Does the effect of pelleting depend on the wheat sample when fed to chickens?

Experimental comparisons of the nutritional value of different wheat cultivars commonly use feeds in meal form even though the large-scale broiler producers use steam pelleted feeds. The aim of this experiment was to examine the effect of steam pelleting on the performance, dietary N-corrected apparent metabolisable energy (AMEn), total tract dry matter retention (DMR), nitrogen retention (NR) and fat digestibility (FD) coefficients, and digestive tract development of broilers fed four different wheat samples in complete diets. Four European wheat samples, with different chemical composition and endosperm characteristics, were used in a broiler experiment. The wheat samples were milled through a 5 mm screen and four basal feeds containing 670 g/kg of each selected wheat sample were mixed. The basal feeds were then split into two batches and one of them was steam pelleted resulting in eight experimental diets. Each diet was fed ad libitum to eight pens of two male Ross 308 broilers from 10 to 24 days of age. Feeding pelleted diets improved (P<0.001) feed intake and weight gain, and daily water intake of the birds. Pelleting also improved dietary AMEn and FD (P<0.001) and DMR (P<0.05). An interaction (P<0.05) was observed between wheat samples and steam pelleting for NR. Steam pelleting improved (P<0.05) NR in the wheat sample with high starch and protein and hard endosperm but not in the rest of the wheat samples. Similar interactions (P<0.05) were also observed between wheat sample and steam pelleting for gain to feed (G : F) and water to feed (W : F) ratios. Pelleting improved G : F ratio the greatest in the wheat sample with high starch and protein and hard endosperm. Feeding the same wheat sample also decreased (P<0.05) W : F but only in the mash diets. Regardless of the wheat sample the values of dietary AMEn did not differ (P>0.05). Feeding different wheat types and pelleting did not (P>0.05) change the development of the gastrointestinal tract of the birds. The study showed that there were differences between four wheat samples when they were fed in pelleted complete feed, but no differences were observed when fed in mash form complete diets. Research on the interaction between pelleting and wheat chemical and quality characteristics is warranted.     

Frequency of the cystic fibrosis ΔF508 mutation in a large sample of the French population

Summary We have determined the frequency of the cystic fibrosis (CF) ΔF508 mutation in a large sample of CF patients originating from different areas of France, including the greater Paris, Brittany, Alsace, Lorraine and Rh?ne-Alpes regions. A total of 422 CF chromosomes were studied, and the defect was found to account for 75% of the mutant alleles. In the course of the survey, a rare nucleotide sequence polymorphism leading to an isoleucine to valine substitution at position 506 of the CF transmembrane conductance regulator protein has been characterized in an unaffected individual. Our data enable the evaluation of the probabilities that a chromosome negative for the ΔF508 mutation carriers another CF defect.     

Is there an alternative to increasing the sample size in microarray studies?

Our answer to the question posed in the title is negative. This intentionally provocative note discusses the issue of sample size in microarray studies from several angles. We suggest that the current view of microarrays as no more than a screening tool be changed and small sample studies no longer be considered appropriate.     

Interproximal wear facets and tooth associations in the Paşalar hominoid sample

Interproximal wear facets were examined on hominoid teeth from the middle Miocene site at Pa?alar, Turkey. The aim was to find matches between adjacent premolar and molar teeth from single individuals that were collected in the field as isolated teeth and use them to reconstruct tooth rows. These were then used to investigate: (1) the wear gradient on the molar teeth; (2) the dispersal of teeth from single mandibles and maxillae; (3) the size ratios among the molars; and (4) the number of individuals represented by the hominoid sample. Facets were scored for size and shape and were assessed visually using photographs and superimposed outline drawings on acetate transparencies. Out of a sample of approximately 1,500 teeth collected between 1983 and 1996, 532 molars and 258 premolars produced apparent matches making up 160 tooth rows. These were then examined rigorously for morphological consistency and state of wear, and, employing the criterion that only the most unequivocal associations should be used, the final number was reduced to 48 tooth rows-31 mandibular and 17 maxillary. The tooth associations represent a minimum of 21 individuals and probably as many as 34. Molar wear was rapid, with M1s having almost twice as much wear as M3s, as measured by a wear-gradient index. The M2s are intermediate but generally closer to M1s in degree of wear, as are P4s. This wear pattern suggests either delayed eruption of M3s or extremely abrasive diets causing rapid, heavy wear. There is some indication that the wear patterns in Griphopithecus alpani and Kenyapithecus kizili are different, with the latter perhaps having a lower wear gradient, but the K. kizili sample is very small. In both species, the M2 is the largest molar and the M1 is the smallest. Separation of individual teeth in the 48 tooth associations varied from widely separated-up to 8.5m apart-to within a few centimeters of each other. One tooth row (D922) was found with the teeth in contact but the maxillary bone had dissolved away. Two dispersal mechanisms have been identified from earlier taphonomic work: transport of disarticulated elements to the fossil site and reworking of sediments by spring action.     

Is the late Neandertal mandibular sample from Vindija Cave (Croatia) biased?

The late Neandertal sample from Vindija (Croatia) has been described as transitional between the earlier Central European Neandertals from Krapina (Croatia) and modern humans. However, the morphological differences indicating this transition may rather be the result of different sex and/or age compositions between the samples. This study tests the hypothesis that the metric differences between the Krapina and Vindija mandibular samples are due to sample bias. Mandibles are the focus of this paper because past studies have posited this region as particularly indicative of the Vindija sample's transitional nature. The results indicate that the metric differences between the Krapina and Vindija mandibular samples are not due to sample bias. This conclusion is consistent with an earlier analysis of sample bias for the Vindija supraorbital sample.     

Does sample length influence the shape of xylem embolism vulnerability curves? A test with the Cavitron spinning technique

The Cavitron spinning technique is used to construct xylem embolism vulnerability curves (VCs), but its reliability has been questioned for species with long vessels. This technique generates two types of VC: sigmoid ‘s’‐shaped and exponential, levelling‐off ‘r’‐shaped curves. We tested the hypothesis that ‘r’‐shaped VCs were anomalous and caused by the presence of vessels cut open during sample preparation. A Cavitron apparatus was used to construct VCs from samples of different lengths in species with contrasting vessel lengths. The results were compared with VCs obtained using other independent techniques. When vessel length exceeded sample length, VCs were ‘r’‐shaped and anomalous. Filling vessels cut open at both ends with air before measurement produced more typical ‘s’‐shaped VCs. We also found that exposing segments of 11 woody species in a Cavitron at the pressure measured in planta before sampling considerably increased the degree of embolism above the native state level for species with long vessels. We concluded that open vessels were abnormally more vulnerable to cavitation than intact vessels. We recommend restricting this technique to species with short conduits. The relevance of our conclusions for other spinning techniques is discussed.     

Understanding sample size: what determines the required number of microarrays for an experiment?

DNA microarray experiments have become a widely used tool for studying gene expression. An important, but difficult, part of these experiments is deciding on the appropriate number of biological replicates to use. Often, researchers will want a number of replicates that give sufficient power to recognize regulated genes while controlling the false discovery rate (FDR) at an acceptable level. Recent advances in statistical methodology can now help to resolve this issue. Before using such methods it is helpful to understand the reasoning behind them. In this Research Focus article we explain, in an intuitive way, the effect sample size has on the FDR and power, and then briefly survey some recently proposed methods in this field of research and provide an example of use.     

Empirical derivation of the reference region for computing diagnostic sensitive ¹⁸fluorodeoxyglucose ratios in Alzheimer's disease based on the ADNI sample

Careful selection of the reference region for non-quantitative positron emission tomography (PET) analyses is critically important for Region of Interest (ROI) data analyses. We introduce an empirical method of deriving the most suitable reference region for computing neurodegeneration sensitive (18)fluorodeoxyglucose (FDG) PET ratios based on the dataset collected by the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. Candidate reference regions are selected based on a heat map of the difference in coefficients of variation (COVs) of FDG ratios over time for each of the Automatic Anatomical Labeling (AAL) atlas regions normalized by all other AAL regions. Visual inspection of the heat map suggests that the portion of the cerebellum and vermis superior to the horizontal fissure is the most sensitive reference region. Analyses of FDG ratio data show increases in significance on the order of ten-fold when using the superior portion of the cerebellum as compared with the traditionally used full cerebellum. The approach to reference region selection in this paper can be generalized to other radiopharmaceuticals and radioligands as well as to other disorders where brain changes over time are hypothesized and longitudinal data is available. Based on the empirical evidence presented in this study, we demonstrate the usefulness of the COV heat map method and conclude that intensity normalization based on the superior portion of the cerebellum may be most sensitive to measuring change when performing longitudinal analyses of FDG-PET ratios as well as group comparisons in Alzheimer's disease. This article is part of a Special Issue entitled: Imaging Brain Aging and Neurodegenerative disease.     

Brief communication: Is variation in the cranial capacity of the Dmanisi sample too high to be from a single species?

This study uses data resampling to test the null hypothesis that the degree of variation in the cranial capacity of the Dmanisi hominid sample is within the range variation of a single species. The statistical significance of the variation in the Dmanisi sample is examined using simulated distributions based on comparative samples of modern humans, chimpanzees, and gorillas. Results show that it is unlikely to find the maximum difference observed in the Dmanisi sample in distributions of female-female pairs from comparative single-species samples. Given that two sexes are represented, the difference in the Dmanisi sample is not enough to reject the null hypothesis of a single species. Results of this study suggest no compelling reason to invoke multiple taxa to explain variation in the cranial capacity of the Dmanisi hominids.     

Evaluation of the SNP tagging approach in an independent population sample—array-based SNP discovery in Sami

Significant efforts have been made to determine the correlation structure of common SNPs in the human genome. One method has been to identify the sets of tagSNPs that capture most of the genetic variation. Here, we evaluate the transferability of tagSNPs between populations using a population sample of Sami, the indigenous people of Scandinavia. Array-based SNP discovery in a 4.4 Mb region of 28 phased copies of chromosome 21 uncovered 5,132 segregating sites, 3,188 of which had a minimum minor allele frequency (mMAF) of 0.1. Due to the population structure and consequently high LD, the number of tagSNPs needed to capture all SNP variation in Sami is much lower than that for the HapMap populations. TagSNPs identified from the HapMap data perform only slightly better in the Sami than choosing tagSNPs at random from the same set of common SNPs. Surprisingly, tagSNPs defined from the HapMap data did not perform better than selecting the same number of SNPs at random from all SNPs discovered in Sami. Nearly half (46%) of the Sami SNPs with a mMAF of 0.1 are not present in the HapMap dataset. Among sites overlapping between Sami and HapMap populations, 18% are not tagged by the European American (CEU) HapMap tagSNPs, while 43% of the SNPs that are unique to Sami are not tagged by the CEU tagSNPs. These results point to serious limitations in the transferability of common tagSNPs to capture random sequence variation, even between closely related populations, such as CEU and Sami. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The stationary distribution of a sample from the Wright–Fisher diffusion model with general small mutation rates

Journal of Mathematical Biology - The stationary distribution of a sample taken from a Wright–Fisher diffusion with general small mutation rates is found using a coalescent approach. The...     

Comparing species richness among assemblages using sample units: why not use extrapolation methods to standardize different sample sizes?

Comparisons of species richness among assemblages using different sample sizes may produce erroneous conclusions due to the strong positive relationship between richness and sample size. A current way of handling the problem is to standardize sample sizes to the size of the smallest sample in the study. A major criticism about this approach is the loss of information contained in the larger samples. A potential way of solving the problem is to apply extrapolation techniques to smaller samples, and produce an estimated species richness expected to occur if sample size were increased to the same size of the largest sample. We evaluated the reliability of 11 potential extrapolation methods over a range of different data sets and magnitudes of extrapolation. The basic approach adopted in the evaluation process was a comparison between the observed richness in a sample and the estimated richness produced by estimators using a sub-sample of the same sample. The Log-Series estimator was the most robust for the range of data sets and sub-sample sizes used, followed closely by Negative Binomial, SO-J1, Logarithmic, Stout and Vandermeer, and Weibull estimators. When applied to a set of independently replicated samples from a species-rich assemblage, 95% confidence intervals of estimates produced by the six best evaluated methods were comparable to those of observed richness in the samples. Performance of estimators tended to be better for species-rich data sets rather than for those which contained few species. Good estimates were found when extrapolating up to 1.8-2.0 times the size of the sample. We suggest that the use of the best evaluated methods within the range of indicated conditions provides a safe solution to the problem of losing information when standardizing different sample sizes to the size of the smallest sample.     

Short communication: Evaluation of the sample size of individual indicators in gestating sows concerning the Welfare Quality® protocol applied to sows and piglets

Sample sizes of welfare assessment protocols must warrant to reflect prevalences on-farm properly – regardless of farm size. Still, solely a fixed sample size was specified for the Welfare Quality® protocol for sows and piglets. The present study investigated whether animals may be assessed from only one body side as applied in the protocol and whether the pre-set sample size of 30 animals mirrors the prevalences of the animal-based indicators on-farm in the gestation unit considering different farm sizes. All indicators were assessed for both sides of an animal’s body by one observer on 13 farms in Germany, which were visited five times within 10 months. The farm visits were treated as independent since different animals were housed in the gestation units. The number of sows in the gestation units varied between 18 and 549 animals. The comparison of sides was carried out calculating exact agreement between animals’ sides and a Wilcoxon signed-rank test (W). The results signified that it is sufficient to assess the animal from one side (exact agreement: 88.3% to 99.5%, except for bursitis (70.0%); W: P-values 0.14 to 0.92). However, if side preferences existed in the indicator bursitis a potential bias must be considered. In the following, the sample size was evaluated by comparing samples’ prevalences against true prevalence, that is, the prevalence of all observed animals in the gestation unit in each farm visit. Therefore, subsets of data were generated by applying simple random sampling without replacement. The samples randomly included the animals’ right or left sides. Linear regression was rated as appropriate provided: coefficient of determination R² ≥ 0.90, slope = 1 and intercept = 0 signifying exact agreement. The results revealed that the sample size required by the protocol and the application of calculation formulas are solely appropriate to mirror the prevalences of frequent indicators in the gestation unit, for example, bursitis (mean prevalence 34.4%). Using a proportion of animals, for example, a sample of 30% of all observed animals in a farm visit, pointed out that proportions must increase with indicators’ underlying prevalence narrowing 0.00%. Local infections (mean prevalence 13.3%) needed samples including 60% of all observed animals in each farm visit, whereas vulva lesions (mean prevalence 7.28%) only reached accuracy with the inclusion of 70% of the animals. Indicators with a mean prevalence of <1% were not analysed but can most likely only be ascertained by the assessment of all animals.     

Is urine a reliable clinical sample for the diagnosis of human visceral leishmaniasis? A systematic review and meta-analysis

Visualization of amastigotes in lymph nodes, bone marrow, and other tissues samples remains the gold standard method for the diagnosis of visceral leishmaniasis (VL) in humans. This gold standard diagnostic method uses a technically challenging microscopy procedure that is often not accessible in many places in the world where VL is endemic. Here, we report the current systematic review and meta-analysis to evaluate whether urine is a reliable clinical sample for diagnosis of human VL. Data were extracted from ten available databases during the period from 2002 to 2017. Overall, 29 articles fulfilled the inclusion criteria and were used for data extraction in this systematic review. Most studies (72.4%) using urine specimens were reported from five countries: India 6 (20.7%), Iran 5 (17.2%), Bangladesh 4 (13.8%), Japan 3 (10.3%) and Spain 3 (10.3%), respectively. The most common diagnostic tests performed on urine were Katex (62.1%), ELISA (24.1%), and the rK39 (17.2%) assays. In meta-analysis the sensitivity and specificity of the three most commonly used diagnostic assays were rK39 (97%; CI: 91–99; 98%;76–100), ELISA (91%; 82–95; 99%; CI: 94–100), and Katex (83%; 73–90; 98%; 98–100), suggesting that the rK39 assay provided the highest sensitivity and the ELISA assay provided the highest specificity for diagnosis of VL from urine samples. Our findings suggest that urine is a valuable clinical sample for the diagnosis of human VL, particularly in areas where the gold standard test for VL is not available.     

Angular transformation – another effect of different sample sizes

Angular transformation has been widely used to analyze proportions or percentages in ecology. A new type of artifact can arise by applying angular transformation to proportions or percentages. Proportions with the same mean or expected value, but with different sample sizes (denominator of proportions), have different means or expected values after this transformation. Overdispersion causes a larger deviation of the expected value after the transformation. Angular transformation should be avoided unless the sample size (denominator of proportions) is the same for all the proportions analyzed.