Accuracy of the interferon-gamma release assay for the diagnosis of tuberculous pleurisy: an updated meta-analysis
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.
Pang et al. (2015) Accuracy of the interferon-gamma release assay for the diagnosis of tuberculous pleurisy: an updated meta-analysis. PeerJ 3:e951 https://doi.org/10.7717/peerj.951
Can parasites halt the invader? Mermithid nematodes parasitizing the yellow-legged Asian hornet in France
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.
Villemant et al. (2015) Can parasites halt the invader? Mermithid nematodes parasitizing the yellow-legged Asian hornet in France. PeerJ 3:e947 https://doi.org/10.7717/peerj.947
Bird biodiversity assessments in temperate forest: the value of point count versus acoustic monitoring protocols
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.
Klingbeil et al. (2015) Bird biodiversity assessments in temperate forest: the value of point count versus acoustic monitoring protocols. PeerJ 3:e973 https://doi.org/10.7717/peerj.973
For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases
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.
Liljekvist et al. (2015) For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases. PeerJ 3:e972 https://doi.org/10.7717/peerj.972
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data
Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted. Materials and Methods. We have developed PANDA (Pathway AND Annotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e., other columns for the table of annotations). Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators. Results. In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user’s own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma. Conclusion. PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website: http://bioinformaticstools.mayo.edu/research/panda-viewer/.
Hart et al. (2015) PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PeerJ 3:e970 https://doi.org/10.7717/peerj.970
Astym treatment vs. eccentric exercise for lateral elbow tendinopathy: a randomized controlled clinical trial
Introduction. Patients with chronic lateral elbow (LE) tendinopathy, commonly known as tennis elbow, often experience prolonged symptoms and frequent relapses. Astym treatment, evidenced in animal studies to promote the healing and regeneration of soft tissues, is hypothesized to improve outcomes in LE tendinopathy patients. This study had two objectives: (1) to compare the efficacy of Astym treatment to an evidence-based eccentric exercise program (EE) for patients with chronic LE tendinopathy, and (2) to quantify outcomes of subjects non-responsive to EE who were subsequently treated with Astym treatment. Study Design. Prospective, two group, parallel, randomized controlled trial completed at a large orthopedic center in Indiana. Inclusion criteria: age range of 18–65 years old, with clinical indications of LE tendinopathy greater than 12 weeks, with no recent corticosteriod injection or disease altering comorbidities. Methods. Subjects with chronic LE tendinopathy (107 subjects with 113 affected elbows) were randomly assigned using computer-generated random number tables to 4 weeks of Astym treatment (57 elbows) or EE treatment (56 elbows). Data collected at baseline, 4, 8, 12 weeks, 6 and 12 months. Primary outcome measure: DASH; secondary outcome measures: pain with activity, maximum grip strength and function. The treating physicians and the rater were blinded; subjects and treating clinicians could not be blinded due to the nature of the treatments. Results. Resolution response rates were 78.3% for the Astym group and 40.9% for the EE group. Astym subjects showed greater gains in DASH scores (p = 0.047) and in maximum grip strength (p = 0.008) than EE subjects. Astym therapy also resolved 20/21 (95.7%) of the EE non-responders, who showed improvements in DASH scores (p < 0.005), pain with activity (p = 0.002), and function (p = 0.004) following Astym treatment. Gains continued at 6 and 12 months. No adverse effects were reported. Conclusion. This study suggests Astym therapy is an effective treatment option for patients with LE tendinopathy, as an initial treatment, and after an eccentric exercise program has failed. Registration/Funding. Ball Memorial Hospital provided limited funding. Trial registration was not required by FDAAA 801. Known about the Subject. Under the new paradigm of degenerative tendinopathy, eccentric exercise (EE) is emerging as a first line conservative treatment for LE tendinopathy. EE and Astym treatment are among the few treatment options aiming to improve the degenerative pathophysiology of the tendon. In this trial, Astym therapy, which has shown success in the treatment of tendinopathy, is compared to EE, which has also shown success in the treatment of tendinopathy. Clinical Relevance. There is a need for more effective, conservative treatment options. Based on the current efficacy study, Astym therapy appears to be a promising, non-invasive treatment option.
Sevier et al. (2015) Astym treatment vs. eccentric exercise for lateral elbow tendinopathy: a randomized controlled clinical trial. PeerJ 3:e967 https://doi.org/10.7717/peerj.967
A white-box model of S-shaped and double S-shaped single-species population growth
Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems.
Kalmykov et al. (2015) A white-box model of S-shaped and double S-shaped single-species population growth. PeerJ 3:e948 https://doi.org/10.7717/peerj.948
Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender
Introduction. Behavioral inattention, working memory (WM), and academic achievement share significant variance, but the direction of relationships across development is unknown. The aim of the present study was to determine whether WM mediates the pathway between inattentive behaviour and subsequent academic outcomes. Methods. 204 students from grades 1–4 (49.5% female) were recruited from elementary schools. Participants received assessments of WM and achievement at baseline and one year later. WM measures included a visual-spatial storage task and auditory-verbal storage and manipulation tasks. Teachers completed the SWAN behaviour rating scale both years. Mediation analysis with PROCESS (Hayes, 2013) was used to determine mediation pathways. Results. Teacher-rated inattention indirectly influenced math addition fluency, subtraction fluency and calculation scores through its effect on visual-spatial WM, only for boys. There was a direct relationship between inattention and math outcomes one year later for girls and boys. Children who displayed better attention had higher WM scores, and children with higher WM scores had stronger scores on math outcomes. Bias-corrected bootstrap confidence intervals for the indirect effects were entirely below zero for boys, for the three math outcomes. WM did not mediate the direct relationship between inattention and reading scores. Discussion. Findings identify inattention and WM as longitudinal predictors for math addition and subtraction fluency and math calculation outcomes one year later, with visual-spatial WM as a significant mediator for boys. Results highlight the close relationship between inattention and WM and their importance in the development of math skills.
Gray et al. (2015) Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender. PeerJ 3:e939 https://doi.org/10.7717/peerj.939
Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam
The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop.
Slabaugh et al. (2015) Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam. PeerJ 3:e915 https://doi.org/10.7717/peerj.915
Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors?
The current commercial production protocols for Atlantic cod depend on enriched rotifers and Artemia during first-feeding, but development and growth remain inferior to fish fed natural zooplankton. Two experiments were conducted in order to identify the underlying factors for this phenomenon. In the first experiment (Exp-1), groups of cod larvae were fed either (a) natural zooplankton, mainly copepods, increasing the size of prey as the larvae grew or (b) enriched rotifers followed by Artemia (the intensive group). In the second experiment (Exp-2), two groups of larvae were fed as in Exp-1, while a third group was fed copepod nauplii (approximately the size of rotifers) throughout the larval stage. In both experiments, growth was not significantly different between the groups during the first three weeks after hatching, but from the last part of the rotifer feeding period and onwards, the growth of the larvae fed copepods was higher than that of the intensive group. In Exp-2, the growth was similar between the two copepod groups during the expeimental period, indicating that nutrient composition, not prey size caused the better growth on copepods. Analyses of the prey showed that total fatty acid composition and the ratio of phospholipids to total lipids was slightly different in the prey organisms, and that protein, taurine, astaxanthin and zinc were lower on a dry weight basis in rotifers than in copepods. Other measured nutrients as DHA, all analysed vitamins, manganese, copper and selenium were similar or higher in the rotifers. When compared to the present knowledge on nutrient requirements, protein and taurine appeared to be the most likely limiting nutrients for growth in cod larvae fed rotifers and Artemia. Larvae fed rotifers/Artemia had a higher whole body lipid content than larvae fed copepods at the end of the experiment (stage 5) after the fish had been fed the same formulated diet for approximately 2 weeks.
Karlsen et al. (2015) Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors?. PeerJ 3:e902 https://doi.org/10.7717/peerj.902