Mario Hasler

Multiple Contrast Tests in the Presence of Heteroscedasticity

This paper proposes a general approach for handling multiple contrast tests for normally distributed data in the presence of heteroscedasticity. Three candidate procedures are described and compared by simulations. Only the procedure with both comparison-specific degrees of freedom and a correlation matrix depending on sample variances maintains the alpha-level over all situations. Other approaches may fail notably as the variances differ more. Furthermore, related approximate simultaneous confidence intervals are given. The approach will be applied to a toxicological experiment.

Proof of Hazard and Proof of Safety in Toxicological Studies Using Simultaneous Confidence Intervals for Differences and Ratios to Control

Simultaneous confidence interval for differences or ratios to control are described for both the proof of hazard and the proof of safety for the typical design in toxicology including several doses and a control. For most endpoints the direction of harmfulness is a priori known; therefore one-sided confidence intervals for Gaussian distributed endpoints, proportions, and poly-k-adjusted tumor rates are used. Special packages in the software R are provided to estimate these confidence intervals. Real data examples are given to demonstrate the estimation of the confidence intervals and their interpretation for selected toxicological studies.

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures

Plant-derived protein sources are the most relevant substitutes for fishmeal in aquafeeds. Nevertheless, the effects of plant based diets on the intestinal microbiome especially of juvenile Rainbow trout (Oncorhynchus mykiss) are yet to be fully investigated. The present study demonstrates, based on 16S rDNA bacterial community profiling, that the intestinal microbiome of juvenile Rainbow trout is strongly affected by dietary plant protein inclusion levels. After first feeding of juveniles with either 0%, 50% or 97% of total dietary protein content derived from plants, statistically significant differences of the bacterial gut community for the three diet-types were detected, both at phylum and order level. The microbiome of juvenile fish consisted mainly of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria, and thus fits the salmonid core microbiome suggested in previous studies. Dietary plant proteins significantly enhanced the relative abundance of the orders Lactobacillales, Bacillales and Pseudomonadales. Animal proteins in contrast significantly promoted Bacteroidales, Clostridiales, Vibrionales, Fusobacteriales and Alteromonadales. The overall alpha diversity significantly decreased with increasing plant protein inclusion levels and with age of experimental animals. In order to investigate permanent effects of the first feeding diet-type on the early development of the microbiome, a diet change was included in the study after 54 days, but no such effects could be detected. Instead, the microbiome of juvenile trout fry was highly dependent on the actual diet fed at the time of sampling.

A Multivariate Williams-Type Trend Procedure

A modified Williams-type approach is proposed, which controls the family-wise error rate globally over both correlated endpoints and over dose comparisons. This order-restricted procedure is formulated for ratio-to-control comparisons, where the comparison of difference-to-control is included directly. Endpoint-specific variances are allowed, and even a modification for dose-group-specific variance heterogeneity is proposed. Therefore, this approach can be used simply for evaluation of real data by means of the R package SimComp. Both multiplicity-adjusted p-values and simultaneous confidence intervals are provided, whereas confidence intervals are clearly recommended to allow the interpretation for clinical relevance.

Effect of dietary Quebracho tannin extract on feed intake, digestibility, excretion of urinary purine derivatives and milk production in dairy cows

ABSTRACT The aim of this study was to evaluate the effects of dietary Quebracho tannin extract (QTE) on feed intake, apparent total tract digestibility (ATTD), excretion of urinary purine derivatives (PD) and milk composition and yield in dairy cows. Fifty Holstein cows were divided into two groups. To reach a similar performance of both groups, cows were divided according to their milk yield, body weight, days in milk and number of lactations at the start of the experiment averaging 33.2 ± 8.2 kg/d, 637 ± 58 kg, 114 ± 73 d and 2.3 ± 1.6 lactations, respectively. The cows were fed a basal diet as total mixed ration containing on dry matter (DM) basis 34% grass silage, 32% maize silage and 34% concentrate feeds. Three dietary treatments were tested, the control (CON, basal diet without QTE), QTE15 (basal diet with QTE at 15 g/kg DM) and QTE30 (basal diet with QTE at 30 g/kg DM). Two treatments were arranged along six periods each 21 d (13 d adaptation phase and 8 d sampling phase). The ATTD of DM and organic matter were reduced only in Diet QTE30, whereas both QTE treatments reduced ATTD of fibre and nitrogen (N), indicating that QTE impaired rumen fermentation. Nevertheless, feed intake was unaffected by QTE. In Diet CON, urinary N excretion accounted for 29.8% of N intake and decreased in treatments QTE15 and QTE30 to 27.5% and 17.9%, respectively. Daily faecal N excretion increased in treatments CON, QTE15 and QTE30 from 211 to 237 and 273 g/d, respectively, which amounted to 39.0%, 42.4% and 51.7% of the N intake, respectively. Hence, QTE shifted N excretion from urine to faeces, whereas the proportion of ingested N appearing in milk was not affected by QTE (average 30.7% of N intake). Daily PD excretion as indicator for microbial crude protein (CP) flow at the duodenum decreased in treatment QTE30 compared with Diet CON from 413 to 280 mmol/d. The ratios of total PD to creatinine suggest that urinary PD excretion was already lower when feeding Diet QTE15. While there was no effect of Diet QTE15, treatment QTE30 reduced milk yield, milk fat and protein. Both QTE treatments reduced milk urea concentration, which suggest that ruminal degradation of dietary CP was reduced. In summary, adding QTE at dosages of 15 and 30 g/kg DM to diets of lactating dairy cows to improve feed and protein use efficiency is not recommended.

Fast responses of metabolites in Vicia faba L. to moderate NaCl stress

Salt stress impairs global agricultural crop production by reducing vegetative growth and yield. Despite this importance, a number of gaps exist in our knowledge about very early metabolic responses that ensue minutes after plants experience salt stress. Surprisingly, this early phase remains almost as a black box. Therefore, systematic studies focussing on very early plant physiological responses to salt stress (in this case NaCl) may enhance our understanding on strategies to develop crop plants with a better performance under saline conditions. In the present study, hydroponically grown Vicia faba L. plants were exposed to 90 min of NaCl stress, whereby every 15 min samples were taken for analyzing short-term physiologic responses. Gas chromatography-mass spectrometry-based metabolite profiles were analysed by calculating a principal component analysis followed by multiple contrast tests. Follow-up experiments were run to analyze downstream effects of the metabolic changes on the physiological level. The novelty of this study is the demonstration of complex stress-induced metabolic changes at the very beginning of a moderate salt stress in V. faba, information that are very scant for this early stage. This study reports for the first that the proline analogue trans-4-hydroxy-L-proline, known to inhibit cell elongation, was increasingly synthesized after NaCl-stress initiation. Leaf metabolites associated with the generation or scavenging of reactive oxygen species (ROS) were affected in leaves that showed a synchronized increase in ROS formation. A reduced glutamine synthetase activity indicated that disturbances in the nitrogen assimilation occur earlier than it was previously thought under salt stress.

Multiple Contrast Tests for Multiple Endpoints in the Presence of Heteroscedasticity

Abstract This article describes an extension of multiple contrast tests to the case of multiple, correlated endpoints. These endpoints are assumed to be normally distributed with different scales and variances. Unlike in previous articles, the covariance matrices are also assumed to be unequal for the treatment groups. Approximate multivariate t-distributions are used to obtain multiplicity-adjusted p-values and quantiles for test decisions or simultaneous confidence intervals. Simulation results show that this approach controls the family-wise error type I over both the comparisons and the endpoints in an admissible range. The approach will be applied to a semi-synthetic example data set of a randomized, placebo-controlled phase IIb dose-finding study of a novel anti-muscarinic agent for five continuous endpoints. A related R package is available.

Silencing of the sulfur rich α-gliadin storage protein family in wheat grains (Triticum aestivum L.) causes no unintended side-effects on other metabolites

Wheat is an important source of proteins and metabolites for human and animal nutrition. To assess the nutritional quality of wheat products, various protein and diverse metabolites have to be evaluated. The grain storage protein family of the α-gliadins are suggested to be the primary initiator of the inflammatory response to gluten in Celiac disease patients. With the technique of RNAi, the α-gliadin storage protein fraction in wheat grains was recently knocked down. From a patients perspective, this is a desired approach, however, this study aims to evaluate whether such a down-regulation of these problematic α-gliadins also has unintended side-effects on other plant metabolites. Such uncontrolled and unknown arbitrary effects on any metabolite in plants designated for food production would surely represent an avoidable risk for the consumer. In general, α-gliadins are rich in sulfur, making their synthesis and content depended of the sulfur supply. For this reason, the influence of the application of increasing sulfur amounts on the metabolome of α-gliadin-deficient wheat was additionally investigated because it might be possible that e.g., considerable high/low amounts of S might increase or even induce such unintended effects that are not observable under moderate S nutrition. By silencing the α-gliadin genes, a recently developed wheat line that lacks the set of 75 corresponding α-gliadin proteins has become available. The plants were subsequently tested for RNAi-induced effects on metabolites that were not directly attributable to the specific effects of the RNAi-approach on the α-gliadin proteins. For this, GC-MS-based metabolite profiles were recorded. A comparison of wild type with gliadin-deficient plants cultivated in pot experiments revealed no differences in all 109 analyzed metabolites, regardless of the S-nutritional status. No unintended effects attributable to the RNAi-based specific genetic deletion of a storage protein fraction were observed.

Multiple comparisons to both a negative and a positive control

This paper addresses multiple comparisons in the presence of both a negative and a positive control. The methodology of the three-arm trial is extended to the case of many experimental treatment arms or different doses of a compound. In contrast to the classic three-arm trial, the focus is on the family-wise error type I. Normally distributed data with either homogeneous or heterogeneous group variances are considered. Explicit criteria for an optimal allocation are proposed. Depending on the pattern of heterogeneity, remarkably unbalanced designs are power-optimal. As an example, the method will be applied to a toxicological experiment.

Effect of dietary quebracho tannin extract on milk fatty acid composition in cows

The aim of this study was to examine the capacity of quebracho tannin extract (QTE) to modulate the fatty acid (FA) profile in the milk fat of cows. Fifty Holstein cows yielding 33.2 ± 8.2 kg/d of milk were divided into 2 groups. The cows were fed a basal diet with a forage-concentrate ratio of 66:34 on a dry matter (DM) basis. Diets tested were control (CON, basal diet without QTE) and basal diet plus 15 or 30 g of QTE/kg of DM (QTE15 and QTE30, respectively). Two treatments could be tested simultaneously and were arranged along 6 periods. The milk FA profile was characterized by increments in the proportion of linoleic (LA) and α-linolenic acid (α-LNA) (QTE15 = 10 and 6.1%; QTE30 = 28 and 25%, respectively) compared to CON, which might indicate reduced ruminal biohydrogenation (BH) of both dietary LA and α-LNA. Vaccenic acid (VA) in the milk fat was reduced (QTE15 8.9% and QTE30 12%) compared to CON, which may be linked to inhibited BH of LA and α-LNA. Rumenic acid (RA), a conjugated LA (cis-9,trans-11 conjugated linoleic acid) and an important human health promoter, was unfortunately decreased (QTE15 8.3% and QTE30 16%) in the milk compared with CON, probably because of inhibited ruminal BH of LA. However, reduced RA in the milk was probably due to reduced availability of VA produced in the rumen and the consequently low VA available to be desaturated to RA in the mammary gland by Δ9-desaturase. The proportions of total polyunsaturated FA were increased with QTE15 and QTE30 by 4.7 and 15% compared to CON, respectively, and the long-chain FA proportions were also increased (QTE15 2.0% and QTE30 8.2%). Moreover, myristic and palmitic acid were reduced by QTE30 (9.6 and 3.3%, respectively) compared to CON, which also contributed to increasing the nutritional quality of milk because they are recognized to increase high-density lipoprotein in humans. Branched-chain FA in milk was reduced with QTE treatments, which indicates inhibited ruminal BH and microbial activity. In general, our findings suggest that dietary QTE have the potential to modulate FA profile of milk fat, and this effect is dosage dependent. Because QTE influenced the FA profile of milk fat both positively and negatively, further research is needed before concluding that QTE may improve the nutritional quality of cow milk fat in human diets.