Effect of Johne's disease status on reproduction and culling in dairy cattle.

Among the costs attributed to Mycobacterium avium ssp. paratuberculosis (MAP) infection in dairy cattle, the effects on reproduction and culling are the least documented. To estimate the cost of MAP infections and Johne's disease in a dairy herd, the rates of calving and culling were calculated for cows in each stage of MAP infection relative to uninfected cows. Data from 6 commercial dairy herds, consisting of 2,818 cows with 2,754 calvings and 1,483 cullings, were used for analysis. Every cow in each study herd was tested regularly for MAP, and herds were followed for between 4 and 7 yr. An ordinal categorical variable for Johne's disease status [test-negative, low-positive (low-shedding or ELISA-positive only), or high-shedding] was defined as a time-dependent variable for all cows with at least 1 positive test result or 2 negative test results. A Cox regression model, stratified on herd and controlling for the time-dependent infection variable, was used to analyze time to culling. Nonshedding animals were significantly less likely to be culled in comparison with animals in the low-shedding or ELISA-positive category, and high-shedding animals had nonsignificantly higher culling rates than low-shedding or ELISA-positive animals. Time to calving was analyzed using a proportional rates model, an analog to the Andersen-Gill regression model suitable for recurrent event data, stratifying on herd and weighted to adjust for the dependent censoring caused by the culling effects described above. High-shedding animals had lower calving rates in comparison with low-shedding or ELISA-positive animals, which tended to have higher calving rates than test-negative animals.

Effects of diseases on reproductive performance in Swedish Red and White dairy cattle.

The objectives of this study were to evaluate the effect of diseases on days open (DO), days to first breeding (DFB) and days from first breeding to conception (DFBC) using survival analysis models, and to assess the significance of the sire component and its possible confounding effect. The data consisted of a random sample of 20% of all herds enrolled in Swedish recording system and using 100% artificial insemination with at least 15 Swedish Red and White cows calving in 1991. The follow-up period was from 45 to 145 d after calving. After editing, the data sets had 23,927, 28,197, and 22,089 cows for days open, days to first breeding, and days from first breeding to conception, respectively. The Cox models included parity, calving season, cow milk production and age at first calving as fixed effects, and herd and sire as random effects. Ten disease groups were considered as possible risk factors for the reproductive traits. Disease groups were treated differently if they occurred before or after 45 d postpartum. Diseases occurring in the first 45 d after calving were treated as time-independent covariates and diseases occurring after day 45 were treated as time-dependent covariates for days open and days to first breeding. The percentages of censored cows were 35% for days open, 19% for days to first breeding, and 33% for days from first breeding to conception. Days open increased in cows with dystocia, stillbirth, retained placenta, metritis, or other diseases occurring in the first 45 d after calving, and in cows with metritis, mastitis, or other diseases occurring after 45 d. Days to first breeding increased in cows with stillbirth, retained placenta, milk fever, mastitis, foot and leg problems, or other diseases occurring before day 45, and in cows with metritis, mastitis, foot and leg problems, or other diseases occurring after 45 d. Days to first breeding decreased in cows treated for ovulatory dysfunctions either before or after 45 d. Days from first breeding to conception increased in cows with dystocia, stillbirth, retained placenta, metritis, or ovulatory dysfunctions occurring before first breeding, and in cows with mastitis occurring after first breeding. Although the additive genetic components were significant for all traits considered, the sires did not act as confounders because only a small amount of variability for the traits considered in this study was explained by the sires, with estimated heritabilities of 2% on the logarithmic scale and from 3 to 4% on the real scale.

Clinical significance of histological classification of idiopathic interstitial pneumonia.

Patients with idiopathic interstitial pneumonias (IIPs) can be subdivided into groups based on the histological appearance of lung tissue obtained by surgical biopsy. The quantitative impact of histological diagnosis, baseline factors and response to therapy on survival has not been evaluated. Surgical lung biopsy specimens from 168 patients with suspected IIP were reviewed according to the latest diagnostic criteria. The impact of baseline clinical, physiological, radiographic and histological features on survival was evaluated using Cox regression analysis. The predictive value of honeycombing on high-resolution computed tomography (HRCT) as a surrogate marker for usual interstitial pneumonia (UIP) was examined. The response to therapy and survival of 39 patients treated prospectively with high-dose prednisone was evaluated. The presence of UIP was the most important factor influencing mortality. The risk ratio of mortality when UIP was present was 28.46 (95% confidence interval (CI) 5.5-148.0; p=0.0001) after controlling for patient age, duration of symptoms, radiographic appearance, pulmonary physiology, smoking history and sex. Honeycombing on HRCT indicated the presence of UIP with a sensitivity of 90% and specificity of 86%. Patients with nonspecific interstitial pneumonia were more likely to respond or remain stable (9 of 10) compared to patients with UIP (14 of 29) after treatment with prednisone. Patients remaining stable had the best prognosis. The risk ratio of mortality for stable patients compared to nonresponders was 0.32 (95% CI 0.11-0.93; p=0.04) in all patients and 0.33 (95% CI 0.12-0.96; p=0.04) in patients with UIP. The histological diagnosis of usual interstitial pneumonia is the most important factor determining survival in patients with suspected idiopathic interstitial pneumonia. The presence of honeycombing on high-resolution computed tomography is a good surrogate for usual interstitial pneumonia and could be utilized in patients unable to undergo surgical lung biopsy. Patients with nonspecific interstitial pneumonia are more likely to respond or remain stable following a course of prednisone. Patients remaining stable following prednisone therapy have the best prognosis.

Histopathologic variability in usual and nonspecific interstitial pneumonias.

Findings of surgical lung biopsy (SLB) are important in categorizing patients with idiopathic interstitial pneumonia (IIP). We investigated whether histologic variability would be evident in SLB specimens from multiple lobes in patients with IIP. SLBs from 168 patients, 109 of whom had multiple lobes biopsied, were reviewed by three pathologists. A diagnosis was assigned to each lobe. A different diagnosis was found between lobes in 26% of the patients. Patients with usual interstitial pneumonia (UIP) in all lobes were categorized as concordant for UIP (n = 51) and those with UIP in at least one lobe were categorized as discordant for UIP (n = 28). Patients with nonspecific interstitial pneumonia (NSIP) in all lobes were categorized as having fibrotic (n = 25) or cellular NSIP (n = 5). No consistent distribution of lobar histology was noted. Patients concordant for UIP were older (63 +/- 9 [mean +/- SD] yr; p < 0.05 as compared with all other groups) than those discordant for UIP (57 +/- 12 yr) or with fibrotic NSIP (56 +/- 11 yr) or cellular NSIP (50 +/- 9 yr). Semiquantitative high-resolution computed tomography demonstrated a varied profusion of fibrosis (p < 0.05 for all group comparisons), with more fibrosis in concordant UIP (2.13 +/- 0.62) than in discordant UIP (1.42 +/- 0.73), fibrotic NSIP (0.83 +/- 0.58), or cellular NSIP (0.44 +/- 0.42). Survival was better for patients with NSIP than for those in both UIP groups (p < 0.001), although survival in the two UIP groups was comparable (p = 0.16). Lobar histologic variability is frequent in patients with IIP, patients with a histologic pattern of UIP in any lobe should be classified as having UIP.

Steroids in idiopathic pulmonary fibrosis: a prospective assessment of adverse reactions, response to therapy, and survival.

PURPOSE: We evaluated the risk and potential benefit of high-dose corticosteroid therapy in patients with idiopathic pulmonary fibrosis. SUBJECTS AND METHODS: We prospectively studied 41 patients with previously untreated, biopsy-proven idiopathic pulmonary fibrosis. Before treatment, we calculated clinical, radiographic, and physiologic severity-of-illness scores for each patient. We scored high-resolution computerized tomographic (CT) scans for ground glass and interstitial opacity. We determined the extent of cellular infiltration, interstitial fibrosis, desquamation, and granulation in open lung biopsy samples. Patients were monitored monthly for steroid-related side effects, response to therapy at 3 months, and mortality. RESULTS: All patients experienced at least one steroid-induced side effect. Eleven (27%) patients were nonresponders, 11 (27%) were responders, and 19 (46%) remained stable. Of the 19 patients who died during a mean (+/- SD) follow-up of 3.3 +/- 2.3 years, 8 (42%) lost weight during the initial 3 months of steroid therapy; only 3 (14%) of the 22 patients still living (P = 0.08) experienced weight loss. In a multivariate analysis, greater fibrosis (hazard ratio [HR] = 1.4 per unit increase; 95% confidence interval [CI]: 1.0 to 1.9; P = 0.03) and cellularity (RR = 1.9 per unit increase; 95% CI: 1.3 to 2.8; 3, P <0.001) in the biopsy sample and whether a patient was classified as a responder (RR = 0.4 versus nonresponder; 95% CI: 0.2 to 1.0; P = 0.05) or stable (RR = 0.2 versus nonresponder; 95% CI: 0.1 to 0.6, P <0.001) after steroid therapy were associated with mortality. CONCLUSION: Corticosteroid treatment for idiopathic pulmonary fibrosis is associated with substantial morbidity. Patients who remain stable or respond to corticosteroid therapy have better survival than those who fail to respond. Whether this difference reflects an effect of treatment or less severe disease can be determined only in a randomized trial.

Cross-sectional and longitudinal predictors of serum albumin in hemodialysis patients.

BACKGROUND: Lower serum albumin concentrations predict increased mortality in hemodialysis (HD) patients. Many demographic, comorbidity, and modifiable treatment-related factors that predict HD patient outcomes may be associated with serum albumin. METHODS: Cross-sectional predictors of baseline albumin on December 31, 1993 were sought (N = 3981). Additional effects of the same baseline predictors on subsequent trends in albumin over one year were examined in a nested subsample of patients (N = 2245). Wave-1 of the United States Renal Data System Dialysis Morbidity and Mortality special study provided the data. RESULTS: Significant associations (P < 0.05) are summarized as older age, female gender, peripheral vascular disease, chronic obstructive pulmonary disease, and cancer predicted a lower baseline albumin and negatively influenced subsequent albumin trends. Baseline albumin was higher for blacks (vs. whites), lower for smoking and diabetes, and lower during the first year of HD treatment (<3 months and 3 to 12 months, vs.> 1 year). Trend analysis showed more positive albumin slopes for patients in their first year on HD and more negative slopes for Native Americans (vs. whites). Baseline albumin was correlated with the type of vascular access being used [arteriovenous (AV) fistulas > AV grafts > permanent catheters > temporary catheters]. Trend analysis predicted more negative albumin slopes for AV grafts and permanent catheters (vs. AV fistula access). Baseline albumin correlated inversely with bicarbonate and directly with hematocrit. Dialysis with unmodified cellulose membranes, without reuse, predicted lower baseline albumin than the other membrane-reuse categories. CONCLUSIONS: Several exposures, which may be modifiable, were associated with serum albumin.

Respiratory response during arm elevation in isolated diaphragm weakness.

Upper extremity exercise is associated with a significant metabolic and ventilatory cost that is particularly evident in patients with severe chronic airflow obstruction. In these patients abnormal ventilatory muscle recruitment has been hypothesized to relate to impaired diaphragm function resulting from hyperinflation. Similar data have never been reported in patients with isolated diaphragm weakness but without airflow obstruction or hyperinflation, a group that would ideally define the role of diaphragm function during arm elevation (AE). We prospectively studied 15 patients with isolated diaphragm weakness of varying severity (Pdi(sniff), 31.74 +/- 3.75 cm H(2)O) as contrasted with eight normal subjects (Pdi(sniff), 111. 77 +/- 13.35 cm H(2)O) of similar age. Patients with diaphragm weakness demonstrated significant lung volume restriction with normal DL(CO)/VA. There was no difference in resting oxygen consumption (V O(2)), carbon dioxide production (V CO(2)), minute ventilation (V E), and tidal volume (VT) between the two groups; however, a borderline difference in resting breathing frequency (f(b)) (p = 0.056) was evident. Both groups demonstrated a rise in V O(2), V CO(2), and V E during 2 min of AE anteriorly. Normal subjects demonstrated a statistically significant rise in VT but a statistically insignificant rise in f(b) during AE. In contrast, patients with diaphragm weakness demonstrated a statistically significant rise in f(b) during AE but a statistically insignificant rise in VT. In patients the observed rise in VT directly correlated with baseline Pdi(sniff) (r = 0.59, p = 0.02) and Pdi(max) (r = 0.81, p = 0.002). Both groups demonstrated a rise in Pdi during AE. The rise in Pdi during AE directly correlated to Pdi(sniff) in the patients (r = 0.69, p = 0.004). Observed end-expiratory Ppl rose during arm elevation in both the patient group and in the normal control group, but no evidence of a differential response to AE was found. In those patients with greater diaphragm weakness (Pdi(sniff) < 30 cm H(2)O), abnormal respiratory muscle function (lesser rise in Pdi) and a lesser increase in VT during AE were more evident. These data highlight the importance of diaphragm function in determining the metabolic and respiratory muscle response to arm elevation.

Simple nutritional indicators as independent predictors of mortality in hemodialysis patients.

A strong association exists between nutritional status and morbidity and mortality in patients with end-stage renal disease who are treated with hemodialysis. Described here is the predictive value for mortality over 5 years of follow-up of a number of risk factors, recorded at baseline, in a national sample of 3,607 hemodialysis patients. Among the variables studied were case-mix covariates, caregiver classifications of nutritional status, serum albumin concentration, and body mass index (BMI). The Case Mix Adequacy special study of the United States Renal Data System (USRDS) provided these measurements as of December 31, 1990. The USRDS patient standard analysis file provided follow-up data on mortality for all patients through December 31, 1995, by which time 64.7% of the patients had died. BMI is a simple anthropometric measurement that has received little attention in dialysis practice. Caregiver classification refers to documentation in a patient's dialysis facility medical records that stated an individual to be "undernourished/cachectic," "obese/overweight," or "well-nourished." The mean serum albumin was 3.7 +/- 0.45 (SD) g/dL, and the mean BMI was 24.4 +/- 5.3 (SD) kg/m2. By caregiver classification, 20.1% of patients were undernourished, and 24.9% obese. In hazard regression models, including but not limited to the Cox proportional hazards model, low BMI, low serum albumin, and the caregiver classification "undernourished" were independently and significantly predictive of increased mortality. In analyses allowing for time-varying relative mortality risks (ie, nonproportional hazards), the greatest predictive value of all three variables occurred early during follow-up, but the independent predictive value of baseline serum albumin and BMI measurements on mortality risk persisted even 5 years later. No evidence of increasing mortality risk was found for higher values of BMI. Serum albumin was confirmed to be a useful predictor of mortality risk in hemodialysis patients; BMI was established as an independently important predictor of mortality; both serum albumin and BMI, measured at baseline, continue to possess predictive value 5 years later; the subjective caregiver classification of nutritional status "undernourished" has independent value in predicting mortality risk beyond the information gained from two other markers of nutritional status--BMI and serum albumin.

Growth rates in pediatric dialysis patients and renal transplant recipients.

We compared growth rates by modality over a 6- to 14-month period in 1,302 US pediatric end-stage renal disese (ESRD) patients treated during 1990. Modality comparisons were adjusted for age, sex, race, ethnicity, and ESRD duration using linear regression models by age group (0.5 to 4 years, 5 to 9 years, 10 to 14 years, and 15 to 18 years). Growth rates were higher in young children receiving a transplant compared with those receiving dialysis (ages 0.5 to 4 years, delta = 3.1 cm/yr v continuous cycling peritoneal dialysis [CCPD], P < 0.01; ages 5 to 9 years, delta = 2.0 to 2.6 cm/yr v CCPD, chronic ambulatory peritoneal dialysis (CAPD), and hemodialysis, P < 0.01). In contrast, growth rates in older children were not statistically different when comparing transplantation with each dialysis modality. For most age groups of transplant recipients, we observed faster growth with alternate-day versus daily steroids that was not fully explained by differences in allograft function. Younger patients (<15 years) grew at comparable rates with each dialysis modality, while older CAPD patients grew faster compared with hemodialysis or CCPD patients (P < 0.02). There was no substantial pubertal growth spurt in transplant or dialysis patients. This national US study of pediatric growth rates with dialysis and transplantation shows differences in growth by modality that vary by age group.

Vascular access survival among incident hemodialysis patients in the United States.

Vascular access failure causes substantial morbidity to hemodialysis patients. We sought to identify factors determining survival of the permanent vascular access in use at the start of end-stage renal disease during 1990 in a national sample of 784 incident hemodialysis patients insured by Medicare. Medicare claims records were used to identify access failures or revisions among patients with an arteriovenous (AV) fistula (n = 245) and an AV vascular graft (n = 539). A proportional hazards analysis of time to first failure or revision, controlled by stratification for sex, race, and cause of end-stage renal disease, was used to determine the effect of age, access type, and peripheral vascular disease on vascular access survival. Patients with an AV fistula and who were older than 65 years had a risk of access failure that was 24% lower than similar patients with an AV graft (P < 0.02). The relative risk of access failure for an AV fistula, but not an AV graft, varied significantly with age for patients younger than 65 years (P < 0.01). The relative risk of access failure for a patient with an AV fistula, compared with a patient of the same age with an AV graft, was 67% lower at the age of 40 years, 54% lower at the age of 50 years, and 24% lower at the age of 65 years. A history of peripheral vascular disease was associated with a 24% higher risk of AV graft or fistula failure (P = 0.05). Measures to decrease vascular access-related morbidity among hemodialysis patients should include reversing the current trend toward increasing use of AV grafts, particularly in patients younger than 65 years.

An asymptotic analysis of the logrank test.

Asymptotic expansions for the null distribution of the logrank statistic and its distribution under local proportional hazards alternatives are developed in the case of iid observations. The results, which are derived from the work of Gu (1992) and Taniguchi (1992), are easy to interpret, and provide some theoretical justification for many behavioral characteristics of the logrank test that have been previously observed in simulation studies. We focus primarily upon (i) the inadequacy of the usual normal approximation under treatment group imbalance; and, (ii) the effects of treatment group imbalance on power and sample size calculations. A simple transformation of the logrank statistic is also derived based on results in Konishi (1991) and is found to substantially improve the standard normal approximation to its distribution under the null hypothesis of no survival difference when there is treatment group imbalance.

Accurate confidence limits for quantiles under random censoring.

In survival analysis, estimates of median survival times in homogeneous samples are often based on the Kaplan-Meier estimator of the survivor function. Confidence intervals for quantiles, such as median survival, are typically constructed via large sample theory or the bootstrap. The former has suspect accuracy for small sample sizes under moderate censoring and the latter is computationally intensive. In this paper, improvements on so-called test-based intervals and reflected intervals (cf., Slud, Byar, and Green, 1984, Biometrics 40, 587-600) are sought. Using the Edgeworth expansion for the distribution of the studentized Nelson-Aalen estimator derived in Strawderman and Wells (1997, Journal of the American Statistical Association 92), we propose a method for producing more accurate confidence intervals for quantiles with randomly censored data. The intervals are very simple to compute, and numerical results using simulated data show that our new test-based interval outperforms commonly used methods for computing confidence intervals for small sample sizes and/or heavy censoring, especially with regard to maintaining specified coverage.

Using USRDS generated hospitalization tables to compare local dialysis patient hospitalization rates to national rates.

Hospitalization tables of the U.S. Renal Data System allow description of national hospitalization rates among incident and prevalent dialysis patients in five-year age groups. These rates are further stratified by sex, race, and four primary disease categories. Based on these tables derived from the data on over 250,000 incident and prevalent patients during 1991 to 1993, a methodology is described that allows comparison of local (for example, dialysis facility) or regional "first admission" rates among incident and prevalent dialysis patients to the national rates. A standardized hospitalization ratio is introduced to facilitate such comparisons, and methods for assessing statistical significance are discussed. Since this methodology allows adjustment for age, race, sex, and primary disease, it can serve as useful tool for dialysis research. It can also be used at the dialysis facility level, alone or in conjunction with the standardized mortality ratio, to facilitate local quality assurance.

Logical and statistical fallacies in the use of Cox regression models.

Time-dependent covariates are an essential data analysis tool for modeling the effect of a study factor whose value changes during follow-up. However, survival analysis models can yield conclusions that are contrary to the truth if such time-dependent factors are not defined and used carefully. We outline some of the biases that can occur when time-dependent covariates are used improperly in a Cox regression model. For example, we discuss why one should almost never use a covariate that has been averaged over a patient's entire follow-up time as a baseline covariate. Instead, the baseline value should be used as a covariate, or the cumulative average up to each point in time should be used as a time-dependent covariate. We also document why one should use time-dependent covariates with great caution in analyses when the evaluation of a baseline factor is the primary objective. Several simulated examples are given to illustrate the direction and magnitude of the biases that can result from not adhering to some basic assumptions that underlie all survival analysis methodologies.