A method to measure completeness of pedigree information is applied to populations of Holstein (registered and grade) and Jersey (largely registered) cows. Inbreeding coefficients where missing ...ancestors make no contribution were compared to a method using average relationships for missing ancestors. Estimated inbreeding depression was from an animal model that simultaneously adjusted for breeding values. Inbreeding and its standard deviation increased with more information, from 0.04±0.84 to 1.65±2.05 and 2.06±2.22 for grade Holsteins with <31%, 31 to 70%, and 71 to 100% complete five-generation pedigrees. Inbreeding from the method of average relationships for missing ancestors was 2.75±1.06, 3.10±2.21, and 2.89±2.37 for the same groups. Pedigrees of registered Holsteins and Jerseys were over 97% and over 89% complete, respectively. Inbreeding depression in days to first service and summit milk yield was estimated from both methods. Inbreeding depression for days to first service was not consistently significant for grade Holsteins and ranged from −0.37 d/1% increase in inbreeding (grade Holstein pedigrees <31% complete) to 0.15 d for grade Holstein pedigrees >70% complete. Estimates were similar for both methods. Inbreeding depression for registered Holsteins and Jerseys were positive (undesirable) but not significant for days to first service. Inbreeding depressed summit milk yield significantly in all groups by both methods. Summit milk yield declined by −0.12 to −0.06kg/d per 1% increase in inbreeding in Holsteins and by −0.08kg/1% increase in inbreeding in Jerseys. Pedigrees of grade animals are frequently incomplete and can yield misleading estimates of inbreeding depression. This problem is not overcome by inserting average relationships for missing ancestors in calculation of inbreeding coefficients.
The General Data Protection Regulation (GDPR) was introduced in 2018 to harmonize data privacy and security laws across the European Union (EU). It applies to any organization collecting personal ...data in the EU. To date, service-level consent has been used as a proportionate approach for clinical trials, which implement low-risk, routine, service-wide interventions for which individual consent is considered inappropriate. In the context of public health research, GDPR now requires that individuals have the option to choose whether their data may be used for research, which presents a challenge when consent has been given by the clinical service and not by individual service users. We report here on development of a pragmatic opt-out solution to this consent paradox in the context of a partner notification intervention trial in sexual health clinics in the UK. Our approach supports the individual's right to withhold their data from trial analysis while routinely offering the same care to all patients.
The effects of inbreeding on the lifetime performance of dairy cattle were examined using data for production, somatic cell score, and linear type for all Holstein cows that were scored between 1983 ...and 1993. The results of fixed and mixed animal models differed. Relative net income adjusted for opportunity cost for the 2,610,123 cows with an 84-mo opportunity for herdlife was depressed by $14.79 for fluid market pricing and by $12.40 for manufacturing pricing per 1% increase in inbreeding. Mixed model estimates of depression per 1% of increase in inbreeding were +0.55 d for age at first calving, –6 d for days of productive life, and –4.8 for days in milk. Inbreeding decreased the mature equivalent production of milk, fat, and protein during first lactation by 27, 0.9, and 0.8kg and the lifetime production of milk, fat, and protein by 177, 6.0, and 5.5kg, respectively, per 1% increase in inbreeding. Inbreeding had little effect on conformation traits. The effects of inbreeding were cumulative, and effects on lifetime profit functions were relatively larger than the effects on lactation traits. Registered cows had higher levels of inbreeding and larger standard deviations than did grade cows. Inbreeding in registered cows depressed relative net income adjusted for opportunity cost for fluid and manufacturing prices by $24.43 and $21.78, respectively; income was depressed $9.43 and $9.02, respectively, for grade cows. The difference between registered and grade cattle is likely due to the incomplete pedigree information in grade animals. Inbreeding among cows in this study was not high on average, but economic losses represented a significant cost to the producer.
Dystocia scores were recorded by producers on 120,434 Holsteins (218,213 records) from 1985 through 1996; dystocia scores 3 to 5 were coded as difficult births. Stillbirths were recorded for deaths ...within the first 48h after birth. Data were restricted to registered cows for pedigree completeness, and inbreeding coefficients were calculated using 5-generation pedigrees. Computational restrictions required that subsets of the data be created by choosing herds at random but using all records from selected herds. Effects of inbreeding in the dam were estimated in a sire-maternal grandsire (of the calf) threshold model using Gibbs sampling. The model included fixed effects of calf sex and inbreeding of the dam and random effects of herd-year-season of birth, additive genetic, and residual effects. First, second, and third parities were analyzed separately. Solutions for sex of calf and inbreeding from different parities were converted to expected change in probability of dystocia or stillbirth per 1% increase in inbreeding. Inbreeding effects were largest for first-parity cows giving birth to male calves at a 0.42% increase in probability of dystocia/1% increase in inbreeding. Effects of inbreeding for first-parity dams giving birth to female calves were smaller, 0.30%/1% increase in inbreeding. Incidence of stillbirths increased 0.25 and 0.20% for male and female calves/1% increase in inbreeding for first parity births. Effects of inbreeding on dystocia and stillbirths declined with parity. Effects of inbreeding were small, especially in later parities, but were consistently unfavorable.
First-lactation Holstein (HH), Jersey (JJ), and crossbred cows (HJ and JH, with sire breed listed first, followed by dam breed) were observed for cumulative energy intake (CEI15) and energy used for ...milk production (CEL15) at wk 15 of lactation in addition to recordings of health problems and pregnancy. Cumulative energy balance (CEB15) was calculated from CEI15 and estimates of expenditures at wk 15 of lactation. Feed efficiency (FE15) was calculated by dividing CEL15 by CEI15. Data included 140 cows with 43, 34, 41, and 22 in the HH, HJ, JH, and JJ groups, respectively. The first incidence of displaced abomasum (DA), ketosis (KET), mastitis (MAST), and metritis (MET) was recorded in the first 100 d of lactation with an incidence of the disease coded as 1 and no incidence coded as 0. Pregnancy (PREG) at d 150 was recorded as 1 if a cow had conceived by d 150 and 0 if she had not. Logistic regression was used to analyze health and fertility with fixed effects in the model including genetic group, linear and quadratic effects for age at calving, and year-season of freshening group. Pregnancy was analyzed with the same variables and the addition of CEB15. In other analyses, CEB15, CEI15, CEL15, and FE15 were response variables with the same explanatory variables plus health events (MAST, DA, MET, and KET), where each health event was a separate analysis. Genetic group effects were significant in the occurrence of MAST and a trend for MET, but were not significant for PREG, DA, and KET. Significant odds ratio for MAST was 19.6 for HJ cows when compared with that for HH cows. Thus, HJ cows were 19.6 times more likely than HH cows to have an incidence of MAST. The trend was for HJ and JH to have a lower odds ratio of MET than that of HH. No other genetic group effects were significant in any of the disease and PREG models. The linear and quadratic terms for age at calving were not significant. An occurrence of MAST decreased FE15 by 5.2±2.2%. Mastitis also decreased CEI15 and CEL15, but the compensatory reductions left the CEB15 unaffected. An occurrence of a DA decreased CEI15 and an incidence of KET decreased CEB15.
Inbreeding depression for 70-d nonreturn rate was estimated in 50,613 Holstein and 47,673 Jersey cows with five-generation pedigrees using an animal model. Heritabilities of 70-d nonreturn rate were ...very low for both breeds (1 to 2%). Maternal inbreeding depression was small (3% reduction for 10% inbreeding) and significant only for Jerseys. Fetal and maternal inbreeding depression was not significant for individual parities in Holsteins, but maternal inbreeding depression was significant in first parity only in Jerseys. Maternal and fetal inbreeding depression of calving rate (verified by a subsequent calving) was estimated on separate datasets by parity from 13,229 to 26,876 Holstein and 7374 to 11,742 Jersey cows. First-parity estimates for heritability of calving rate were 1% or less, whereas estimates for later parities varied from 1 to 6%. Significant inbreeding depression in first-parity Holsteins reduced calving rate by 4% per 10% maternal or fetal inbreeding, but effects, while undesirable, were not consistently significant in other parities. In Jerseys, maternal inbreeding significantly reduced calving rate by 6% per 10% inbreeding in first parity, and was undesirable but not significant for second through fourth parities. Fetal inbreeding depression was not significant in Jerseys. Maternal inbreeding depression of 70-d nonreturn and calving rate was small, undesirable, but not consistently significant across breeds and parities. The cumulative economic impact of maternal or fetal inbreeding on lifetime reproductive performance of Holstein or Jersey cows would be more dramatic than results for a single breeding.
This study explored whether seasonal and/or climatic factors influenced detection of specific genotypes of Pneumocystis jirovecii. Between 1989 and 2001, 155 isolates of P. jirovecii were obtained ...from patients undergoing bronchoscopic alveolar lavage. For each isolate, the month and climatic conditions were noted. Genotypes of P. jirovecii were distinguished by polymorphisms in the mitochondrial large-subunit rRNA gene. There were monthly and seasonal variations in the frequency of detection of mixed genotypes (p 0.018 and p 0.031, respectively) and genotype 2 (p 0.029 and p 0.086, respectively). There was no association between month/season and genotypes 1, 3 and 4, or between monthly temperature or rainfall and any genotype.
To provide nationally representative data on trends in HIV testing in primary care and to estimate the proportion of diagnosed HIV positive individuals known to general practitioners (GPs).
We ...undertook a retrospective cohort study between 1995 and 2005 of all general practices contributing data to the UK General Practice Research Database (GPRD), and data on persons accessing HIV care (Survey of Prevalent HIV Infections Diagnosed). We identified all practice-registered patients where an HIV test or HIV positive status is recorded in their general practice records. HIV testing in primary care and prevalence of recorded HIV positive status in primary care were estimated.
Despite 11-fold increases in male testing and 19-fold increases in non-pregnant female testing between 1995 and 2005, HIV testing rates remained low in 2005 at 71.3 and 61.2 tests per 100,000 person years for males and females, respectively, peaking at 162.5 and 173.8 per 100,000 person years at 25-34 years of age. Inclusion of antenatal tests yielded a 129-fold increase in women over the 10-year period. In 2005, 50.7% of HIV positive individuals had their diagnosis recorded with a lower proportion in London (41.8%) than outside the capital (60.1%).
HIV testing rates in primary care remain low. Normalisation of HIV testing and recording in primary care in antenatal testing has not been accompanied by a step change in wider HIV testing practice. Recording of HIV positive status by GPs remains low and GPs may be unaware of HIV-related morbidity or potential drug interactions.
Our objective was to evaluate breed differences for heat-stress resistance as reflected by age at first calving and first calving interval. We examined the effect of geographic location and birth ...season on age at first calving, and geographic location and first calving season on first calving interval on Holsteins and Jerseys, and Holsteins and Brown Swiss located on the same farm. We defined 7 regions within the United States: Northwest, Central north, Northeast, Central, Central south, Southwest, and Southeast, and analyzed 7 individual states: Ohio, Wisconsin, Oregon, California, Arizona, Texas, and Florida. Brown Swiss were older than Holsteins at first calving (833±2.4 vs. 806±2.0 d in regions, and 830±3.1 vs. 803±2.4 d in states), but Holsteins and Brown Swiss did not differ for first calving interval. Jerseys were younger than Holsteins at first calving and had shorter first calving intervals. In data from individual states, Holsteins housed with Brown Swiss were older at first calving than were Holsteins housed with Jerseys (800±2.7 vs. 780±2.5 d). Holsteins housed with one breed or the other were analyzed as a separate data set, and referred to as “type of Holstein.” The interaction of “type of Holstein” with first calving season was highly significant for first calving interval. Geographic location and season effects were smaller for Jerseys than for Holsteins; thus, Jerseys showed evidence of heat-stress resistance with respect to Holsteins. Management modified age at first calving in Holsteins to more nearly match that of the other breed. Longer calving intervals might be partly due to voluntary waiting period to breed the cows.
We present a measurement of the left-right cross-section asymmetry ( A(LR)) for Z boson production by e(+)e(-) collisions. The measurement includes the final data taken with the SLD detector at the ...SLAC Linear Collider during the period 1996-1998. Using a sample of 383 487 Z decays collected during the 1996-1998 runs we measure the pole value of the asymmetry, A(0)(LR), to be 0.150 56+/-0.002 39 which is equivalent to an effective weak mixing angle of sin (2)straight theta(eff)(W) = 0.231 07+/-0.000 30. Our result for the complete 1992-1998 data set comprising approximately 537 000 Z decays is sin (2)straight theta(eff)(W) = 0.230 97+/-0.000 27.
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