EM Estimation of Diagnosis

The diagnosis/prognosis problem has already been introduced by the authors in previous papers as a classification problem for survival data. In this paper, the specific aspects of the estimation of the survival functions in diagnostic classes and the evaluation of the posterior probabilities of the diagnostic classes are addressed; a latent random variable Z is defined to denote the classification of censored and uncensored individuals, where early censored individuals cannot be immediately classified as Z is not observed. Parameter estimation of the mixture survival model thus derived is carried out using a proper version of the EM algorithm with given prior probabilities on Z and diagnostic/prognostic information provided by the observable covariates is also included into the model. Numerical examples using AIDS data and a simulation study are used to better outline the main features of the model and of the estimation methodology.     

Books on biodiversity and conservation

Reviews are provided for 24 books published over the years 2006–2011 which have been received by Biodiversity and Conservation. These are in the general areas of ecology and the environment, mammals, birds, plants, evolution, and the human dimension of biodiversity, plus a miscellaneous work. Such batches of synoptic reviews are a new feature for Biodiversity and Conservation, and it is envisaged that 3–4 such groups of reviews will now be issued each year.     

Point count summary statistics differentially predict reproductive activity in bird-habitat relationship studies

Point count summary statistics (e.g. mean abundance, maximum abundance, frequency and presence/absence) reflect different assumptions about behavioral and population processes. In this paper we (1) determine the frequency and usage trends of different point count summary statistics in recent ornithological literature, and (2) assess how well point count data, summarized using five common statistics, predict an alternate measure of habitat quality–reproductive activity. For the 100 journal years we reviewed (10 journals over 10 years), 148 papers used point counts to evaluate bird habitat relationships. The number of papers using point counts has increased over the decade. Mean abundance, the most common summary statistic, was used more than twice as frequently as the next most common summary statistics. Only 25.7% (38 papers) provided a justification for use of a particular summary technique. We conducted point counts in three Canadian study regions (New Brunswick, Nova Scotia, and Newfoundland and Labrador) comprised of two ecosystem types (forest and grassland). While there was a statistically significant positive correlation between point count data and reproductive activity data for most species, we found that point counts were often unsuccessful at predicting reproductive activity in forest birds. For species where point counts adequately predicted reproductive activity mean abundance and frequency were consistently the best predictors. Our results indicate that statistics using information on intra-season (multiple-visit) occupancy tend to be better estimators of reproductive activity.     

One Dog,but Which Dog? How Researchers Guide Participants to Select Dogs in Surveys of Human–Dog Relationships

Surveys and questionnaires are regularly used in studies of human–animal relationships. However, little attention has been given to understanding how survey participants are provided with instructions for the selection of a single animal within a multi-pet household, let alone the implications for reporting and interpreting data. We reviewed the instructions for the selection of an individual animal in studies addressing emotional or psychological attachment between people and dogs. By searching multidisciplinary journals from the year 2000 onwards, we identified a total of 128 papers, of which 63 met the inclusion criteria. Where selection criteria/instructions were not clear, authors were contacted. One in five studies (21%, or n = 13) did not report their instructions. When provided, instructions varied considerably. The most commonly provided direction was “favorite/closest relationship” (n = 12, or 19%). The remainder (n = 38, or 60%) were spread across eight different categories. Around half of the studies used a validated questionnaire that already contained an instruction, though a similar proportion of studies implemented author-designed instruments. Overall, the common absence and inconsistency of instructions for individual dog selection is taken to imply that there is no standard expectation or approach for instructions to be reported in studies of human relationships with dogs, or human–animal relationships more generally. We recommend further research on the implication of selection methods to ensure that instructions can be matched with specific research aims.     

In vitro biological properties of flavonoid conjugates found in vivo

For some flavonoids such as quercetin, isoflavones and catechins, the pathways of absorption and metabolism are now reasonably well characterised and understood. By definition, for biological activity of flavonoids to be manifest, the target tissue, which includes the blood and vascular system, must respond to the form(s) of flavonoid that it encounters. Bioavailability studies have shown that the circulating form of most flavonoids is as conjugates, with a few notable exceptions. There have been several recent papers on the in vitro biological properties of conjugates that have been found in vivo. This paper reviews the properties of these conjugates. Most of the information currently available is on quercetin glucuronides, but also on isoflavone and catechin conjugates. In addition to the biological properties of the conjugates, the partition coefficients and methods of synthesis are also presented.     

Non-Surgical Interventions for Adolescents with Idiopathic Scoliosis: An Overview of Systematic Reviews

Background

Non-surgical interventions for adolescents with idiopathic scoliosis remain highly controversial. Despite the publication of numerous reviews no explicit methodological evaluation of papers labeled as, or having a layout of, a systematic review, addressing this subject matter, is available.

Objectives

Analysis and comparison of the content, methodology, and evidence-base from systematic reviews regarding non-surgical interventions for adolescents with idiopathic scoliosis.

Design

Systematic overview of systematic reviews.

Methods

Articles meeting the minimal criteria for a systematic review, regarding any non-surgical intervention for adolescent idiopathic scoliosis, with any outcomes measured, were included. Multiple general and systematic review specific databases, guideline registries, reference lists and websites of institutions were searched. The AMSTAR tool was used to critically appraise the methodology, and the Oxford Centre for Evidence Based Medicine and the Joanna Briggs Institute’s hierarchies were applied to analyze the levels of evidence from included reviews.

Results

From 469 citations, twenty one papers were included for analysis. Five reviews assessed the effectiveness of scoliosis-specific exercise treatments, four assessed manual therapies, five evaluated bracing, four assessed different combinations of interventions, and one evaluated usual physical activity. Two reviews addressed the adverse effects of bracing. Two papers were high quality Cochrane reviews, Three were of moderate, and the remaining sixteen were of low or very low methodological quality. The level of evidence of these reviews ranged from 1 or 1+ to 4, and in some reviews, due to their low methodological quality and/or poor reporting, this could not be established.

Conclusions

Higher quality reviews indicate that generally there is insufficient evidence to make a judgment on whether non-surgical interventions in adolescent idiopathic scoliosis are effective. Papers labeled as systematic reviews need to be considered in terms of their methodological rigor; otherwise they may be mistakenly regarded as high quality sources of evidence.

Protocol registry number

CRD42013003538, PROSPERO     

Soil and rhizosphere as habitats for Pseudomonas inoculants: new knowledge on distribution,activity and physiological state derived from micro-scale and single-cell studies

Pseudomonas spp. comprise an important group of bacteria used for biological control of microfungi in the plant rhizosphere. Successful performance of microbial inoculants requires both establishment, proliferation and activity under in situ conditions. To identify the factors controlling fate and performance of the inoculants, small-scale analyses are needed due to the heterogeneity characterizing the complex soil and rhizosphere environments. Direct staining techniques and advanced microscopy have provided the first detailed single-cell images of root colonization by these bacteria using fluorescent antibodies, fluorescent in situ hybridization and marker gene technology. These tracking methods have, in conjunction with activity assays, provided high-resolution data on the metabolic activity and growth of the inoculants. Finally, Pseudomonas reporter bacteria constructed to sense phosphorus, nitrogen, iron, and oxygen limitations have provided new insight into the significance of growth-limiting factors in the soil and along the root. The present work reviews the current knowledge on Pseudomonas inoculants in soil and rhizosphere based on these modern techniques. Finally, some perspectives for future studies are discussed.     

Insights on Using Morphologic Data for Phylogenetic Analysis in Sedges (Cyperaceae)

Sedges are often viewed as difficult subjects for morphology-based phylogenetic analysis, due to several difficulties, including finding an adequate number of characters to yield well-resolved and well-supported trees, correctly assessing homology of characters and character states, and selecting appropriate outgroups for character state polarizations. The published literature holds only 11 papers with morphology-based phylogenetic analyses of sedges. This paper reviews those studies, and presents the phylogeny of two groups of sedges: (1) Carex section Deweyanae, and (2) Carex sections Careyanae, Granulares, and Griseae. This paper also presents recommendations for using morphologic data to reconstruct sedge phylogenies, based on comparisons of the trees resulting from the present study with the previous sedge studies and with similar studies of phylogeny of other groups of flowering plants. In the two groups of Carex examined, morphology does provide sufficient characters to infer well-resolved trees, with some nodes having good to strong support at levels consistent with those found in morphology-based analyses of other groups of flowering plants. The inclusion of micromorphologic and anatomic characters substantially enhances the resolving power of macromorphologic characters in sedge analyses, and increases the support for some clades.     

Does lethal control of top‐predators release mesopredators? A re‐evaluation of three Australian case studies

Top‐predators can sometimes be important for structuring fauna assemblages in terrestrial ecosystems. Through a complex trophic cascade, the lethal control of top‐predators has been predicted to elicit positive population responses from mesopredators that may in turn increase predation pressure on prey species of concern. In support of this hypothesis, many relevant research papers, opinion pieces and literature reviews identify three particular case studies as supporting evidence for top‐predator control‐induced release of mesopredators in Australia. However, many fundamental details essential for supporting this hypothesis are missing from these case studies, which were each designed to investigate alternative aims. Here, we re‐evaluate the strength of evidence for top‐predator control‐induced mesopredator release from these three studies after comprehensive analyses of associated unpublished correlative and experimental data. Circumstantial evidence alluded to mesopredator releases of either the European Red Fox (Vulpes vulpes) or feral Cat (Felis catus) coinciding with Dingo (Canis lupus dingo) control in each case. Importantly, however, substantial limitations in predator population sampling techniques and/or experimental designs preclude strong assertions about the effect of lethal control on mesopredator populations from these studies. In all cases, multiple confounding factors and plausible alternative explanations for observed changes in predator populations exist. In accord with several critical reviews and a growing body of demonstrated experimental evidence on the subject, we conclude that there is an absence of reliable evidence for top‐predator control‐induced mesopredator release from these three case studies. Well‐designed and executed studies are critical for investigating potential top‐predator control‐induced mesopredator release.     

Introduction: Aging and the Multifaceted Influences on Adaptation to Working Time

This special issue of Chronobiology International presents a selection of papers originally delivered at the 18th International Symposium on Shift Work and Working Time, held at Yeppoon, Australia, in August 2007. The key theme of the symposium was “Aging and Working Time: Creating Safe Environments.” Older workers are widely believed to experience greater difficulty than younger workers adapting to shift work and irregular work schedules. However, while the three reviews of age effects published here (Costa & Di Milia, ; Folkard, ; Gander & Signal, ) identify evidence that older workers do indeed adapt less well, they also demonstrate that much more research is urgently required. The remaining papers address various aspects of the impact of work schedules on health, safety, sleep, and performance. They can be divided into three broad categories: circadian and other periodic factors; sleep, sleepiness, and fatigue; and other aspects of health and adjustment. This collection of papers showcases the best of contemporary research on the safety and health effects of working hours, continuing the tradition established by the two previous issues of the journal devoted to earlier symposia on shift work and working time.     

Molecular immunology: At the border of centuries and at the interface of disciplines

This is a special issue of the journal Molekulyarnaya biologiya (Molecular Biology) focusing on topical problems in molecular immunology, virology, and the related fields of science, including molecular genetics, biochemistry, and cell biology. Several reviews are offered to the attention of our readers, as well as original experimental papers. This issue was prepared on a tight schedule and, certainly, cannot pretend to cover all the areas of the state-of-the-art science.     

Annual Progress in Bioinformatics 2006

In this issue, Briefings in Bioinformatics is happy to presentthe next installment of our special annual issue devoted toreviews of very active subdisciplines within our field. Theeditors surveyed recent publications in order to identify fieldsthat are moving rapidly and would be good targets for summaryand review. We asked authors to provide brief introductionsto their field, and then to concentrate on contributions inthe last 12–24 months of particular interest. In somecases, they also provided annotated bibliographies in whichthey highlighted papers of particularly high interest. The resultis seven outstanding reviews. The influence of high-throughputgenomic experimental techniques and the increasing intereston synthesis of information comes through strongly in this year'sselections. We     

Solving the problem of how to eat something as big as yourself: Diverse bacterial strategies for degrading polysaccharides

Polysaccharide digestion by bacteria is an important activity in many ecosystems, and a number of bacterial genera can perform this function. Although many papers have been published about the properties of isolated polysaccharide-degrading enzymes, relatively little is known about how intact bacteria degrade polysaccharides. This review summarizes recent findings suggesting that there are at least three different strategies. the most familiar one is the excretion of extracellular polysaccharidases, which diffuse to and degrade nearby polysaccharides. An example of this type of strategy is provided by the plant pathogen,Erwinia spp. A second strategy is to have the enzyme exposed to the extracellular medium but attached to the surface of the cell. Examples of this strategy are provided by the pullulanase system ofKlebsiella oxytoca and the cellulosomes ofClostridium thermocellum. A strategy that could be seen as a combination of the extracellular enzyme strategy and the surface organelle strategy is provided byVibrio harveyi, which attaches to its substrate, chitin, via proteins that appear to be specialized for attachment and produces extracellular enzymes that attack the chitin. A third strategy is to import the polysaccharide, as appears to be done byBacteroides spp. In this instance, the polysaccharide is bound to an outer membrane receptor, then passes into the periplasm where the degradative enzymes are located. The ecological advantages and disadvantages of these systems are discussed, and areas where further research is needed are defined.     

A comparison and critique of different scat‐analysis methods for determining carnivore diet

• 1 For terrestrial carnivores, scat analysis is the technique most often used to determine diets. Various methods of interpreting scat‐analysis data exist; however, little is known about how the choice of method affects the results.
• 2 We reviewed 50 scat‐analysis papers to assess the range of methods currently used. Furthermore, we used a large data set from cape fox Vulpes chama and black‐backed jackal Canis mesomelas scats to compare 11 scat‐analysis methods. Techniques tested included five biomass calculation methods, four frequency of occurrence methods, one method that estimated volume in scats, and another that estimated mass of food items in scats.
• 3 Frequency of occurrence methods were used in 94% of reviewed papers, and in 50% of papers they were the sole methods used. However, we conclude that frequency of occurrence has the least ecological significance and results can be misleading. Although biomass calculations probably provide the best approximation to true diets, only 23% of reviewed papers used suitable biomass calculation methods when models were available for the study species.
• 4 Analysis of fox and jackal scats showed that there were significant differences among methods when calculating percent diet composition and niche breadth. Additionally, dietary overlap between species differed considerably among the methods (range of R₀ = 0.29–0.79). We conclude that the choice of method can have a significant impact on the results of dietary analysis, and can lead to very different conclusions about a species' ecology.
• 5 The best approximation of the true diet can be obtained by using a biomass calculation model that was developed for the same species, or for a closely related species with a similar food spectrum. When no such model is available, either the volume or mass of diet components in the scats should be used. To document rare food items, frequency of occurrence data could also be given.