-related and the non-associated groups of haplotypes, results of both GAW14 and our own simulation encourage us to improve the efficiency and sensitivity of the estimation algorithm and to further compare the proposed method with more traditional methods

The effects of simultaneous large acidic and alkaline airborne pollutants on forest soil

http://www.elsevier.com/locate/issn/02697491The effects of air pollutants on soil were studied in Scots pine (Pinus sylvestris L.) forests near the boundary of Russia and Estonia. The study area is characterized by large amounts of acidic and basic pollutants, mainly sulphur dioxide (SO*) and calcium (Ca) . Several variables were measured in different horizons of the podzolic soil polluted by emissions from local sources in areas of several thousands of square kilometres. Alkalinization dominates the processes in the soil, since sulphur is absorbed only in small quantities and Ca is much better absorbed. Ca content in humus horizon may rise even to 100 000 mg kg-’ and the pH of originally very acidic soil may rise to 8.3. Total aluminum (Al) content was high in the heavily polluted plots, since emissions contain much Al. On the other hand, the exchangeable Al was very low in these alkaline sites. A larger quantity of exchangeable Al occurred farther from the pollutant sources, even though total Al in these plots was low. These plots had acidic soils in which Al is in exchangeable form. Due to the neutralizing effect of acidic and basic pollutants, forest damage in the study area was not as serious as might be supposed, Complicated pollutant situations must be taken into consideration when pollution-caused environmental protection measures are planned. It is not reasonable to reduce only SO2 emissions, but necessary to lower the basic emissions at the same time

Awareness and practice of patient's rights law in Lithuania

BACKGROUND: Patient's rights law is intended to secure good medical practice, but it can also serve to improve understanding between patients and medical staff if both were aware of their rights. METHODS: Awareness and practice of the new patient's rights law in Lithuanian health care institutions was explored through a survey of 255 medical staff and 451 patients in the four Kaunas city medical units in 2002. Participation rates were 74% and 66%, respectively. RESULTS: Majority of the medical staff (85%) and little over one half of the patients (56%) had heard or read about the Law on Patient's Rights (p < 0.001). Only 50% of professionals compared to 69% of patients thought information for patients about diagnosis, treatment results and alternative treatments is necessary (p < 0.001). A clear discrepancy was indicated between physicians informing the patients (80% – 98% of physicians) and patients actually knowing (37% – 54%) their treatment prognosis, disease complications or possible alternative treatment methods. CONCLUSION: These results suggest a need for awareness-raising among patients to improve the practical implementation of the Patient's Rights Law in Lithuania

Comparison of Finnish meat inspection records and average daily gain for cattle herds differing in Mycoplasma bovis test-status

Detecting Mycoplasma bovis on cattle farms represents a challenge in the absence of an outbreak or cases of M. bovis mastitis, yet identification of an infection is essential to control the spread of the disease successfully. The objectives of this study were: (1) to determine whether meat inspection records can aid identification of cattle farms supporting M. bovis infection, and (2) to compare the average daily weight gain estimated from carcass weight for cattle originating from farms differing in M. bovis test-status. Meat inspection records were collected from two abattoirs in 2015; 80 677 animals in total. All the dairy and mixed breed cows and bulls used for meat production were categorized according to known M. bovis infection status of the farms from which the cattle were derived; positive, contact or control farms. The associations between animals from different M. bovis categories and lung lesions of bulls and cows (pneumonia and pleuritis), identified during meat inspection, and estimated average daily gain (ADG) of bulls, were investigated. The odds ratios for lung lesions, especially pleuritis, were higher in M. bovis test-positive or contact farms compared with control farms. Additionally, odds ratios for pleuritis were higher among animals from M. bovis test-positive farms and animals from contact slaughtering farms originating from M. bovis-free rearing farms. Bulls originating from M. bovis test-positive farms had higher estimated average daily gain than cattle from control farms. Meat inspection records can be used alongside other methods to detect M. bovis-positive farms where M. bovis causes lung lesions. (C) 2019 The Authors. Published by Elsevier Ltd.Peer reviewe

Characterisation of the course of Mycoplasma bovis infection in naturally infected dairy herds

Mycoplasma bovis causes bovine respiratory disease, mastitis, arthritis and otitis. The importance of M. bovis has escalated because of recent outbreaks and introductions into countries previously free of M. bovis. We characterized the course of M. bovis infection on 19 recently infected dairy farms over 24 months. Our objective was to identify diagnostic tools to assess the efficacy of control measures to assess low risk infection status on M. bovis infected farms. PCR assays and culture were used to detect M. bovis, and in-house and BioX ELISAs were used to follow antibody responses. Cows and young stock were sampled on four separate occasions, and clinical cases were sampled when they arose. On 17 farms, a few cases of clinical mastitis were detected, mostly within the first eight weeks after the index case. Antibodies detected by in-house ELISA persisted in the serum of cows at least for 1.5 years on all farms, regardless of the M. bovis infection status or signs of clinical disease or subclinical mastitis on the farm. Six out of 19 farms became low risk as the infection was resolved. Our results suggest that, for biosecurity purposes, regular monitoring should be conducted on herds by screening for M. bovis in samples from cows with clinical mastitis and calves with pneumonia, in conjunction with testing young stock by screening longitudinally collected nasal swabs for M. bovis and sequential serum samples for antibody against recombinant antigen.Peer reviewe

Decline after immobilisation and recovery after remobilisation of synovial fluid IL1, TIMP, and chondroitin sulphate levels in young beagle dogs

OBJECTIVE: To monitor the concentration of markers of cartilage and synovium metabolism in the knee (stifle) joint synovial fluid of young beagles subjected to immobilisation and subsequent remobilisation.METHODS: The right hind limb of 17 dogs was immobilised in flexion for 11 weeks. Simultaneously, the contralateral left knee was exposed to increased weight bearing. The remobilisation period lasted 50 weeks. Litter mates served as controls. The concentration in joint lavage fluid of interleukin 1 (IL1) was measured by immunoassay, the activity of phospholipase A2 (PLA2) was determined by an extraction method, chondroitin sulphate (CS) concentration by precipitation with Alcian blue, hyaluronan (HA) by an ELISA-like assay using biotinylated HA-binding complexes, matrix metalloproteinase 3 (MMP-3), and tissue inhibitor of metalloproteinases 1 (TIMP-1) by sandwich ELISA, and synovitis was scored by light microscopy.RESULTS: Synovitis or effusion was absent in all experimental and control groups. Immobilisation decreased the joint lavage fluid levels of IL1 (p<0.05), TIMP (p< 0.05), and the concentration of CS down to 38 (p<0.05) in comparison with untreated litter mates with normal weight bearing. Immobilisation did not affect the activity of PLA2, or the concentration of MMP-3 or HA in synovial fluid. Joint remobilisation restored the decreased concentrations of markers to control levels. Increased weight bearing did not change the concentrations of markers in comparison with the control joints with normal weight bearing.CONCLUSIONS: 11 weeks joint immobilisation decreased the concentration of markers of cartilage and synovium metabolism in the synovial fluid, and remobilisation restored the concentrations to control levels. The changes in joint metabolism induced by immobilisation, as reflected by the markers, are thus different from those found in osteoarthritis, where increased levels of these markers are associated with enhanced degradation and synthesis. These findings suggest that the change induced in joint metabolism by immobilisation is reversible in its early stages

Association between serum keptin concentrations and insulin resistance: A population-based study from China

BACKGROUND Insulin resistance contributes to the cardio-metabolic risk. The effect of leptin in obese and overweight population on insulin resistance was seldom reported. METHODS A total of 1234 subjects (572 men and 662 women) aged ≥18 y was sampled by the procedure. Adiposity measures included BMI, waist circumference, hip circumference, WHR, upper arm circumference, triceps skinfold and body fat percentage. Serum leptin concentrations were measured by an ELISA method. The homeostasis model (HOMA-IR) was applied to estimate insulin resistance. RESULTS In men, BMI was the variable which was most strongly correlated with leptin, whereas triceps skinfold was most sensitive for women. More importantly, serum leptin levels among insulin resistant subjects were almost double compared to the subjects who had normal insulin sensitivity at the same level of adiposity in both men and women, after controlling for potential confounders. In addition, HOMA-IR increased significantly across leptin quintiles after adjustment for age, BMI, total energy intake, physical activity and smoking status in both men and women (p for trend <0.0001). CONCLUSIONS There was a significant association between HOMA-IR and serum leptin concentrations in Chinese men and women, independently of adiposity levels. This may suggest that serum leptin concentration is an important predictor of insulin resistance and other metabolic risks irrespective of obesity levels. Furthermore, leptin levels may be used to identify the cardio-metabolic risk in obese and overweight population.Hui Zuo, Zumin Shi, Baojun Yuan, Yue Dai, Gaolin Wu, Akhtar Hussai

Optimization of xylanase production by filamentous fungi in solid state fermentation and scale-up to horizontal tube bioreactor

Five microorganisms, namely Aspergillus niger CECT 2700, A. niger CECT 2915, A. niger CECT 2088, Aspergillus terreus CECT 2808, and Rhizopus stolonifer CECT 2344, were grown on corncob to produce cell wall polysaccharide-degrading enzymes, mainly xylanases, by solid-state fermentation (SSF). A. niger CECT 2700 produced the highest amount of xylanases of 504±7 U/g dry corncob (dcc) after 3 days of fermentation. The optimization of the culture broth (5.0 g/L NaNO3, 1.3 g/L (NH4)2SO4, 4.5 g/L KH2PO4, and 3 g/L yeast extract) and operational conditions (5 g of bed loading, using an initial substrate to moistening medium of 1:3.6 (w/v)) allowed increasing the predicted maximal xylanase activity up to 2,452.7 U/g dcc. However, different pretreatments of materials, including destarching, autoclaving, microwave, and alkaline treatments, were detrimental. Finally, the process was successfully established in a laboratory-scale horizontal tube biore- actor, achieving the highest xylanase activity (2,926 U/g dcc) at a flow rate of 0.2 L/min. The result showed an overall 5.8-fold increase in xylanase activity after optimization of culture media, operational conditions, and scale-up.We are grateful to the Spanish Ministry of Science and Innovation for the financial support of this work (project CTQ2011-28967), which has partial financial support from the FEDER funds of the European Union; to the Leonardo da Vinci Programme for founding the stay of Felisbela Oliveira in Vigo University; to MAEC-AECID (Spanish Government) for the financial support for Perez-Bibbins, B. and to Spanish Ministry of Education, Culture and Sports for Perez-Rodriguez's FPU; and to Solla E. and Mendez J. (CACTI-University of Vigo) for their excellent technical assistance in microscopy

Ice structures, patterns, and processes: A view across the ice-fields

We look ahead from the frontiers of research on ice dynamics in its broadest sense; on the structures of ice, the patterns or morphologies it may assume, and the physical and chemical processes in which it is involved. We highlight open questions in the various fields of ice research in nature; ranging from terrestrial and oceanic ice on Earth, to ice in the atmosphere, to ice on other solar system bodies and in interstellar space