Maintaining data integrity in microarray data management

Gene expression microarrays are a relatively new technology, dating back just a few years, yet they have already become a very widely used tool in biology, and have evolved to a wide range of applications well beyond their original design intent. However, while the use of microarrays has expanded, and the issues of performance optimization have been intensively studied, the fundamental issue of data integrity management has largely been ignored. Now that performance has improved so greatly, the shortcomings of data integrity control methods constitute a greater percent of the stumbling blocks for investigators. Microarray data are cumbersome, and the rule up to this point has mostly been one of hands-on transformations, leading to human errors which often have dramatic consequences. We show in this review that the time lost on such mistakes is enormous and dramatically affects results; therefore, mistakes should be mitigated in any way possible. We outline the scope of the data integrity issue, to survey some of the most common and dangerous data transformations, and their shortcomings. To illustrate, we review some case studies. We then look at the work done by the research community on this issue (which admittedly is meager up to this point). Some data integrity issues are always going to be difficult, while others will become easier-one of our goals is to expedite the use of integrity control methods. Finally, we present some preliminary guidelines and some specific approaches that we believe should be the focus of future research.     

Skin grafts and local flaps

Expedited healing of skin wounds is essential regardless of surgical specialty. Any skin deficiency will thwart this basic intent, and an alternative must be sought. The autogenous skin graft or local flap has long had a major role in satisfying this objective. Various forms of autogenous skin grafts are to be differentiated from local flaps, primarily on the basis of vascularization. The indications for either, their surgical anatomy, harvest techniques, and limitations, including pitfalls, need to be outlined. Skin grafts are the simplest means to restore skin integrity. If skin grafts are contraindicated, a flap may be essential. For this purpose, the "top ten" local "workhorse" flaps are briefly described in this article. Accompanying videos further elaborate the requisite surgical anatomy and harvest techniques. As a problem-solving specialty, it is incumbent upon us to first prevent, then be able to provide rapid, efficient, and efficacious healing of, any surgical wound, iatrogenic or otherwise. Skin grafts and local flaps are fundamental elements for achieving this goal when healing by primary or secondary intent is not possible. Whether one is a "reconstructive" or "aesthetic" plastic surgeon, knowledge of these basic tenets will ensure maintenance of competency.     

Before, During and After: The Need for Long-term Monitoring in Invasive Plant Species Management

The invasion of non-indigenous plants is considered one of the primary threats to rare and endangered species as well as to the integrity and function of North American ecosystems. However, many of the suspected negative ecosystem impacts are based on anecdotal evidence. For example, there is almost unanimous agreement among natural resource managers of the detrimental ecological impacts of species such as Lythrum salicaria (purple loosestrife), Phragmites australis (common reed) and Alliaria petiolata (garlic mustard) but convincing documentation is scarce. Experimental and theoretical ecology predicts large ecosystem impacts of the most widespread invasive species. However, it is difficult to prioritize control of species that occur at intermediate densities. Long-term monitoring before and during the invasion as well as before, during and after any control attempts can provide valuable ecological information. In particular, it is important to understand how changes in the abundance of species influence ecosystem properties and processes which, in turn, will help guide management decisions. Ideally, this monitoring has to go beyond 'simple impacts on plant communities, involve cross-disciplinary teams of scientists and should incorporate many different taxa and their interactions. Monitoring design and data collection should be sophisticated enough to allow statistically sound data analysis. The available information will be paramount in (1) developing new political and scientific guidelines in invasive species management, (2) helping resolve potential conflicts of interest and (3) helping change public attitudes regarding growth, sale, and control of non-indigenous species.     

国家公园生态系统完整性的内涵及评价框架: 以东北虎豹国家公园为例

保护自然生态系统的完整性是我国建立国家公园的主要目标之一, 《国家公园设立规范》(GB/T 39737-2021)已将生态系统完整性作为国家公园的准入条件生态重要性的认定指标之一, 但目前对国家公园生态系统完整性的内涵还没有统一定义, 并缺乏具体的评价体系。本文在国内外相关研究的基础上, 结合我国国家公园体制试点成果及第一批国家公园设立实践, 提出了国家公园生态系统完整性的基本内涵及评价指标体系, 以期为今后设立国家公园时划定边界范围或评估国家公园管理成效提供理论依据。作者提出, 应从生态系统结构和过程完整性、功能完整性、空间格局完整性3个维度对我国国家公园生态系统完整性进行综合评价。以东北虎豹国家公园为例, 体制试点以来, 东北虎(Panthera tigris altaica)和东北豹(P. pardus orientalis)等顶级食肉动物的食物链相对完整, 虎、豹野生种群从俄罗斯进入、定居、繁衍、扩散的路径清晰, 种群稳定增长、栖息地质量持续改善, 生物多样性日益丰富, 国家公园正式设立范围划定时充分考虑了生态系统完整性保护, 生态系统完整性评级为优秀, 为国家公园可持续发展奠定了良好基础。     

Necrotic and apoptotic cell death induced by Captan on <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Captan is one of the most widely used broad-spectrum fungicide applied to control several early and late diseases of grapes, apples, and other fruits and vegetables, and as other phthalimide fungicides is defined as a multisite compound with thiol-reactivity. Captan can affect non-target organisms as yeasts, modifying microbial populations and fermentation processes. In this study, we asked whether Captan thiol-reactivity and other mechanisms are involved in acute Captan-induced cell death on aerobic growing Saccharomyces cerevisiae. Thus for, we analyze cellular protein and non-protein thiols, cell membrane integrity, reactive oxygen species accumulation, phosphatidylserine externalization, and apoptotic mutants behavior. The results showed that when submitted to acute Captan treatment most cells lost their membrane integrity and died by necrosis due to Captan reaction with thiols. However, part of the cells, even maintaining their membrane integrity, lost their culture ability. These cells showed an apoptotic behavior that may be the result of non-protein thiol depletion and consequent increase of reactive oxygen species (ROS). ROS accumulation triggers a metacaspase-dependent apoptotic cascade, as shown by the higher viability of the yca1-deleted mutant. Together, necrosis and apoptosis are responsible for the high mortality detected after acute Captan treatment of aerobically growing cells of S. cerevisiae.     

Identifying conservation units within captive chimpanzee populations

One of the primary objectives in the captive management of any endangered primate is to preserve as much as possible the genetic diversity that has evolved and still exists in wild gene pools. The rationale for this is based on the theoretical understanding of the relationship between genetic diversity and fitness in response to selection. There remains little consensus, however, as to the type of genetic data that should be used to monitor captive populations. In order to develop a deeper understanding of the degree and nature of genetic diversity among "wild" chimpanzee gene pools, as well as to determine if one type of genetic data is more useful than others, DNA sequence data were generated at three unlinked, nonrepetitive nuclear loci, one polymorphic microsatellite, and the mitochondrial D-loop for 59 unrelated common and pygmy chimpanzees. The results suggest that: 1) data from nuclear loci can be used to differentiate common chimpanzee subspecies; 2) pygmy chimpanzees may have less genetic diversity than common chimpanzees; 3) shared microsatellite alleles do not always indicate identity by descent; and 4) nonrepetitive loci provide unique insights into evolutionary relationships and provide useful information for captive management programs.     

中国国家公园原真性与完整性概念及其评价框架

国家公园保护管理的首要目的是有效保护国家重要自然生态系统原真性和完整性。我们提出了面向管理的中国国家公园原真性与完整性概念, 国家公园原真性是指国家公园内生态系统及构成国家公园价值或与国家公园价值紧密联系的自然与文化要素保持在原生状态, 强调“不受损”; 国家公园完整性是指国家公园具有足够面积和充分的组成要素, 以维持生态系统的结构、功能与过程, 维持自然区域的价值与特征, 强调“不缺失”。我们还提出了国家公园原真性和完整性评价框架, 从自然度、气候变化强度、传统文化及其载体的真实性、人类干扰程度、人与自然和谐关系的原真性5个方面评价国家公园原真性; 从生态系统组成完整性、生态系统结构完整性、生态系统功能完整性、景观组成要素完整性和文化景观的完整性5个层面评价国家公园完整性。此外, 我们还提出了国家公园原真性与完整性保护的建议, 包括重塑保护管理目标、更新保护管理理念与提升保护管理技术3个方面。国家公园原真性与完整性的讨论尚未成熟, 对评价指标设定、指标间的相互关系、保护管理技术等的研究均尚待深入。     

Designing and implementing a research integrity promotion plan: Recommendations for research funders

Various stakeholders in science have put research integrity high on their agenda. Among them, research funders are prominently placed to foster research integrity by requiring that the organizations and individual researchers they support make an explicit commitment to research integrity. Moreover, funders need to adopt appropriate research integrity practices themselves. To facilitate this, we recommend that funders develop and implement a Research Integrity Promotion Plan (RIPP). This Consensus View offers a range of examples of how funders are already promoting research integrity, distills 6 core topics that funders should cover in a RIPP, and provides guidelines on how to develop and implement a RIPP. We believe that the 6 core topics we put forward will guide funders towards strengthening research integrity policy in their organization and guide the researchers and research organizations they fund.

Research funders are prominently placed to foster research integrity by requiring that researchers make an explicit commitment to research integrity. This Consensus View suggests 6 core topics that funders should cover in a research integrity promotion plan and provides practical recommendations for how to implement one.

To improve research quality and validity, foster responsible research cultures, and maintain public trust in science, various stakeholders have put research integrity high on their agenda. Among them, research funders are increasingly acknowledging their pivotal role in contributing to a culture of research integrity. For example, the European Commission (EC) is mandating research organizations receiving funding from the €95 billion Horizon Europe program to have, at the institutional level, policies and processes in place for research integrity covering the promotion of good practice, prevention of misconduct and questionable practices, and procedures to deal with breaches of research integrity [1]. To meet these obligations, the EC requires beneficiaries to respect the principles of research integrity as set out in the European Code of Conduct for Research Integrity (ECoC) and suggests that research organizations develop and implement a Research Integrity Promotion Plan (RIPP) [2]. In this Consensus View, we have adopted the World Conference on Research Integrity’s approach to research integrity, by having “research integrity” refer to “the principles and standards that have the purpose to ensure validity and trustworthiness of research” [3]. More specifically, we mostly adhere to the principles outlined in the ECoC: reliability, honesty, respect, and accountability. While many definitions of research integrity exist [4,5], for example, those that distinguish between the integrity of a researcher, integrity of research, and integrity of the research record, the ECoC combines these approaches in a balanced way [1].We believe that funders are prominently placed to foster a culture of research integrity by requiring that the organizations and individual researchers they support make an explicit commitment to research integrity. At the same time, funders need to adopt appropriate research integrity practices themselves. Of late, attention to research integrity among funders has gathered pace, as reflected in several initiatives around the globe that demonstrate how funders can support a culture of research integrity. For example, the US National Science Foundation (NSF) [6] requires applicants’ research organizations to provide training and oversight in the responsible conduct of research, designate individuals responsible for research integrity, and have an institutional certification to testify of its commitment. Also, in 2016, 3 Canadian federal funders joined forces to support research integrity in the Canadian Tri-Agency Framework: Responsible Conduct of Research–Harmony and Responsibility [7]. The framework was subsequently updated in 2021. This framework sets out responsible practices that research organizations and researchers should follow, including rigor, record keeping, accurate referencing, responsible authorship, and the management of conflicts of interest. It also acknowledges the responsibilities of the funders, including “helping to promote the responsible conduct of research and to assist individuals and institutions with the interpretation or implementation of this Responsible Conduct of Research (RCR) Framework”.It is not only major funding organizations in highly developed research environments that are taking steps. Smaller funders are also acting to mandate compliance with research integrity standards. The constantly growing literature on the topic is another sign of development within this area [2,3]. In the USA, research integrity recently reached the political arena, when, following a call from researchers [8], President Biden’s administration published a memorandum on restoring trust [9] that highlights the importance of integrity in research. The memorandum will be supported by the reintroduction of the Scientific Integrity Act. This act will prohibit research misconduct and the manipulation of research findings. It talks of a “culture of research integrity” and demands that funding agencies adopt and enforce research integrity policies, appoint a research integrity officer, and provide regular research integrity and ethics training. The US are not alone in their endeavors. Governments in other countries are equally gearing up to support the integrity and reproducibility of research [10]. However, so far, there is only limited evidence about the effectiveness of such initiatives, although it is generally accepted that they raise awareness among various stakeholders concerning research integrity challenges, strengthen the sense of responsibility of those stakeholders to address those challenges, and thereby ultimately contribute to fostering a culture of research integrity.In a collective effort to foster research integrity, research organizations and funders have their own, complementary roles. The Standard Operating Procedures for Research Integrity (SOPs4RI) consortium has recommended that both research organizations and funders develop a RIPP. A RIPP outlines the key responsibilities of an organization concerning research integrity and details methods and procedures to foster it. For example, in the case of research organizations, a RIPP should facilitate and stimulate a healthy research environment, proper mentoring and supervision, research ethics structures, research integrity training, high-quality dissemination practices, research collaboration, effective data management, and open and fair procedures to deal with breaches of research integrity [11]. Funders have a different role. They can support, safeguard, and incentivise, or even mandate, responsible research practices from research organizations and researchers. Equally important, funders should make sure that their internal processes live up to the highest standards of research integrity. We recognize that funders are many and varied in their scale, portfolio, disciplinary focus, and the extent to which they have procedures and governance arrangements to support research integrity. For all funders, adopting a RIPP will structure and coordinate research integrity practices, giving clarity and transparency to applicant institutions and researchers.In this Consensus View, we highlight examples of best practice of funders worldwide to foster a research integrity culture. With these examples in mind, we suggest guidelines to support funders in taking a leading role in fostering research integrity. In so doing, we acknowledge the local contexts in which funders operate, but we believe that all funders, large and small, in all parts of the world, can and should contribute to improving research validity and building and maintaining trust in science through incentivising and mandating a culture of research integrity. Our core argument is that developing a tailored RIPP will contribute to building an institutional culture of research integrity, both within funding organizations and among the research organizations and individual researchers they fund. Based on empirical work from the SOPs4RI project, we have identified 6 key research integrity topics: researchers’ compliance with research integrity standards; expectations for research organizations; selection of grant applications; declaration of interests; monitoring funded research; and dealing with internal integrity breaches (Fig 1). We recommend that these topics should be included in a RIPP and provide guidelines on developing and implementing a RIPP.Open in a separate windowFig 1Topics to be covered in a RIPP for funders.An overview of the 6 most important topics identified by the SOPs4RI to be included in research funding organization’s RIPP. RIPP, Research Integrity Promotion Plan; SOPs4RI, Standard Operating Procedures for Research Integrity.     

Seahorses in focus: local ecological knowledge of seahorse-watching operators in a tropical estuary

Background

Seahorses are endangered teleost fishes under increasing human pressures worldwide. In Brazil, marine conservationists and policy-makers are thus often skeptical about the viability of sustainable human-seahorse interactions. This study focuses on local ecological knowledge on seahorses and the implications of their non-lethal touristic use by a coastal community in northeastern Brazil. Community-based seahorse-watching activities have been carried out in Maracaípe village since 1999, but remained uninvestigated until the present study. Our goal is to provide ethnoecological understanding on this non-extractive use to support seahorse conservation and management.

Methods

We interviewed 32 informants through semi-structured questionnaires to assess their socioeconomic profile, their knowledge on seahorse natural history traits, human uses, threats and abundance trends.

Results

Seahorse-watching has high socioeconomic relevance, being the primary income source for all respondents. Interviewees elicited a body of knowledge on seahorse biology largely consistent with up-to-date research literature. Most informants (65.5 %) perceived no change in seahorse abundance. Their empirical knowledge often surpassed scientific reports, i.e. through remarks on trophic ecology; reproductive aspects, such as, behavior and breeding season; spatial and temporal distribution, suggesting seahorse migration related to environmental parameters.

Conclusions

Seahorse-watching operators were aware of seahorse biological and ecological aspects. Despite the gaps remaining on biological data about certain seahorse traits, the respondents provided reliable information on all questions, adding ethnoecological remarks not yet assessed by conventional scientific surveys. We provide novel ethnobiological insight on non-extractive modes of human-seahorse interaction, eliciting environmental policies to integrate seahorse conservation with local ecological knowledge and innovative ideas for seahorse sustainable use. Our study resonates with calls for more active engagement with communities and their local ecologies if marine conservation and development are to be reconciled.

     

Spatial variance and spatial skewness: leading indicators of regime shifts in spatial ecological systems

Ecosystems can undergo large-scale changes in their states, known as catastrophic regime shifts, leading to substantial losses to services they provide to humans. These shifts occur rapidly and are difficult to predict. Several early warning signals of such transitions have recently been developed using simple models. These studies typically ignore spatial interactions, and the signal provided by these indicators may be ambiguous. We employ a simple model of collapse of vegetation in one and two spatial dimensions and show, using analytic and numerical studies, that increases in spatial variance and changes in spatial skewness occur as one approaches the threshold of vegetation collapse. We identify a novel feature, an increasing spatial variance in conjunction with a peaking of spatial skewness, as an unambiguous indicator of an impending regime shift. Once a signal has been detected, we show that a quick management action reducing the grazing activity is needed to prevent the collapse of vegetated state. Our results show that the difficulties in obtaining the accurate estimates of indicators arising due to lack of long temporal data can be alleviated when high-resolution spatially extended data are available. These results are shown to hold true independent of various details of model or different spatial dispersal kernels such as Gaussian or heavily fat tailed. This study suggests that spatial data and monitoring multiple indicators of regime shifts can play a key role in making reliable predictions on ecosystem stability and resilience. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ecological integrity assessment as a metric of biodiversity: are we measuring what we say we are?

As the recognition of the importance of biological diversity in biological conservation grows, an ongoing challenge is to develop metrics that can be used for effective conservation and management. The ecological integrity assessment has been proposed as such a metric. It is held by some to measure species composition, diversity, and habitat quality, as well as ecosystem structure, composition, and function. The methodology relies on proxy variables that include data on landscape characteristics such as patch size, abiotic factors such as hydrology, and some features of vegetation structure and composition. We suggest that the measure is flawed on four levels. First, its putative representation of general ecological form and function, and its lack of specific detail about how it actually represents those attributes, leaves the metric without the focus needed to be useful for measuring ecological features on the ground and testing associated hypotheses and predictions. Second, the proxy variables used to represent biological diversity, such as habitat (vegetation) metrics and vascular plant species diversity, are not empirically correlated with diversity of a range of taxa or of other components of the biota. Third, like other ecological indices that integrate many distinct features, the ecological integrity index is subject to the loss of information in its condensation of multi-dimensional variability into a one-dimensional index, and it may be subject to systematic bias from the conversion of raw data into categorical scores. Fourth, the sampling protocols are at risk of sampling bias, observer bias, and measurement error, any of which can confound the estimation of conservation value. In terms of biological diversity, the methodology produces an unreliable estimate of the number of vascular plant species and their relative percentages of occurrence, and an absence of any protocols for taxa other than plants. For these reasons we believe that ecological integrity assessment is currently of limited value as a measure of site-specific biological diversity and its change over time. A considerable amount of investigation is needed in order to have confidence in the results of an ecological integrity assessment, especially if it is to be used for regulatory purposes. We suggest further refinements and discuss alternative measures of biological diversity that provide reliable metrics for assessing change. A thoughtful choice among measures can help to identify the most appropriate assessment for conservation decisions.     

Differential enumeration of intact and damaged marine planktonic bacteria based on cell membrane integrity

Viable but non-culturable (VBNC) bacteria are a much discussed issue in microbial ecology. Quantitative aspects are not understood, due mostly to the lack of suitable techniques. A widely accepted approach is dependent on the integrity of cell membranes. Recently developed fluorescence dyes differ in permeability with respect to the integrity of membranes: one dye permeates the intact membranes, which another permeates those which are damaged. Although the dyes were developed originally for determining the viability of cultured bacteria, here they are used to enumerate live and dead bacterial cells (designated as having intact and damaged membranes, respectively) in natural environments. Preliminary results from coastal waters of Seto Inland Sea, Japan, were: 1) the sums of the intact and damaged cells were very similar in each case to the total number of acridine orange-stained cells; and 2) about 50–60% of the total bacteriaoplankton populations are intact with respect to membrane integrity.     

Contemporary issues,current best practice and ways forward in soil protist ecology

Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.     

Ecosystem integrity and the “fish wars”

The problems of fisheries and aquatic ecosystems in Canada have been analyzed primarily from the standpoint of the conservation of these resources, without much emphasis on the value of aquatic ecosystems for themselves, including their life-support function, vital to all the biota within them. This represents a purely anthropocentric approach, that is flawed from the standpoint of sustainability practically and theoretically (Westra, 1996; Norton, 1995). Without entering in the anthropocentrism debate, the intent of this study is to indicate the apparent conflict between theoretical legislative and regulative aims, and most forms of management principles, even when these are presented in their most enlightened forms. Starting with the examination of a recent Canadian case, the failure of present management practices is outlined, even when these are democratically chosen and support worthwhile social goals. The Canadian fish wars example shows clearly why the ethics of integrity provide better guidelines for public policy, as they alone take as primary biological and ecological objectives.     

Growing floricultural crops with brackish water

In the current review we focus on the opportunity to use brackish water in the cultivation of floricultural plants, plants for which, due to their high economic value, growers have traditionally used good quality water for irrigation. Now, even for these crops the use of alternative water sources for irrigating nursery plants is needed because of the limited supplies of fresh water in many countries; understanding how saline water can be used will also enhance sustainable development in floriculture. While salt stress usually reduces plant growth, any such reduction might not be negative for ornamentals, where shoot vigour is sometime undesirable, although on flower crops salt stress can delay flowering or decrease flower quality characteristics. However, a decrease in growth rate is not enough to characterize the salt tolerance of ornamental plants, but traits like tip and marginal leaf burn, as consequence of sodium and chlorine accumulation, have to be considered for their effects on aesthetical value. With this in mind, some halophytes should be considered for floriculture because of their ability to cope with saline environments; their potential to tolerate salt is an important factor in reducing production costs. Consequently, the identification of ornamental halophytes is important for producing a commercially acceptable crop when irrigated with brackish waters. Many aspects of a plant's reaction to salt are genetically determined, so selection of suitable genotypes or breeding for salt tolerance in ornamentals are interesting options. Developing salt-tolerant floricultural crops, together with typical management practices that avoid excessive salinity stress in the root media, will provide the grower with economically and environmentally sound wastewater reuse options.     

Implications of global change for the maintenance of water quality and ecological integrity in the context of current water laws and environmental policies

There is both a fundamental and applied need to define expectations of changes in aquatic ecosystems due to global changes. It is clear that programs using biological indicators and reference-based comparisons as the foundation for assessments are likely to make increasingly erroneous decisions if the impacts of global change are ignored. Global changes influence all aspects of water resource management decisions based on comparisons to reference conditions with impacts making it increasingly problematic to find an “undisturbed” water body to define acceptable conditions of ecological integrity. Using a more objective scale for characterizing reference conditions that is anchored in expectations for what would be attainable under undisturbed conditions, such as the Biological Condition Gradient (BCG) is one approach that maintains consistent definitions for ecosystem conditions. In addition, protection of reference stations and of unique or undisturbed aquatic resources is imperative, though the scope of protection options is limited. Projections indicate that encroaching land use will affect 36–48% of current reference surface waters by the year 2100. The interpretation of biological indicators is also at risk from global changes. Distinguishing taxonomic attributes based on temperature or hydrologic preferences can be used to enhance the ability to make inferences about global change effects compared to other stressors. Difficulties arise in categorizing unique indicators of global changes, because of similarities in some of the temperature and hydrologic effects resulting from climate change, land use changes, and water removal. In the quest for biological indicators that might be uniquely sensitive to one global stressor as an aid in recognizing probable causes of ecosystem damage, the potential similarities in indicator responses among global and landscape-scale changes needs to be recognized as a limiting factor. Many aspects of global changes are not tractable at the local to regional scales at which water quality regulations are typically managed. Our ability to implement water policies through bioassessment will require a shift in the scale of assessment, planning, and adaptations in order to fulfill our ultimate regulatory goals of preserving good water quality and ecological integrity. Providing clear expectations of effects due to global change for key species and communities in freshwater ecosystems will help water quality programs achieve their goals under changing environmental conditions.     

Modeling effective dosages in hormetic dose-response studies

Background

Two hormetic modifications of a monotonically decreasing log-logistic dose-response function are most often used to model stimulatory effects of low dosages of a toxicant in plant biology. As just one of these empirical models is yet properly parameterized to allow inference about quantities of interest, this study contributes the parameterized functions for the second hormetic model and compares the estimates of effective dosages between both models based on 23 hormetic data sets. Based on this, the impact on effective dosage estimations was evaluated, especially in case of a substantially inferior fit by one of the two models.

Methodology/Principal Findings

The data sets evaluated described the hormetic responses of four different test plant species exposed to 15 different chemical stressors in two different experimental dose-response test designs. Out of the 23 data sets, one could not be described by any of the two models, 14 could be better described by one of the two models, and eight could be equally described by both models. In cases of misspecification by any of the two models, the differences between effective dosages estimates (0–1768%) greatly exceeded the differences observed when both models provided a satisfactory fit (0–26%). This suggests that the conclusions drawn depending on the model used may diverge considerably when using an improper hormetic model especially regarding effective dosages quantifying hormesis.

Conclusions/Significance

The study showed that hormetic dose responses can take on many shapes and that this diversity can not be captured by a single model without risking considerable misinterpretation. However, the two empirical models considered in this paper together provide a powerful means to model, prove, and now also to quantify a wide range of hormetic responses by reparameterization. Despite this, they should not be applied uncritically, but after statistical and graphical assessment of their adequacy.     

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.     

Caries-preventive effect of glass ionomer and resin-based fissure sealants on permanent teeth: An update of systematic review evidence

Background

The 1980s marked the occasion when Geographical Information System (GIS) technology was broadly introduced into the geo-spatial community through the establishment of a strong GIS industry. This technology quickly disseminated across many countries, and has now become established as an important research, planning and commercial tool for a wider community that includes organisations in the public and private health sectors. The broad acceptance of GIS technology and the nature of its functionality have meant that numerous datasets have been created over the past three decades. Most of these datasets have been created independently, and without any structured documentation systems in place. However, search and retrieval systems can only work if there is a mechanism for datasets existence to be discovered and this is where proper metadata creation and management can greatly help. This situation must be addressed through support mechanisms such as Web-based portal technologies, metadata editor tools, automation, metadata standards and guidelines and collaborative efforts with relevant individuals and organisations. Engagement with data developers or administrators should also include a strategy of identifying the benefits associated with metadata creation and publication.

Findings

The establishment of numerous Spatial Data Infrastructures (SDIs), and other Internet resources, is a testament to the recognition of the importance of supporting good data management and sharing practices across the geographic information community. These resources extend to health informatics in support of research, public services and teaching and learning. This paper identifies many of these resources available to the UK academic health informatics community. It also reveals the reluctance of many spatial data creators across the wider UK academic community to use these resources to create and publish metadata, or deposit their data in repositories for sharing. The Go-Geo! service is introduced as an SDI developed to provide UK academia with the necessary resources to address the concerns surrounding metadata creation and data sharing. The Go-Geo! portal, Geodoc metadata editor tool, ShareGeo spatial data repository, and a range of other support resources, are described in detail.

Conclusions

This paper describes a variety of resources available for the health research and public health sector to use for managing and sharing their data. The Go-Geo! service is one resource which offers an SDI for the eclectic range of disciplines using GIS in UK academia, including health informatics. The benefits of data management and sharing are immense, and in these times of cost restraints, these resources can be seen as solutions to find cost savings which can be reinvested in more research.