On misinterpretations of pseudoreplication and related matters: a reply to Oksanen

Pseudoreplication has become a widely accepted label for a certain class of statistical error common in the literature of ecology as well as of other fields. A wide-ranging critique by L. Oksanen recently published in this journal criticizes the term and concept and concludes it to be a "pseudoissue," one reflecting an intellectual disease, "a totally outdated epistemology" known as "inductionism." The present article addresses some of Oksanen's complaints. His critique is based on a misconception of pseudoreplication, reflects unawareness of most of the literature on the topic, and mistakenly argues that the seriousness of the error is a function of whether an experiment is conducted in an inductive or deductive spirit. Oksanen's advocacy of using resources available for large scale ecology more for large numbers of experiments with unreplicated treatments than for fewer experiments with modest replication of treatments is unrealistic. It is based on an overly optimistic view of the ability of a meta-analysis to compensate for deficiencies, such as very noisy estimates of treatment effects, of the individual studies that are fed into it. A definition is offered of the term manipulative experiment, since adequate ones are lacking in the literature. Attention is called to the fact that for certain types of manipulative experiments lacking treatment replication, there are valid ways to test for treatment effects.     

HLA associations in classical Hodgkin lymphoma: EBV status matters

The pathogenesis of classical Hodgkin lymphoma (cHL) involves environmental and genetic factors. To explore the role of the human leukocyte antigen (HLA) genes, we performed a case-control genotyping study in 338 Dutch cHL patients using a PCR-based sequence-specific oligonucleotide probe (SSOP) hybridization approach. The allele frequencies were compared to HLA typings of more than 6,000 controls. The age of the cHL patients varied between 13 and 81 years with a median of 35 years. Nodular sclerosis subtype was the most common subtype (87%) and EBV was detected in 25% of the cHL patients. HLA-B5 was significantly increased and HLA-DR7 significantly decreased in the total cHL patient population as compared to controls. Two class II associations were observed to be specific for the EBV- cHL population with an increase of HLA-DR2 and HLA-DR5. Allele frequencies of HLA-A1, HLA-B37 and HLA-DR10 were significantly increased in the EBV+ cHL population; these alleles are in strong linkage disequilibrium and form a common haplotype in Caucasians. The allele frequency of HLA-A2 was significantly decreased in the EBV+ cHL population. Analysis of haplotypes with a frequency of >1% revealed a significant increase of HLA-A2-B7-DR2 in EBV- cHL as compared to controls. SSOP association analysis revealed significant differences between EBV+ and EBV- cHL patients for 19 probes that discriminate between HLA-A*01 and HLA-A*02. In conclusion, the HLA-A1 and HLA-A2 antigens and not specific single nucleotide variants shared by multiple alleles are responsible for the association with EBV+ cHL. Furthermore several new protective and predisposing HLA class I and II associations for the EBV+, the EBV- and the entire cHL population were identified.     

Epidemiology and control of onchocerciasis: The threshold biting rate of savannah onchocerciasis in Africa

Control of onchocerciasis currently focuses on community-directed treatment with the microfilaricide ivermectin which effectively kills Onchocerca volvulus microfilariae in the human host. The feasibility of elimination by this control strategy has recently been reported for some foci in Africa which has rekindled discussions on evaluating the threshold conditions of elimination of onchocerciasis. We developed a stochastic model based on a master equation which predicts, based on data from West and Central Africa, that elimination of savannah onchocerciasis can be expected around a threshold biting rate of 730 bites per person per year, ranging region-specifically roughly from 230 to 2300 bites per person and year. The threshold values give rise to optimism that elimination of onchocerciasis is feasible, but the associated measures of parasite prevalence and density suggest that onchocerciasis can remain endemic at very low infection intensities. Endemicity at a low level is a risk factor for elimination strategies, and we point to the necessity of investigating these issues on the basis of breakpoints which refer to threshold conditions based on parasite prevalence and density.     

Control of onchocerciasis today: status and challenges

The filarid parasite Onchocerca volvulus is the causative agent of human onchocerciasis (river blindness), an infection characterized by chronic skin and eye lesions. There are three regional programs currently dedicated to controlling onchocerciasis in the endemic areas of Africa and the Americas: the Onchocerciasis Control Programme of West Africa, the African Programme for Onchocerciasis Control and the Onchocerciasis Elimination Program for the Americas. All three programs use periodic mass treatment with the microfilaricidal drug ivermectin with differing strategic purposes and, as a result, face different challenges to reach their goals. This paper will review the strategies, status and challenges of these three programs.     

Decision-making: Context matters

Research and theory in human decision-making has increasingly stressed the importance of the context in which the problem is embedded. This emphasis is consistent with that supported by research of behavior analysts on natural concept formation and in problem solving, as well as in the study of choice. We present data on reasoning problems that further support the role of context in decision-making.     

Malaria: seroepidemiology and serologic diagnosis

Recent advances on the application of serologic methods employing the indirect hemagglutination test with a Plasmodium knowlesi antigen for the study of malaria epidemiology are outlined. Work in progress on the stabilization of malaria antigens and the preparation of gluteraldehyde sensitized cells were reviewed. Fluorescent antibody studies in progress are discussed and work on the cross reactivity of Babesia antigens with malaria is mentioned.     

On the Population Dynamics of the Malaria Vector

A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can established itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing.     

Malaria: medical and surgical complications

The resurgence of malaria in Venezuela as an epidemic has caused an increase in the number of cases of this disease. 898 cases were registered in 1962 in contrast to 46,279 cases in 1988. This reality implies that all hospitals will have to face the increase of patients with this disease. Ten cases of malaria have been described and analyzed. These have been chosen for their medical and surgical complications, for which they were admitted to the "Hospital Universitario de Caracas" and "Hospital de Clínicas Caracas". Of these ten cases, eight were acquired in a natural way and two in an induced form. In six cases, the agent was P. falciparum; in three, P. vivax; in one, P. ovale and P.vivax combined. Five of the cases by P.falciparum were resistant to chloroquine, being necessary to treat them with a combination of quinine and other antimalaric drugs. Among the 10 described patients, there were: one case of splenic rupture in malaria by P. vivax, a severe case of anemia in a child with malaria by this same species and a case of relapse produced by P.vivax in another child with an insufficient radical treatment. The usual mistakes are observed in the management of malaria, such as a delay in the diagnosis and inappropriate radical treatment. As conclusion, publication of epidemiological, clinical and parasitological problems which are causing the actual epidemic, is recommended. This will be a guide in the fight against malaria, that must be considered again a national emergency.     

Context matters: On the road to responsible biosafety technologies in synthetic biology

Biosafety is a major challenge for developing for synthetic organisms. An early focus on application and their context could assist with the design of appropriate genetic safeguards. Subject Categories: Synthetic Biology & Biotechnology, S&S: Economics & Business

One of the goals of synthetic biology is the development of robust chassis cells for their application in medicine, agriculture, and the food, chemical and environmental industries. These cells can be streamlined by removing undesirable features and can be augmented with desirable functionalities to design an optimized organism. In a direct analogy with a car chassis, they provide the frame for different modules or “plug‐in” regulatory networks, metabolic pathways, or safety elements. In an effort to ensure a safe microbial chassis upfront, safety measures are implemented as genetic safeguards to limit risks such as unwanted cellular proliferation or horizontal gene transfer. Examples of this technology include complex genetic circuits, sophisticated metabolic dependencies (auxotrophies), and altered genomes (Schmidt & de Lorenzo, 2016; Asin‐Garcia et al, 2020). Much like seat belts or airbags in cars, these built‐in measures increase the safety of the chassis and of any organisms derived from it. Indeed, when it comes to safety, synthetic biology can still learn from a century‐old technology such as cars about the significance of context for the development of biosafety technologies.Every car today has seat belts installed by default. Yet, seat belts were not always a standard component; in fact, they were not even designed for cars to begin with. The original 2‐point belts were first used in aviation and only slowly introduced for motorized vehicles. Only after some redesign, the now‐common 3‐point car seat belts would become the life‐saving equipment that they are today. A proper understanding of the context of their application was therefore one of the crucial factors for their success and wide adoption. Context matters: It provides meaning for and defines what a technological application is best suited for. What was true for seat belts may be also true for biosafety technologies such as genetic safeguards.

… when it comes to safety, synthetic biology can still learn from a century‐old technology such as cars about the significance of context for the development of biosafety technologies.

Society has a much higher awareness of technology’s risks compared to the early days of cars. Society today requires that technological risks are anticipated and assessed before an innovation or its applications are widely deployed. In addition, society increasingly demands that research and innovation take into account societal needs and values. This has led to, among others, the Responsible Research and Innovation (RRI; von Schomberg, 2013) concept that has become prominent in European science policy. In a nutshell, RRI requires that innovative products and processes align with societal needs, expectations, and values in consultation with stakeholders. RRI and similar frameworks suggest that synthetic biology must anticipate and respond not only to risks, but also to societal views that frame its evaluation and risk assessment.     

Body size matters in provision of help: factors related to children's willingness to help overweight peers

Although children who are overweight may be vulnerable to negative social experiences, little is known about whether children will offer help to peers who are overweight. The present study examined whether children would offer aid to peers who are overweight with everyday tasks (such as picking up toys). This study also examined whether weight stereotypes and intentions to befriend these peers are related to intentions to help. Fifty-one children, aged 4-8, were interviewed about their stereotypes and behavioral intentions. Findings revealed that children were less likely to help overweight than average weight peers. Children who did not hold positive stereotypes about thinness and those who chose to play with overweight peers were more likely to help peers who are overweight. Results suggest that weight prejudice is pervasive and that children who are overweight might not be offered aid in classroom settings, highlighting the need for early intervention.