Association between days open and milk spectral data in dairy cows.

Data on 19,489 Brown Swiss cows reared in northeastern Italy were used to associate absorbances of individual wavenumbers within the mid-infrared range with days open (DO). Different postcalving days in milk (DIM) intervals were studied to determine the most informative milk sampling periods for predicting DO. Milk samples were analyzed using a MilkoScan (Foss Electric, Hillerød, Denmark) Fourier-transform infrared (FTIR) spectrometer for 1,060 wavenumbers (wn) ranging from 5,011 to 925 cm-1. To determine DO, we considered an insemination to lead to conception when there was no return of heat (i.e., no successive insemination) and the cow had a subsequent calving date whereby gestation length was required to be within ±30 d of 290 d. Only milk records within the first 90 DIM were considered. Associations were inferred by (1) fitting linear regression models between the DO and each individual wavenumber or milk component, and (2) fitting a Bayesian regression model that included the complete FTIR spectral data. The effects of including systematic effects (parity number, year-season, herd) in the model on these associations were also studied. These analyses were performed for the complete data (5-90 DIM) and for data stratified by DIM period (5 to 30, 31 to 60, and 61 to 90 DIM). Overall, regions of wavenumbers of the milk FTIR spectra that were associated with DO included wn 2,973 to 2,830 cm-1 [related to fat-B (C-H stretch)], wn 2,217 to 1,769 cm-1 [related to fat-A (C = O stretch)], wn 1,546 cm-1 (related to protein), wn 1,465 cm-1 (related to urea and fat), wn 1,399 to 1,245 cm-1 (related to acetone), and wn 1,110 cm-1 (related to lactose). Estimated effects depended on the DIM period, with milk samples drawn during DIM intervals 31 to 60 d and 61 to 90 d being most strongly associated with DO. These DIM intervals are also typically most associated with negative energy balance and peak lactation.

Prediction of fatty acid composition using milk spectral data and its associations with various mid-infrared spectral regions in Michigan Holsteins.

Fatty acid composition in milk is not only reflective of nutritional quality but also potentially predictive of other attributes (e. g. including the cow's energy balance and its relative output of methane emissions). Furthermore, a higher ratio of long-chain to short-chain fatty acids or mean carbon number has been associated with negative energy balance in dairy cows, whereas enhanced nutritional properties have been generally associated with higher levels of unsaturation. We set out to directly compare Bayesian regression strategies with partial least squares for the prediction of various milk fatty acids using Fourier-transform infrared spectrum data on 777 milk samples taken from 579 cows on 4 Michigan dairy herds between 5 and 90 d in milk. We also set out to identify those spectral regions that might be associated with fatty acids and whether carbon number or level of unsaturation might contribute to the strength of these associations. These associations were based on adaptively clustered windows of wavenumbers to mitigate the distorting effects of severe multicollinearity on marginal associations involving individual wavenumbers. In general, Bayesian regression methods, particularly the variable selection method BayesB, outperformed partial least squares regression for cross-validation prediction accuracy for both individual fatty acids and fatty acid groups. Strong signals for wavenumber associations using BayesB were well distributed throughout the mid-infrared spectrum, particularly between 910 and 3,998 cm-1. Carbon number appeared to be linearly related to strength of wavenumber associations for 38 moderately to highly predicted fatty acids within the spectral regions of 2,286 to 2,376 and 2,984 to 3,100 cm-1, whereas nonlinear associations were determined within 1,141 to 1,205; 1,570 to 1,630; and 1,727 to 1,768 cm-1. However, no such associations were detected with level of unsaturation. Spectral regions where there were significant relationships between strength of association and carbon number may be useful targets for inferring the relative proportion of long-chain to short-chain fatty acids, and hence energy balance.

Association of spontaneous abortion and Ureaplasma parvum detected in placental tissue.

Spontaneous abortion is considered a public health problem having several causes, including infections. Among the infectious agents, bacteria of the vaginal microbiota and Ureaplasma parvum have been associated with abortion, but their participation needs to be further elucidated. This study aims to evaluate the influence of Mollicutes on the development of spontaneous abortion. Women who underwent spontaneous abortion and those with normal birth (control) were studied. Samples of cervical mucus (CM) and placental tissue were collected to identify Mollicutes using the quantitative polymerase chain reaction methodology. Eighty-nine women who had a miscarriage and 20 women with normal pregnancies were studied. The presence of Mollicutes in placental tissue increased the chance of developing miscarriage sevenfold. The prevalence of U. parvum in women who experienced spontaneous abortion was 66.3% in placental tissue. A positive association was observed between the detection of U. parvum in samples of placental tissue and abortion. There was a significant increase in microbial load in placental tissue for M. hominis, U. urealyticum and U. parvum compared to the control group. Detection of U. parvum in CM in pregnant women can ascend to the region of the placental tissue and trigger a spontaneous abortion.

Genetic parameters for fertility traits assessed in herds divergent in milk energy output in Holstein-Friesian, Brown Swiss, and Simmental cattle.

In this study, we aimed to investigate differences in the genetics of fertility traits (heritability of traits and correlations between traits in divergent environments) in dairy cows of different production levels defined on the basis of the herd-average daily milk energy output (herd-dMEO). Data were obtained from Holstein-Friesian (n = 37,359 for fertility traits, 381,334 for dMEO), Brown Swiss (n = 79,638 for fertility traits, 665,697 for dMEO), and Simmental cows (n = 63,048 for fertility traits, 448,445 for dMEO) reared in northeastern Italy. Fertility traits under study were interval from calving to first service, interval from first service to conception, days open, calving interval, calving rate, and nonreturn rate at d 56. We classified herds into low and high productivity based on the herd-average dMEO (inferred using mixed effects models). We estimated genetic parameters using Bayesian bivariate animal models, where expressions of a phenotype in the low and high dMEO herds were taken as being different-albeit correlated-traits. Fertility traits were more favorable in Simmental than in Holstein-Friesian cows, whereas for all traits, Holstein-Friesian had the highest estimates of intraherd heritability [ranging from 0.021 (0.006-0.038) to 0.126 (0.10-0.15)] and Simmental the lowest [ranging from 0.008 (0.001-0.017) to 0.101 (0.08-0.12)]. The genetic correlations between fertility traits and dMEO were moderate and unfavorable, ranging, in absolute values, from 0.527 (0.37-0.68) to 0.619 (0.50-0.73) in Holstein-Friesian; from 0.339 (0.20-0.47) to 0.556 (0.45-0.66) in Brown Swiss; and from 0.340 (0.10-0.60) to 0.475 (0.33-0.61) in Simmental cattle. The only exception was the nonreturn rate at d 56, which had weak genetic correlations with dMEO in all 3 breeds. The herd correlations between fertility and dMEO tended to be modest and favorable and the residual correlations modest and variable. The heritability of fertility traits tended to be greater in the low dMEO than in the high dMEO herds in the case of the Holstein-Friesians, but not in the case of the Brown Swiss or Simmentals. The additive genetic correlations between fertility traits in the low and high dMEO herds were always lower than 1 [0.329 (-0.17 to 0.85) to 0.934 (0.86 to 0.99)] for all traits considered in all breeds. The correlation was particularly low for the threshold characters and the interval from first service to conception in Holstein-Friesian, suggesting that the relative performances of genotypes vary significantly between herds of different dMEO levels. Although there was large variability in the estimates, results might support making separate genetic evaluations of fertility in the different herd production groups. Our results also indicate that Simmental, a dual-purpose breed, has higher fertility and lower environmental sensitivity than Holstein-Friesian, with Brown Swiss being intermediate.

Genotoxicity in fishes environmentally exposed to As, Se, Hg, Pb, Cr and toxaphene in the lower Colorado River basin, at Mexicali valley, Baja California, México.

The environmental exposure to As, Se, Hg, Pb, Cr and toxaphene was assessed for 11 freshwater fish species in irrigation channels, agricultural return flow drains, a drain collecting lagoon and sections of the Colorado River at the Mexicali valley in Baja California, México, during August 2015-April 2016. Arsenic (2.90 ng ml-1) and Se (1.41 ng ml-1) in water had the highest concentrations in the return flow drains (Hardy River and Xochimilco Lagoon, respectively). However, fish axial muscle tissue had the highest concentration of Se (8.3 µg g-1) and Hg (0.36 µg g-1) in Colorado River fresh water, while As (1.7 µg g-1) in Hardy River fish was highest. Selenium concentrations in all fishes and toxaphene in Cyprinus carpio and Ameiurus natalis are above the safe levels for human consumption (0.3 µg g-1 and 180 ng g-1 respectively). Toxaphene was detected in the fish axial tissue, having the highest concentrations in Poecilia latipinna (690 ng g-1) in the Colorado River. The low proportion of the 8-Cl toxaphene congeners in fish suggests degradation of this pollutant. Tilapia. sp. cf. zillii had the most genotoxic damage with 7.4 micronucleated erythrocytes per 10,000 erythrocytes in Xochimilco Lagoon and 2 in Hardy River. The genotoxicity in all the fish species studied was significantly correlated to the concentrations of As and Se in water.

Association of high-fat diet with neuroinflammation, anxiety-like defensive behavioral responses, and altered thermoregulatory responses in male rats.

Overweight and obesity are a worldwide pandemic affecting billions of people. These conditions have been associated with a chronic low-grade inflammatory state that is recognized as a risk factor for a range of somatic diseases as well as neurodevelopmental disorders, anxiety disorders, trauma- and stressor-related disorders, and affective disorders. We previously reported that the ingestion of a high-fat diet (HFD; 45% fat kcal/g) for nine weeks was capable of inducing obesity in rats in association with increased reactivity to stress and increased anxiety-related defensive behavior. In this study, we conducted a nine-week diet protocol to induce obesity in rats, followed by investigation of anxiety-related defensive behavioral responses using the elevated T-maze (ETM), numbers of FOS-immunoreactive cells after exposure of rats to the avoidance or escape task of the ETM, and neuroinflammatory cytokine expression in hypothalamic and amygdaloid nuclei. In addition, we investigated stress-induced cutaneous thermoregulatory responses during exposure to an open-field (OF). Here we demonstrated that nine weeks of HFD intake induced obesity, in association with increased abdominal fat pad weight, increased anxiety-related defensive behavioral responses, and increased proinflammatory cytokines in hypothalamic and amygdaloid nuclei. In addition, HFD exposure altered avoidance- or escape task-induced FOS-immunoreactivity within brain structures involved in control of neuroendocrine, autonomic, and behavioral responses to aversive stimuli, including the basolateral amygdala (BLA) and dorsomedial (DMH), paraventricular (PVN) and ventromedial (VMH) hypothalamic nuclei. Furthermore, rats exposed to HFD, relative to control diet-fed rats, responded with increased tail skin temperature at baseline and throughout exposure to an open-field apparatus. These data are consistent with the hypothesis that HFD induces neuroinflammation, alters excitability of brain nuclei controlling neuroendocrine, autonomic, and behavioral responses to stressful stimuli, and enhances stress reactivity and anxiety-like defensive behavioral responses.

A landscape of the heritability of Fourier-transform infrared spectral wavelengths of milk samples by parity and lactation stage in Holstein cows.

Fourier-transform near- and mid-infrared (FTIR) milk spectral data are routinely collected in many countries worldwide. Establishing an optimal strategy to use spectral data in genetic evaluations requires knowledge of the heritabilities of individual FTIR wavelength absorbances. Previous FTIR heritability estimates have been based on relatively small sample sizes and have not considered the possibility that heritability may vary across parities and stages of the lactation. We used data from ∼370,000 test-day records of Canadian Holstein cows to produce a landscape of the heritability of FTIR spectra, 1,060 wavelengths in the near- and mid-infrared spectrum (5,011-925 cm-1), by parity and month of the lactation (mo 1 to 3 and mo 1 to 6, respectively). The 2 regions of the spectrum associated with absorption of electromagnetic energy by water molecules were estimated to have very high phenotypic variances, very low heritabilities, and very low proportion of variance explained by herd-year-season (HYS) subclasses. The near- or short-wavelength infrared (SWIR: 5,066-3,672 cm-1) region was also characterized by low heritability estimates, whereas the estimated proportion of the variance explained by HYS was high. The mid-wavelength infrared region (MWIR: 3,000-2,500 cm-1) and the transition between mid and long-wavelength infrared region (MWIR-LWIR: 1,500-925 cm-1) harbor several waves characterized by moderately high (≥0.4) heritabilities. Most of the high-heritability regions contained wavelengths that are reported to be associated with important milk metabolites and components. Interestingly, these 2 same regions tended to show more variability in heritabilities between parity and lactation stage. Second parity showed heritability patterns that were distinctly different from those of the first and third parities, whereas the first 2 mo of the lactation had clearly distinct heritability patterns compared with mo 3 to 6.

Involvement of human monogenic cardiomyopathy genes in experimental polygenic cardiac hypertrophy.

Hypertrophic cardiomyopathy thickens heart muscles, reducing functionality and increasing risk of cardiac disease and morbidity. Genetic factors are involved, but their contribution is poorly understood. We used the hypertrophic heart rat (HHR), a unique normotensive polygenic model of cardiac hypertrophy and heart failure, to investigate the role of genes associated with monogenic human cardiomyopathy. We selected 42 genes involved in monogenic human cardiomyopathies to study: 1) DNA variants, by sequencing the whole genome of 13-wk-old HHR and age-matched normal heart rat (NHR), its genetic control strain; 2) mRNA expression, by targeted RNA-sequencing in left ventricles of HHR and NHR at 5 ages (2 days old and 4, 13, 33, and 50 wk old) compared with human idiopathic dilated cardiomyopathy data; and 3) microRNA expression, with rat microRNA microarrays in left ventricles of 2-day-old HHR and age-matched NHR. We also investigated experimentally validated microRNA-mRNA interactions. Whole-genome sequencing revealed unique variants mostly located in noncoding regions of HHR and NHR. We found 29 genes differentially expressed in at least 1 age. Genes encoding desmoglein 2 ( Dsg2) and transthyretin ( Ttr) were significantly differentially expressed at all ages in the HHR, but only Ttr was also differentially expressed in human idiopathic cardiomyopathy. Lastly, only two microRNAs differentially expressed in the HHR were present in our comparison of validated microRNA-mRNA interactions. These two microRNAs interact with five of the genes studied. Our study shows that genes involved in monogenic forms of human cardiomyopathies may also influence polygenic forms of the disease.

Protective effect of black relative to white race against non-alcoholic fatty liver disease in patients with severe obesity, independent of type 2 diabetes.

Severe obesity (body mass index ⩾35 kg m-2) and type 2 diabetes (T2D) are potent and additive risk factors for non-alcoholic fatty liver disease (NAFLD), including non-alcoholic steatohepatitis (NASH). Scant available evidence indicates that black relative to white patients with severe obesity are less susceptible to NAFLD, but it is unclear if T2D abolishes this apparent racial disparity. Therefore, we compared biopsy-proven NAFLD and its progression between black (n=71) and white (n=155) patients with severe obesity stratified by presence or absence of T2D. Although prevalence of T2D was similar between races (37%, P>0.9), whites were significantly more likely than blacks to have NAFLD, NASH and advanced fibrosis (defined as bridging fibrosis and/or cirrhosis). Importantly, T2D was associated with increased odds of NAFLD, NASH and advanced fibrosis (defined as bridging fibrosis or cirrhosis) in whites only (P<0.05). In turn, a higher proportion of blacks than whites with T2D were free of NAFLD (58 versus 22%, P<0.01). These preliminary findings question translation of the powerful interconnection between T2D and NAFLD in whites with severe obesity to blacks and point to an important role of race in the pathophysiology and treatment of these diseases.

The role of posttraumatic stress and posttraumatic growth on online information use in breast cancer survivors.

OBJECTIVE: Changes perceived as both positive (eg, posttraumatic growth [PTG]) and negative (eg, posttraumatic stress symptoms [PTSS]) have been associated with intensive Internet use among breast cancer survivors. In this multicenter study, we analyzed the role of PTG and PTSS on the amount of time spent looking for online cancer information, its content, and its psychological impact. METHODS: Posttraumatic stress symptoms and PTG were assessed in 182 breast cancer survivors by using the Post-traumatic Stress Disorder Checklist and Post-traumatic Growth Inventory questionnaires. Subjects also completed a questionnaire about their behavior when looking for online illness-related information (ie, time spent, type of contents, and psychological impact). RESULTS: Posttraumatic stress symptoms positively correlated with the amount of time spent looking for cancer-related information, including both medical and psychosocial content. By contrast, PTG showed no relationships with the amount of time, but with a predominant search for cancer-related psychosocial information. The psychological impact of online information was associated with participants' levels of PTG and/or PTSS. Whereas PTG was related to a decrease of women's hope, PTSS was linked to the perception of being less conscious or inadequately informed about the illness, thereby increasing feelings of distress. CONCLUSIONS: Posttraumatic stress symptoms and PTG show relationships with the amount of time spent online, the type of information accessed online, and the psychological impact of Internet use. Health professionals should prescribe online information according to the psychological response to cancer. There is a need for professional-led online resources to provide patients with timely information as well as support sites to facilitate psychological adjustment.

Joint lavage followed by viscosupplementation and triamcinolone in patients with severe haemophilic arthropathy: objective functional results.

INTRODUCTION: Viscosupplementation can improve function in haemophilia patients. Viscosupplementation results can be improved by prior joint lavage and triamcinolone administration. AIM: To objectively assess whether viscosupplementation and associated triamcinolone use in patients with severe haemophilic arthropathy following joint lavage improves force and balance and reduces bleeding events. METHODS: Fourteen patients with haemophilic knee arthritis with and without the involvement of other joints underwent joint lavage and subsequent injections of Hylan G-F20 and triamcinolone into all affected joints. Patients were evaluated with NeuroCom® force and balance platforms using the step-up-and-over task (STP), sit-to-stand test (STS), one-leg stance (UNI) and weight-bearing squat (WBS) at baseline and at 1, 3, 6 and 12 months after the procedure. Bleeding events in the year prior to and the year after the procedure were analysed. RESULTS: Sixteen knees, 15 ankles, eight elbows and one shoulder were treated. The STP results indicated improvements in the lift-up indices (right leg) at all time points evaluated (P = 0.03). The STS results revealed coupled improvement in weight transfer and the rising index for up to a year (P = 0.02). Balance (UNI) with eyes open or closed improved in all evaluations. The WBS results revealed improvements at all degrees of flexion (0, P = 0.003; 30°, P = 0.001; 60°, P < 0.001 and 90°, P < 0.001). The numbers of total and traumatic bleeding events were reduced (P = 0.04). CONCLUSION: Joint lavage followed by injections of triamcinolone and Hylan G-F20 improved balance, function and bleeding events in severe haemophilic arthropathy patients.

The 'heritability' of domestication and its functional partitioning in the pig.

We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regression approach proposed in this study revealed molecular processes not apparent through typical differentiation statistics. We propose that at least some of these processes are likely new discoveries because domestication is a dynamic process of genetic selection, which may not be completely characterized by a static metric like Fst. Nevertheless, and despite some particularly influential mutation types or pathways, our analyses tend to rule out a simplistic genetic basis for the domestication process: neither a single pathway nor a unique set of SNPs can explain the process as a whole.

Ureaplasma urealyticum and U. parvum in sexually active women attending public health clinics in Brazil.

Ureaplasma urealyticum and U. parvum have been associated with genital infections. The purpose of this study was to detect the presence of ureaplasmas and other sexually transmitted infections in sexually active women from Brazil and relate these data to demographic and sexual health, and cytokines IL-6 and IL-1ß. Samples of cervical swab of 302 women were examined at the Family Health Units in Vitória da Conquista. The frequency of detection by conventional PCR was 76·2% for Mollicutes. In qPCR, the frequency found was 16·6% for U. urealyticum and 60·6% U. parvum and the bacterial load of these microorganisms was not significantly associated with signs and symptoms of genital infection. The frequency found for Trichomonas vaginalis, Neisseria gonorrhoeae, Gardnerella vaginalis and Chlamydia trachomatis was 3·0%, 21·5%, 42·4% and 1·7%, respectively. Higher levels of IL-1ß were associated with control women colonized by U. urealyticum and U. parvum. Increased levels of IL-6 were associated with women who exhibited U. parvum. Sexually active women, with more than one sexual partner in the last 3 months, living in a rural area were associated with increased odds of certain U. parvum serovar infection.

How does temperature influences the development of lactococcosis? Transcriptomic and immunoproteomic in vitro approaches.

Lactococcus garvieae is the aetiological agent of lactococcosis, a haemorrhagic septicaemia that affects marine and freshwater fish, with special incidence and economic relevance in farmed rainbow trout. Water temperature is one of the most important predisposing factors in the development of lactococcosis outbreaks. Lactococcosis in trout usually occur when water temperatures rise to about 18 °C, while fish carriers remain asymptomatic at temperatures below 13 °C. The aim of this work was to analyse the differences in the complete transcriptome response of L. garvieae grown at 18 °C and at 13 °C and to identify the immunogenic proteins expressed by this bacterium at 18 °C. Our results show that water temperature influences the expression of L. garvieae genes involved in the lysis of part of the bacterial cell population and in the cold response bacterial adaptation. Moreover, the surface immunogenic protein profile at 18 °C suggests an important role of the lysozyme-like enzyme, WxL surface proteins and some putative moonlighting proteins (proteins with more than one function, usually associated with different cellular locations) as virulence factors in L. garvieae. The results of this study could provide insights into the understanding of the virulence mechanisms of L. garvieae in fish.

Genotype by environment (climate) interaction improves genomic prediction for production traits in US Holstein cattle.

Genotype by environment interaction (G × E) in dairy cattle productive traits has been shown to exist, but current genetic evaluation methods do not take this component into account. As several environmental descriptors (e.g., climate, farming system) are known to vary within the United States, not accounting for the G × E could lead to reranking of bulls and loss in genetic gain. Using test-day records on milk yield, somatic cell score, fat, and protein percentage from all over the United States, we computed within herd-year-season daughter yield deviations for 1,087 Holstein bulls and regressed them on genetic and environmental information to estimate variance components and to assess prediction accuracy. Genomic information was obtained from a 50k SNP marker panel. Environmental effect inputs included herd (160 levels), geographical region (7 levels), geographical location (2 variables), climate information (7 variables), and management conditions of the herds (16 total variables divided in 4 subgroups). For each set of environmental descriptors, environmental, genomic, and G × E components were sequentially fitted. Variance components estimates confirmed the presence of G × E on milk yield, with its effect being larger than main genetic effect and the environmental effect for some models. Conversely, G × E was moderate for somatic cell score and small for milk composition. Genotype by environment interaction, when included, partially eroded the genomic effect (as compared with the models where G × E was not included), suggesting that the genomic variance could at least in part be attributed to G × E not appropriately accounted for. Model predictive ability was assessed using 3 cross-validation schemes (new bulls, incomplete progeny test, and new environmental conditions), and performance was compared with a reference model including only the main genomic effect. In each scenario, at least 1 of the models including G × E was able to perform better than the reference model, although it was not possible to find the overall best-performing model that included the same set of environmental descriptors. In general, the methodology used is promising in accounting for G × E in genomic predictions, but challenges exist in identifying a unique set of covariates capable of describing the entire variety of environments.

Use of genotype × environment interaction model to accommodate genetic heterogeneity for residual feed intake, dry matter intake, net energy in milk, and metabolic body weight in dairy cattle.

Feed efficiency in dairy cattle has gained much attention recently. Due to the cost-prohibitive measurement of individual feed intakes, combining data from multiple countries is often necessary to ensure an adequate reference population. It may then be essential to model genetic heterogeneity when making inferences about feed efficiency or selecting efficient cattle using genomic information. In this study, we constructed a marker × environment interaction model that decomposed marker effects into main effects and interaction components that were specific to each environment. We compared environment-specific variance component estimates and prediction accuracies from the interaction model analyses, an across-environment analyses ignoring population stratification, and a within-environment analyses using an international feed efficiency data set. Phenotypes included residual feed intake, dry matter intake, net energy in milk, and metabolic body weight from 3,656 cows measured in 3 broadly defined environments: North America (NAM), the Netherlands (NLD), and Scotland (SAC). Genotypic data included 57,574 single nucleotide polymorphisms per animal. The interaction model gave the highest prediction accuracy for metabolic body weight, which had the largest estimated heritabilities ranging from 0.37 to 0.55. The within-environment model performed the best when predicting residual feed intake, which had the lowest estimated heritabilities ranging from 0.13 to 0.41. For traits (dry matter intake and net energy in milk) with intermediate estimated heritabilities (0.21 to 0.50 and 0.17 to 0.53, respectively), performance of the 3 models was comparable. Genomic correlations between environments also were computed using variance component estimates from the interaction model. Averaged across all traits, genomic correlations were highest between NAM and NLD, and lowest between NAM and SAC. In conclusion, the interaction model provided a novel way to evaluate traits measured in multiple environments in which genetic heterogeneity may exist. This model allowed estimation of environment-specific parameters and provided genomic predictions that approached or exceeded the accuracy of competing within- or across-environment models.

Genomic variance estimates: With or without disequilibrium covariances?

Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance. The classical estimate of genomic variance that ignores covariances underestimated the genomic variance in the data. The second method accounts for LD explicitly and leads to genomic variance estimates that when added to error variance estimates match the sample variance of phenotypes. This method also allows estimating the covariance between sets of markers when partitioning the genome into subunits. Large covariance estimates between the five Arabidopsis chromosomes indicated that the population structure in the data led to strong LD also between physically unlinked QTL. By consecutively removing population structure from the phenotypic variance using principal component analysis, we show how population structure affects the magnitude of LD contribution and the genomic variance estimates obtained with the two methods.

[Evaluation of an instrument assessing the satisfaction of ophthalmological emergency service users in Chile]. / Satisfacción usuaria en urgencia oftalmológica: evaluación de la consistencia interna y validez de constructo de un instrumento aplicado en Chile.

BACKGROUND: Ocular trauma is a distressing condition feared by the general public. AIM: To evaluate the construct validity and internal consistency of an instrument to measure the level of user satisfaction in patients treated at an Ocular Trauma and Ophthalmological Emergency Unit. MATERIAL AND METHODS: A survey to measure user satisfaction was applied to patients consulting at the Ocular Trauma Unit in a public hospital on April 2014. Internal consistency and construct validity from the estimated Cronbach alpha coefficient and factor analysis were assessed. RESULTS: Surveys answered by 138 patients aged 45 ± 15 years (93% men), were analyzed. The reliability obtained for the final questionnaire was 0.88. The factor analysis yielded four factors responsible for explaining 74.1% of the total variance, related to "quality of clinical information", "treatment by health care personnel", "lighting conditions, environment and noise" and "waiting time and overall assessment of service". CONCLUSIONS: These results allow to consider the instrument as a useful and reliable tool that can be applied to ophthalmological emergency service users in Chile.