The Perils of Straying from Protocol: Sampling Bias and Interviewer Effects

Fidelity to research protocol is critical. In a contingent valuation study in an informal urban settlement in Nairobi, Kenya, participants responded differently to the three trained interviewers. Interviewer effects were present during the survey pilot, then magnified at the start of the main survey after a seemingly slight adaptation of the survey sampling protocol allowed interviewers to speak with the “closest neighbor” in the event that no one was home at a selected household. This slight degree of interviewer choice led to inferred sampling bias. Multinomial logistic regression and post-estimation tests revealed that the three interviewers’ samples differed significantly from one another according to six demographic characteristics. The two female interviewers were 2.8 and 7.7 times less likely to talk with respondents of low socio-economic status than the male interviewer. Systematic error renders it impossible to determine which of the survey responses might be “correct.” This experience demonstrates why researchers must take care to strictly follow sampling protocols, consistently train interviewers, and monitor responses by interview to ensure similarity between interviewers’ groups and produce unbiased estimates of the parameters of interest.     

Robot-Mediated Interviews - How Effective Is a Humanoid Robot as a Tool for Interviewing Young Children?

Robots have been used in a variety of education, therapy or entertainment contexts. This paper introduces the novel application of using humanoid robots for robot-mediated interviews. An experimental study examines how children’s responses towards the humanoid robot KASPAR in an interview context differ in comparison to their interaction with a human in a similar setting. Twenty-one children aged between 7 and 9 took part in this study. Each child participated in two interviews, one with an adult and one with a humanoid robot. Measures include the behavioural coding of the children’s behaviour during the interviews and questionnaire data. The questions in these interviews focused on a special event that had recently taken place in the school. The results reveal that the children interacted with KASPAR very similar to how they interacted with a human interviewer. The quantitative behaviour analysis reveal that the most notable difference between the interviews with KASPAR and the human were the duration of the interviews, the eye gaze directed towards the different interviewers, and the response time of the interviewers. These results are discussed in light of future work towards developing KASPAR as an ‘interviewer’ for young children in application areas where a robot may have advantages over a human interviewer, e.g. in police, social services, or healthcare applications.     

Precision and Disclosure in Text and Voice Interviews on Smartphones

As people increasingly communicate via asynchronous non-spoken modes on mobile devices, particularly text messaging (e.g., SMS), longstanding assumptions and practices of social measurement via telephone survey interviewing are being challenged. In the study reported here, 634 people who had agreed to participate in an interview on their iPhone were randomly assigned to answer 32 questions from US social surveys via text messaging or speech, administered either by a human interviewer or by an automated interviewing system. 10 interviewers from the University of Michigan Survey Research Center administered voice and text interviews; automated systems launched parallel text and voice interviews at the same time as the human interviews were launched. The key question was how the interview mode affected the quality of the response data, in particular the precision of numerical answers (how many were not rounded), variation in answers to multiple questions with the same response scale (differentiation), and disclosure of socially undesirable information. Texting led to higher quality data—fewer rounded numerical answers, more differentiated answers to a battery of questions, and more disclosure of sensitive information—than voice interviews, both with human and automated interviewers. Text respondents also reported a strong preference for future interviews by text. The findings suggest that people interviewed on mobile devices at a time and place that is convenient for them, even when they are multitasking, can give more trustworthy and accurate answers than those in more traditional spoken interviews. The findings also suggest that answers from text interviews, when aggregated across a sample, can tell a different story about a population than answers from voice interviews, potentially altering the policy implications from a survey.     

The reliability of adult self-reported height: The role of interviewers

Surveys serve as an important source of information on key anthropometric characteristics such as body height or weight in the population. Such data are often obtained by directly asking respondents to report those values. Numerous studies have examined measurement errors in this context by comparing reported to measured values. However, little is known on the role of interviewers on the prevalence of irregularities in anthropometric survey data. In this study, we explore such interviewer effects in two ways. First, we use data from the US National Health and Nutrition Examination Survey and the UK Household Longitudinal Study to evaluate whether differences between reported and measured values are clustered within interviewers. Second, we investigate changes in adult self-reported height over survey waves in two German large-scale panel surveys. Here, we exploit that height should be constant over time for the majority of adult age groups. In both analyses, we use multilevel location-scale models to identify interviewers who enhance reporting errors and interviewers for whom unlikely height changes over waves occur frequently. Our results reveal that interviewers can play a prominent role in differences between reported and measured height values and changes in reported height over survey waves. We further provide an analysis of the consequences of height misreporting on substantive regression coefficients where we especially focus on the role of interviewers who reinforce reporting errors and unlikely height changes.     

Social network- and community-level influences on contraceptive use: evidence from rural Poland

The diffusion of ‘modern’ contraceptives—as a proxy for the spread of low-fertility norms—has long interested researchers wishing to understand global fertility decline. A fundamental question is how local cultural norms and other people''s behaviour influence the probability of contraceptive use, independent of women''s socioeconomic and life-history characteristics. However, few studies have combined data at individual, social network and community levels to simultaneously capture multiple levels of influence. Fewer still have tested if the same predictors matter for different contraceptive types. Here, we use new data from 22 high-fertility communities in Poland to compare predictors of the use of (i) any contraceptives—a proxy for the decision to control fertility—with those of (ii) ‘artificial’ contraceptives—a subset of more culturally taboo methods. We find that the contraceptive behaviour of friends and family is more influential than are women''s own characteristics and that community level characteristics additionally influence contraceptive use. Highly educated neighbours accelerate women''s contraceptive use overall, but not their artificial method use. Highly religious neighbours slow women''s artificial method use, but not their contraceptive use overall. Our results highlight different dimensions of sociocultural influence on contraceptive diffusion and suggest that these may be more influential than are individual characteristics. A comparative multilevel framework is needed to understand these dynamics.     

Racial ambiguity among the Brazilian population

I investigate the extent to which interviewers and respondents in a 1995 national survey consistently classify race in Brazil, overall and in particular contexts. Overall, classification as white, brown or black is consistent 79 per cent of the time. However, persons at the light end of the colour continuum tend to be consistently classified, whereas ambiguity is greater for those at the darker end. Based on statistical estimation, the findings also reveal that consistency varies from 20 to 100 per cent depending on one's education, age, sex and local racial composition. Inconsistencies are in the direction of both ''whitening'' and ''darkening'', depending on whether the reference is interviewer or respondent. For example, interviewers ''whitened'' the classification of higher educated persons who self-identified as brown, especially in mostly non-white regions. Finally, I discuss the role of the Brazilian state in constructing race and the implications of these findings for survey research and comparative analysis.     

“How” and “Why” prompts in forensic investigative interviews with preschool children

Although young children may frequently be asked “How” and “Why” questions, it is unclear whether they have the ability to respond well enough to justify the use of these words during investigative interviews. The range of possible uses and interpretations of the words “How” and “Why” makes it critical to examine their use when communicatively immature children are interviewed. In this study, police interviews of 3- to 5-year-old suspected victims of sexual abuse (n = 49) were examined. The use of How/Why prompts by interviewers and children’s responses to interviewers’ How/Why prompts were coded. How/Why prompts represented 22% of all interviewer prompts. Of all details provided by children, however, 8.5% were in response to How/Why prompts. In addition, children provided the information sought in response to only 20% of the interviewers’ How/Why prompts, whereas uninformative responses were relatively common. Children responded to more How/Why prompts with the information sought by interviewers as they grew older. The findings suggest that How/Why prompts may not be particularly effective when interviewing preschool children.     

Proportionality: A Valid Alternative to Correlation for Relative Data

In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative—or compositional—data, differential expression needs careful interpretation, and correlation—a statistical workhorse for analyzing pairwise relationships—is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the strength of proportionality between two variables can be meaningfully and interpretably described by a new statistic ϕ which can be used instead of correlation as the basis of familiar analyses and visualisation methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes.     

Learning a Prior on Regulatory Potential from eQTL Data

Genome-wide RNA expression data provide a detailed view of an organism's biological state; hence, a dataset measuring expression variation between genetically diverse individuals (eQTL data) may provide important insights into the genetics of complex traits. However, with data from a relatively small number of individuals, it is difficult to distinguish true causal polymorphisms from the large number of possibilities. The problem is particularly challenging in populations with significant linkage disequilibrium, where traits are often linked to large chromosomal regions containing many genes. Here, we present a novel method, Lirnet, that automatically learns a regulatory potential for each sequence polymorphism, estimating how likely it is to have a significant effect on gene expression. This regulatory potential is defined in terms of “regulatory features”—including the function of the gene and the conservation, type, and position of genetic polymorphisms—that are available for any organism. The extent to which the different features influence the regulatory potential is learned automatically, making Lirnet readily applicable to different datasets, organisms, and feature sets. We apply Lirnet both to the human HapMap eQTL dataset and to a yeast eQTL dataset and provide statistical and biological results demonstrating that Lirnet produces significantly better regulatory programs than other recent approaches. We demonstrate in the yeast data that Lirnet can correctly suggest a specific causal sequence variation within a large, linked chromosomal region. In one example, Lirnet uncovered a novel, experimentally validated connection between Puf3—a sequence-specific RNA binding protein—and P-bodies—cytoplasmic structures that regulate translation and RNA stability—as well as the particular causative polymorphism, a SNP in Mkt1, that induces the variation in the pathway.     

DNA diet profiles with high‐resolution animal tracking data reveal levels of prey selection relative to habitat choice in a crepuscular insectivorous bird

Given the global decline of many invertebrate food resources, it is fundamental to understand the dietary requirements of insectivores. We give new insights into the functional relationship between the spatial habitat use, food availability, and diet of a crepuscular aerial insectivore, the European Nightjar (Caprimulgus europaeus) by relating spatial use data with high‐throughput sequencing (HTS) combined with DNA metabarcoding. Our study supports the predictions that nightjars collect a substantial part of their daily nourishment from foraging locations, sometimes at considerable distance from nesting sites. Lepidopterans comprise 65% of nightjars'' food source. Nightjars tend to select larger species of Lepidoptera (>19 mm) which suggests that nightjars optimize the efficiency of foraging trips by selecting the most energetically favorable—larger—prey items. We anticipate that our findings may shed additional light on the interactions between invertebrate communities and higher trophic levels, which is required to understand the repercussions of changing food resources on individual‐ and population‐level processes.     

Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)

The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data–mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera—an estimated 80% of extant plant diversity—to illustrate the potential of public sequence data for broad phylogenetic inference in plants, and we explore the limits to inference imposed by the structure of these data using theoretical foundations from phylogenetic data decisiveness. We find that despite very high levels of missing data (over 96%), the present data retain the potential to inform over 86.3% of all possible phylogenetic relationships. Most of these relationships, however, are informed by small amounts of data—approximately half are informed by fewer than four loci, and more than 99% are informed by fewer than fifteen. We also apply an information theoretic measure of branch support to assess the strength of phylogenetic signal in the data, revealing many poorly supported branches concentrated near the tips of the tree, where data are sparse and the limiting effects of this sparseness are stronger. We argue that limits to phylogenetic inference and signal imposed by low data coverage may pose significant challenges for comprehensive phylogenetic inference at the species level. Computational requirements provide additional limits for large reconstructions, but these may be overcome by methodological advances, whereas insufficient data coverage can only be remedied by additional sampling effort. We conclude that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing these resources to their full potential.     

Chromatin Hydrodynamics

Following recent observations of large scale correlated motion of chromatin inside the nuclei of live differentiated cells, we present a hydrodynamic theory—the two-fluid model—in which the content of a nucleus is described as a chromatin solution with the nucleoplasm playing the role of the solvent and the chromatin fiber that of a solute. This system is subject to both passive thermal fluctuations and active scalar and vector events that are associated with free energy consumption, such as ATP hydrolysis. Scalar events drive the longitudinal viscoelastic modes (where the chromatin fiber moves relative to the solvent) while vector events generate the transverse modes (where the chromatin fiber moves together with the solvent). Using linear response methods, we derive explicit expressions for the response functions that connect the chromatin density and velocity correlation functions to the corresponding correlation functions of the active sources and the complex viscoelastic moduli of the chromatin solution. We then derive general expressions for the flow spectral density of the chromatin velocity field. We use the theory to analyze experimental results recently obtained by one of the present authors and her co-workers. We find that the time dependence of the experimental data for both native and ATP-depleted chromatin can be well-fitted using a simple model—the Maxwell fluid—for the complex modulus, although there is some discrepancy in terms of the wavevector dependence. Thermal fluctuations of ATP-depleted cells are predominantly longitudinal. ATP-active cells exhibit intense transverse long wavelength velocity fluctuations driven by force dipoles. Fluctuations with wavenumbers larger than a few inverse microns are dominated by concentration fluctuations with the same spectrum as thermal fluctuations but with increased intensity.     

Metabolic Bone Disease Secondary to Renal and Intestinal Disorders

Metabolic bone disease occurring in renal or intestinal disorders has been reviewed with particular reference to etiological factors.Hyperparathyroidism is seen as a recurring cycle of renal damage—hyperphosphatemia—hypocalcemia—parathyroid stimulation—mobilization of bone calcium and phosphate—renal tubular phosphate rejection. In intestinal cases, the initial stimulus is presumably hypocalcemia.Osteomalacia is seen as resulting from phosphate depletion for the following reasons:1. Experimentally, rickets results from dietary phosphate restriction in rats.2. Such rickets is not prevented by the presence of normally adequate amounts of dietary vitamin D, and may therefore be termed “resistant” in the clinical sense.3. Osteomalacia or rickets in intestinal malabsorption and renal tubular disorders is associated with hypophosphatemia due to excessive fecal or urinary loss.4. Renal tubular rickets has been healed by oral phosphate loading in some studies.5. Acidosis may induce osteomalacic changes, experimentally and clinically (for example, in uretero-sigmoidostomy). Reversal of systemic acidosis with oral bicarbonate has resulted in phosphate retention and a rising serum phosphate in one such case.6. Preliminary data from analysis of full-thickness bone biopsy in two osteomalacic patients shows a significant reduction in calcium and phosphate content.7. Despite the hyperphosphatemia of azotemic renal failure, over-all phosphate depletion may be present in this situation also due to: • Diminished dietary phosphate in low protein diets • Nausea and vomiting • Occasional diarrhea • The use of oral phosphatebinding antacids • Perpetuation of urinary phosphate losses by reduction in proportion of tubular reabsorbed phosphate (secondary hyperparathyroidism) and possibly high filtered load per nephron • Repeated losses of phosphate to bath fluid during dialysis.     

Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data

We present a rigorous statistical model that infers the structure of P. falciparum mixtures—including the number of strains present, their proportion within the samples, and the amount of unexplained mixture—using whole genome sequence (WGS) data. Applied to simulation data, artificial laboratory mixtures, and field samples, the model provides reasonable inference with as few as 10 reads or 50 SNPs and works efficiently even with much larger data sets. Source code and example data for the model are provided in an open source fashion. We discuss the possible uses of this model as a window into within-host selection for clinical and epidemiological studies.     

Relating Land Use and Human Intra-City Mobility

Understanding human mobility patterns—how people move in their everyday lives—is an interdisciplinary research field. It is a question with roots back to the 19^th century that has been dramatically revitalized with the recent increase in data availability. Models of human mobility often take the population distribution as a starting point. Another, sometimes more accurate, data source is land-use maps. In this paper, we discuss how the intra-city movement patterns, and consequently population distribution, can be predicted from such data sources. As a link between land use and mobility, we show that the purposes of people’s trips are strongly correlated with the land use of the trip’s origin and destination. We calibrate, validate and discuss our model using survey data.     

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria

Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs—which dominate in carbon-rich environments—and oligotrophs—which dominate in carbon-poor environments—as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis–Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs.     

Minimization of Childhood Maltreatment Is Common and Consequential: Results from a Large,Multinational Sample Using the Childhood Trauma Questionnaire

Childhood maltreatment has diverse, lifelong impact on morbidity and mortality. The Childhood Trauma Questionnaire (CTQ) is one of the most commonly used scales to assess and quantify these experiences and their impact. Curiously, despite very widespread use of the CTQ, scores on its Minimization-Denial (MD) subscale—originally designed to assess a positive response bias—are rarely reported. Hence, little is known about this measure. If response biases are either common or consequential, current practices of ignoring the MD scale deserve revision. Therewith, we designed a study to investigate 3 aspects of minimization, as defined by the CTQ’s MD scale: 1) its prevalence; 2) its latent structure; and finally 3) whether minimization moderates the CTQ’s discriminative validity in terms of distinguishing between psychiatric patients and community volunteers. Archival, item-level CTQ data from 24 multinational samples were combined for a total of 19,652 participants. Analyses indicated: 1) minimization is common; 2) minimization functions as a continuous construct; and 3) high MD scores attenuate the ability of the CTQ to distinguish between psychiatric patients and community volunteers. Overall, results suggest that a minimizing response bias—as detected by the MD subscale—has a small but significant moderating effect on the CTQ’s discriminative validity. Results also may suggest that some prior analyses of maltreatment rates or the effects of early maltreatment that have used the CTQ may have underestimated its incidence and impact. We caution researchers and clinicians about the widespread practice of using the CTQ without the MD or collecting MD data but failing to assess and control for its effects on outcomes or dependent variables.     

Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740_bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population.     

The Scientific Competitiveness of Nations

We use citation data of scientific articles produced by individual nations in different scientific domains to determine the structure and efficiency of national research systems. We characterize the scientific fitness of each nation—that is, the competitiveness of its research system—and the complexity of each scientific domain by means of a non-linear iterative algorithm able to assess quantitatively the advantage of scientific diversification. We find that technological leading nations, beyond having the largest production of scientific papers and the largest number of citations, do not specialize in a few scientific domains. Rather, they diversify as much as possible their research system. On the other side, less developed nations are competitive only in scientific domains where also many other nations are present. Diversification thus represents the key element that correlates with scientific and technological competitiveness. A remarkable implication of this structure of the scientific competition is that the scientific domains playing the role of “markers” of national scientific competitiveness are those not necessarily of high technological requirements, but rather addressing the most “sophisticated” needs of the society.