To sample or not to sample? That is the question ... for the vegetation scientist

Lájer (2007) raised the problem of using a non-random sample for statistical testing of plant community data. He argued that this violates basic assumptions of the tests, resulting thus in non-significant results. However, a huge part of present-day knowledge of vegetation science is still based on non-random, preferentially collected data of plant communities. I argue that, given the inherent limits of preferential sampling, a change of approach is now necessary, with the adoption of sampling based on random principles seeming the obvious choice. However, a complete transition to random-based sampling designs in vegetation science is limited by the yet undefined nature of plant communities and by the still diffused opinion that plant communities have a discrete nature. Randomly searching for such entities is almost impossible, given their dependence on scale of observation, plot size and shape, and the need for finding well-defined types. I conclude that the only way to solve this conundrum is to consider and study plant communities as operational units. If the limits of the plant communities are defined operationally, they can be investigated using proper sampling techniques and the collected data analyzed using adequate statistical tools.     

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.     

A representative pond net sample: Fiction or reality?

The occurrence of chironomids in a standard pond net sample was studied. The standard pond net sample is quite biased; its qualitative to semi-quantitive character should always be taken into account. It is advised to transform abundances (log-normal) of chironomids when collected with the standard pond net. Despite disadvantages the pond net can be used in water quality surveys because of their general objectives.     

Can Malaise traps be used to sample spiders for biodiversity assessment?

Malaise traps are typically used to sample a range of flying insect groups; however non-target taxa such as spiders may also be collected in large numbers. In this study, spiders were sampled in peatlands and wet grasslands and catches in Malaise and pitfall traps were compared in order to determine the adequacy of Malaise traps for use in spider biodiversity assessment. Overall, the number of species and individuals caught in Malaise and pitfall traps were comparable, although more species were sampled in Malaise traps in locations with a greater structural diversity of the vegetation. The spider fauna sampled by the Malaise traps differed from that of the pitfall traps, but both methods consistently separated the species assemblages by biotope. These results demonstrate that Malaise traps are effective at sampling spiders and indicate that they can be used in biodiversity assessment. In addition the complementary species sampled by each method mean that employing both techniques will be useful where a full inventory of the species is required. The authors do not suggest that Malaise traps should be used solely to sample spiders; however, if traps are set to collect insects, identification of the spiders sampled may reduce the need to employ additional sampling techniques.     

Do polymorphic loci require large sample sizes to estimate genetic distances?

The coefficient of variation of estimates of three genetic distances (standard genetic distance of Nei, chord distance, FST) was examined with computer simulation to determine if large samples (per population) are necessary to precisely estimate genetic distances at loci with high levels of polymorphism. These simulations showed that loci with high mutation rates produce estimates of genetic distance with lower coefficients of variation than loci with lower mutation rates--without requiring larger sample sizes from each population. In addition, the rate at which increasing sample sizes decreases the coefficient of variation of estimates of genetic distances was shown to be approximately determined by the value of FST between the populations being sampled. When FST was greater than 0.05, sampling fewer than 20 individuals (per population) should be sufficient. When FST was less than 0.01, sampling 100 individuals (per population) or more will be useful.     

Can Mosquito Magnet® substitute for human-landing catches to sample anopheline populations?

The efficiency of the Mosquito Magnet Liberty Plus? (MMLP) trap was evaluated in comparison to human-landing catches (HLCs) to sample anopheline populations in Jabillal, state of Bolivar, southern Venezuela. The village comprised 37 houses and a population of 101; malaria in this village is primarily due to Plasmodium vivax and the Annual Parasite Index is 316.8 per 1,000 population. A longitudinal study was conducted between June 2008-January 2009 for three nights per month every two months between 17:30 pm-21:30 pm, a time when biting mosquitoes are most active. Anopheles darlingi and Anopheles nuneztovari were the most common species collected by both methods, whereas Anopheles marajoara was more abundant according to the HLC method. The MMLP trap was more efficient for collecting An. nuneztovari [63%, confidence interval (CI): 2.53] than for collecting An. darlingi (31%, CI: 1.57). There were significant correlations (p < 0.01) between the two methods for An. darlingi [Pearson correlation (R2) = 0.65] and An. nuneztovari (R2 = 0.48). These preliminary results are encouraging for further investigations of the use of the MMLP trap for monitoring anopheline populations in remote malaria-endemic areas in the Amazon Basin.     

Do sampling method and sample size affect basic measures of dolphin sociality?

Although the fission–fusion social patterns of bottlenose dolphins have been described, defining and measuring sociality is difficult. No study to date has investigated how much data are necessary to accurately depict social patterns in a fission–fusion species and whether this amount differs depending on the measure used. Using the long-term Shark Bay bottlenose dolphin study we examined four different measures of sociality for mothers and dependent calves ( n = 89). Our objectives were to determine (1) the amount of observation time necessary to accurately depict sociality using these measures, (2) correlations among these measures, and (3) if sampling method affects the validity of sociality measurements. A minimum of 10 h and 5 h of observations, respectively, were necessary to accurately capture calf associate numbers and percent time alone. A pairwise comparison of calf sociality measurements from focal and survey data found that calves spent from 0% to 70.2% of their time alone in focal data, but these same calves spent only 0%–7.7% alone in survey data. These findings indicate that (1) results differ depending on the type of sampling method and (2) the amount of observation time necessary to adequately capture individual variation differs depending on the measure of sociality.     

Anticipation or ascertainment bias in schizophrenia? Penrose's familial mental illness sample.

Several studies have observed anticipation (earlier age at onset [AAO] in successive generations) in familial schizophrenia. However, whether true anticipation or ascertainment bias is the principal originating mechanism remains unclear. In 1944 L. S. Penrose collected AAO data on a large, representative sample of familial mental illness, using a broad ascertainment strategy. These data allowed examination of anticipation and ascertainment biases in five two-generation samples of affected relative pairs. The median intergenerational difference (MID) in AAO was used to assess anticipation. Results showed significant anticipation in parent-offspring pairs with schizophrenia (n = 137 pairs; MID 15 years; P = .0001) and in a positive control sample with Huntington disease (n = 11; P = .01). Broadening the diagnosis of the schizophrenia sample suggested anticipation of severity of illness. However, other analyses provided evidence for ascertainment bias, especially in later-AAO parents, in parent-offspring pairs. Aunt/uncle-niece/nephew schizophrenia pairs showed anticipation (n = 111; P = .0001), but the MID was 8 years and aunts/uncles had earlier median AAO than parents. Anticipation effects were greatest in pairs with late-AAO parents but remained significant in a subgroup of schizophrenia pairs with early parental AAO (n = 31; P = .03). A small control sample of other diseases had MID of 5 years but no significant anticipation (n = 9; P = .38). These results suggest that, although ascertainment-bias effects were observed in parent-offspring pairs, true anticipation appears to be inherent in the transmission of familial schizophrenia. The findings support investigations of unstable mutations and other mechanisms that may contribute to true anticipation in schizophrenia.     

Are pan traps colors complementary to sample community of potential pollinator insects?

The global initiatives of monitoring and conserving pollinators require worldwide assessments with comparable data sets collected through standardized methods. The use of pan traps is a passive method widely applied to sample flower visitors, standing out for its simplicity. Despite its wide use to sample pollinator diversity, the influence of color on trap efficiency is not well understood. The available studies are particularly scarce in the tropics and have generated divergent results. The main goal of the present study was to assess whether blue, yellow and white pan traps are complementary to sample Hymenoptera community. For this, we placed 49 sample units of blue, white and yellow pan traps in agricultural and natural (savanna-like) areas in Chapada Diamantina, Bahia, Brazil. We found that the species richness from blue and yellow pan traps were not significantly different, but both were significantly greater than the species richness from white pan traps. However, bees were significantly more attracted to the blue pan traps and wasps to the yellow ones; thus, color attractiveness was group-specific. Pan traps of different color showed low species composition overlap with 61 % of species collected exclusively in one of the three pan trap colors, and the species composition in the blue traps differed consistently from that in the traps of the other colors. In the article we discuss the implication of the results and defend the combined use of pan traps with different colors as a solution for the differential variable sample bias.     

Efficient sample processing for proteomics applications—Are we there yet?

The ability to solubilize and digest protein extracts and recover peptides with high efficiency is of paramount importance in proteomics. A novel proteomic sample preparation protocol by Krijgsveld and colleagues (Hughes et al, 2014) provides significant advantages by enabling all sample processing steps to be carried out in a single tube to minimize sample losses, thereby enhancing sensitivity, throughput, and scalability of proteomics analyses.     

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.     

Ethnic differences in sleep duration and morning–evening type in a population sample

This cross-sectional population study examined associations of sleep duration and morning–evening type with sociodemographic and cardiometabolic disease in adults participating in the UK Biobank study (N = 439 933). Multivariable Poisson regression models of sleep duration and morning–evening type with a robust error variance were generated to estimate adjusted prevalence ratios and their 95% confidence intervals. All models were adjusted for sex, race, college attendance, employment status and age. Twenty five percent of the sample reported short sleep; 27% were morning, 64% intermediate and 9% evening type. Black ethnicity emerged as most strongly associated with sleep behavior. Short sleep was twice as prevalent, and morning versus intermediate type was 1.4 times more prevalent in Black than White participants. The greater prevalence of short sleep and morning type among Blacks suggests that sleep-based approaches to improving cardiometabolic outcomes may require a more multidimensional approach that encompasses adequate sleep and circadian alignment in this population.     

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.     

Premenstrual dysphoric disorder--a neglected diagnosis? Preliminary study on a sample of Croatian students

The aims of this study were to assess prevalence and symptom profile of premenstrual dysphoric disorder (PMDD) in a sample of Croatian students and young university graduates. We obtained data for 87 healthy women, aged 18-30, at their regular gynecologic outpatient visits over the period of 2003 to 2004. The severity of premenstrual symptoms were assessed daily, during two cycles, with the Daily Record of Severity of Problems (DRSP) and criteria for PMDD according to DSM-IV were applied. Fifteen out of 87 women fulfilled PMDD criteria and reported statistically significantly higher prevalence of co morbid disorders in their medical history compared to non-PMDD group. The most common symptoms in the PMDD group were psychological, while in non-PMDD group were vegetative. Overall, relatively high prevalence of PMDD in studied group indicates the need to continue the study.     

Does bone mineralization reflect economic conditions? An examination using a national US sample

BACKGROUND: Bone density is the most important determinant of osteoporotic fractures, which lead to significant morbidity, disability and mortality for older persons, particularly women. Sensitive periods for bone mineralization in infancy, childhood and adolescence overlap with those for height attainment. After peak density is reached in early adulthood, there is age-related decline. We ask whether bone density, as height, reflects economic conditions. SUBJECTS AND METHODS: Using the third National Health and Nutrition Examination Survey, a probability sample of the US population which over-sampled Blacks and Mexican Americans, we examine the associations between adult bone mineral content (BMC) adjusted for bone and body size and three economic indicators: education, height and the poverty income ratio (PIR). We compare four groups: US-born Whites, Blacks and Mexican Americans and Mexican-born Mexican Americans. RESULTS: Education is positively associated with BMC only for White women, although there are similar, non-significant associations for Black women and White and Black men. For women, BMC is more strongly associated with height for Mexican Americans, especially the Mexican-born, than for Whites. For men, the only significant association is a negative one with education for men born in Mexico. PIR is not significantly associated with BMC, although there is pattern of lower income being associated with lower BMC for Whites and Blacks and higher BMC for Mexican Americans. CONCLUSION: Bone density does not reflect economic conditions as strongly or consistently as does physical stature. However, for women there is evidence that lower economic status in childhood or adolescence is associated with lower bone density.     

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.