A pilot study to investigate if New Zealand men with prostate cancer benefit from a Mediterranean-style diet
Carcinoma of the prostate is the most commonly diagnosed malignancy and the third leading cause of mortality in New Zealand men, making it a significant health issue in this country. Global distribution patterns suggest that diet and lifestyle factors may be linked to the development and progression of this cancer. Twenty men with diagnosed prostate cancer adhered to a Mediterranean diet, with specific adaptations, for three months. Prostate-specific antigen, C-reactive protein and DNA damage were evaluated at baseline and after three months of following the diet. Dietary data were collated from diet diaries and an adaptation of a validated Mediterranean diet questionnaire. A significant reduction in DNA damage compared to baseline was apparent, with particular benefit noted for overall adherence to the diet (p = 0.013), increased intake of folate (p = 0.023), vitamin C (p = 0.007), legumes (p = 0.004) and green tea (p = 0.002). Higher intakes of red meat and dairy products were inversely associated with DNA damage (p = 0.003 and p = 0.008 respectively). The results from this small feasibility study suggest that a high-antioxidant diet, modelled on Mediterranean traditions, may be of benefit for men with prostate cancer. Protection against DNA damage appears to be associated with the diet implemented, ostensibly due to reduction in reactive oxidant species. These findings warrant further exploration in a longer trial, with a larger cohort.
Erdrich et al. (2015) A pilot study to investigate if New Zealand men with prostate cancer benefit from a Mediterranean-style diet. PeerJ 3:e1080 https://doi.org/10.7717/peerj.1080
Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries
Climate change over the last two centuries has been associated with significant shifts in diatom community structure in lakes from the high arctic to temperate latitudes. To test the hypotheses that recent climate warming selects for species of smaller size within communities and a decrease in the average size of species within populations, we quantified the size of individual diatom valves from 10 depths in a sediment core covering the last ∼200 years from a pristine subarctic lake. Over the last ∼200 years, changes in the relative abundance of species of different average size and changes in the average valve size of populations of species contribute equally to the changes in community size structure, but are often opposite in sign, compensating for one another and moderating temporal changes in community size structure. In the surface sediments that correspond to the recent decades when air temperatures have warmed, the mean size of valves in the diatom community has significantly decreased due to an increase in the proportion of smaller-sized planktonic diatom species.
Kerrigan et al. (2015) Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries. PeerJ 3:e1074 https://doi.org/10.7717/peerj.1074
Comparing cestode infections and their consequences for host fitness in two sexual branchiopods: alien Artemia franciscana and native A. salina from syntopic-populations
The American brine shrimp Artemia franciscana is invasive in the Mediterranean region where it has displaced native species (the sexual A. salina, and the clonal A. parthenogenetica) from many salt pond complexes. Artemia populations are parasitized by numerous avian cestodes whose effects have been studied in native species. We present a study from the Ebro Delta salterns (NE Spain), in a salt pond where both A. franciscana and native A. salina populations coexist, providing a unique opportunity to compare the parasite loads of the two sexual species in syntopy. The native species had consistently higher infection parameters, largely because the dominant cestode in A. salina adults and juveniles (Flamingolepis liguloides) was much rarer in A. franciscana. The most abundant cestodes in the alien species were Eurycestus avoceti (in adults) and Flamingolepis flamingo (in juveniles). The abundance of E. avoceti and F. liguloides was higher in the A. franciscana population syntopic with A. salina than in a population sampled at the same time in another pond where the native brine shrimp was absent, possibly because the native shrimp provides a better reservoir for parasite circulation. Infection by cestodes caused red colouration in adult and juvenile A. salina, and also led to castration in a high proportion of adult females. Both these effects were significantly stronger in the native host than in A. franciscana with the same parasite loads. However, for the first time, significant castration effects (for E. avoceti and F. liguloides) and colour change (for six cestode species) were observed in infected A. franciscana. Avian cestodes are likely to help A. franciscana outcompete native species. At the same time, they are likely to reduce the production of A. franciscana cysts in areas where they are harvested commercially.
Redón et al. (2015) Comparing cestode infections and their consequences for host fitness in two sexual branchiopods: alien Artemia franciscana and native A. salina from syntopic-populations. PeerJ 3:e1073 https://doi.org/10.7717/peerj.1073
Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes
Larger benthic foraminifera (LBF) are important and prolific carbonate producers both in modern and ancient shallow tropical seas. During the Paleogene the genus Nummulites was particularly abundant with a global distribution, leading it to be frequently used in biostratigraphy. However, their evolution is poorly understood as classification is Europe-centered and mostly based on external characters and equatorial thin sections. New occurrences from regions outside the northern Tethys which poorly fit in thus reference frame, show that a more rigid framework for the classification of Nummulites is needed. Here we apply micro computed-tomographical scanning, a tool that recently has become available, to visualise 3D chamber shape of Nummulites djokdjokartae and compare these to traditional morphometrical characters. We find that despite the regular shape in equatorial and axial thin section the irregular 3D chamber shape is not predicted by these sections. We argue that 3D reconstructions of Nummulites tests will be a great aid in improving our understanding of lineages within the genus Nummulites, and to elucidate its evolutionary and biogeographical history.
Renema et al. (2015) Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes. PeerJ 3:e1072 https://doi.org/10.7717/peerj.1072
Depressive symptoms and other risk factors predicting suicide in middle-aged men: a prospective cohort study among Korean Vietnam War veterans
Background. Few studies have prospectively examined whether depressive symptoms and other risk factors are associated with a higher risk of suicide death in individuals other than high-risk populations such as psychiatric patients and individuals with self-harm histories. The purpose of the study is to prospectively examine whether depressive symptoms assessed by the Beck Depression Inventory (BDI) are associated with greater risk of suicide death and whether depressive symptoms and other risk factors are independent predictors of suicide in general-risk populations. Another aim is to evaluate the sensitivity of the BDI for predicting suicide death. Methods. 10,238 Korean Vietnam War veterans (mean age: 56.3 years) who participated in two surveys in 2001 were followed up for suicide mortality over 7.5 years. Results. 41 men died by suicide. Severely depressed participants had a higher adjusted hazard ratio (aHR = 3.4; 95% CI [1.5–7.7]) of suicide than non-to-moderately depressed ones. Higher suicide risk was associated with more severe depressive symptoms (p for trend = 0.009). After adjustment for depressive symptoms and other factors, very poor health, low education, and past drinking were associated with higher suicide risk, while good health, body mass index, and marital status were not associated with suicide. The sensitivity at the cut-off score of 31 for detecting suicide was higher during the earlier 3.5 years of the follow-up (75%; 95% CI [50–90]) than during the latter 4 years (60%; 95% CI [41–76]). Conclusions. Depressive symptoms are a strong independent predictor and very poor health, low education, and drinking status may be independent predictors of future suicide. The BDI may have acceptable diagnostic properties as a risk assessment tool for identifying people with depression and suicidal potential among middle-aged men.
Yi et al. (2015) Depressive symptoms and other risk factors predicting suicide in middle-aged men: a prospective cohort study among Korean Vietnam War veterans. PeerJ 3:e1071 https://doi.org/10.7717/peerj.1071
Identification of the underlying factor structure of the Derriford Appearance Scale 24
Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.
Moss et al. (2015) Identification of the underlying factor structure of the Derriford Appearance Scale 24. PeerJ 3:e1070 https://doi.org/10.7717/peerj.1070
Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease
Introduction. The metabolic syndrome (MS) affects 21–53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also affect natural course of COPD—number of exacerbations, quality of life and lung function. Aim. To examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. Material and methods. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. Results. 25% of patients have MS. 23.1% of the male and 29.5% of the female patients have MS (p > 0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44.6% in subjects over 45 years). 69.1% of all patients and 97.4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p = 0.002 and p = 0.001 respectively) and higher total CAT score (p = 0.017). Average BMI is 27.31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p = 0.008) and with the number of exacerbations in the last year (p = 0.015). There is no correlation between the presence of MS and the pulmonary function. Conclusion. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21–53%) and lower prevalence compared to general population (44.6%). MS may impact quality of life and the number of exacerbations of COPD. Having in mind that MS is more common in the early stages and decreases with COPD progression, the COPD patients admitted for exacerbation may be considered as having advanced COPD.
Mekov et al. (2015) Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease. PeerJ 3:e1068 https://doi.org/10.7717/peerj.1068
Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber
Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers), to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR) spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene) resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.
Seyfullah et al. (2015) Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber. PeerJ 3:e1067 https://doi.org/10.7717/peerj.1067
Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect
Background. Previous research (Tkach & Lyubomirsky, 2006) shows that there are eight general happiness-increasing strategies: social affiliation, partying, mental control, goal pursuit, passive leisure, active leisure, religion, and direct attempts. The present study investigates the factor structure of the happiness-increasing strategies scales (H-ISS) and their relationship to positive and negative affect. Method. The present study used participants’ (N = 1,050 and age mean = 34.21 sd = 12.73) responses to the H-ISS in structural equation modeling analyses. Affect was measured using the Positive Affect Negative Affect Schedule. Results. After small modifications we obtained a good model that contains the original eight factors/scales. Moreover, we found that women tend to use social affiliation, mental control, passive leisure, religion, and direct attempts more than men, while men preferred to engage in partying and clubbing more than women. The H-ISS explained significantly the variance of positive affect (R2 = .41) and the variance of negative affect (R2 = .27). Conclusions. Our study is an addition to previous research showing that the factor structure of the happiness-increasing strategies is valid and reliable. However, due to the model fitting issues that arise in the present study, we give some suggestions for improving the instrument.
Al Nima et al. (2015) Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect. PeerJ 3:e1059 https://doi.org/10.7717/peerj.1059
Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae
Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein–protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein–protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent).
Zubek et al. (2015) Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae. PeerJ 3:e1041 https://doi.org/10.7717/peerj.1041