The indispensability of labelled groups to vulnerability in bioethics

Regarding the determination of vulnerability, the bioethics community has univocally jettisoned “labelled groups”, groups whose membership confers a context‐invariant “vulnerable” status to their members. While the usual reasons against the sole use of labelled groups to determine the vulnerability of individuals are sound, labelled groups as exemplars of vulnerability can play indispensable roles in bioethical reasoning. In this article, I argue against the wholesale jettisoning of labelled groups by showing how they can be useful.     

IS IT TIME FOR BIOETHICS TO GO EMPIRICAL?

Observers who note the increasing popularity of bioethics discussions often complain that the social sciences are poorly represented in discussions about things like abortion and stem-cell research. Critics say that bioethicists should be incorporating the methods and findings of social scientists, and should move towards making the discipline more empirically oriented. This way, critics argue, bioethics will remain relevant, and truly reflect the needs of actual people. Such recommendations ignore the diversity of viewpoints in bioethics, however. Bioethics can gain much from the methods and findings from ethnographies and similar research. But it is misleading to suggest that bioethicists are unaware of this potential benefit. Not only that, bioethicists are justified in having doubts about the utility of the social science approach in some cases. This is not because there is some inherent superiority in non-empirical approaches to moral argument. Rather, the doubts concern the nature of the facts that the sciences would provide. Perhaps the larger point is that disagreements about the relationship between facts and normative arguments should be seen as part of the normal inquiry in bioethics, not evidence that reform is needed.     

On small‐sample inference in group randomized trials with binary outcomes and cluster‐level covariates

Group randomized trials (GRTs) randomize groups, or clusters, of people to intervention or control arms. To test for the effectiveness of the intervention when subject‐level outcomes are binary, and while fitting a marginal model that adjusts for cluster‐level covariates and utilizes a logistic link, we develop a pseudo‐Wald statistic to improve inference. Alternative Wald statistics could employ bias‐corrected empirical sandwich standard error estimates, which have received limited attention in the GRT literature despite their broad utility and applicability in our settings of interest. The test could also be carried out using popular approaches based upon cluster‐level summary outcomes. A simulation study covering a variety of realistic GRT settings is used to compare the accuracy of these methods in terms of producing nominal test sizes. Tests based upon the pseudo‐Wald statistic and a cluster‐level summary approach utilizing the natural log of observed cluster‐level odds worked best. Due to weighting, some popular cluster‐level summary approaches were found to lead to invalid inference in many settings. Finally, although use of bias‐corrected empirical sandwich standard error estimates did not consistently result in nominal sizes, they did work well, thus supporting the applicability of marginal models in GRT settings.     

A New Testing Approach for Comparing the Overall Homogeneity of Survival Curves

The assessment of overall homogeneity of time‐to‐event curves is a key element in survival analysis. The currently commonly used methods, e.g., log‐rank and Wilcoxon tests, may have a significant loss of statistical testing power under certain circumstances. In this paper a new statistical testing approach is developed to compare the overall homogeneity of survival curves. The proposed new method has greater power than the commonly used tests to detect overall differences between crossing survival curves. The small‐sample performance of the new test is investigated under a variety of situations by means of Monte Carlo simulations. Furthermore, the applicability of the proposed testing approach is illustrated by a real data example from a kidney dialysis trial. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Multiplexed MRM‐based quantitation of candidate cancer biomarker proteins in undepleted and non‐enriched human plasma

An emerging approach for multiplexed targeted proteomics involves bottom‐up LC‐MRM‐MS, with stable isotope‐labeled internal standard peptides, to accurately quantitate panels of putative disease biomarkers in biofluids. In this paper, we used this approach to quantitate 27 candidate cancer‐biomarker proteins in human plasma that had not been treated by immunoaffinity depletion or enrichment techniques. These proteins have been reported as biomarkers for a variety of human cancers, from laryngeal to ovarian, with breast cancer having the highest correlation. We implemented measures to minimize the analytical variability, improve the quantitative accuracy, and increase the feasibility and applicability of this MRM‐based method. We have demonstrated excellent retention time reproducibility (median interday CV: 0.08%) and signal stability (median interday CV: 4.5% for the analytical platform and 6.1% for the bottom‐up workflow) for the 27 biomarker proteins (represented by 57 interference‐free peptides). The linear dynamic range for the MRM assays spanned four orders‐of‐magnitude, with 25 assays covering a 10³–10⁴ range in protein concentration. The lowest abundance quantifiable protein in our biomarker panel was insulin‐like growth factor 1 (calculated concentration: 127 ng/mL). Overall, the analytical performance of this assay demonstrates high robustness and sensitivity, and provides the necessary throughput and multiplexing capabilities required to verify and validate cancer‐associated protein biomarker panels in human plasma, prior to clinical use.     

Patterns of dental caries and treatment experience in elderly Lithuanians

Objective: The aim of the study was to evaluate patterns of caries experience in a representative sample of Lithuanians, aged 65‐74. Methods: This cross‐sectional study included 301 participants (response rate 54%). Information was obtained from a clinical examination (caries experience, stimulated salivary flow rates and oral hygiene levels) and a questionnaire. The questionnaire comprised questions about oral, general, physical, mental and social health and about background, knowledge, attitudes and lifestyle. The study had a multidimensional approach to negative consequences of disease and positive aspects of health. For bivariate testing, t‐test, ANOVA and Spearman's correlation were used. Factor analysis was combined with linear multiple regression for a multivariate study of caries experience patterns. Results: Elderly Lithuanians were found to have lower levels of edentulousness (range 11‐15%) than elderly people in other European countries. The mean number of missing teeth was also lower than in any of the neighbouring countries. A comparison of dentate and edentulous groups did not show any major differences. Those who reported that they had general disease had higher levels of oral health maintenance. In dentate elderly, caries experience differed according to place of residence, fluoride content in the drinking water, socio‐economic status, gender, lifestyle, and many other factors. The multivariate approach explained 52%. 61% and 55% of the variation in the number of filled or sound teeth (FS‐T), delayed (DT) and missing teeth (MT) respectively. Conclusion: Levels of oral health maintenance and caries experience show substantial variation among elderly Lithuanians, according to many health‐related characteristics. These elderly people require appropriate oral care, just as much as people in other population sub‐groups.     

Thermodynamic Constraints in Kinetic Modeling: Thermodynamic‐Kinetic Modeling in Comparison to Other Approaches

Kinetic models of reaction networks may easily violate the laws of thermodynamics and the principle of detailed balance. In large network models, the constraints that are imposed by these laws are particularly difficult to address. This hinders modeling of biochemical reaction networks. Thermodynamic‐kinetic modeling is a method that provides a thermodynamically sound and formally appealing way for deriving dynamic model equations of reaction systems. State variables of this approach are thermokinetic potentials that describe the ability of compounds to drive a reaction. A compound has a parameter called capacity, which is the ratio of its concentration and thermokinetic potential. A reaction is described by its resistance which is the ratio of the thermokinetic driving force and flux. In these aspects, the formalism is similar to the modeling formalism for electrical networks and an analogous graphical representation is possible. The thermodynamic‐kinetic modeling formalism is equivalent to the traditional kinetic modeling formalism with the exception that it is not possible to build thermodynamically infeasible models. Here, the thermodynamic‐kinetic modeling formalism is reviewed, compared to other approaches, and some of its advantages are worked out. In contrast to other approaches, thermodynamic‐kinetic modeling does not rely on an explicit enumeration of stoichiometric cycles. It is capable of describing rate laws far from equilibrium. Further, the parameterization by capacities and resistances is particularly intuitive and powerful.     

TWO CONCEPTS OF EMPIRICAL ETHICS

The turn to empirical ethics answers two calls. The first is for a richer account of morality than that afforded by bioethical principlism, which is cast as excessively abstract and thin on the facts. The second is for the facts in question to be those of human experience and not some other, unworldly realm. Empirical ethics therefore promises a richer naturalistic ethics, but in fulfilling the second call it often fails to heed the metaethical requirements related to the first. Empirical ethics risks losing the normative edge which necessarily characterizes the ethical, by failing to account for the nature and the logic of moral norms. I sketch a naturalistic theory, teleological expressivism (TE), which negotiates the naturalistic fallacy by providing a more satisfactory means of taking into account facts and research data with ethical implications. The examples of informed consent and the euthanasia debate are used to illustrate the superiority of this approach, and the problems consequent on including the facts in the wrong kind of way.     

Non-invasive diagnosis methods of coronary disease based on wavelet denoising and sound analyzing

The heart sound is the characteristic signal of cardiovascular health status. The objective of this project is to explore the correlation between Wavelet Transform and noise performance of heart sound and the adaptability of classifying heart sound using bispectrum estimation. Since the wavelet has multi-scale and multi-resolution characteristics, in this paper, the heart sound signal with different frequency ranges is decomposed through wavelet and displayed on different scales of the resolving wavelet result. According to distribution features of frequency of heart sound signals, the interference components in heart sound signal can be eliminated by selecting reconstruction coefficients. Comparing de-noising effects of four wavelets which are haar, db6, sym8 and coif6, the db6 wavelet has achieved an optimal denoising effect to heart sound signals. The de-noising result of contrasting different layers in the db6 wavelet shows that decomposing with five layers in db6 provide the optimal performance. In practice, the db6 wavelet also shows commendable denoising effects when applying to 51 clinical heart signals. Furthermore, through the clinic analyses of 29 normal signals from healthy people and 22 abnormal heart signals from coronary heart disease patients, this method can fairly distinguish abnormal signals from normal signals by applying bispectrum estimation to denoised signals via ARMA coefficients model.     

Developing a vision for improved monitoring and reporting of riparian restoration projects

Representatives from agencies involved in natural resource management in the Murray‐Darling Basin gathered for a workshop in November 2010 to develop a vision for improved monitoring and reporting of riparian restoration projects. The resounding message from this workshop was that the effectiveness of riparian restoration depends on having sound, documented and agreed evidence on the ecological responses to restoration efforts. Improving our capacity to manage and restore riparian ecosystems is constrained by (i) a lack of ecological evidence on the effects of restoration efforts, and (ii) short‐termism in commitment to restoration efforts, in funding of monitoring and in expected time spans for ecosystem recovery. Restoration at the effective spatial scope will invariably require a long‐term commitment by researchers, funding agencies, management agencies and landholders. To address the knowledge gaps that constrain riparian restoration in the Basin, participants endorsed four major fields for future research: the importance of landscape context to restoration outcomes; spatio‐temporal scaling of restoration outcomes; functional effects of restoration efforts; and developing informative and effective indicators of restoration. To improve the monitoring and restoration of riparian zones throughout the Basin, participants advocated an integrated approach: a hierarchical adaptive management framework that incorporates long‐term ecological research.     

[Re]considering Respect for Persons in a Globalizing World

Contemporary clinical ethics was founded on principlism, and the four principles: respect for autonomy, nonmaleficence, beneficence and justice, remain dominant in medical ethics discourse and practice. These principles are held to be expansive enough to provide the basis for the ethical practice of medicine across cultures. Although principlism remains subject to critique and revision, the four‐principle model continues to be taught and applied across the world. As the practice of medicine globalizes, it remains critical to examine the extent to which both the four‐principle framework, and individual principles among the four, suffice patients and practitioners in different social and cultural contexts. Using the four‐principle model we analyze two accounts of surrogate decision making – one from the developed and one from the developing world – in which the clinician undertakes medical decision‐making with apparently little input from the patient and/or family. The purpose of this analysis is to highlight challenges in assessing ethical behaviour according to the principlist model. We next describe cultural expectations and mores that inform both patient and clinician behaviors in these scenarios in order to argue that the principle of respect for persons informed by culture‐specific ideas of personhood may offer an improved ethical construct for analyzing and guiding medical practice in a globalized and plural world.     

Is maximization of molar yield in metabolic networks favoured by evolution?

Stoichiometric analysis of metabolic networks allows the calculation of possible metabolic flux distributions in the absence of kinetic data. In order to predict which of the possible fluxes are present under certain conditions, additional constraints and optimization principles can be applied. One approach of calculating unknown fluxes (frequently called flux balance analysis) is based on the optimality principle of maximizing the molar yield of biotransformations. Here, the relevance and applicability of that approach are examined, and it is compared with the principle of maximizing pathway flux. We discuss diverse experimental evidence showing that, often, those biochemical pathways are operative that allow fast but low-yield synthesis of important products, such as fermentation in Saccharomyces cerevisiae and several other yeast species. Together with arguments based on evolutionary game theory, this leads us to the conclusion that maximization of molar yield is by no means a universal principle.     

Gastropod palaeohabitats of Miocene Lake Randeck Maar and its hinterland defined by an actualistic genus-level approach

The Randeck Maar lake sediments from SW Germany were deposited during a climatic phase known as the Mid-Miocene Climatic Optimum, providing a unique window into this last favourable period for a more thermophilous fauna in Central Europe. Previous palaeoecological reconstructions of Randeck Maar's environment focused on the flora and vertebrate fauna. Here, we present a palaeoecological analysis using gastropods as proxies by means of an actualistic genus-level approach. This approach is grounded in comparisons of habitat preferences between extant and fossil congeners and thus obviously requires a sound taxonomic framework. Despite being commonly applied in the literature, this approach has hardly been defined so far. Therefore, we thoroughly delineate it, exploring its applicability, potential and shortcomings. The molluscan fauna of Randeck Maar counts with 32 species of continental snails, mostly terrestrial pulmonates, related to the following palaeohabitats: littoral, supralittoral, rocky walls, shrubland, forests and open habitats. The gastropods indicate a warm-temperate climate with a dry season, in line with previous works on Randeck Maar's flora and vertebrates.     

Assessment of spatial habitat heterogeneity by coupling data-driven habitat suitability models with a 2D hydrodynamic model in small-scale streams

Habitat assessment considering habitat quality and quantity is a key approach in conservation and restoration works for biodiversity and ecosystems. In this regard, application of hydrodynamic model for modeling instream habitat conditions and machine learning (ML) methods for modeling habitat suitability of a target species can contribute to better modeling practices in ecohydraulics. Despite the importance of small streams for aquatic ecosystems, previous studies in ecohydraulics have been conducted mainly in medium to large rivers, often disregarding small-scale streams such as agricultural canals. The aim of this study is to demonstrate the applicability of a coupled use of ML and a two-dimensional (2D) hydrodynamic model for assessing spatial habitat heterogeneity in small-scale agricultural canals in Japan. Using abundance data of Japanese medaka (Oryzias latipes), four ML methods, namely artificial neural networks (ANNs), classification and regression trees (CARTs), random forests (RF) and support vector machines (SVMs), were applied to develop habitat suitability models considering water depth and flow velocity. A 2D hydrodynamic model was developed based on field surveys in two types of agricultural canals, namely earthen and concrete-lined canals. Information entropy was used for assessing the spatial heterogeneity of instream habitat conditions. As a result, the hydrodynamic models could model instream habitat conditions in a reasonable accuracy. Despite the differences in accuracies in habitat modeling, the four ML methods illustrated similar habitat suitability information for Japanese medaka. The coupled ecohydraulics modeling approach could quantify habitat quality and its spatial heterogeneity, based on which the differences between the earthen and concrete-lined canals were quantitatively assessed. This study demonstrated the applicability of ML-based habitat suitability evaluation and a 2D hydrodynamic model for modeling the spatial distribution of habitat suitability and assessing its spatial heterogeneity. Further study, assessing the spatial heterogeneity in various types of flows including natural/artificial and small/large streams, can contribute to establish quantitative criteria for an ecologically sound habitat and improved ecofriendly construction works in small-scale rivers and streams.     

Phonotactic behaviour and vertical sound source localisation of the parasitoid fly Emblemasoma auditrix (Diptera: Sarcophagidae)

1. Acoustically guided movement in a three‐dimensional space is a complex behavioural task performed notably by birds, bats, and some insect species. The precision of acoustic orientation depends on the directionality of the hearing system as well as on auditory behaviour. 2. The fly Emblemasoma auditrix Diptera (Sarcophagidae) is a parasitoid of the cicada Okanagana rimosa Auchenorrhyncha (Cicadidae) and locates its host in the complex habitat of a forest. The phonotactic behaviour of the fly was analysed experimentally with emphasis on the vertical domain in the field. Different experimental setups allowed discriminating subsequent steps in the phonotactic behaviour of E. auditrix. 3. During the phonotactic flight, flies first landed on landmarks, which were used to re‐adjust to the elevation of the sound source. Acoustic targets were located from these resting positions. The sound source elevation was detected at the start of the flight as the longitudinal body axis was adjusted to the inclination of the target sound source. 4. Flies usually did not land directly upon the sound source, but landed nearby, and most often above the target. Within the target area, types of movement for the final approach differed in respect to target position; flies walked predominantly if the final target was located above or below, but for horizontally located targets much of the distance was covered by flight. 5. In conclusion, E. auditrix can locate the acoustic target in complex habitats and uses a flexible multi‐step approach for short‐range phonotaxis.     

Protease cleavage site fingerprinting by label‐free in‐gel degradomics reveals pH‐dependent specificity switch of legumain

Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel‐based label‐free proteomic approach (DIPPS—direct in‐gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in‐gel digestion of the gel‐separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction, and subsequent mass spectrometry analysis combined with a length‐limited unspecific database search. We applied the methodology to profile ten proteases ranging from highly specific (trypsin, endoproteinase GluC, caspase‐7, and legumain) to broadly specific (matrix‐metalloproteinase‐3, thermolysin, and cathepsins K, L, S, and V). Using DIPPS, we were able to perform specificity profiling of thermolysin at its optimal temperature of 75°C, which confirmed the applicability of the method to extreme experimental conditions. Moreover, DIPPS enabled the first global specificity profiling of legumain at pH as low as 4.0, which revealed a pH‐dependent change in the specificity of this protease, further supporting its broad applicability.     

Bias in population growth rate estimation: sparse data,partial life cycle analysis and Jensen's inequality

Demographic matrix models have become an integral part of population viability analysis for threatened and endangered species, but their use is often limited by data availability. A common solution to this problem is to assume constant annual rates within a multi‐year stage. Partial life cycle analysis (PLC), which incorporates only juvenile and adult stages, is a noteworthy example of this approach because it has been described in the literature as a reliable approximation of age‐structured populations. However, we predict from Jensen's Inequality that the required lumping of age classes leads to over‐ or underestimation of population fitness when survival rates are truly age‐dependent. We illuminate this problem by comparing fitness estimates from Leslie matrix and PLC models for theoretical populations having different levels of age‐dependence in their survival rates. We also propose a modification of the PLC approach to address this problem and demonstrate its applicability using data from a published long‐term study of red deer Cervus elephas.     

Multiplex single‐cell quantification of rare RNA transcripts from protoplasts in a model plant system

Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface‐enhanced Raman spectroscopy (SERS) and gold nanoprobes at single‐cell resolution. We show the applicability of nanoparticle‐based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold‐nanoparticles decorated with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by transmission electron microscopy, inductively‐coupled plasma‐mass spectrometry and fluorescence imaging. Second, we show the utility of a SERS platform to monitor individual alternatively spliced (AS) variants and miRNA copies within single cells. Finally, the distinctive spectral features of Raman‐active dyes were exploited for multiplex analysis of AtPTB2, AtDCL2, miR156a and miR172a. Furthermore, single‐cell studies were validated by in vitro quantification and evaluation of nanotoxicity of gold probes. Raman tag functionalized gold nanosensors yielded an approach for the tracking of rare RNAs within the protoplasts. The SERS‐based approach for quantification of RNAs has the capability to be a highly sensitive, accurate and discerning method for single‐cell studies including AS variants quantification and rare miRNA detection in specific plant species.