A fast method for implementing Generalized Cross-Validation in multi-dimensional nonparametric regression

This article presents a modified Newton method for minimizing the Generalized Cross-Validation criterion, a commonly used smoothing parameter selection method in nonparametric regression. The method is applicable to higher dimensional problems such as additive and generalized additive models, and provides a computationally efficient alternative to full grid search in such cases. The implementation of the proposed method requires the estimation of a number of auxiliary quantities, and simple estimators are suggested. This article describes the methodology for local polynomial regression smoothing

Local Likelihood Estimation in Generalized Additive Models

Generalized additive models are a popular class of multivariate nonparametric regression models, due in large part to the ease of use of the local scoring estimation algorithm. However, the theoretical properties of the local scoring estimator are poorly understood. In this article, we propose a local likelihood estimator for generalized additive models that is closely related to the local scoring estimator fitted by local polynomial regression. We derive the statistical properties of the estimator and show that it achieves the same asymptotic convergence rate as a one-dimensional local polynomial regression estimator. We also propose a wild bootstrap estimator for calculating pointwise confidence intervals for the additive component functions. The practical behavior of the proposed estimator is illustrated through simulation experiments and an example

Environmental effects on progesterone profile measures of dairy cow fertility

Environmental effects on fertility measures early in lactation, such as the interval from calving to first luteal activity (CLA), proportion of samples with luteal activity during the first 60 days after calving (PLA) and interval to first ovulatory oestrus (OOE) were studied. In addition, traditional measurements of fertility, such as pregnancy to first insemination, number of inseminations per service period and interval from first to last insemination were studied as well as associations between the early and late measurements. Data were collected from an experimental herd during 15 years and included 1106 post-partum periods from 191 Swedish Holsteins and 325 Swedish Red and White dairy cows. Individual milk progesterone samples were taken twice a week until cyclicity and thereafter less frequently. First parity cows had 14.8 and 18.1 days longer CLA (LS-means difference) than second parity cows and older cows, respectively. Moreover, CLA was 10.5 days longer for cows that calved during the winter season compared with the summer season and 7.5 days longer for cows in tie-stalls than cows in loose-housing system. Cows treated for mastitis and lameness had 8.4 and 18.0 days longer CLA, respectively, compared with healthy cows. OOE was affected in the same way as CLA by the different environmental factors. PLA was a good indicator of CLA, and there was a high correlation (−0.69) between these two measurements. Treatment for lameness had a significant influence on all late fertility measurements, whereas housing was significant only for pregnancy to first insemination. All fertility traits were unfavourably associated with increased milk production. Regression of late fertility measurements on early fertility measurements had only a minor association with conception at first AI and interval from first to last AI for cows with conventional calving intervals, i.e. a 22 days later, CLA increased the interval from first to last insemination by 3.4 days. Early measurements had repeatabilities of 0.14–0.16, indicating a higher influence by the cow itself compared with late measurements, which had repeatabilities of 0.09–0.10. Our study shows that early fertility measurements have a possibility to be used in breeding for better fertility. To improve the early fertility of the cow, there are a number of important factors that have to be taken into account

Influence of the Cu-Te composition and microstructure on the resistive switching of Cu-Te/Al(2)O(3)/Si cells

In this letter, we explore the influence of the Cu(x)Te(1-x) layer composition (0.2 0.7 leads to large reset power, similar to pure-Cu electrodes, x < 0.3 results in volatile forming properties. The intermediate range 0.5< x < 0.7 shows optimum memory properties, featuring improved control of filament programming using <5 mu A as well as state stability at 85 degrees C. The composition-dependent programming control and filament stability are closely associated with the phases in the Cu(x)Te(1-x) layer and are explained as related to the chemical affinity between Cu and Te. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3621835

Te-based chalcogenide materials for selector applications

The implementation of dense, one-selector one-resistor (1S1R), resistive switching memory arrays, can be achieved with an appropriate selector for correct information storage and retrieval. Ovonic threshold switches (OTS) based on chalcogenide materials are a strong candidate, but their low thermal stability is one of the key factors that prevents rapid adoption by emerging resistive switching memory technologies. A previously developed map for phase change materials is expanded and improved for OTS materials. Selected materials from different areas of the map, belonging to binary Ge-Te and Si-Te systems, are explored. Several routes, including Si doping and reduction of Te amount, are used to increase the crystallization temperature. Selector devices, with areas as small as 55 x 55 nm(2), were electrically assessed. Sub-threshold conduction models, based on Poole-Frenkel conduction mechanism, are applied to fresh samples in order to extract as-processed material parameters, such as trap height and density of defects, tailoring of which could be an important element for designing a suitable OTS material. Finally, a glass transition temperature estimation model is applied to Te-based materials in order to predict materials that might have the required thermal stability. A lower average number of p-electrons is correlated with a good thermal stability

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including , , , , and inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows

Assessment of associations between transition diseases and reproductive performance of dairy cows using survival analysis and decision tree algorithms

This study aimed to evaluate the associations between transition cow conditions and diseases TD with fertility in Holstein cows, and to compare analytic methods for doing so. Kaplan-Meier, Cox proportional hazard, and decision tree models were used to analyze the associations of TD with the pregnancy risk at 120 and 210 DIM from a 1-year cohort with 1946 calvings from one farm. The association between TD and fertility was evaluated as follows: 1 cows with TD whether complicated with another TD or not TD-all, versus healthy cows, and 2 cows with uncomplicated TD TD-single, versus cows with multiple TD TD+; complicated cases, versus healthy cows. The occurrence of twins, milk fever, retained placenta, metritis, ketosis, displaced abomasum, and clinical mastitis were recorded. Using Kaplan-Meier models, in primiparous cows the 120 DIM pregnancy risk was 62% (95% CI: 57-67 %) for healthy animals. This was not significantly different for TD-single (58%; 95% CI: 51-66 %) but was reduced for TD+ (45%; 95% CI: 33-60 %). Among healthy primiparous cows, 80% (95% CI: 75-84 %) were pregnant by 210 DIM, but pregnancy risk at that time was reduced for primiparous cows with TD-single (72%; 95% CI: 65-79 %) and TD+ (62%; 95% CI: 49-75 %). In healthy multiparous cows, the 120 DIM pregnancy risk was 53% (95% CI: 49-56 %), which was reduced for TD-single (36%; 95% CI: 31-42 %) and TD+ (30%; 95% CI: 24-38 %). The 210 DIM pregnancy risk for healthy multiparous cows was 70% (95% CI: 67-72 %), being higher than the 210 DIM pregnancy risk for multiparous cows with TD-single (47%; 95% CI: 42-53 %) or TD+ (46%; 95% CI: 38-54 %). Cows with TD-all presented similar pregnancy risk estimates as for TD+. Cox proportional hazards regressions provided similar magnitudes of effects as the Kaplan-Meier estimates. Survival analysis and decision tree models identified parity as the most influential variable affecting fertility. Both modeling techniques concurred that TD + had a greater effect than TD-single on the probability of pregnancy at 120 and 210 DIM. Decision trees for individual TD identified that displaced abomasum affected fertility at 120 DIM in primiparous while metritis was the most influential TD at 120 and 210 DIM for multiparous cows. The data were too sparse to assess multiple interactions in multivariable Cox proportional hazard models for individual TD. Machine learning helped to explore interactions between individual TD to study their hierarchical effect on fertility, identifying conditional relationships that merit further investigation

Effect of yeast culture on milk production and metabolic and reproductive performance of early lactation dairy cows

<p>Abstract</p> <p>Background</p> <p>The main objective of this study was to estimate the effect of supplementation with <it>Saccaromyces cerevisiae (SC</it>) (Yea-Sacc^®1026) on milk production, metabolic parameters and the resumption of ovarian activity in early lactation dairy cows.</p> <p>Methods</p> <p>The experiment was conducted during 2005/2006 in a commercial tied-house farm with an average of 200 milking Estonian Holstein Friesian cows. The late pregnant multiparous cows (n = 46) were randomly divided into two groups; one group received 10 g yeast culture from two weeks before to 14 weeks after calving. The groups were fed a total mixed ration with silages and concentrates. Milk recording data and blood samples for plasma metabolites were taken. Resumption of luteal activity was determined using milk progesterone (P₄) measurements. Uterine bacteriology and ovarian ultrasonography (US) were performed and body condition scores (BCS) and clinical disease occurrences were recorded. For analysis, the statistical software Stata 9.2 and R were used to compute Cox proportional hazard and linear mixed models.</p> <p>Results</p> <p>The average milk production per cow did not differ between the groups (32.7 ± 6.4 vs 30.7 ± 5.3 kg/day in the SC and control groups respectively), but the production of milk fat (<it>P </it>< 0.001) and milk protein (<it>P </it>< 0.001) were higher in the SC group. There was no effect of treatment on BCS. The analysis of energy-related metabolites in early lactation showed no significant differences between the groups. In both groups higher levels of β-hydroxybutyrate (BHB) appeared from days 14 to 28 after parturition and the concentration of non-esterfied fatty acid (NEFA) was higher from days 1–7 post partum (PP). According to US and P₄results, all cows in both groups ovulated during the experimental period. The resumption of ovarian activity (first ovulations) and time required for elimination of bacteria from the uterus did not differ between the groups.</p> <p>Conclusion</p> <p>Supplementation with SC had an effect on milk protein and fat production, but did not influence the milk yield. No effects on PP metabolic status, bacterial elimination from the uterus nor the resumption of ovarian activity were found.</p

Internal validity of a household food security scale is consistent among diverse populations participating in a food supplement program in Colombia

Objective: We assessed the validity of a locally adapted Colombian Household Food Security Scale (CHFSS) used as a part of the 2006 evaluation of the food supplement component of the Plan for Improving Food and Nutrition in Antioquia, Colombia (MANA – Plan Departamental de Seguridad Alimentaria y Nutricional de Antioquia). Methods: Subjects included low-income families with pre-school age children in MANA that responded affirmatively to at least one CHFSS item (n = 1,319). Rasch Modeling was used to evaluate the psychometric characteristics of the items through measure and INFIT values. Differences in CHFSS performance were assessed by area of residency, socioeconomic status and number of children enrolled in MANA. Unidimensionality of a scale by group was further assessed using Differential Item Functioning (DIF). Results: Most CHFSS items presented good fitness with most INFIT values within the adequate range of 0.8 to 1.2. Consistency in item measure values between groups was found for all but two items in the comparison by area of residency. Only two adult items exhibited DIF between urban and rural households. Conclusion: The results indicate that the adapted CHFSS is a valid tool to assess the household food security of participants in food assistance programs like MANA