EXPERTS VERSUS CONSUMERS: A CRITIQUE

In a recent paper Moskowitz (1996) refuted the notion that consumers are incapable of validly rating the sensory aspects of products. An analysis of this paper reveals that references are not presented to support his introduction, there is lack of experimental detail, parameters to compare panels were questionable, the degree of expertise of the expert panel is put to doubt and the model proposed to relate data between panels was not compared to existing models.     

DISCUSSION II ON FITTING EQUATIONS TO SENSORY DATA

In his article " On Fitting Equations to Sensory Data." Moskowitz suggests many strategies for model fitting which depart from current statistical methodology. Four areas discussed by Moskowitz are addressed here: (1) Forcing terms into a model; (2) The use of hold-out samples; (3) The use of aggregate data (averaging across people, suppressing the person-to-person variation); and (4) The use of random data as a predictor variable in a regression equation. All four of these points will be examined within this article.     

On the Other "Phylogenetic Systematics"

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor "widely held belief" systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new "Phylogenetic Systematics"—instead we have been presented with a vague and sketchy manifesto based upon the assertion that "clades are individuals" and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for "node pointing," yet even their own examples show that the opposite is true, and their node pointing system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the node pointing system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.     

Compositional Analysis and "Sources" of Pottery: An Ethnoarcheological Approach

One of the important assumptions of compositional analysis is that the elemental composition of an artifact reflects the source of the materials used to make it. Thus, pottery from a particular source will be chemically similar to the raw materials from that source. This "commonsense" assumption seems beyond dispute, but the fact that pottery is a mixture of clay, water, and often temper added by the potter, complicates the interpretation of compositional data from ceramics. This article examines the relationship between potters' behavior in obtaining and using raw materials, on the one hand, and the chemical composition of their finished pottery, on the other, by comparing the elemental composition of ethnographic pottery and raw materials from contemporary pottery-making communities in the Valley of Guatemala. The results of this research show that the relationship between pottery and its constituent raw materials is not as obvious as was first supposed. The article concludes with an alternative approach to compositional analysis that is more in line with the realities of real-world pottery production.     

BH3‐only proteins are part of a regulatory network that control the sustained signalling of the unfolded protein response sensor IRE1α

Correction to: The EMBO Journal (2012) 31: 2322–2335. DOI 10.1038/emboj.2012.84 ¦ Published online 17 April 2012 Figure 4A. Original.Source data are available online for this figure. Figure 4A. Corrected. Source data are available online for this figure. The journal was alerted to the claim that the IRE input panels are identical in Figure 1G. Since the IRE input panels show a high degree of similarity, the source data for both panels are published with this notice for the avoidance of doubt.The HSP90 blot looks very similar in Fig 3F and Fig S4A. The authors confirmed that they had stripped and re‐probed the original HSP90 blot in Fig 3F and Fig S4A. Specifically, the membrane was probed with antibodies to IRE1, and HSP90, and then re‐probed with anti‐PERK antibodies. For that reason, HSP90 was presented in both figures because it is the same experiment. In the source data published with this correction, the authors have marked the original data with contrast boxes and arrows to indicate which blots were presented in the figure. The legends have been updated to state that a control originating from one blot is displayed in both figures.The authors acknowledge that they had removed one set of experimental conditions with wild‐type parental DKO cells when preparing Fig 4A and state that this does not change the conclusions of the figure. The figure is herewith updated with a demarcating line and source data for the full experiment is published with this notice.All authors agree with this corrigendum. The authors apologize for any confusion caused by these errors.     

Desired Division, Disavowed Division: An Analysis of the Labeling of the Bilingual Unit as Separatist in an Aotearoa/New Zealand School

In this article, I offer a new interpretation of non-Mäori parents' claim that a Mäori/English bilingual school unit in Aotearoa/New Zealand is separatist. I show that while some use such a claim to defend monoculturalism and white hegemony, others use it to come to terms with Aotearoa/New Zealand's postcolonial nationhood, globalization, and a changing meaning of "ethnic harmony." I suggest collaborations to rearticulate the latter parents' concerns, thereby creating new alliances to support minority education.     

The effect of gramicidin A on phospholipid bilayers

The helical polypeptide, gramicidin A has been widely studied as a model for the interactions of hydrophobic proteins with lipid bilayer membranes. Many reports are now available of the physical effects of mixing gramicidin A with phospholipid membranes, however, the interpretation of these data remains unclear. The purpose of this communication is to examine the controversial claim that high concentrations of gramicidin A cause disorder within the L phase of phosphatidylcholine-water dispersions. Solid-state nuclear magnetic resonance (NMR), density gradient and X-ray diffraction techniques are used to confirm the existence of such an effect and mechanisms are discussed which account for the known effects of gramicidin A on lipid bilayers.     

Getting into Shape: An Empirical Comparison of Traditional Truss-Based Morphometric Methods with a Newer Geometric Method Applied to New World Cichlids

Body shape is a difficult, but important, trait to quantify. Researchers have traditionally used multivariate analysis of several linear measures ('trusses') across the body form to quantify shape. Newer geometric morphometric methods claim to better estimate shape because they analyze the geometry among the locations of all landmarks simultaneously rather than the linear distances between pairs of landmarks. We tested this claim by comparing the results of several traditional morphometric analyses against a newer geometric analysis involving thin-plate splines (TPS), all applied to a common data set of morphologically variable new world cichlids Amphilophus citrinellus and A. zaliosus. The TPS method yielded slightly stronger evidence of morphological differences among forms, although traditional methods also distinguished the two species. Perhaps our most important result was the idiosyncratic interpretation of shape variation among the traditional truss-based methods, whereas the generation of deformation grids using the TPS approach yielded clear and visually interpretable figures. Our results indicate that geometric morphometrics can be a more effective way to analyze and interpret body form, but also that traditional methods can be relied upon to provide statistical evidence of shape differences, although not necessarily accurate information about the nature of variation in shape.     

The impact of multifunctional genes on "guilt by association" analysis

Many previous studies have shown that by using variants of "guilt-by-association", gene function predictions can be made with very high statistical confidence. In these studies, it is assumed that the "associations" in the data (e.g., protein interaction partners) of a gene are necessary in establishing "guilt". In this paper we show that multifunctionality, rather than association, is a primary driver of gene function prediction. We first show that knowledge of the degree of multifunctionality alone can produce astonishingly strong performance when used as a predictor of gene function. We then demonstrate how multifunctionality is encoded in gene interaction data (such as protein interactions and coexpression networks) and how this can feed forward into gene function prediction algorithms. We find that high-quality gene function predictions can be made using data that possesses no information on which gene interacts with which. By examining a wide range of networks from mouse, human and yeast, as well as multiple prediction methods and evaluation metrics, we provide evidence that this problem is pervasive and does not reflect the failings of any particular algorithm or data type. We propose computational controls that can be used to provide more meaningful control when estimating gene function prediction performance. We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies.     

"Property" and Aboriginal Land Claims in the Canadian Subarctic: Some Theoretical Considerations

Many of the world's aboriginal peoples are currently engaged in struggles over land and self-government with the states that encompass them. In Canada, aboriginal people have effectively used the concept of "aboriginal title" to force the government to negotiate land and self-government agreements with them. Such agreements, however, along with the notion of "aboriginal title" itself, are based on the European concept of "property"; they grant First Nations "ownership" of certain lands and spell out the rights they possess in relation to those lands. This means that aboriginal people have had to learn to think and speak in the "language of property" as a precondition for even engaging government officials in a dialogue over land and sovereignty. Yet the concept of property is in many ways incompatible with many Canadian First Nation people's views about proper human-animal/land relations. In this article, I argue that the land claim process—because it forces aboriginal people to think and speak in the language of property—tends to undermine the very beliefs and practices that a land claim agreement is meant to preserve. [Key words: property, First Nations, aboriginal land claims, Canada, Subarctic]     

"Infant mortality in Armenia 1992-2003": a comment.

The purpose of this comment is to counsel caution in some of the conclusions drawn in an otherwise fine article recently published in Economics and Human Biology on infant mortality in Armenia by Hakobyan, Mkrtchyan and Yepiskoposyan. These relate first, to the reliability of estimates and trends in infant mortality estimated from DHS data; second, to the interpretation of what the authors consider to be a 'low' infant mortality rate in former communist countries given their level of economic development; and third, to the role of the health care infrastructure in countries of the former Soviet Union in producing these 'low' infant mortality levels. This comment argues that trends in infant mortality in Armenia and other CIS countries, although probably declining, are perhaps less certain than the authors allow, that existing evidence does not suggest that they are uniformly low by global standards, or that the health care systems in CIS countries are uniformly effective in reducing infant deaths.     

The "unfrozen fraction" hypothesis of freezing injury to human erythrocytes: a critical examination of the evidence

This paper examines the experimental evidence presented by Mazur and his colleagues to support their hypothesis that the survival of slowly frozen human red blood cells is primarily dependent on the fraction of water that remains unfrozen, rather than on the high concentrations of sodium chloride produced by the formation of ice. This hypothesis is in direct conflict with the general belief that freezing injury under such conditions is caused by the concentration of solutes in the solution surrounding the cells: if the "unfrozen fraction" hypothesis is true, then much of the evidence supporting that belief must be dismissed as mere coincidence. We have reexamined Mazur's data, and have suggested an alternative explanation--that cells which are initially suspended in solutions that are not isotonic differ in their susceptibility to subsequent freezing and thawing, shrunken cells being more resistant and swollen cells more susceptible than normal cells. If this is true then the data can be explained without invoking a direct effect of the unfrozen fraction, solely on the basis of changes in the concentration of the solution surrounding the cells. We cite other experimental evidence, obtained in the absence of freezing, that red blood cells do indeed possess the required property. We further argue that the known effects of variations in cooling and warming rate, and in hematocrit, are able to account for the features observed by Mazur and his colleagues in their three published studies.     

Analysis of the link between a definition of sustainability and the life cycle methodologies

Purpose

It has been claimed that in order to assess the sustainability of products, a combination of the results from a life cycle assessment (LCA), social life cycle assessment (SLCA) and life cycle costing (LCC) is needed. Despite the frequent reference to this claim in the literature, very little explicit analysis of the claim has been made. The purpose of this article is to analyse this claim.

Methods

An interpretation of the goals of sustainability, as outlined in the report Our Common Future (WCED 1987), which is the basis for most literature on sustainability assessment in the LCA community, is presented and detailed to a level enabling an analysis of the relation to the impact categories at midpoint level considered in life cycle (LC) methodologies.

Results

The interpretation of the definition of sustainability as outlined in Our Common Future (WCED 1987) suggests that the assessment of a product's sustainability is about addressing the extent to which product life cycles affect poverty levels among the current generation, as well as changes in the level of natural, human and produced and social capital available for the future population. It is shown that the extent to which product life cycles affect poverty to some extent is covered by impact categories included in existing SLCA approaches. It is also found that the extent to which product life cycles affect natural capital is well covered by LCA, and human capital is covered by both LCA and SLCA but in different ways. Produced capital is not to any large extent considered in any of the LC methodologies. Furthermore, because of the present level of knowledge about what creates and destroys social capital, it is difficult to assess how it relates to the LC methodologies. It is also found that the LCC is only relevant in the context of a life cycle sustainability assessment (LCSA) if focusing on the monetary gains or losses for the poor. Yet, this is an aspect which is already considered in several SLCA approaches.

Conclusions

The current consensus that LCSA can be performed through combining the results from an SLCA, LCA and LCC is only partially supported in this article: The LCSA should include both an LCA and an SLCA, which should be expanded to better cover how product life cycles affect poverty and produced capital. The LCC may be included if it has as a focus to asses income gains for the poor.     

Alternative statistical parameter for high-throughput screening assay quality assessment

High-throughput screening is an essential process in drug discovery. The ability to identify true active compounds depends on the high quality of assays and proper analysis of data. The Z factor, presented by Zhang et al. in 1999, provides an easy and useful summary of assay quality and has been a widely accepted standard. However, as data analysis has undergone much improvement recently, the assessment of assay quality has not evolved in parallel. In this article, the authors study the implications of Z factor values under different conditions and link the Z factor with the power of discovering true active compounds. They discuss the different interpretations of Z factor depending on error distributions and advocate direct analysis of power as assay quality assessment. They also propose that in estimating assay quality parameters, adjustments in data analysis should be taken into account. Studying the power of identifying true "hits" gives a more direct interpretation of assay quality and may provide guidance in assay optimization on some occasions.     

On sieve tube function

Summary Several theories of phloem transport are currently being considered in various laboratories on the basis of recent evidence. Proponents of the activated diffusion or protoplasmic theories claim support in the disclosure of fibrils, longitudinally arranged, in the connecting strands passing across sieve plates, and in the close connection between respiratory activity and transport. Those favoring a surface migration theory claim support in the demonstrated systems of sieve element lamellae, along whose surfaces one could imagine solute transport to occur. Proponents of the pressure flow theory point to results of exudation studies, tracer investigations, and to histochemical evidence indicating that sieve elements are relatively inactive, metabolically, as well as to the suggestion that perhaps the connecting strands are more open (tubular) than they have been considered to be up to now.Callose formation is stimulated by turgor changes, promoted by foreign chemicals, viruses, and, in the sieve element, by a relatively alkaline pH, a high sucrose concentration, and doubtless by the unique unbalanced character of sieve sap composition. The function of callose in older or wounded elements appears to be a constricting or plugging action, but its function in young mature elements is essentially obscure.Recent evidence augments the view that sieve elements display an extraordinary sensitivity towards experimental manipulation.     

Men Who Are Called "Women" in Toba-Batak: Marriage, Fundamental Sex-Role Differences, and the Suitability of the Gloss "Wife-Receiver"

This article gives brief accounts of affinal relations, marriage, gender roles, and long-term lineage relationships among Toba Bataks of Samosir, north Sumatra, Indonesia. Ethnographic data, presented in tandem with data on the Kachin and similar cultures, are used to call into question the use of the term "wife-taker" as opposed to "wife-receiver," as it is generally employed with reference to the groom, his family, and lineage-mates, in glossing a major conceptual category of Southeast Asian hinterland societies that have preferred matrilateral cross-cousin marriage. It is argued that "wife-taker" is more distorting of Batak practice and of their system of values than "wife-receiver."     

TWO TYPES OF SENSORY PANELS OR ARE THERE MORE?

The purpose of this article is to discuss the issues associated with selecting assessors for sensory panels. It develops the argument that although there are many variations in the detail of how assessors are selected, all panels can be considered as either (1) selecting respondents to measure ingredient concentrations via perceptions or (2) selecting respondents to represent the response that would be obtained from a wider consumer population. The validity of the data collected, i.e., the extent to which the data collected measures what was originally intended, depends on the detail of how assessors were selected as well as a number of other factors.     

Evaluating the accuracy of AIM panels at quantifying genome ancestry

Background

There is a growing interest among geneticists in developing panels of Ancestry Informative Markers (AIMs) aimed at measuring the biogeographical ancestry of individual genomes. The efficiency of these panels is commonly tested empirically by contrasting self-reported ancestry with the ancestry estimated from these panels.

Results

Using SNP data from HapMap we carried out a simulation-based study aimed at measuring the effect of SNP coverage on the estimation of genome ancestry. For three of the main continental groups (Africans, East Asians, Europeans) ancestry was first estimated using the whole HapMap SNP database as a proxy for global genome ancestry; these estimates were subsequently compared to those obtained from pre-designed AIM panels. Panels that consider >400 AIMs capture genome ancestry reasonably well, while those containing a few dozen AIMs show a large variability in ancestry estimates. Curiously, 500-1,000 SNPs selected at random from the genome provide an unbiased estimate of genome ancestry and perform as well as any AIM panel of similar size. In simulated scenarios of population admixture, panels containing few AIMs also show important deficiencies to measure genome ancestry.

Conclusions

The results indicate that the ability to estimate genome ancestry is strongly dependent on the number of AIMs used, and not primarily on their individual informativeness. Caution should be taken when making individual (medical, forensic, or anthropological) inferences based on AIMs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-543) contains supplementary material, which is available to authorized users.     

"Rates" of birth defects

The proportion of children born with a particular defect is not a "birth defect rate" but, rather, a prevalence proportion. The implications of confusing a rate and a proportion are discussed in terms of the interpretation of birth defect data. It is recommended that "prevalence proportion" or "prevalence" be used to report the frequency of various defects rather than the often-used "prevalence rate."