Pollution from drug manufacturing: review and perspectives

As long ago as the sixteenth century, Paracelsus recognized that ‘the dose makes the poison’. Indeed, environmental concentrations of pharmaceuticals excreted by humans are limited, most importantly because a defined dose is given to just a fraction of the population. By contrast, recent studies have identified direct emission from drug manufacturing as a source of much higher environmental discharges that, in some cases, greatly exceed toxic threshold concentrations. Because production is concentrated in specific locations, the risks are not linked to usage patterns. Furthermore, as the drugs are not consumed, metabolism in the human body does not reduce concentrations. The environmental risks associated with manufacturing therefore comprise a different, wider set of pharmaceuticals compared with those associated with risks from excretion. Although pollution from manufacturing is less widespread, discharges that promote the development of drug-resistant microorganisms can still have global consequences. Risk management also differs between production and excretion in terms of accountability, incentive creation, legal opportunities, substitution possibilities and costs. Herein, I review studies about industrial emissions of pharmaceuticals and the effects associated with exposure to such effluents. I contrast environmental pollution due to manufacturing with that due to excretion in terms of their risks and management and highlight some recent initiatives.     

Conjugative plasmids: vessels of the communal gene pool

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.     

Communicating and Dealing with Uncertainty in General Practice: The Association with Neuroticism

Background

Diagnostic reasoning in primary care setting where presented problems and patients are mostly unselected appears as a complex process. The aim was to develop a questionnaire to describe how general practitioners (GPs) deal with uncertainty to gain more insight into the decisional process. The association of personality traits with medical decision making was investigated additionally.

Methods

Raw items were identified by literature research and focus group. Items were improved by interviewing ten GPs with thinking-aloud-method. A personal case vignette related to a complex and uncertainty situation was introduced. The final questionnaire was administered to 228 GPs in Germany. Factorial validity was calculated with explorative and confirmatory factor analysis. The results of the Communicating and Dealing with Uncertainty (CoDU) – questionnaire were compared with the scales of the ‘Physician Reaction to Uncertainty’ (PRU) questionnaire and with the personality traits which were determined with the Big Five Inventory (BFI-K).

Results

The items could be assigned to four scales with varying internal consistency, namely ‘communicating uncertainty’ (Cronbach alpha 0.79), ‘diagnostic action’ (0.60), ‘intuition’ (0.39) and ‘extended social anamnesis’ (0.69). Neuroticism was positively associated with all PRU scales ‘anxiety due to uncertainty’ (Pearson correlation 0.487), ‘concerns about bad outcomes’ (0.488), ‘reluctance to disclose uncertainty to patients’ (0.287), ‘reluctance to disclose mistakes to physicians’ (0.212) and negatively associated with the CoDU scale ‘communicating uncertainty’ (−0.242) (p<0.01 for all). ‘Extraversion’ (0.146; p<0.05), ‘agreeableness’ (0.145, p<0.05), ‘conscientiousness’ (0.168, p<0.05) and ‘openness to experience’ (0.186, p<0.01) were significantly positively associated with ‘communicating uncertainty’. ‘Extraversion’ (0.162), ‘consciousness’ (0.158) and ‘openness to experience’ (0.155) were associated with ‘extended social anamnesis’ (p<0.05).

Conclusion

The questionnaire allowed describing the diagnostic decision making process of general practitioners in complex situations. Personality traits are associated with diagnostic reasoning and communication with patients, which might be important for medical education and quality improvement purposes.     

Virtual bargaining: a theory of social decision-making

An essential element of goal-directed decision-making in social contexts is that agents'' actions may be mutually interdependent. However, the most well-developed approaches to such strategic interactions, based on the Nash equilibrium concept in game theory, are sometimes too broad and at other times ‘overlook’ good solutions to fundamental social dilemmas and coordination problems. The authors propose a new theory of social decision-making—virtual bargaining—in which individuals decide among a set of moves on the basis of what they would agree to do if they could openly bargain. The core principles of a formal account are outlined (vis-à-vis the notions of ‘feasible agreement’ and explicit negotiation) and further illustrated with the introduction of a new game, dubbed the ‘Boobytrap game’ (a modification on the canonical Prisoner''s Dilemma paradigm). In the first empirical data of how individuals play the Boobytrap game, participants'' experimental choices accord well with a virtual bargaining perspective, but do not match predictions from a standard Nash account. Alternative frameworks are discussed, with specific empirical tests between these and virtual bargaining identified as future research directions. Lastly, it is proposed that virtual bargaining underpins a vast range of human activities, from social decision-making to joint action and communication.     

galign: A Tool for Rapid Genome Polymorphism Discovery

Background

Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale. However, the development of customized software to analyze data produced by these methods has lagged behind.

Methods/Principal Findings

Here I describe a tool, ‘galign’, designed to identify polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome. The ‘galign’ alignment tool does not use Smith-Waterman matrices for sequence comparisons. Instead, a simple algorithm comparing parsed sequence reads to parsed reference genome sequences is used. ‘galign’ output is geared towards immediate user application, displaying polymorphism locations, nucleotide changes, and relevant predicted amino-acid changes for ease of information processing. To do so, ‘galign’ requires several accessory files easily derived from an annotated reference genome. Direct sequencing as well as in silico studies demonstrate that ‘galign’ provides lesion predictions comparable in accuracy to available prediction programs, accompanied by greater processing speed and more user-friendly output. We demonstrate the use of ‘galign’ to identify mutations leading to phenotypic consequences in C. elegans.

Conclusion/Significance

Our studies suggest that ‘galign’ is a useful tool for polymorphism discovery, and is of immediate utility for sequence mining in C. elegans.     

Association between Obesity and Cardiometabolic Health Risk in Asian-Canadian Sub-Groups

Objectives

To quantify and compare the association between the World Health Organizations’ Asian-specific trigger points for public health action [‘increased risk’: body mass index (BMI) ≥23 kg/m², and; ‘high risk’: BMI ≥27.5 kg/m²] with self-reported cardiovascular-related conditions in Asian-Canadian sub-groups.

Methods

Six cycles of the Canadian Community Health Survey (2001–2009) were pooled to examine BMI and health in Asian sub-groups (South Asians, Chinese, Filipino, Southeast Asians, Arabs, West Asians, Japanese and Korean; N = 18 794 participants, ages 18–64 y). Multivariable logistic regression, adjusting for demographic, lifestyle characteristics and acculturation measures, was used to estimate the odds of cardiovascular-related health (high blood pressure, heart disease, diabetes, ‘at least one cardiometabolic condition’) outcomes across all eight Asian sub-groups.

Results

Compared to South Asians (OR = 1.00), Filipinos had higher odds of having ‘at least one cardiometabolic condition’ (OR = 1.29, 95% CI: 1.04–1.62), whereas Chinese (0.63, 0.474–0.9) and Arab-Canadians had lower odds (0.38, 0.28–0.51). In ethnic-specific analyses (with ‘acceptable’ risk weight as the referent), ‘increased’ and ‘high’ risk weight categories were the most highly associated with ‘at least one cardiometabolic condition’ in Chinese (‘increased’: 3.6, 2.34–5.63; ‘high’: 8.9, 3.6–22.01). Compared to normal weight South Asians, being in the ‘high’ risk weight category in all but the Southeast Asian, Arab, and Japanese ethnic groups was associated with approximately 3-times the likelihood of having ‘at least one cardiometabolic condition’.

Conclusion

Differences in the association between obesity and cardiometabolic health risks were seen among Asian sub-groups in Canada. The use of WHO’s lowered Asian-specific BMI cut-offs identified obesity-related risks in South Asian, Filipino and Chinese sub-groups that would have been masked by traditional BMI categories. These findings have implications for public health messaging, especially for ethnic groups at higher odds of obesity-related health risks.     

A common perceptual temporal limit of binding synchronous inputs across different sensory attributes and modalities

The human brain processes different aspects of the surrounding environment through multiple sensory modalities, and each modality can be subdivided into multiple attribute-specific channels. When the brain rebinds sensory content information (‘what’) across different channels, temporal coincidence (‘when’) along with spatial coincidence (‘where’) provides a critical clue. It however remains unknown whether neural mechanisms for binding synchronous attributes are specific to each attribute combination, or universal and central. In human psychophysical experiments, we examined how combinations of visual, auditory and tactile attributes affect the temporal frequency limit of synchrony-based binding. The results indicated that the upper limits of cross-attribute binding were lower than those of within-attribute binding, and surprisingly similar for any combination of visual, auditory and tactile attributes (2–3 Hz). They are unlikely to be the limits for judging synchrony, since the temporal limit of a cross-attribute synchrony judgement was higher and varied with the modality combination (4–9 Hz). These findings suggest that cross-attribute temporal binding is mediated by a slow central process that combines separately processed ‘what’ and ‘when’ properties of a single event. While the synchrony performance reflects temporal bottlenecks existing in ‘when’ processing, the binding performance reflects the central temporal limit of integrating ‘when’ and ‘what’ properties.     

Electronically Monitored Labial Dabbing and Stylet ‘Probing’ Behaviors of Brown Marmorated Stink Bug,Halyomorpha halys,in Simulated Environments

Brown marmorated stink bug, Halyomorpha halys (Stål), (Hemiptera: Pentatomidae) is an invasive polyphagous agricultural and urban nuisance pest of Asian origin that is becoming widespread in North America and Europe. Despite the economic importance of pentatomid pests worldwide, their feeding behavior is poorly understood. Electronically monitored insect feeding (EMIF) technology is a useful tool in studies of feeding behavior of Hemiptera. Here we examined H. halys feeding behavior using an EMIF system designed for high throughput studies in environmental chambers. Our objectives were to quantify feeding activity by monitoring proboscis contacts with green beans, including labial dabbing and stylet penetration of the beans, which we collectively define as ‘probes’. We examined frequency and duration of ‘probes’ in field-collected H. halys over 48 hours and we determined how environmental conditions could affect diel and seasonal periodicity of ‘probing’ activity. We found differences in ‘probing’ activity between months when the assays were conducted. These differences in activity may have reflected different environmental conditions, and they also coincide with what is known about the phenology of H. halys. While a substantial number of ‘probes’ occurred during scotophase, including some of the longest mean ‘probe’ durations, activity was either lower or similar to ‘probing’ activity levels during photophase on average. We found that temperature had a significant impact on H. halys ‘probing’ behavior and may influence periodicity of activity. Our data suggest that the minimal temperature at which ‘probing’ of H. halys occurs is between 3.5 and 6.1°C (95% CI), and that ‘probing’ does not occur at temperatures above 26.5 to 29.6°C (95% CI). We estimated that the optimal temperature for ‘probing’ is between 16 and 17°C.     

What Are Fair Study Benefits in International Health Research? Consulting Community Members in Kenya

Background

Planning study benefits and payments for participants in international health research in low- income settings can be a difficult and controversial process, with particular challenges in balancing risks of undue inducement and exploitation and understanding how researchers should take account of background inequities. At an international health research programme in Kenya, this study aimed to map local residents'' informed and reasoned views on the effects of different levels of study benefits and payments to inform local policy and wider debates in international research.

Methods and Findings

Using a relatively novel two-stage process community consultation approach, five participatory workshops involving 90 local residents from diverse constituencies were followed by 15 small group discussions, with components of information-sharing, deliberation and reflection to situate normative reasoning within debates. Framework Analysis drew inductively and deductively on voice- recorded discussions and field notes supported by Nvivo 10 software, and the international research ethics literature. Community members'' views on study benefits and payments were diverse, with complex contextual influences and interplay between risks of giving ‘too many’ and ‘too few’ benefits, including the role of cash. While recognising important risks for free choice, research relationships and community values in giving ‘too many’, the greatest concerns were risks of unfairness in giving ‘too few’ benefits, given difficulties in assessing indirect costs of participation and the serious consequences for families of underestimation, related to perceptions of researchers'' responsibilities.

Conclusions

Providing benefits and payments to participants in international research in low-income settings is an essential means by which researchers meet individual-level and structural forms of ethical responsibilities, but understanding how this can be achieved requires a careful account of social realities and local judgment. Concerns about undue inducement in low-income communities may often be misplaced; we argue that greater attention should be placed on avoiding unfairness, particularly for the most-poor.     

Can the meaning of multiple words be integrated unconsciously?

What are the limits of unconscious language processing? Can language circuits process simple grammatical constructions unconsciously and integrate the meaning of several unseen words? Using behavioural priming and electroencephalography (EEG), we studied a specific rule-based linguistic operation traditionally thought to require conscious cognitive control: the negation of valence. In a masked priming paradigm, two masked words were successively (Experiment 1) or simultaneously presented (Experiment 2), a modifier (‘not’/‘very’) and an adjective (e.g. ‘good’/‘bad’), followed by a visible target noun (e.g. ‘peace’/‘murder’). Subjects indicated whether the target noun had a positive or negative valence. The combination of these three words could either be contextually consistent (e.g. ‘very bad - murder’) or inconsistent (e.g. ‘not bad - murder’). EEG recordings revealed that grammatical negations could unfold partly unconsciously, as reflected in similar occipito-parietal N400 effects for conscious and unconscious three-word sequences forming inconsistent combinations. However, only conscious word sequences elicited P600 effects, later in time. Overall, these results suggest that multiple unconscious words can be rapidly integrated and that an unconscious negation can automatically ‘flip the sign’ of an unconscious adjective. These findings not only extend the limits of subliminal combinatorial language processes, but also highlight how consciousness modulates the grammatical integration of multiple words.     

A Drosophila Toolkit for the Visualization and Quantification of Viral Replication Launched from Transgenic Genomes

Arthropod RNA viruses pose a serious threat to human health, yet many aspects of their replication cycle remain incompletely understood. Here we describe a versatile Drosophila toolkit of transgenic, self-replicating genomes (‘replicons’) from Sindbis virus that allow rapid visualization and quantification of viral replication in vivo. We generated replicons expressing Luciferase for the quantification of viral replication, serving as useful new tools for large-scale genetic screens for identifying cellular pathways that influence viral replication. We also present a new binary system in which replication-deficient viral genomes can be activated ‘in trans’, through co-expression of an intact replicon contributing an RNA-dependent RNA polymerase. The utility of this toolkit for studying virus biology is demonstrated by the observation of stochastic exclusion between replicons expressing different fluorescent proteins, when co-expressed under control of the same cellular promoter. This process is analogous to ‘superinfection exclusion’ between virus particles in cell culture, a process that is incompletely understood. We show that viral polymerases strongly prefer to replicate the genome that encoded them, and that almost invariably only a single virus genome is stochastically chosen for replication in each cell. Our in vivo system now makes this process amenable to detailed genetic dissection. Thus, this toolkit allows the cell-type specific, quantitative study of viral replication in a genetic model organism, opening new avenues for molecular, genetic and pharmacological dissection of virus biology and tool development.     

Social Cognition in Individuals at Ultra-High Risk for Psychosis: A Meta-Analysis

Objective

Treatment in the ultra-high risk stage for a psychotic episode is critical to the course of symptoms. Markers for the development of psychosis have been studied, to optimize the detection of people at risk of psychosis. One possible marker for the transition to psychosis is social cognition. To estimate effect sizes for social cognition based on a quantitative integration of the published evidence, we conducted a meta-analysis of social cognitive performance in people at ultra high risk (UHR).

Methods

A literature search (1970-July 2015) was performed in PubMed, PsychINFO, Medline, Embase, and ISI Web of Science, using the search terms ‘social cognition’, ‘theory of mind’, ‘emotion recognition’, ‘attributional style’, ‘social knowledge’, ‘social perception’, ‘empathy’, ‘at risk mental state’, ‘clinical high risk’, ‘psychosis prodrome’, and ‘ultra high risk’. The pooled effect size (Cohen’s D) and the effect sizes for each domain of social cognition were calculated. A random effects model with 95% confidence intervals was used.

Results

Seventeen studies were included in the analysis. The overall significant effect was of medium magnitude (d = 0.52, 95% Cl = 0.38–0.65). No moderator effects were found for age, gender and sample size. Sub-analyses demonstrated that individuals in the UHR phase show significant moderate deficits in affect recognition and affect discrimination in faces as well as in voices and in verbal Theory of Mind (TOM). Due to an insufficient amount of studies, we did not calculate an effect size for attributional bias and social perception/ knowledge. A majority of studies did not find a correlation between social cognition deficits and transition to psychosis, which may suggest that social cognition in general is not a useful marker for the development of psychosis. However some studies suggest the possible predictive value of verbal TOM and the recognition of specific emotions in faces for the transition into psychosis. More research is needed on these subjects.

Conclusion

The published literature indicates consistent general impairments in social cognition in people in the UHR phase, but only very specific impairments seem to predict transition to psychosis.     

'Asking the Right Question'. A Comparison of Two Approaches to Gathering Data on 'Herbals' Use in Survey Based Studies

Background

Over the last decade academic interest in the prevalence and nature of herbal medicines use by pregnant women has increased significantly. Such data are usually collected by means of an administered questionnaire survey, however a key methodological limitation using this approach is the need to clearly define the scope of ‘herbals’ to be investigated. The majority of published studies in this area neither define ‘herbals’ nor provide a detailed checklist naming specific ‘herbals’ and CAM modalities, which limits inter-study comparison, generalisability and the potential for meta-analyses. The aim of this study was to compare the self-reported use of herbs, herbal medicines and herbal products using two different approaches implemented in succession.

Methods

Cross-sectional questionnaire surveys of women attending for their mid-trimester scan or attending the postnatal unit following live birth at the Royal Aberdeen Maternity Hospital, North-East Scotland. The questionnaire utilised two approaches to collect data on ‘herbals’ use, a single closed yes/no answer to the question “have you used herbs, herbal medicines and herbal products in the last three months”; and a request to tick which of a list of 40 ‘herbals’ they had used in the same time period.

Results

A total of 889 responses were obtained of which 4.3% (38) answered ‘yes’ to herbal use via the closed question. However, using the checklist 39% (350) of respondents reported the use of one or more specific ‘herbals’ (p<0.0001). The 312 respondents who reported ‘no’ to ‘herbals’ use via the closed question but “yes” via the checklist consumed a total of 20 different ‘herbals’ (median 1, interquartile range 1–2, range 1–6).

Conclusions

This study demonstrates that the use of a single closed question asking about the use of ‘herbals’, as frequently reported in published studies, may not yield valid data resulting in a gross underestimation of actual use.     

Accumulation of cadmium in near-isogenic lines of durum wheat (Triticum turgidum L. var durum): the role of transpiration

Concentrations of cadmium in the grain of durum wheat (Triticum turgidum L. var durum) are often above the internationally acceptable limit of 0.2 mg kg⁻¹. Cultivars that vary in concentrations of cadmium in the grain have been identified but the physiology behind differential accumulation has not been determined. Three pairs of near-isogenic lines (isolines) of durum wheat that vary in aboveground cadmium accumulation (8982-TL ‘high’ and ‘low’, W9260-BC ‘high’ and ‘low’, and W9261-BG ‘high’ and ‘low’) were used to test the hypothesis that the greater amounts of cadmium in shoots of the ‘high’ isolines are correlated with greater volumes of water transpired. In general, cadmium content was positively correlated with transpiration only in the ‘low’ isolines. Although shoots of the ‘high’ isolines of W9260-BC and W9261-BG contained higher concentrations of cadmium than did their corresponding ‘low’ isolines, they did not transpire larger volumes of water. In addition, isolines of 8982-TL transpired less water than did the other pairs of isolines yet both ‘high’ and ‘low’ isolines of 8982-TL contained higher amounts of cadmium than did the other pairs. The difference between ‘high’ and ‘low’ isolines appears to be related to the relative contribution of transpiration to cadmium translocation to the shoot. Increased transpiration was associated with increased cadmium content in the ‘low’ isolines but in the ‘high’ isolines increased cadmium in the shoot occurred independently of the volume of water transpired.     

A Simple,Low-Cost Conductive Composite Material for 3D Printing of Electronic Sensors

3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes (‘rapid prototyping’) before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and emoH@baF has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term ‘carbomorph’ and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes.     

Dark extinction: the problem of unknown historical extinctions

The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the ‘pre-taxonomic’ period (approx. 1500–1800 CE) and, to some extent, in the ‘taxonomic period’ (approx. 1800–present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the ‘taxonomic period’. For the ‘pre-taxonomic period’, simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the ‘taxonomic period’ (1800–present) and approximately 180 in the ‘pre-taxonomic period’ (1500–1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).     

Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies

Gene set-based analysis of genome-wide association study (GWAS) data has recently emerged as a useful approach to examine the joint effects of multiple risk loci in complex human diseases or phenotypes. Dental caries is a common, chronic, and complex disease leading to a decrease in quality of life worldwide. In this study, we applied the approaches of gene set enrichment analysis to a major dental caries GWAS dataset, which consists of 537 cases and 605 controls. Using four complementary gene set analysis methods, we analyzed 1331 Gene Ontology (GO) terms collected from the Molecular Signatures Database (MSigDB). Setting false discovery rate (FDR) threshold as 0.05, we identified 13 significantly associated GO terms. Additionally, 17 terms were further included as marginally associated because they were top ranked by each method, although their FDR is higher than 0.05. In total, we identified 30 promising GO terms, including ‘Sphingoid metabolic process,’ ‘Ubiquitin protein ligase activity,’ ‘Regulation of cytokine secretion,’ and ‘Ceramide metabolic process.’ These GO terms encompass broad functions that potentially interact and contribute to the oral immune response related to caries development, which have not been reported in the standard single marker based analysis. Collectively, our gene set enrichment analysis provided complementary insights into the molecular mechanisms and polygenic interactions in dental caries, revealing promising association signals that could not be detected through single marker analysis of GWAS data.