New mutation within a common haplotype is associated with calf muscle weakness in Holsteins.

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7-80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency.

Initial elevation bias in subjective reports.

People's reports of their thoughts, feelings, and behaviors are used in many fields of biomedical and social science. When these states have been studied over time, researchers have often observed an unpredicted and puzzling decrease with repeated assessment. When noted, this pattern has been called an "attenuation effect," suggesting that the effect is due to bias in later reports. However, the pattern could also be consistent with an initial elevation bias. We present systematic, experimental investigations of this effect in four field studies (study 1: n = 870; study 2: n = 246; study 3: n = 870; study 4: n = 141). Findings show clear support for an initial elevation bias rather than a later decline. This bias is larger for reports of internal states than for behaviors and for negative mental states and physical symptoms than for positive states. We encourage increased awareness and investigation of this initial elevation bias in all research using subjective reports.

Blind at First Sight: The Role of Distinctively Accurate and Positive First Impressions in Romantic Interest.

Viewing other people with distinctive accuracy-the degree to which personality impressions correspond with targets' unique characteristics-often predicts positive interpersonal experiences, including liking and relationship satisfaction. Does this hold in the context of first dates, or might distinctive accuracy have negative links with romantic interest in such evaluative settings? We examined this question using two speed-dating samples (Sample 1: N = 172, N = 2,407 dyads; Sample 2: N = 397, N = 1,849 dyads). Not surprisingly, positive impressions of potential dating partners were strongly associated with greater romantic interest. In contrast, distinctively accurate impressions were associated with significantly less romantic interest. This association was even stronger for potential partners whose personalities were less romantically appealing, specifically, those lower in extraversion. In sum, on a first date, distinctive accuracy tends to be paired with lower romantic interest. The potential implications of distinctive accuracy for romantic interest and of romantic interest for distinctive accuracy are discussed.

Severe childhood trauma and clinical and neurocognitive features in schizotypal personality disorder.

OBJECTIVE: Literature suggests that childhood trauma increases vulnerability for schizophrenia-spectrum disorders, including schizotypal personality disorder (SPD). Yet, it remains unexplored whether childhood trauma predicts symptom load and the level of neurocognitive functioning in SPD. METHOD: We included 225 individuals with SPD and 127 healthy controls. Childhood trauma was evaluated using the Childhood Trauma Questionnaire, and schizotypal traits were assessed using the Schizotypal Personality Questionnaire. Standard neurocognitive assessments covered six cognitive domains. RESULTS: All types of reported childhood trauma were significantly associated with SPD, in a linear fashion. Severe sexual abuse showed the greatest magnitude of association with higher cognitive-perceptual load (e.g., ideas of reference, odd belief or magical thinking); severe emotional neglect was associated with interpersonal scores (e.g., excessive social anxiety, constricted affect) within the SPD group. SPD individuals who reported severe trauma showed worse cognitive functioning (i.e., working memory, verbal/visual learning and memory, as well as verbal fluency). CONCLUSIONS: Particular severe childhood trauma types were associated with higher cognitive-perceptual and interpersonal symptoms in SPD, along with worse cognitive functioning. These findings highlight the need for clinicians to enquire about childhood trauma in SPD patients, since unaddressed early adverse experiences may carry long-term negative consequences.

InterPrEP: internet-based pre-exposure prophylaxis with generic tenofovir disoproxil fumarate/emtrictabine in London - analysis of pharmacokinetics, safety and outcomes.

OBJECTIVES: The National Health Service in England (NHS England) does not provide pre-exposure prophylaxis (PrEP) against HIV, forcing people to purchase generic versions on the internet. However, there are concerns about the authenticity of medicines purchased online. We established an innovative service offering plasma tenofovir (TFV) and emcitrabine (FTC) therapeutic drug monitoring for people buying generic PrEP online, to ensure that drug concentrations in vivo were consistent with those of propriety brands and previously published data. METHODS: TFV/FTC concentrations were measured by ultra-performance liquid chromatography ultraviolet detection. Evaluation of renal function and testing for HIV, hepatitis B virus (HBV) and hepatitis C virus (HCV) were also carried out, at baseline and every 3-6 months, with risk reduction advice. RESULTS: A total of 293 individuals presented having purchased PrEP on the internet: 85% were white, 84% were taking daily PrEP, and 16% were event-driven. Most were on generic TFV disoproxil fumarate (TDF)/FTC from Cipla Ltd. Median (range) TFV and FTC plasma concentrations were 104 (21-597) ng/mL and 140 (17-1876) ng/mL, respectively. All concentrations were above our established plasma TFV and FTC targets, based on previously published data. Renal function was normal in all evaluable individuals and no new cases of HIV, HBV or HCV infection were seen. CONCLUSIONS: In a population at high risk of HIV acquisition, who cannot yet access PrEP on the NHS, concentrations of TFV and FTC in generic formulations purchased over the internet were similar to (or slightly higher than) those measured in phase I studies with the original formulation from Gilead (Truvada™), which has demonstrated high levels of protection against HIV infection in previous PrEP clinical trials.

Proportion of Tubal Factor Infertility due to Chlamydia: Finite Mixture Modeling of Serum Antibody Titers.

In this study, we examined whether the proportion of tubal factor infertility (TFI) that is attributable to Chlamydia trachomatis, the population excess fraction (PEF), can be estimated from serological data using finite mixture modeling. Whole-cell inclusion immunofluorescence serum antibody titers were recorded among infertile women seen at St. Michael's Hospital in Bristol, United Kingdom, during the period 1985-1995. Women were classified as TFI cases or controls based on laparoscopic examination. Finite mixture models were used to identify the number of component titer distributions and the proportion of serum samples in each, from which estimates of PEF were derived. Four titer distributions were identified. The component at the highest titer was found only in samples from women with TFI, but there was also an excess of the second-highest titer component in TFI cases. Minimum and maximum estimates of the PEF were 28.0% (95% credible interval: 6.9, 50.0) and 46.8% (95% credible interval: 23.2, 64.1). Equivalent estimates based on the standard PEF formula from case-control studies were 0% and over 65%. Finite mixture modeling can be applied to serological data to obtain estimates of the proportion of reproductive damage attributable to C. trachomatis Further studies using modern assays in contemporary, representative populations should be undertaken.

Understanding the costs of support transactions in daily life.

The benefits of close relationships for mental and physical health are well documented. One of the mechanisms presumed to underlie these effects is social support, whereby close others provide practical and emotional assistance in times of need. Although there is no doubt that generalized perceptions of support availability are beneficial, research examining actual instances of support receipt has found unexpectedly mixed results. Receiving support sometimes has positive effects, but null or even negative effects are common. In this article, we review our multimethod program of research that seeks to understand and explain the costs of receiving social support. We focus on reductions in the recipient's sense of relationship equity and self-efficacy as mechanisms of this effect and examine a number of other moderating factors. Although we have found that receiving support incurs costs on average, there is considerable variability yet to be explained. Using diary data from 312 persons preparing to take a challenging exam, we examined the potential of individual differences in neuroticism, agreeableness, and attachment insecurity to explain variability in experienced support costs. We close with new questions about why received support may be beneficial or benign in some situations while being especially toxic in others.

Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes.

The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777,962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47,770 autosomal SNPs) and high density (HD; 735,151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD.

Uncovering and overcoming ambivalence: the role of chronic and contextually activated attachment in two-person social dilemmas.

OBJECTIVE: Humans face an enduring conflict between desires to affiliate with others but to protect the self; effective social functioning often requires reconciling the resulting ambivalence between these motives. Attachment anxiety is characterized by chronically heightened concerns about affiliation and self-protection; we investigated how anxious individuals' chronic relational ambivalence affects interpersonal behavior. METHOD: We used the Prisoner's Dilemma and the Assurance Game to examine how the ambivalence associated with attachment anxiety affects pro-social behavior, comparing chronic attachment anxiety with both chronic (Study 1; N = 94) and contextually activated (Study 2; N = 56) security. RESULTS: Chronic attachment anxiety was associated with ambivalent behavior in the social dilemma games. Specifically, the chronically anxious were mistrustfully inconsistent in their strategic choices and took more time to make these choices. However, priming the chronically anxious with attachment security decreased ambivalence by promoting more fluent cooperative behavior. CONCLUSIONS: To our knowledge, these are the first studies to examine the effect of the anxiously attached's chronic relational ambivalence on pro-social behavior. These findings illustrate that the simultaneous activation of affiliation and self-protection can have interpersonal consequences, increasing mistrust and hesitance. Importantly, however, we were able to attenuate these effects by priming felt security.

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

We performed a genome-wide association study for Warner-Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within µ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31-0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1 SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.

Genome-wide association analysis for feed efficiency in Angus cattle.

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.

Assessment of plant biomass and nitrogen nutrition with plant height in early-to mid-season corn.

BACKGROUND: The physiological basis for using non-destructive high-resolution measurements of plant height through plant height sensing to guide variable-rate nitrogen (N) applications on corn (Zea mays L.) during early (six-leaf growth stage, V6) to mid (V12) season is largely unknown. This study was conducted to assess the relationships of plant biomass and leaf N with plant height in early- to mid-season corn under six different N rate treatments. RESULTS: Corn plant biomass was significantly and positively related to plant height under an exponential model when both were measured at V6. This relationship explained 62-78% of the variations in corn biomass production. Leaf N concentration was, in general, significantly and positively related to plant height when both were measured at V6, V8, V10 and V12. This relationship became stronger as the growing season progressed from V6 to V12. The relationship of leaf N with plant height in early- to mid-season corn was affected by initial soil N fertility and abnormal weather conditions. CONCLUSION: The relationship of leaf N concentration with plant height may provide a physiological basis for using plant height sensing to guide variable-rate N applications on corn.

Pharmacokinetic and safety profile of raltegravir and ribavirin, when dosed separately and together, in healthy volunteers.

BACKGROUND: Treatment of chronic hepatitis C virus (HCV) infection in HIV-1-co-infected individuals remains challenging due to numerous factors, including drug-drug interactions. The aim of this study was to assess the safety and pharmacokinetic (PK) profile of raltegravir and ribavirin when dosed separately and together. METHODS: Fourteen healthy volunteers [mean (standard deviation) age 35 (10) years, 71% male] entered this phase 1 PK study and received single-dose ribavirin (800 mg) on day 1 (phase 1). Following a washout period, subjects received raltegravir (400 mg twice daily) on days 15-19 (phase 2) and single-dose ribavirin (800 mg) with raltegravir (400 mg) on day 20 (phase 3). Intensive PK sampling was undertaken on days 1, 19 and 20 and differences in geometric mean ratios (GMRs) for PK parameters between study periods were assessed. RESULTS: No statistically significant differences in PK parameters were observed for raltegravir between phases 2 and 3. A statistically significant decrease in maximum plasma concentration (C(max)) and an increase in time to maximum plasma concentration (T(max)) were observed for ribavirin in phase 3 compared with phase 1 [GMR (95% confidence interval) 0.79 (0.62-1.00) and 1.39 (1.08-1.78), respectively], whereas no significant differences in other ribavirin PK parameters were observed between study phases. No clinically significant safety concerns were reported. CONCLUSIONS: The PK profile of ribavirin is altered when administered with raltegravir (reduced C(max) and increased T(max)), with no safety concerns identified. This is unlikely to be of clinical significance or have an impact on the antiviral effects of ribavirin in HIV-1- and HCV-co-infected subjects.

Improvement in regression of corn yield with plant height using relative data.

BACKGROUND: The traditional approach of analyzing absolute variable data across multiple locations and/or years has drawbacks in precision agriculture. This study was conducted to evaluate the impacts of using relative yield and plant height data of corn (Zea mays L.) on the regression of yield with plant height using linear and exponential models in a nitrogen (N) rate field trial under four cropping systems. RESULTS: The use of relative yield to replace absolute yield frequently increased the determination coefficient (R(2) ) values in the regression of yield with plant height on datasets combined across cropping systems or/and years. Relative yield and relative plant height sometimes further enhanced the R(2) values compared with relative yield and absolute plant height. All these improvements mostly occurred when the fit of the model was not strong with absolute yield and absolute plant height or relative yield and absolute plant height. The advantages of using relative data of yield or/and plant height were similar for the two regression models. CONCLUSION: The use of relative yield or relative data of both yield and plant height may be effective in improving the regression of corn yield with plant height across multiple cropping systems/locations and years in precision agriculture.

Genome-wide association study of economically important traits in Charolais and Limousin beef cows.

Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.

Progress and prospects: foamy virus vectors enter a new age.

Foamy viruses, distantly related to the major subfamily of Retroviruses, Orthoretroviruses that include oncoviruses (for example, murine leukemia virus (MLV)) and lentiviruses (human immunodeficiency virus (HIV)), are endemic in mammalian species, but not in human populations. Humans infected by accidental or occupational exposure remain well. The virus is not transmitted to others, nor is it associated with any disease. These features added to its broad host range, efficient transduction of progenitor cells and an integration profile less likely to induce insertional mutagenesis, make these viruses attractive as vectors. Long-term reversal of disease phenotype in dogs with the genetic defect, leukocyte adhesion deficiency, by foamy virus vector therapy strengthens the case for their clinical exploitation.

HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection.

Human immunodeficiency virus type 1 (HIV-1) can evade immunity shortly after transmission to a new host but the clinical significance of this early viral adaptation in HIV infection is not clear. We present an analysis of sequence variation from a longitudinal cohort study of HIV adaptation in 189 acute seroconverters followed for up to 3 years. We measured the rates of variation within well-defined epitopes to determine associations with the HLA-linked hazard of disease progression. We found early reversion across both the gag and pol genes, with a 10-fold faster rate of escape in gag (2.2 versus 0.27 forward mutations/1,000 amino acid sites). For most epitopes (23/34), variation in the HLA-matched and HLA-unmatched controls was similar. For a minority of epitopes (8/34, and generally associated with HLA class I alleles that confer clinical benefit), new variants appeared early and consistently over the first 3 years of infection. Reversion occurred early at a rate which was HLA-dependent and correlated with the HLA class 1-associated relative hazard of disease progression and death (P = 0.0008), reinforcing the association between strong cytotoxic T-lymphocyte responses, viral fitness, and disease status. These data provide a comprehensive overview of viral adaptation in the first 3 years of infection. Our findings of HLA-dependent reversion suggest that costs are borne by some escape variants which may benefit the host, a finding contrary to a simple immune evasion paradigm. These epitopes, which are both strongly and frequently recognized, and for which escape involves a high cost to the virus, have the potential to optimize vaccine design.

A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle.

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.

The role of human endogenous retroviruses in melanoma.

Sequencing of the human genome has established that our DNA harbours many endogenous retrovirus (ERV) sequences, remnants of ancestral exogenous retroviral infections fixed in the germline DNA. In recent years, human ERVs (HERVs) have been implicated in melanomagenesis. Retrovirus-like particles and the expression of HERV mRNA and proteins have been demonstrated in melanoma tissue. In addition, antibodies to HERV proteins have been observed in patients with melanoma. In vitro and mouse models have provided fascinating insights into the potential mechanisms of HERVs in melanomagenesis. This review considers the evidence associating HERVs with melanoma.