title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1962 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species link: https://peerj.com/articles/976 last-modified: 2015-05-21 description: Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection. creator: Katrín Halldórsdóttir creator: Einar Árnason uri: https://doi.org/10.7717/peerj.976 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Halldórsdóttir and Árnason title: Causes of mortality across different immigrant groups in Northeastern Italy link: https://peerj.com/articles/975 last-modified: 2015-05-21 description: Background. Despite massive immigration towards Southern Europe in the last two decades, data on mortality by cause among immigrants in Italy are scarce. The aim of this study was to investigate mortality from all and from specific causes of death among immigrants residing in the Veneto Region (Northeastern Italy).Methods. Mortality records for the period 2008–2013 were extracted from the regional archive of causes of death, whereas population data were obtained from the 2011 Italian census. Immigrants were grouped by area of provenience based on the information on country of citizenship available both in mortality and census data. Standardized Mortality Ratios (SMR) with 95% Confidence Intervals (CI) were computed for the period 2008–2013 in subjects aged 20–59 years, with rates of Italian citizens as a reference.Results. Overall mortality was reduced both in male (SMR 0.86, CI [0.80–0.92]) and female immigrants (SMR 0.72, CI [0.65–0.78]), although an increased risk was observed for subjects from Sub-Saharan Africa. Significantly raised SMR for circulatory diseases were found among Sub-Saharan Africans and Southern Asians in both genders. Sub-Saharan Africans experienced a higher risk of death, especially from cerebrovascular diseases: SMR 4.78 (CI [2.67–7.89]) and SMR 6.09 (CI [1.96–14.2]) in males and females, respectively. Among Southern Asians, the increase in mortality from ischemic heart diseases reached statistical significance in males (SMR 2.53, CI [1.42–4.18]). In spite of a lower risk of death for all neoplasms combined, mortality from cancer of cervix uteri was increased among immigrants (SMR 2.61, CI [1.35–4.56]), as well as for other cancer sites in selected immigrant groups. A raised mortality was found for infectious diseases in Sub-Saharan Africans (both genders), and for transport accidents among females from Eastern Europe.Conclusion. Our study showed great variations in mortality by cause and area of provenience among immigrants resident in the Veneto Region and highlighted specific health issues that should be addressed through tailored efforts in chronic diseases prevention. creator: Ugo Fedeli creator: Eliana Ferroni creator: Mara Pigato creator: Francesco Avossa creator: Mario Saugo uri: https://doi.org/10.7717/peerj.975 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Fedeli et al. title: Sex differences in human gregariousness link: https://peerj.com/articles/974 last-modified: 2015-05-21 description: Research on human sociality rarely includes kinship, social structure, sex, and familiarity, even though these variables influence sociality in non-human primates. However, cross-cultural ethnographic and observational studies with humans indicate that, beginning after age 5 years, males and females form differing social structures with unrelated individuals in a community. Specifically, compared with females, human males exhibit greater tolerance for and form larger, interconnected groups of peers which we term “gregariousness.” To examine sex differences in gregariousness early in life when children first interact with peers without adult supervision, 3- to 6-year-old children were given the choice to enter one of three play areas: an empty one, one with an adult, or one with a familiar, same-sex peer. More males than females initially chose the play area with the same-sex peer, especially after age 5 years. Sex differences in gregariousness with same-sex peers likely constitute one facet of human sociality. creator: Joyce F. Benenson creator: Sandra Stella creator: Anthony Ferranti uri: https://doi.org/10.7717/peerj.974 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Benenson et al. title: Identification of miR-194-5p as a potential biomarker for postmenopausal osteoporosis link: https://peerj.com/articles/971 last-modified: 2015-05-21 description: The incidence of osteoporosis is high in postmenopausal women due to altered estrogen levels and continuous calcium loss that occurs with aging. Recent studies have shown that microRNAs (miRNAs) are involved in the development of osteoporosis. These miRNAs may be used as potential biomarkers to identify women at a high risk for developing the disease. In this study, whole blood samples were collected from 48 postmenopausal Chinese women with osteopenia or osteoporosis and pooled into six groups according to individual T-scores. A miRNA microarray analysis was performed on pooled blood samples to identify potential miRNA biomarkers for postmenopausal osteoporosis. Five miRNAs (miR-130b-3p, -151a-3p, -151b, -194-5p, and -590-5p) were identified in the microarray analysis. These dysregulated miRNAs were subjected to a pathway analysis investigating whether they were involved in regulating osteoporosis-related pathways. Among them, only miR-194-5p was enriched in multiple osteoporosis-related pathways. Enhanced miR-194-5p expression in women with osteoporosis was confirmed by quantitative reverse transcription–polymerase chain reaction analysis. For external validation, a significant correlation between the expression of miR-194-5p and T-scores was found in an independent patient collection comprised of 24 postmenopausal women with normal bone mineral density, 30 postmenopausal women with osteopenia, and 32 postmenopausal women with osteoporosis (p < 0.05). Taken together, the present findings suggest that miR-194-5p may be a viable miRNA biomarker for postmenopausal osteoporosis. creator: Jia Meng creator: Dapeng Zhang creator: Nanan Pan creator: Ning Sun creator: Qiujun Wang creator: Jingxue Fan creator: Ping Zhou creator: Wenliang Zhu creator: Lihong Jiang uri: https://doi.org/10.7717/peerj.971 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Meng et al. title: Rapid cessation of acute diarrhea using a novel solution of bioactive polyphenols: a randomized trial in Nicaraguan children link: https://peerj.com/articles/969 last-modified: 2015-05-21 description: Goal. We assessed the effectiveness of bioactive polyphenols contained in solution (LX) to restore normal bowel function in pediatric patients with acute diarrhea.Background. While providing oral rehydration solution (ORS) is standard treatment for diarrhea in developing countries, plant-derived products have been shown to positively affect intestinal function. If a supplement to ORS resolves diarrhea more rapidly than ORS alone, it is an improvement to current care.Study. In a randomized, double-blind, placebo-controlled cross-over study, 61 pediatric patients with uncontrolled diarrhea were randomized to receive either ORS + LX on day 1 and then ORS + water on day 2 (study arm) or ORS + water on day 1 and then ORS + LX on day 2 (control arm). Time to resolution and number of bowel movements were recorded.Results. On day 1, the mean time to diarrhea resolution was 3.1 h (study arm) versus 9.2 h (control arm) (p = 0.002). In the study arm, 60% of patients had normal stool at their first bowel movement after consumption of the phenolic redoxigen solution (LX). On day 2, patients in the study arm continued to have normal stool while patients in the control arm achieved normal stool within 24 h after consuming the test solution. Patients in the control arm experienced a reduction in the mean number of bowel movements from day 1 to day 2 after consuming the test solution (p = 0.0001). No adverse events were observed.Conclusions. Significant decreases in bowel movement frequency and rapid normalization of stool consistency were observed with consumption of this novel solution. creator: Arthur Dover creator: Neema Patel creator: KT Park uri: https://doi.org/10.7717/peerj.969 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dover et al. title: Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus link: https://peerj.com/articles/968 last-modified: 2015-05-21 description: An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic. creator: Rochelle M. Soo creator: Ben J. Woodcroft creator: Donovan H. Parks creator: Gene W. Tyson creator: Philip Hugenholtz uri: https://doi.org/10.7717/peerj.968 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Soo et al. title: Accuracy of the interferon-gamma release assay for the diagnosis of tuberculous pleurisy: an updated meta-analysis link: https://peerj.com/articles/951 last-modified: 2015-05-21 description: Background and Objectives. The best method for diagnosing tuberculous pleurisy (TP) remains controversial. Since a growing number of publications focus on the interferon-gamma release assay (IGRA), we meta-analyzed the available evidence on the overall diagnostic performance of IGRA applied to pleural fluid and peripheral blood.Materials and Methods. PubMed and Embase were searched for relevant English papers up to October 31, 2014. Statistical analyses were performed using Stata and Meta-DiSc. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), positive predictive value (PPV), negative predictive value (NPV) and diagnostic odds ratio (DOR) were count. Summary receiver operating characteristic curves and area under the curve (AUC) were used to summarize the overall diagnostic performance.Results. Fifteen publications met our inclusion criteria and were included in the meta analysis. The following pooled estimates for diagnostic parameters of pleural IGRA were obtained: sensitivity, 0.82 (95% CI [0.79–0.85]); specificity, 0.87 (95% CI [0.84–0.90]); PLR, 4.94 (95% CI [2.60–9.39]); NLR, 0.22 (95% CI [0.13–0.38]); PPV, 0.91 (95% CI [0.85–0.96]); NPV, 0.79 (95% CI [0.71–0.85]); DOR, 28.37 (95% CI [10.53–76.40]); and AUC, 0.91. The corresponding estimates for blood IGRA were as follows: sensitivity, 0.80 (95% CI [0.76–0.83]); specificity, 0.70 (95% CI [0.65–0.75]); PLR, 2.48 (95% CI [1.95–3.17]); NLR, 0.30 (95% CI [0.24–0.37]); PPV, 0.79 (95% CI [0.60–0.87]); NPV, 0.75 (95% CI [0.62–0.83]); DOR, 9.96 (95% CI [6.02–16.48]); and AUC, 0.89.Conclusions. This meta analysis suggested that pleural IGRA has potential for serving as a complementary method for diagnosing TP; however, its cost, high turn around time, and sub-optimal performance make it unsuitable as a stand-alone diagnostic tool. Better tests for the diagnosis of TP are required. creator: Cai-Shuang Pang creator: Yong-Chun Shen creator: Pan-Wen Tian creator: Jing Zhu creator: Mei Feng creator: Chun Wan creator: Fu-Qiang Wen uri: https://doi.org/10.7717/peerj.951 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pang et al. title: Can parasites halt the invader? Mermithid nematodes parasitizing the yellow-legged Asian hornet in France link: https://peerj.com/articles/947 last-modified: 2015-05-21 description: Since its introduction in France 10 years ago, the yellow-legged Asian bee-hawking hornet Vespa velutina has rapidly spread to neighboring countries (Spain, Portugal, Belgium, Italy, and Germany), becoming a new threat to beekeeping activities. While introduced species often leave behind natural enemies from their original home, which benefits them in their new environment, they can also suffer local recruitment of natural enemies. Three mermithid parasitic subadults were obtained from V. velutina adults in 2012, from two French localities. However, these were the only parasitic nematodes reported up to now in Europe, in spite of the huge numbers of nests destroyed each year and the recent examination of 33,000 adult hornets. This suggests that the infection of V. velutina by these nematodes is exceptional. Morphological criteria assigned the specimens to the genus Pheromermis and molecular data (18S sequences) to the Mermithidae, due to the lack of Pheromermis spp. sequences in GenBank. The species is probably Pheromermis vesparum, a parasite of social wasps in Europe. This nematode is the second native enemy of Vespa velutina recorded in France, after a conopid fly whose larvae develop as internal parasitoids of adult wasps and bumblebees. In this paper, we provide arguments for the local origin of the nematode parasite and its limited impact on hornet colony survival. We also clarify why these parasites (mermithids and conopids) most likely could not hamper the hornet invasion nor be used in biological control programs against this invasive species. creator: Claire Villemant creator: Dario Zuccon creator: Quentin Rome creator: Franck Muller creator: George O. Poinar Jr creator: Jean-Lou Justine uri: https://doi.org/10.7717/peerj.947 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Villemant et al. title: Bird biodiversity assessments in temperate forest: the value of point count versus acoustic monitoring protocols link: https://peerj.com/articles/973 last-modified: 2015-05-19 description: Effective monitoring programs for biodiversity are needed to assess trends in biodiversity and evaluate the consequences of management. This is particularly true for birds and faunas that occupy interior forest and other areas of low human population density, as these are frequently under-sampled compared to other habitats. For birds, Autonomous Recording Units (ARUs) have been proposed as a supplement or alternative to point counts made by human observers to enhance monitoring efforts. We employed two strategies (i.e., simultaneous-collection and same-season) to compare point count and ARU methods for quantifying species richness and composition of birds in temperate interior forests. The simultaneous-collection strategy compares surveys by ARUs and point counts, with methods matched in time, location, and survey duration such that the person and machine simultaneously collect data. The same-season strategy compares surveys from ARUs and point counts conducted at the same locations throughout the breeding season, but methods differ in the number, duration, and frequency of surveys. This second strategy more closely follows the ways in which monitoring programs are likely to be implemented. Site-specific estimates of richness (but not species composition) differed between methods; however, the nature of the relationship was dependent on the assessment strategy. Estimates of richness from point counts were greater than estimates from ARUs in the simultaneous-collection strategy. Woodpeckers in particular, were less frequently identified from ARUs than point counts with this strategy. Conversely, estimates of richness were lower from point counts than ARUs in the same-season strategy. Moreover, in the same-season strategy, ARUs detected the occurrence of passerines at a higher frequency than did point counts. Differences between ARU and point count methods were only detected in site-level comparisons. Importantly, both methods provide similar estimates of species richness and composition for the region. Consequently, if single visits to sites or short-term monitoring are the goal, point counts will likely perform better than ARUs, especially if species are rare or vocalize infrequently. However, if seasonal or annual monitoring of sites is the goal, ARUs offer a viable alternative to standard point-count methods, especially in the context of large-scale or long-term monitoring of temperate forest birds. creator: Brian T. Klingbeil creator: Michael R. Willig uri: https://doi.org/10.7717/peerj.973 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Klingbeil and Willig title: For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases link: https://peerj.com/articles/972 last-modified: 2015-05-19 description: Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases.Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined.Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ.Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. creator: Mads Svane Liljekvist creator: Kristoffer Andresen creator: Hans-Christian Pommergaard creator: Jacob Rosenberg uri: https://doi.org/10.7717/peerj.972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Liljekvist et al.