A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications

Over the years, ad-hoc procedures were used for designing SNP arrays, but the procedures and strategies varied considerably case by case. Recently, a multiple-objective, local optimization (MOLO) algorithm was proposed to select SNPs for SNP arrays, which maximizes the adjusted SNP information (E score) under multiple constraints, e.g. on MAF, uniformness of SNP locations (U score), the inclusion of obligatory SNPs and the number and size of gaps. In the MOLO, each chromosome is split into equally spaced segments and local optima are selected as the SNPs having the highest adjusted E score within each segment, conditional on the presence of obligatory SNPs. The computation of the adjusted E score, however, is empirical, and it does not scale well between the uniformness of SNP locations and SNP informativeness. In addition, the MOLO objective function does not accommodate the selection of uniformly distributed SNPs. In the present study, we proposed a unified local function for optimally selecting SNPs, as an amendment to the MOLO algorithm. This new local function takes scalable weights between the uniformness and informativeness of SNPs, which allows the selection of SNPs under varied scenarios. The results showed that the weighting between the U and the E scores led to a higher imputation concordance rate than the U score or E score alone. The results from the evaluation of six commercial bovine SNP chips further confirmed this conclusion.

Cardiac sympathetic denervation and synucleinopathy in Alzheimer's disease with brain Lewy body disease

Comorbid Lewy body pathology is very common in Alzheimer’s disease and may confound clinical trial design, yet there is no in vivo test to identify patients with this. Tissue (and/or radioligand imaging) studies have shown cardiac sympathetic denervation in Parkinson’s disease and dementia with Lewy bodies, but this has not been explored in Alzheimer’s subjects with Lewy bodies not meeting dementia with Lewy bodies clinicopathological criteria. To determine if Alzheimer’s disease with Lewy bodies subjects show sympathetic cardiac denervation, we analysed epicardial and myocardial tissue from autopsy-confirmed cases using tyrosine hydroxylase and neurofilament immunostaining. Comparison of tyrosine hydroxylase fibre density in 19 subjects with Alzheimer’s disease/dementia with Lewy bodies, 20 Alzheimer’s disease with Lewy bodies, 12 Alzheimer’s disease subjects without Lewy body disease, 19 Parkinson’s disease, 30 incidental Lewy body disease and 22 cognitively normal without Alzheimer’s disease or Lewy body disease indicated a significant group difference (P < 0.01; Kruskal–Wallis analysis of variance) and subsequent pair-wise Mann–Whitney U tests showed that Parkinson’s disease (P < 0.05) and Alzheimer’s disease/dementia with Lewy bodies (P < 0.01) subjects, but not Alzheimer’s disease with Lewy bodies subjects, had significantly reduced tyrosine hydroxylase fibre density as compared with cognitively normal. Both Parkinson’s disease and Alzheimer’s disease/dementia with Lewy bodies subjects also showed significant epicardial losses of neurofilament protein-immunoreactive nerve fibre densities within the fibre bundles as compared with cognitively normal subjects (P < 0.01) and both groups showed high pathologic alpha-synuclein densities (P < 0.0001). Cardiac alpha-synuclein densities correlated significantly with brain alpha-synuclein (P < 0.001), while cardiac tyrosine hydroxylase and neurofilament immunoreactive nerve fibre densities were negatively correlated with the densities of both brain and cardiac alpha-synuclein, as well as Unified Parkinson’s Disease Rating Scale scores (P < 0.05). The clear separation of Alzheimer’s disease/dementia with Lewy bodies subjects from Alzheimer’s disease and cognitively normal, based on cardiac tyrosine hydroxylase fibre density, is the first report of a statistically significant difference between these groups. Our data do not show significant sympathetic cardiac denervation in Alzheimer’s disease with Lewy bodies, but strongly confirm that cardiac nuclear imaging with a noradrenergic radioligand is worthy of further study as a potential means to separate Alzheimer’s disease from Alzheimer’s disease/dementia with Lewy bodies during life.

Prevalence of REM sleep behavior disorder in Sun City, Arizona

Objective

To determine prevalence of REM sleep behavior disorder (RBD) [prodromal Lewy body disease] in Sun City, Arizona.

Patients and methods

We attempted, by telephone and mail, a survey using the RBD single item question for probable RBD (pRBD) and the Innsbruck RBD Inventory. Individuals answering “yes” to 4/5 Inventory questions were considered to have high likelihood RBD (HL-RBD.)

Results

Response rate was 484/3000 individuals contacted (16%), mean age 78; 48 (9.9%) endorsed pRBD by RBD1Q; 16 (3.3%) had HL-pRBD. Prevalence of idiopathic cases (without neurodegenerative disease) was 8.8% pRBD and 2.8% HL-RBD.

Conclusion

Our estimated definite RBD prevalence of 1.7% (61.3% of HL-RBD) was similar to previous community-based studies.

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

Cross-sectional survey of pet ownership, veterinary service utilisation, and pet-related expenditures in New Zealand

Aims: To describe the demographics of and predictors for pet ownership, reasons for visiting a veterinarian, and pet-related expenditure in pet owners in New Zealand. Methods: A cross-sectional online survey was conducted from 18-22 June 2015 using a permission-based panel of New Zealand residents aged ≥18 years. Questions included demographics of respondents, number of pets and reasons for owning or not owning pets, number of visits and reasons for visiting a veterinarian, and pet-related expenditure. Results: Of the 1,572 respondents who completed the survey, 1,013 (64.4%) owned ≥1 pet. Of these, 443 owned dogs, 696 cats, 32 horses, 103 birds, 55 rabbits, and 159 owned fish. Companionship was the most common reason for getting dogs, cats, and birds; horses were mostly owned as a hobby, rabbits to provide fun for children, and fish as a source of relaxation. The majority of dog, cat, and rabbit owners considered their pets to be family members; horse owners almost equally considered their horses a hobby or a family member. The odds of pet ownership increased for respondents from a rural region, having a higher household income, having children and being female. Overall, 711/1,013 (70.2%) pet-owning respondents had taken ≥1 animal to the veterinarian in the previous year, with the most common reasons being for vaccination or annual check-ups or health issues. Respondents who considered their pets trusted companions, had a higher income, and owned dogs or cats compared with other species, were most likely to have taken their pet to a veterinarian. The greatest pet-related expenditure for all species was food. The median yearly veterinary expenditure was $200-499 by dog owners, $100-199 by cat owners, and <$100 by horse, bird, rabbit, and fish owners. The best source of information for pet-related issues was considered to be veterinarians by 724/1,001 (72.3%) owners, and the internet by 509/1,001 (50.8%) owners. Conclusions: Among survey respondents, pet ownership was common and pets filled a variety of roles in the household. Pet owners reported spending considerable amounts of money on their pets each year, but some of them may be underutilising veterinary services despite veterinarians being considered as valuable sources of information about pet-related issues.

A survey of opinions towards dog and cat management policy issues in New Zealand

Aims: To describe the opinions of respondents to an online survey on desexing, microchipping and pet registration, and the management of cats, and aggressive dogs in New Zealand. Methods: A cross-sectional survey was conducted online from 18-22 June 2015 using a permission-based panel of New Zealand residents aged ≥18 years. Questions included demographics of respondents, number of dogs and cats owned, and opinions on desexing, microchipping, pet registration, management of cats and aggressive dogs. Results: Of the 1,572 survey respondents, 216 (13.7%) owned ≥1 dog and ≥1 cat, 227 (14.4%) owned ≥1 dog and no cats, 480 (30.5%) owned ≥1 cat and no dogs, and 559 (35.6%) did not own any pets. The majority of dogs (456/613; 74.8%) and cats (974/1,045; 93.2%) were desexed. The most common reasons for not desexing pets were cost, feeling that it was not needed, or keeping the dog for breeding. Of the 613 dogs, 557 (90.9%) were registered with the local council, and 434 (71.0%) were microchipped, but only 290 (47.3%) were registered in the national database. Of the 1,045 cats, 326 (31.2%) were microchipped and 279/486 (57.4%) owners felt that it was unnecessary. Of the 1,572 respondents, 947 (60.2%) were unaware of stray cats in their local community, and 479 (30.5%) stated that local councils, or animal welfare organisations (546/1,572; 34.7%) should be responsible for managing strays. Among all 1,572 respondents, 787 (50.1%) thought stray cats should be assessed and subjected to euthanasia. Compared with non-pet owners, a lower percentage of cat owners agreed that cats should be confined (p < 0.001). When asked to choose the most appropriate course of action for dogs that had bitten people or other animals, 849 (54.0%) and 820 (52.5%) respondents, respectively, agreed that the dog should be assessed by an expert who would then determine the appropriate action. Compared with non-pet owners, a lower percentage of dog owners supported registration and education of dog owners, aggressive dogs being destroyed, and giving more power to local councils (p < 0.05). Conclusions: The results highlight opportunities to improve owner compliance with desexing, microchipping and registration of dogs and cats. Opinions towards management of stray cat and aggressive dogs varied between pet owners and non-owners. Further research is needed to better understand how to engage the public in important dog and cat management policy issues.

Estimated workload intensity during volunteer aquarium dives

BACKGROUND

This study aimed to characterize the physiological demands of working dives on volunteer divers at a public aquarium in the USA.

AIMS

To estimate the workloads associated with volunteer dives in a US aquarium.

METHODS

Participants completed a medical and diving history questionnaire. Measurements included blood pressure before and after diving and continuous ECG (Holter) monitoring during diving. Dive profiles were recorded using loggers. Mean workload was estimated from total air consumption.

RESULTS

Twenty-seven divers recorded 49 air dives over 5 days. Two-thirds were male and ages ranged from 40 to 78 years. Typically, each diver made two dives with a 30-60 min surface interval. Mean heart rate while diving was 100 beats per minute (bpm). Mean estimated workload during the dives recorded during this study was 5.8 metabolic equivalents (METS), with a range from 4.1 to 10.5. The highest mean recorded heart rate was 120 bpm over 40 min, vacuuming the floor in the shark exhibit.

CONCLUSIONS

Given the mean age of this sample and the prevalence of cardiovascular risk factors (body mass index, high cholesterol and hypertension), it may be prudent for aquariums to regularly monitor SAC/kg and heart rate in volunteer divers, to identify which tasks require the highest workload intensity. Divers with existing cardiovascular risk factors might then be employed in dives with lighter workloads. In conclusion, volunteer dives at this aquarium required a mean workload intensity that was described by recreational divers as moderate. The highest workload, at 10 METS for 23 min, would be considered by many recreational divers as exhausting.

Evaluation of the self-directed format of Walk With Ease in patients with systemic lupus erythematosus: the Walk-SLE Pilot Study

OBJECTIVE

To conduct a proof-of-concept pilot evaluation of the self-directed format of Walk With Ease (WWE), a 6-week walking program developed for adults with arthritis, in patients with systemic lupus erythematosus (SLE).

METHODS

This was a single arm, 6-week pre- and post-evaluation of the self-directed WWE program to assess feasibility, tolerability, safety, acceptability, and effectiveness. Adult patients with physician-diagnosed SLE were recruited to participate during regularly scheduled visits to an academic rheumatology clinic. Self-reported outcomes of pain, stiffness, and fatigue were assessed by visual analog scales (VAS) and the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-fatigue) scale at baseline and at completion of the 6-week program. Patients also completed a satisfaction survey at the end of the program. Multivariate linear regression models were used to calculate mean changes between baseline and 6-week follow-up scores, adjusting for covariates. Mean change scores were used to estimate effect sizes (ES).

RESULTS

At 6 weeks, 48 of the 75 recruited participants completed the WWE program. Participants experienced modest improvements in stiffness and fatigue (ES = 0.12 and ES = 0.23, respectively, for VAS scores; ES = 0.16 for FACIT-fatigue score) following the intervention. The majority of participants reported satisfaction with the program (98%) and benefitted from the workbook (96%).

CONCLUSIONS

The self-directed format of WWE appears to reduce stiffness and fatigue in patients with SLE. It also seems to be a feasible and acceptable exercise program to patients with SLE. Larger studies are needed to confirm these findings.

A Preliminary Description of Companion Cat, Managed Stray Cat, and Unmanaged Stray Cat Welfare in Auckland, New Zealand Using a 5-Component Assessment Scale

Free-roaming cats are a polarizing issue in New Zealand and there is strong need for a comprehensive evaluation of their welfare to better inform population management decisions. In this study, a 5-component visual health-related welfare assessment scale was developed and piloted on a convenience sample of 213 free-roaming companion cats (CC), 210 managed stray cats (MS), and 253 unmanaged stray cats (UMS) from various locations in Auckland, New Zealand. The welfare assessment was performed through distance observation and consisted of body condition score (BCS); coat condition score; nose and eye discharge score; ear crusting score; and injury score. The majority of cats in all groups appeared generally healthy with no nose or eye discharge, ear crusting, or injuries. Although there were no appreciable differences in the apparent welfare of CC and MS cats, future studies with more robust sampling designs are needed to draw accurate inferences. The scale also requires further validation by comparing the visual observations against more detailed physical examination and biochemical data. Nonetheless, the results from this study provide preliminary information about assessing the health and welfare of stray cats as well as considerations for developing and implementing robust assessment scales.

Search for CP Violation in Neutrino and Antineutrino Oscillations by the T2K Experiment with 2.2×10^{21} Protons on Target

The T2K experiment measures muon neutrino disappearance and electron neutrino appearance in accelerator-produced neutrino and antineutrino beams. With an exposure of 14.7(7.6)×10^{20} protons on target in the neutrino (antineutrino) mode, 89 ν_{e} candidates and seven anti-ν_{e} candidates are observed, while 67.5 and 9.0 are expected for δ_{CP}=0 and normal mass ordering. The obtained 2σ confidence interval for the CP-violating phase, δ_{CP}, does not include the CP-conserving cases (δ_{CP}=0, π). The best-fit values of other parameters are sin^{2}θ_{23}=0.526_{-0.036}^{+0.032} and Δm_{32}^{2}=2.463_{-0.070}^{+0.071}×10^{-3}  eV^{2}/c^{4}.