Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well‐known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., ?entelodonts, “?anthracotheriids” and ?mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct ?Mesonychia was more closely related to Cetacea than was any “artiodactylan.”“?Anthracotheriids” were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological–dental data alone, however, did not support inclusion of cetaceans within crown “Artiodactyla.” Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other “artiodactylans”. © The Willi Hennig Society 2007.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub

Background and Aims

Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas.

Methods

Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates.

Key Results

Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle.

Conclusions

Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management.     

Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine

Background

Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations.

Methodology/Principals Findings

A DNA extraction of a ∼6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.

Conclusions

A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.     

Common Avian Infection Plagued the Tyrant Dinosaurs

Background

Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name ‘Sue’) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids.

Methodology/Principal Findings

We conducted an extensive survey of tyrannosaurid specimens and identified ten individuals with full-thickness erosive lesions. These lesions were described, measured and photographed for comparison with one another. We also conducted an extensive survey of related archosaurs for similar lesions. We show here that these lesions are consistent with those caused by an avian parasitic infection called trichomonosis, which causes similar abnormalities on the mandible of modern birds, in particular raptors.

Conclusions/Significance

This finding represents the first evidence for the ancient evolutionary origin of an avian transmissible disease in non-avian theropod dinosaurs. It also provides a valuable insight into the palaeobiology of these now extinct animals. Based on the frequency with which these lesions occur, we hypothesize that tyrannosaurids were commonly infected by a Trichomonas gallinae-like protozoan. For tyrannosaurid populations, the only non-avian dinosaur group that show trichomonosis-type lesions, it is likely that the disease became endemic and spread as a result of antagonistic intraspecific behavior, consumption of prey infected by a Trichomonas gallinae-like protozoan and possibly even cannibalism. The severity of trichomonosis-related lesions in specimens such as Tyrannosaurus rex FMNH PR2081 and Tyrannosaurus rex MOR 980, strongly suggests that these animals died as a direct result of this disease, mostly likely through starvation.     

First Record of Eocene Bony Fishes and Crocodyliforms from Canada’s Western Arctic

Background

Discovery of Eocene non-marine vertebrates, including crocodylians, turtles, bony fishes, and mammals in Canada’s High Arctic was a critical paleontological contribution of the last century because it indicated that this region of the Arctic had been mild, temperate, and ice-free during the early – middle Eocene (∼53–50 Ma), despite being well above the Arctic Circle. To date, these discoveries have been restricted to Canada’s easternmost Arctic – Ellesmere and Axel Heiberg Islands (Nunavut). Although temporally correlative strata crop out over 1,000 km west, on Canada’s westernmost Arctic Island – Banks Island, Northwest Territories – they have been interpreted as predominantly marine. We document the first Eocene bony fish and crocodyliform fossils from Banks Island.

Principal Findings

We describe fossils of bony fishes, including lepisosteid (Atractosteus), esocid (pike), and amiid, and a crocodyliform, from lower – middle Eocene strata of the Cyclic Member, Eureka Sound Formation within Aulavik National Park (∼76°N. paleolat.). Palynology suggests the sediments are late early to middle Eocene in age, and likely spanned the Early Eocene Climatic Optimum (EECO).

Conclusions/Significance

These fossils extend the geographic range of Eocene Arctic lepisosteids, esocids, amiids, and crocodyliforms west by approximately 40° of longitude or ∼1100 km. The low diversity bony fish fauna, at least at the family level, is essentially identical on Ellesmere and Banks Islands, suggesting a pan-High Arctic bony fish fauna of relatively basal groups around the margin of the Eocene Arctic Ocean. From a paleoclimatic perspective, presence of a crocodyliform, gar and amiid fishes on northern Banks provides further evidence that mild, year-round temperatures extended across the Canadian Arctic during early – middle Eocene time. Additionally, the Banks Island crocodyliform is consistent with the phylogenetic hypothesis of a Paleogene divergence time between the two extant alligatorid lineages Alligator mississippiensis and A. sinensis, and high-latitude dispersal across Beringia.     

DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivity

Background

Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus) once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry.

Methodology/Findings

We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males) exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a “Floreana-like” mitochondrial DNA haplotype.

Significance

Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C. elephantopus ancestry currently reside at a centralized breeding facility on Santa Cruz, these findings permit breeding efforts to commence in support of the reestablishment of this extinct species to its native range.     

A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge,Tanzania

Background

The fossil record reveals surprising crocodile diversity in the Neogene of Africa, but relationships with their living relatives and the biogeographic origins of the modern African crocodylian fauna are poorly understood. A Plio-Pleistocene crocodile from Olduvai Gorge, Tanzania, represents a new extinct species and shows that high crocodylian diversity in Africa persisted after the Miocene. It had prominent triangular “horns” over the ears and a relatively deep snout, these resemble those of the recently extinct Malagasy crocodile Voay robustus, but the new species lacks features found among osteolaemines and shares derived similarities with living species of Crocodylus.

Methodology/Principal Findings

The holotype consists of a partial skull and skeleton and was collected on the surface between two tuffs dated to approximately 1.84 million years (Ma), in the same interval near the type localities for the hominids Homo habilis and Australopithecus boisei. It was compared with previously-collected material from Olduvai Gorge referable to the same species. Phylogenetic analysis places the new form within or adjacent to crown Crocodylus.

Conclusions/Significance

The new crocodile species was the largest predator encountered by our ancestors at Olduvai Gorge, as indicated by hominid specimens preserving crocodile bite marks from these sites. The new species also reinforces the emerging view of high crocodylian diversity throughout the Neogene, and it represents one of the few extinct species referable to crown genus Crocodylus.     

The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization

A recent total evidence analysis of the position of cetaceans(whales, dolphins and porpoises and extinct relatives) amongmammals indicated that the phylogeny of these taxa remains poorlyresolved. Molecular data show that 1) the order Artiodactyla(even-toed ungulates) is paraphyletic unless whales are includedwithin it and 2) that the traditional relationships of cladeswithin Artiodactyla are not supported. This controversy alsoaffects the position of a wholly extinct clade, Mesonychia,which has been argued to be the group of terrestrial mammalsmost closely related to whales. Here I update a previous totalevidence analysis by adding several hundred new informativemolecular characters from the literature. Even with the additionof these characters the phylogeny remains unresolved. All mostparsimonious trees, however, indicate a paraphyletic Artiodactylawith conflict existing over the exact sister taxon of Cetacea.Congruence between different equally parsimonious cladogramsand the stratigraphic record as measured using the modifiedManhattan Stratigraphic Measure shows that all of the competingtopologies, including those with a paraphyletic Artiodactyla,are significantly congruent with the stratigraphic record. Infossil taxa cladistic optimization can be used as an alternativeto "argument from design" (Lauder, 1996) to reconstruct behaviorand soft tissues that do not fossilize or osteological charactersthat have not preserved. In certain scenarios of cetacean phylogeny,optimization indicates that taxa such as the archaic whalesAmbulocetus and Pakicetus, and possibly mesonychians, are morecorrectly reconstructed without hair.     

Health-Related Quality of Life and Its Correlates among Chinese Migrants in Small- and Medium-Sized Enterprises in Two Cities of Guangdong

Objectives

To explore the relationship between health-related quality of life (HRQOL) status and associated factors among rural-to-urban migrants in China.

Methods

A cross-sectional survey was conducted with 856 rural-to-urban migrants working at small- and medium-size enterprises (SMEs) in Shenzhen and Zhongshan City in 2012. Andersen''s behavioral model was used as a theoretical framework to exam the relationships among factors affecting HRQOL. Analysis was performed using structural equation modeling (SEM).

Results

Workers with statutory working hours, higher wages and less migrant experience had higher HRQOL scores. Need (contracting a disease in the past two weeks and perception of needing health service) had the greatest total effect on HRQOL (β = −0.78), followed by enabling (labor contract, insurance purchase, income, physical examination during work and training) (β = 0.40), predisposing (age, family separation, education) (β = 0.22) and health practices and use of health service (physical exercise weekly, health check-up and use of protective equipments) (β = −0.20).

Conclusions

Priority should be given to satisfy the needs of migrant workers, and improve the enabling resources.     

Distinct Transmission Networks of Chlamydia trachomatis in Men Who Have Sex with Men and Heterosexual Adults in Amsterdam,The Netherlands

Background

Genovar distributions of Chlamydia trachomatis based on ompA typing differ between men who have sex with men (MSM) and heterosexuals. We investigated clonal relationships using a high resolution typing method to characterize C. trachomatis types in these two risk groups.

Methods

C. trachomatis positive samples were collected at the STI outpatient clinic in Amsterdam between 2008 and 2010 and genotyped by multilocus sequence typing. Clusters were assigned using minimum spanning trees and these were combined with epidemiological data of the hosts.

Results

We typed 526 C. trachomatis positive samples: 270 from MSM and 256 from heterosexuals. Eight clusters, containing 10–128 samples were identified of which 4 consisted of samples from MSM (90%–100%), with genovars D, G, J, and L2b. The other 4 clusters consisted mainly of samples from heterosexuals (87%–100%) with genovars D, E, F, I, and J. Genetic diversity was much lower in the MSM clusters than in heterosexual clusters. Significant differences in number of sexual partners and HIV-serostatus were observed for MSM–associated clusters.

Conclusions

C. trachomatis transmission patterns among MSM and heterosexuals were largely distinct. We hypothesize that these differences are due to sexual host behavior, but bacterial factors may play a role as well.     

Ancestor–descendant relationships in evolution: origin of the extant pygmy right whale,Caperea marginata

Ancestor–descendant relationships (ADRs), involving descent with modification, are the fundamental concept in evolution, but are usually difficult to recognize. We examined the cladistic relationship between the only reported fossil pygmy right whale, †Miocaperea pulchra, and its sole living relative, the enigmatic pygmy right whale Caperea marginata, the latter represented by both adult and juvenile specimens. †Miocaperea is phylogenetically bracketed between juvenile and adult Caperea marginata in morphologically based analyses, thus suggesting a possible ADR—the first so far identified within baleen whales (Cetacea: Mysticeti). The †Miocaperea–Caperea lineage may show long-term morphological stasis and, in turn, punctuated equilibrium.     

Dietary Restriction and Exercise for Diabetic Patients with Chronic Kidney Disease: A Systematic Review

Background

Obesity and sedentary lifestyle are major health problems and key features to develop cardiovascular disease. Data on the effects of lifestyle interventions in diabetics with chronic kidney disease (CKD) have been conflicting.

Study Design

Systematic review.

Population

Diabetes patients with CKD stage 3 to 5.

Search Strategy and Sources

Medline, Embase and Central were searched to identify papers.

Intervention

Effect of a negative energy balance on hard outcomes in diabetics with CKD.

Outcomes

Death, cardiovascular events, glycaemic control, kidney function, metabolic parameters and body composition.

Results

We retained 11 studies. There are insufficient data to evaluate the effect on mortality to promote negative energy balance. None of the studies reported a difference in incidence of Major Adverse Cardiovascular Events. Reduction of energy intake does not alter creatinine clearance but significantly reduces proteinuria (mean difference from −0.66 to −1.77 g/24 h). Interventions with combined exercise and diet resulted in a slower decline of eGFR (−9.2 vs. −20.7 mL/min over two year observation; p<0.001). Aerobic and resistance exercise reduced HbA1c (−0.51 (−0.87 to −0.14); p = 0.007 and −0.38 (−0.72 to −0.22); p = 0.038, respectively). Exercise interventions improve the overall functional status and quality of life in this subgroup. Aerobic exercise reduces BMI (−0.74% (−1.29 to −0.18); p = 0.009) and body weight (−2.2 kg (−3.9 to −0.6); p = 0.008). Resistance exercise reduces trunk fat mass (−0,7±0,1 vs. +0,8 kg ±0,1 kg; p = 0,001−0,005). In none of the studies did the intervention cause an increase in adverse events.

Limitations

All studies used a different intervention type and mixed patient groups.

Conclusions

There is insufficient evidence to evaluate the effect of negative energy balance interventions on mortality in diabetic patients with advanced CKD. Overall, these interventions have beneficial effects on glycaemic control, BMI and body composition, functional status and quality of life, and no harmful effects were observed.     

Inflammatory thresholds and the species-specific effects of colonising bacteria in stable chronic obstructive pulmonary disease

Background

There has been increasing interest in the use of newer, culture-independent techniques to study the airway microbiome of COPD patients. We investigated the relationships between the three common potentially pathogenic microorganisms (PPMs) Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis, as detected by quantitative PCR (qPCR), and inflammation and health status in stable patients in the London COPD cohort.

Methods

We prospectively collected sputum, serum and plasma samples for analysis of airway bacterial presence and load, and airway and systemic inflammation from 99 stable COPD patients between January 2011 and October 2012. Health status was measured with St George’s Respiratory Questionnaire and COPD Assessment Test.

Results

Airway inflammation and plasma fibrinogen, but not C-reactive protein, were greater in samples with PPM detection (p < 0.001, p = 0.049 and p = 0.261, respectively). Increasing total bacterial load was associated with increasing airway (p < 0.01) but not systemic inflammation (p > 0.05). Samples with high total bacterial loads had significantly higher airway inflammation than both samples without PPM detection and those with lower loads. Haemophilus influenzae presence was associated with significantly higher levels of airway but not systemic inflammation for all given pathogen loads (p < 0.05), and was significantly greater than with other PPMs. No association was observed between inflammation and health status (p > 0.05).

Conclusions

Airway and systemic inflammation, as measured by fibrinogen, is greater in stable COPD patients with PPMs detected using the culture-independent qPCR technique. The airway, but not systemic inflammatory response, appears to have a total pathogen-load threshold and appears attributable to Haemophilus influenzae. However, discordance between inflammation and health status was observed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0114-1) contains supplementary material, which is available to authorized users.     

Salt-Restriction-Spoon Improved the Salt Intake among Residents in China

Objective

To evaluate the effect of an improved salt-restriction spoon on the attitude of salt-restriction, the using rate of salt-restriction-spoon, the actual salt intake, and 24-hour urinary sodium excretion (24HUNa).

Design

A community intervention study.

Setting

Two villages in Beijing.

Participants

403 local adult residents being responsible for home cooking.

Intervention

Participants were randomly assigned to the intervention group or the control group. Those in the intervention group were provided with an improved salt-restriction-spoon and health education, and were informed of their actual salt intake and 24HUNa. Not any intervention was given to those in the control group.

Main Outcome Measures

The scores on the variables of Health Belief Model, the using rate of salt-restriction-spoon, the actual salt intake, and 24HUNa.

Analysis

Covariance analyses, Chi-square tests, Student’s t tests, and repeated measures analyses of variance.

Results

After 6 months of intervention, the intervention group felt significantly less objective barriers, and got access to significantly more cues to action as compared to the control group. The using rate and the correctly using rate of salt-restriction-spoon were significantly higher in the intervention group. The daily salt intake decreased by 1.42 g in the intervention group and by 0.28 g in the control group, and repeated measures analysis of variance showed significant change over time (F = 7.044, P<0.001) and significant difference between groups by time (F = 2.589, P = 0.041). The 24HUNa decreased by 34.84 mmol in the intervention group and by 33.65 mmol in the control group, and repeated measures analysis of variance showed significant change over time (F = 14.648, P<0.001) without significant difference between groups by time (F = 0.222, P = 0.870).

Conclusions

The intervention effect was acceptable, therefore, the improved salt-restriction-spoon and corresponding health education could be considered as an alternative for salt reduction strategy in China and other countries where salt intake comes mainly from home cooking.     

A Role for SPARC in the Moderation of Human Insulin Secretion

Aims/Hypothesis

We have previously shown the implication of the multifunctional protein SPARC (Secreted protein acidic and rich in cysteine)/osteonectin in insulin resistance but potential effects on beta-cell function have not been assessed. We therefore aimed to characterise the effect of SPARC on beta-cell function and features of diabetes.

Methods

We measured SPARC expression by qRT-PCR in human primary pancreatic islets, adipose tissue, liver and muscle. We then examined the relation of SPARC with glucose stimulated insulin secretion (GSIS) in primary human islets and the effect of SPARC overexpression on GSIS in beta cell lines.

Results

SPARC was expressed at measurable levels in human islets, adipose tissue, liver and skeletal muscle, and demonstrated reduced expression in primary islets from subjects with diabetes compared with controls (p< = 0.05). SPARC levels were positively correlated with GSIS in islets from control donors (p< = 0.01). Overexpression of SPARC in cultured beta-cells resulted in a 2.4-fold increase in insulin secretion in high glucose conditions (p< = 0.01).

Conclusions

Our data suggest that levels of SPARC are reduced in islets from donors with diabetes and that it has a role in insulin secretion, an effect which appears independent of SPARC’s modulation of obesity-induced insulin resistance in adipose tissue.     

Accuracy of the Interpretation of Chest Radiographs for the Diagnosis of Paediatric Pneumonia

Introduction

World Health Organization (WHO) radiological classification remains an important entry criterion in epidemiological studies of pneumonia in children. We report inter-observer variability in the interpretation of 169 chest radiographs in children suspected of having pneumonia.

Methods

An 18-month prospective aetiological study of pneumonia was undertaken in Northern England. Chest radiographs were performed on eligible children aged ≤16 years with clinical features of pneumonia. The initial radiology report was compared with a subsequent assessment by a consultant cardiothoracic radiologist. Chest radiographic changes were categorised according to the WHO classification.

Results

There was significant disagreement (22%) between the first and second reports (kappa = 0.70, P<0.001), notably in those aged <5 years (26%, kappa = 0.66, P<0.001). The most frequent sources of disagreement were the reporting of patchy and perihilar changes.

Conclusion

This substantial inter-observer variability highlights the need for experts from different countries to create a consensus to review the radiological definition of pneumonia in children.     

Quilt Plots: A Simple Tool for the Visualisation of Large Epidemiological Data

Background

Graphical representation of data is one of the most easily comprehended forms of explanation. The current study describes a simple visualization tool which may allow greater understanding of medical and epidemiological data.

Method

We propose a simple tool for visualization of data, known as a “quilt plot”, that provides an alternative to presenting large volumes of data as frequency tables. Data from the Australian Needle and Syringe Program survey are used to illustrate “quilt plots”.

Conclusion

Visualization of large volumes of data using “quilt plots” enhances interpretation of medical and epidemiological data. Such intuitive presentations are particularly useful for the rapid assessment of problems in the data which cannot be readily identified by manual review. We recommend that, where possible, “quilt plots” be used along with traditional quantitative assessments of the data as an explanatory data analysis tool.     

Association between an Alzheimer’s Disease-Related Index and APOE ε4 Gene Dose

Background

We introduced a hypometabolic convergence index (HCI) to characterize in a single measurement the extent to which a person’s fluorodeoxyglucose positron emission tomogram (FDG PET) corresponds to that in Alzheimer’s disease (AD). Apolipoprotein E ε4 (APOE ε4) gene dose is associated with three levels of risk for late-onset AD. We explored the association between gene dose and HCI in cognitively normal ε4 homozygotes, heterozygotes, and non-carriers.

Methods

An algorithm was used to characterize and compare AD-related HCIs in cognitively normal individuals, including 36 ε4 homozygotes, 46 heterozygotes, and 78 non-carriers.

Results

These three groups differed significantly in their HCIs (ANOVA, p = 0.004), and there was a significant association between HCIs and gene dose (linear trend, p = 0.001).

Conclusions

The HCI is associated with three levels of genetic risk for late-onset AD. This supports the possibility of using a single FDG PET measurement to help in the preclinical detection and tracking of AD.