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Showing papers in "PeerJ in 2013"


Journal ArticleDOI
01 Oct 2013-PeerJ
TL;DR: There is a direct effect of third-party data reuse that persists for years beyond the time when researchers have published most of the papers reusing their own data, and a robust citation benefit from open data is found, although a smaller one than previously reported.
Abstract: Background. Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain estimates of the “citation benefit”. Furthermore, little is known about patterns in data reuse over time and across datasets. Method and Results. Here, we look at citation rates while controlling for many known citation predictors and investigate the variability of data reuse. In a multivariate regression on 10,555 studies that created gene expression microarray data, we found that studies that made data available in a public repository received 9% (95% confidence interval: 5% to 13%) more citations than similar studies for which the data was not made available. Date of publication, journal impact factor, open access status, number of authors, first and last author publication history, corresponding author country, institution citation history, and study topic were included as covariates. The citation benefit varied with date of dataset deposition: a citation benefit was most clear for papers published in 2004 and 2005, at about 30%. Authors published most papers using their own datasets within two years of their first publication on the dataset, whereas data reuse papers published by third-party investigators continued to accumulate for at least six years. To study patterns of data reuse directly, we compiled 9,724 instances of third party data reuse via mention of GEO or ArrayExpress accession numbers in the full text of papers. The level of third-party data use was high: for 100 datasets deposited in year 0, we estimated that 40 papers in PubMed reused a dataset by year 2, 100 by year 4, and more than 150 data reuse papers had been published by year 5. Data reuse was distributed across a broad base of datasets: a very conservative estimate found that 20% of the datasets deposited between 2003 and 2007 had been reused at least once by third parties. Conclusion. After accounting for other factors affecting citation rate, we find a robust citation benefit from open data, although a smaller one than previously reported. We conclude there is a direct effect of third-party data reuse that persists for years beyond the time when researchers have published most of the papers reusing their own data. Other factors that may also contribute to the citation benefit are considered. We further conclude that, at least for gene expression microarray data, a substantial fraction of archived datasets are reused, and that the intensity of dataset reuse has been steadily increasing since 2003.

423 citations


Journal ArticleDOI
19 Feb 2013-PeerJ
TL;DR: The gaming EEG system may prove a valid alternative to laboratory ERP systems for recording reliable late auditory ERPs over the frontal cortices, and less reliable ERPs, such as the MMN, if the reliability of such ERPs can be boosted to the same level as late auditoryERPs.
Abstract: Background. Auditory event-related potentials (ERPs) have proved useful in investigating the role of auditory processing in cognitive disorders such as developmental dyslexia, specific language impairment (SLI), attention deficit hyperactivity disorder (ADHD), schizophrenia, and autism. However, laboratory recordings of auditory ERPs can be lengthy, uncomfortable, or threatening for some participants – particularly children. Recently, a commercial gaming electroencephalography (EEG) system has been developed that is portable, inexpensive, and easy to set up. In this study we tested if auditory ERPs measured using a gaming EEG system (Emotiv EPOC®, www.emotiv.com) were equivalent to those measured by a widely-used, laboratory-based, research EEG system (Neuroscan). Methods. We simultaneously recorded EEGs with the research and gaming EEG systems, whilst presenting 21 adults with 566 standard (1000 Hz) and 100 deviant (1200 Hz) tones under passive (non-attended) and active (attended) conditions. The onset of each tone was marked in the EEGs using a parallel port pulse (Neuroscan) or a stimulus-generated electrical pulse injected into the O1 and O2 channels (Emotiv EPOC®). These markers were used to calculate research and gaming EEG system late auditory ERPs (P1, N1, P2, N2, and P3 peaks) and the mismatch negativity (MMN) in active and passive listening conditions for each participant. Results. Analyses were restricted to frontal sites as these are most commonly reported in auditory ERP research. Intra-class correlations (ICCs) indicated that the morphology of the research and gaming EEG system late auditory ERP waveforms were similar across all participants, but that the research and gaming EEG system MMN waveforms were only similar for participants with non-noisy MMN waveforms (N = 11 out of 21). Peak amplitude and latency measures revealed no significant differences between the size or the timing of the auditory P1, N1, P2, N2, P3, and MMN peaks. Conclusions. Our findings suggest that the gaming EEG system may prove a valid alternative to laboratory ERP systems for recording reliable late auditory ERPs (P1, N1, P2, N2, and the P3) over the frontal cortices. In the future, the gaming EEG system may also prove useful for measuring less reliable ERPs, such as the MMN, if the reliability of such ERPs can be boosted to the same level as late auditory ERPs.

352 citations


Journal ArticleDOI
16 Jul 2013-PeerJ
TL;DR: The acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON), a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings, is described.
Abstract: Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON), a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net). Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica.

336 citations


Journal ArticleDOI
03 Oct 2013-PeerJ
TL;DR: A new predictor called iSNO-AAPair was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains, and shown that the new predictor outperformed the existing predictors.
Abstract: As one of the most important and universal posttranslational modifications (PTMs) of proteins, S-nitrosylation (SNO) plays crucial roles in a variety of biological processes, including the regulation of cellular dynamics and many signaling events. Knowledge of SNO sites in proteins is very useful for drug development and basic research as well. Unfortunately, it is both time-consuming and costly to determine the SNO sites purely based on biological experiments. Facing the explosive protein sequence data generated in the post-genomic era, we are challenged to develop automated vehicles for timely and effectively determining the SNO sites for uncharacterized proteins. To address the challenge, a new predictor called iSNO-AAPair was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains. The cross-validation results on a state-of-the-art benchmark have shown that the new predictor outperformed the existing predictors. The same was true when tested by the independent proteins whose experimental SNO sites were known. A user-friendly web-server for iSNO-AAPair was established at http://app.aporc.org/iSNO-AAPair/, by which users can easily obtain their desired results without the need to follow the mathematical equations involved during its development.

259 citations


Journal ArticleDOI
09 Jul 2013-PeerJ
TL;DR: Empirical data from the Swedish community collected in this study provide point prevalence rates of depression, anxiety disorders and their comorbidity, which were shown to be undertreated and associated with lower quality of life.
Abstract: Background. Depression and anxiety disorders are major world-wide problems. There are no or few epidemiological studies investigating the prevalence of depression, generalized anxiety disorder and anxiety disorders in general in the Swedish population. Methods. Data were obtained by means of a postal survey administered to 3001 randomly selected adults. After two reminders response rate was 44.3%. Measures of depression and general anxiety were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). The PHQ-9 identified participants who had experienced clinically significant depression (PHQ-9 ≥ 10), and who had a diagnosis of major depression (defined by using a PHQ-9 scoring algorithm). Clinically significant anxiety was defined as having a GAD-7 score ≥ 8. To specifically measure generalized anxiety disorder, the Generalized Anxiety Disorder Questionnaire-IV (GAD-Q-IV) was used with an established cut-off. Health-related quality of life was measured using the EuroQol (EQ-5D). Experiences of treatments for psychiatric disorders were also assessed. Results. Around 17.2% (95% CI: 15.1–19.4) of the participants were experiencing clinically significant depression (10.8%; 95% CI: 9.1–12.5) and clinically significant anxiety (14.7%; 95% CI: 12.7–16.6). Among participants with either clinically significant depression or anxiety, nearly 50% had comorbid disorders. The point prevalence of major depression was 5.2% (95% CI: 4.0–6.5), and 8.8% (95% CI: 7.3–10.4) had GAD. Among those with either of these disorders, 28.2% had comorbid depression and GAD. There were, generally, significant gender differences, with more women having a disorder compared to men. Among those with depression or anxiety, only between half and two thirds had any treatment experience. Comorbidity was associated with higher symptom severity and lower health-related quality of life. Conclusions. Epidemiological data from the Swedish community collected in this study provide point prevalence rates of depression, anxiety disorders and their comorbidity. These conditions were shown in this study to be undertreated and associated with lower quality of life, that need further efforts regarding preventive and treatment interventions.

251 citations


Journal ArticleDOI
05 Sep 2013-PeerJ
TL;DR: An experiment to ascertain the “identifiability” of research resources in the biomedical literature and provides recommendations to authors, reviewers, journal editors, vendors, and publishers show that identifiability is a serious problem for reproducibility.
Abstract: Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem. We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the "identifiability" of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines. We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility. Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problem in science today.

224 citations


Journal ArticleDOI
19 Nov 2013-PeerJ
TL;DR: The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.
Abstract: Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.

197 citations


Journal ArticleDOI
22 Oct 2013-PeerJ
TL;DR: It is suggested that barnacle ingestion of microplastic is relatively common, with unknown trophic impacts on the rafting community and the NPSG ecosystem, and this work examines the gastrointestinal tracts of 385 barnacles collected from the North Pacific Subtropical Gyre.
Abstract: Substantial quantities of small plastic particles, termed "microplastic," have been found in many areas of the world ocean, and have accumulated in particularly high densities on the surface of the subtropical gyres. While plastic debris has been documented on the surface of the North Pacific Subtropical Gyre (NPSG) since the early 1970s, the ecological implications remain poorly understood. Organisms associated with floating objects, termed the "rafting assemblage," are an important component of the NPSG ecosystem. These objects are often dominated by abundant and fast-growing gooseneck barnacles (Lepas spp.), which predate on plankton and larval fishes at the sea surface. To assess the potential effects of microplastic on the rafting community, we examined the gastrointestinal tracts of 385 barnacles collected from the NPSG for evidence of plastic ingestion. We found that 33.5% of the barnacles had plastic particles present in their gastrointestinal tract, ranging from one plastic particle to a maximum of 30 particles. Particle ingestion was positively correlated to capitulum length, and no blockage of the stomach or intestines was observed. The majority of ingested plastic was polyethylene, with polypropylene and polystyrene also present. Our results suggest that barnacle ingestion of microplastic is relatively common, with unknown trophic impacts on the rafting community and the NPSG ecosystem.

195 citations


Journal ArticleDOI
05 Nov 2013-PeerJ
TL;DR: It is found that most abundant exosomal RNA species are the fragments of 28S and 18S rRNA subunits, which limits the number of reads from other RNAs, and protocols allowing depletion of fragmented rRNA should be utilized in the future RNA-seq analyses on exosomes.
Abstract: Exosomes are nanosized (30–100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs. In this study, we utilized RNA-Seq technology to analyze RNAs present in microvesicles secreted by human breast cancer cell lines. Exosomes were isolated from the media conditioned by two human breast cancer cell lines, MDA-MB-231 and MDA-MB-436. Exosomal RNA was profiled using the Ion Torrent semiconductor chip-based technology. Exosomes were found to contain various classes of RNA with the major class represented by fragmented ribosomal RNA (rRNA), in particular 28S and 18S rRNA subunits. Analysis of exosomal RNA content revealed that it reflects RNA content of the donor cells. Although exosomes produced by the two cancer cell lines shared most of the RNA species, there was a number of non-coding transcripts unique to MDA-MB-231 and MDA-MB-436 cells. This suggests that RNA analysis might distinguish exosomes produced by low metastatic breast cancer cell line (MDA-MB-436) from that produced by highly metastatic breast cancer cell line (MDA-MB-231). The analysis of gene ontologies (GOs) associated with the most abundant transcripts present in exosomes revealed significant enrichment in genes encoding proteins involved in translation and rRNA and ncRNA processing. These GO terms indicate most expressed genes for both, cellular and exosomal RNA. For the first time, using RNA-seq, we examined the transcriptomes of exosomes secreted by human breast cancer cells. We found that most abundant exosomal RNA species are the fragments of 28S and 18S rRNA subunits. This limits the number of reads from other RNAs. To increase the number of detectable transcripts and improve the accuracy of their expression level the protocols allowing depletion of fragmented rRNA should be utilized in the future RNA-seq analyses on exosomes. Present data revealed that exosomal transcripts are representative of their cells of origin and thus could form basis for detection of tumor specific markers.

183 citations


Journal ArticleDOI
26 Feb 2013-PeerJ
TL;DR: The results suggest that several members of the Firmicutes, Actinobacteria and Proteobacteria may be involved in the metabolism of dietary and endogenous lipids, and provide a scientific rationale for further human studies to explore the role of intestinal microbes in host lipid metabolism.
Abstract: Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae). These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes, Actinobacteria and Proteobacteria may be involved in the metabolism of dietary and endogenous lipids, and provide a scientific rationale for further human studies to explore the role of intestinal microbes in host lipid metabolism.

169 citations


Journal ArticleDOI
19 Nov 2013-PeerJ
TL;DR: Findings support the inclusion of resilience as a component of optimal functioning and well being in doctors and identify the key traits that promote or impair resilience.
Abstract: Objective. The health and well being of medical doctors is vital to their longevity and safe practice. The concept of resilience is recognised as a key component of well being and is an important factor in medical training to help doctors learn to cope with challenge, stress, and adversity. This study examined the relationship of resilience to personality traits and resilience in doctors in order to identify the key traits that promote or impair resilience. Methods. A cross sectional cohort of 479 family practitioners in practice across Australia was studied. The Temperament and Character Inventory measured levels of the seven basic dimensions of personality and the Resilience Scale provided an overall measure of resilience. The associations between resilience and personality were examined by Pearson product-moment correlation coeYcients, controlling for age and gender ( D 0:05 with an accompanying 95% confidence level) and multiple regression analyses. Results. Strong to medium positive correlations were found between Resilience and Self-directedness (rD:614, p< :01), Persistence (rD:498, p< :01), and Cooperativeness (rD:363, p< :01) and negative with Harm Avoidance (rD: 555, p< :01). Individual diVerences in personality explained 39% of the variance in resilience [F.7;460/D 38:40, p< :001]. The three traits which contributed significantly to this variance were Self-directedness ( D:33, p< :001), Persistence ( D:22, p< :001) and Harm Avoidance ( D:19, p< :001). Conclusion. Resilience was associated with a personality trait pattern that is mature, responsible, optimistic, persevering, and cooperative. Findings support the inclusion of resilience as a component of optimal functioning and well being in doctors. Strategies for enhancing resilience should consider the key traits that drive or impair it.

Journal ArticleDOI
17 Sep 2013-PeerJ
TL;DR: A broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy are presented.
Abstract: The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

Journal ArticleDOI
25 Jun 2013-PeerJ
TL;DR: It is indicated that non-pneumococcal species can confound serotype-specific PCR and other sequence-based assays due to evolutionarily conserved genes most likely involved in biosynthesis of surface polysaccharide structures.
Abstract: We performed culture-based and PCR-based tests for pneumococcal identification and serotyping from carriage specimens collected in rural and urban Kenya. Nasopharyngeal specimens from 237 healthy children 98.7%) with the reference cmPCR amplicon for the st, while cmPCR amplicons from lytA-negative specimens were generally more divergent. Separate testing of 56 A-OPs and 56 A-NPs revealed that ∼94% of the positive cmPCR results from A-NP/OPs were from OP microbiota. In contrast, A-NPs yielded >2-fold more pneumococcal isolates than A-OPs. Verified and suspected non-pneumococcal cmPCR serotypes/serogroups appeared to be relatively rare in C-NPs and A-NPs compared to A-OPs. Our findings indicate that non-pneumococcal species can confound serotype-specific PCR and other sequence-based assays due to evolutionarily conserved genes most likely involved in biosynthesis of surface polysaccharide structures.

Journal ArticleDOI
19 Feb 2013-PeerJ
TL;DR: The relevant abundances of the M methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.
Abstract: We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with 13C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.

Journal ArticleDOI
04 Jun 2013-PeerJ
TL;DR: A retrospective computerized analysis of electronically recorded FHR tracings of singleton pregnancies in three German medical centers from 2000 to 2007 found normal ranges for FHR are 120 to 160 bpm, which seem to be safe in daily practice.
Abstract: Aim. There is no consensus about the normal fetal heart rate. Current international guidelines recommend for the normal fetal heart rate (FHR) baseline different ranges of 110 to 150 beats per minute (bpm) or 110 to 160 bpm. We started with a precise definition of "normality" and performed a retrospective computerized analysis of electronically recorded FHR tracings. Methods. We analyzed all recorded cardiotocography tracings of singleton pregnancies in three German medical centers from 2000 to 2007 and identified 78,852 tracings of sufficient quality. For each tracing, the baseline FHR was extracted by eliminating accelerations/decelerations and averaging based on the "delayed moving windows" algorithm. After analyzing 40% of the dataset as "training set" from one hospital generating a hypothetical normal baseline range, evaluation of external validity on the other 60% of the data was performed using data from later years in the same hospital and externally using data from the two other hospitals. Results. Based on the training data set, the "best" FHR range was 115 or 120 to 160 bpm. Validation in all three data sets identified 120 to 160 bpm as the correct symmetric "normal range". FHR decreases slightly during gestation. Conclusions. Normal ranges for FHR are 120 to 160 bpm. Many international guidelines define ranges of 110 to 160 bpm which seem to be safe in daily practice. However, further studies should confirm that such asymmetric alarm limits are safe, with a particular focus on the lower bound, and should give insights about how to show and further improve the usefulness of the widely used practice of CTG monitoring.

Journal ArticleDOI
12 Feb 2013-PeerJ
TL;DR: There is a crucial need for broader studies of ecological, behavioural, physiological and life history responses to be addressed across a greater range of geographic locations, particularly Asia, Africa and Australasia, and in areas of high human population growth and habitat modification.
Abstract: To understand how researchers are tackling globally important issues, it is crucial to identify whether current research is comprehensive enough to make substantive predictions about general responses. We examined how research on climate change affecting insects is being assessed, what factors are being tested and the localities of studies, from 1703 papers published between 1985 and August 2012. Most published research (64%) is generated from Europe and North America and being dedicated to core data analysis, with 29% of the studies analysed dedicated to Lepidoptera and 22% Diptera: which are well above their contribution to the currently identified insect species richness (estimated at 13% and 17% respectively). Research publications on Coleoptera fall well short of their proportional contribution (19% of publications but 39% of insect species identified), and to a lesser extent so do Hemiptera, and Hymenoptera. Species specific responses to changes in temperature by assessing distribution/range shifts or changes in abundance were the most commonly used methods of assessing the impact of climate change on insects. Research on insects and climate change to date is dominated by manuscripts assessing butterflies in Europe, insects of economic and/or environmental concern in forestry, agriculture, and model organisms. The research on understanding how insects will respond to a rapidly changing climate is still in its infancy, but the current trends of publications give a good basis for how we are attempting to assess insect responses. In particular, there is a crucial need for broader studies of ecological, behavioural, physiological and life history responses to be addressed across a greater range of geographic locations, particularly Asia, Africa and Australasia, and in areas of high human population growth and habitat modification. It is still too early in our understanding of taxa responses to climate change to know if charismatic taxa, such as butterflies, or disease vectors, including Diptera, can be used as keystone taxa to generalise other insect responses to climate change. This is critical as the basic biology of most species is still poorly known, and dominant, well studied taxa may show variable responses to climate change across their distribution due to regional biotic and abiotic influences. Indeed identifying if insect responses to climate change can be generalised using phylogeny, functional traits, or functional groups, or will populations and species exhibit idiosyncratic responses, should be a key priority for future research.

Journal ArticleDOI
28 May 2013-PeerJ
TL;DR: Spatial patterns in their benthic communities across reef habitats and depths are described, and these in the context of oceanographic gradients are considered to reflect increasingly efficient heterotrophic abilities.
Abstract: Kingman Reef and Palmyra Atoll in the central Pacific are among the most remote coral reefs on the planet. Here we describe spatial patterns in their benthic communities across reef habitats and depths, and consider these in the context of oceanographic gradients. Benthic communities at both locations were dominated by calcifying organisms (54-86% cover), namely hard corals (20-74%) and crustose coralline algae (CCA) (10-36%). While turf algae were relatively common at both locations (8-22%), larger fleshy macroalgae were virtually absent at Kingman (<1%) and rare at Palmyra (0.7-9.3%). Hard coral cover was higher, but with low diversity, in more sheltered habitats such as Palmyra's backreef and Kingman's patch reefs. Almost exclusive dominance by slow-growing Porites on Kingman's patch reefs provides indirect evidence of competitive exclusion, probably late in a successional sequence. In contrast, the more exposed forereef habitats at both Kingman and Palmyra had higher coral diversity and were characterized by fast-growing corals (e.g., Acropora and Pocillopora), indicative of more dynamic environments. In general at both locations, soft coral cover increased with depth, likely reflecting increasingly efficient heterotrophic abilities. CCA and fleshy macroalgae cover decreased with depth, likely due to reduced light. Cover of other calcified macroalgae, predominantly Halimeda, increased with depth. This likely reflects the ability of many calcifying macroalgae to efficiently harvest light at deeper depths, in combination with an increased nutrient supply from upwelling promoting growth. At Palmyra, patterns of hard coral cover with depth were inconsistent, but cover peaked at mid-depths at Kingman. On Kingman's forereef, benthic community composition was strongly related to wave energy, with hard coral cover decreasing and becoming more spatially clustered with increased wave energy, likely as a result of physical damage leading to patches of coral in localized shelter. In contrast, the cover of turf algae at Kingman was positively related to wave energy, reflecting their ability to rapidly colonize newly available space. No significant patterns with wave energy were observed on Palmyra's forereef, suggesting that a more detailed model is required to study biophysical coupling there. Kingman, Palmyra, and other remote oceanic reefs provide interesting case studies to explore biophysical influences on benthic ecology and dynamics.

Journal ArticleDOI
21 Nov 2013-PeerJ
TL;DR: The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types.
Abstract: Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.

Journal ArticleDOI
16 Jul 2013-PeerJ
TL;DR: The results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.
Abstract: Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

Journal ArticleDOI
07 May 2013-PeerJ
TL;DR: Using dynamic light scattering, size exclusion chromatography and small angle X-ray scattering, it is shown that HFIP pretreated Aβ peptide solutions displaying an increased proportion of oligomeric and aggregated material and an increased propensity to aggregate.
Abstract: Alzheimer's disease is the leading cause of dementia in the elderly. Pathologically it is characterized by the presence of amyloid plaques and neuronal loss within the brain tissue of affected individuals. It is now widely hypothesised that fibrillar structures represent an inert structure. Biophysical and toxicity assays attempting to characterize the formation of both the fibrillar and the intermediate oligomeric structures of Aβ typically involves preparing samples which are largely monomeric; the most common method by which this is achieved is to use the fluorinated organic solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). Recent evidence has suggested that this method is not 100% effective in producing an aggregate free solution. We show, using dynamic light scattering, size exclusion chromatography and small angle X-ray scattering that this is indeed the case, with HFIP pretreated Aβ peptide solutions displaying an increased proportion of oligomeric and aggregated material and an increased propensity to aggregate. Furthermore we show that an alternative technique, involving treatment with strong alkali results in a much more homogenous solution that is largely monomeric. These techniques for solubilising and controlling the oligomeric state of Aβ are valuable starting points for future biophysical and toxicity assays.

Journal ArticleDOI
08 Aug 2013-PeerJ
TL;DR: This work has developed a web-based tool called Kinome Render (KR) that produces customized annotations on the human kinome tree that allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on theHuman Kinome tree.
Abstract: Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains 518 members. Most studies that focus on the human kinome require, at some point, the visualization of large amounts of data. The visualization of such data within the framework of a phylogenetic tree may help identify key relationships between different protein kinases in view of their evolutionary distance and the information used to annotate the kinome tree. For example, studies that focus on the promiscuity of kinase inhibitors can benefit from the annotations to depict binding affinities across kinase groups. Images involving the mapping of information into the kinome tree are common. However, producing such figures manually can be a long arduous process prone to errors. To circumvent this issue, we have developed a web-based tool called Kinome Render (KR) that produces customized annotations on the human kinome tree. KR allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on the human kinome tree. The web interface can be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A stand-alone version is also available and can be run locally.

Journal ArticleDOI
12 Sep 2013-PeerJ
TL;DR: Optimal transparency and reproducibility of studies of YouTube health-related videos can be achieved by following guidance designed for systematic review reporting, with attention to several elements specific to the video medium.
Abstract: Background. YouTube is an increasingly important medium for consumer health information – with content provided by healthcare professionals, government and non-government organizations, industry, and consumers themselves. It is a rapidly developing area of study for healthcare researchers. We examine the methods used in reviews of YouTube consumer health videos to identify trends and best practices. Methods and Materials. Published reviews of consumer-oriented health-related YouTube videos were identified through PubMed. Data extracted from these studies included type of journal, topic, characteristics of the search, methods of review including number of reviewers and method to achieve consensus between reviewers, inclusion and exclusion criteria, characteristics of the videos reported, ethical oversight, and follow-up. Results. Thirty-three studies were identified. Most were recent and published in specialty journals. Typically, these included more than 100 videos, and were examined by multiple reviewers. Most studies described characteristics of the videos, number of views, and sometime characteristics of the viewers. Accuracy of portrayal of the health issue under consideration was a common focus. Conclusion. Optimal transparency and reproducibility of studies of YouTube health-related videos can be achieved by following guidance designed for systematic review reporting, with attention to several elements specific to the video medium. Particularly when seeking to replicate consumer viewing behavior, investigators should consider the method used to select search terms, and use a snowballing rather than a sequential screening approach. Discontinuation protocols for online screening of relevance ranked search results is an area identified for further development.

Journal ArticleDOI
02 Apr 2013-PeerJ
TL;DR: Overall, the data show that heat stress-induced targeting of HsfA2 by MPK6 participates in the complex regulatory mechanism how plants respond to heat stress.
Abstract: So far little is known on the functional role of phosphorylation in the heat stress response of plants. Here we present evidence that heat stress activates the Arabidopsis mitogen-activated protein kinase MPK6. In vitro and in vivo evidence is provided that MPK6 specifically targets the major heat stress transcription factor HsfA2. Activation of MPK6 results in complex formation with HsfA2. MPK6 phosphorylates HsfA2 on T249 and changes its intracellular localisation. Protein kinase and phosphatase inhibitor studies indicate that HsfA2 protein stability is regulated in a phosphorylation-dependent manner, but this mechanism is independent of MPK6. Overall, our data show that heat stress-induced targeting of HsfA2 by MPK6 participates in the complex regulatory mechanism how plants respond to heat stress.

Journal ArticleDOI
09 Jul 2013-PeerJ
TL;DR: Initial support is provided for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders and the results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet.
Abstract: Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated aVective experience and outcome in psychodynamic therapy. AVect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of aVect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the eYcacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders. Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up. Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction eVects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group eVect size of Cohen’s dD 0:77 (95% CI: 0.37‐1.18) was found on the PHQ-9 and a moderately

Journal ArticleDOI
12 Mar 2013-PeerJ
TL;DR: This study conducted a study during a flat track roller derby tournament and found that teammates shared distinct skin microbial communities before and after playing against another team, but that opposing teams’ bacterial communities converged during the course of a roller derby bout.
Abstract: Diverse bacterial communities live on and in human skin. These complex communities vary by skin location on the body, over time, between individuals, and between geographic regions. Culture-based studies have shown that human to human and human to surface contact mediates the dispersal of pathogens, yet little is currently known about the drivers of bacterial community assembly patterns on human skin. We hypothesized that participation in a sport involving skin to skin contact would result in detectable shifts in skin bacterial community composition. We conducted a study during a flat track roller derby tournament, and found that teammates shared distinct skin microbial communities before and after playing against another team, but that opposing teams’ bacterial communities converged during the course of a roller derby bout. Our results are consistent with the hypothesis that the human skin microbiome shifts in composition during activities involving human to human contact, and that contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people.

Journal ArticleDOI
12 Feb 2013-PeerJ
TL;DR: Direct access to BRCA mutation tests, considered a model for high-risk actionable genetic tests of proven clinical utility, provided clear benefits to participants and broader screening of Ashkenazi Jewish women for these three BRCa mutations should be considered.
Abstract: Background. Inherited BRCA gene mutations convey a high risk for breast and ovarian cancer, but current guidelines limit BRCA mutation testing to women with early-onset cancer and relatives of mutation-positive cases. Benefits and risks of providing this information directly to consumers are unknown. Methods. To assess and quantify emotional and behavioral reactions of consumers to their 23andMe Personal Genome Service® report of three BRCA mutations that are common in Ashkenazi Jews, we invited all 136 BRCA1 and BRCA2 mutation-positive individuals in the 23andMe customer database who had chosen to view their BRCA reports to participate in this IRB-approved study. We also invited 160 mutation-negative customers who were matched for age, sex and ancestry. Semi-structured phone interviews were completed for 32 mutation carriers, 16 women and 16 men, and 31 non-carriers. Questions addressed personal and family history of cancer, decision and timing of viewing the BRCA report, recollection of the result, emotional responses, perception of personal cancer risk, information sharing, and actions taken or planned. Results. Eleven women and 14 men had received the unexpected result that they are carriers of a BRCA1 185delAG or 5382insC, or BRCA2 6174delT mutation. None of them reported extreme anxiety and four experienced moderate anxiety that was transitory. Remarkably, five women and six men described their response as neutral. Most carrier women sought medical advice and four underwent risk-reducing procedures after confirmatory mutation testing. Male carriers realized that their test results implied genetic risk for female relatives, and several of them felt considerably burdened by this fact. Sharing mutation information with family members led to screening of at least 30 relatives and identification of 13 additional carriers. Non-carriers did not report inappropriate actions, such as foregoing cancer screening. All but one of the 32 mutation-positive participants appreciated learning their BRCA mutation status. Conclusions. Direct access to BRCA mutation tests, considered a model for high-risk actionable genetic tests of proven clinical utility, provided clear benefits to participants. The unexpected information demonstrated a cascade effect as relatives of newly identified carriers also sought testing and more mutation carriers were identified. Given the absence of evidence for serious emotional distress or inappropriate actions in this subset of mutation-positive customers who agreed to be interviewed for this study, broader screening of Ashkenazi Jewish women for these three BRCA mutations should be considered.

Journal ArticleDOI
23 Dec 2013-PeerJ
TL;DR: Overall, the succession of the ileum bacterial microbiome in commercial turkeys proceeds in a predictable manner, and efforts to prevent disease and promote growth in the absence of antibiotics could involve target dominant bacteria identified in the turkey ilesum that are associated with increased weight gain.
Abstract: Because of concerns related to the use of antibiotics in animal agriculture, antibiotic-free alternatives are greatly needed to prevent disease and promote animal growth One of the current challenges facing commercial turkey production in Minnesota is difficulty obtaining flock average weights typical of the industry standard, and this condition has been coined "Light Turkey Syndrome" or LTS This condition has been identified in Minnesota turkey flocks for at least five years, and it has been observed that average flock body weights never approach their genetic potential However, a single causative agent responsible for these weight reductions has not been identified despite numerous efforts to do so The purpose of this study was to identify the bacterial community composition within the small intestines of heavy and light turkey flocks using 16S rRNA sequencing, and to identify possible correlations between microbiome and average flock weight This study also sought to define the temporal succession of bacteria occurring in the turkey ileum Based upon 27 million sequences across nine different turkey flocks, dominant operational taxonomic units (OTUs) were identified and compared between the flocks studied OTUs that were associated with heavier weight flocks included those with similarity to Candidatus division Arthromitus and Clostridium bartlettii, while these flocks had decreased counts of several Lactobacillus species compared to lighter weight flocks The core bacterial microbiome succession in commercial turkeys was also defined Several defining markers of microbiome succession were identified, including the presence or abundance of Candidatus division Arthromitus, Lactobacillus aviarius, Lactobacillus ingluviei, Lactobacillus salivarius, and Clostridium bartlettii Overall, the succession of the ileum bacterial microbiome in commercial turkeys proceeds in a predictable manner Efforts to prevent disease and promote growth in the absence of antibiotics could involve target dominant bacteria identified in the turkey ileum that are associated with increased weight gain

Journal ArticleDOI
12 Feb 2013-PeerJ
TL;DR: Among non-sauropods, their saurischian relatives the theropod dinosaurs seem to have been best placed to evolve long necks, and indeed their necks probably surpassed those of giraffes, but 150 million years of evolution did not suffice for them to exceed a relatively modest 2.5 m.
Abstract: The necks of the sauropod dinosaurs reached 15 m in length: six times longer than that of the world record giraffe and five times longer than those of all other terrestrial animals. Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stable platform for a long neck; a small, light head that did not orally process food; cervical vertebrae that were both numerous and individually elongate; an efficient air-sac-based respiratory system; and distinctive cervical architecture. Relevant features of sauropod cervical vertebrae include: pneumatic chambers that enabled the bone to be positioned in a mechanically efficient way within the envelope; and muscular attachments of varying importance to the neural spines, epipophyses and cervical ribs. Other long-necked tetrapods lacked important features of sauropods, preventing the evolution of longer necks: for example, giraffes have relatively small torsos and large, heavy heads, share the usual mammalian constraint of only seven cervical vertebrae, and lack an air-sac system and pneumatic bones. Among non-sauropods, their saurischian relatives the theropod dinosaurs seem to have been best placed to evolve long necks, and indeed their necks probably surpassed those of giraffes. But 150 million years of evolution did not suffice for them to exceed a relatively modest 2.5 m.

Journal ArticleDOI
12 Feb 2013-PeerJ
TL;DR: It is shown here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection.
Abstract: Fragments of prostatic acid phosphatase (PAP248-286) in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection), however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide) and Aβ1-40) with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1-40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.

Journal ArticleDOI
12 Feb 2013-PeerJ
TL;DR: The results have implications for previous and future research conducted under fixation conditions, and should encourage forthcoming studies to report the size of fixation targets to aid the interpretation and replication of their results.
Abstract: A large amount of classic and contemporary vision studies require subjects to fixate a target. Target fixation serves as a normalizing factor across studies, promoting the field's ability to compare and contrast experiments. Yet, fixation target parameters, including luminance, contrast, size, shape and color, vary across studies, potentially affecting the interpretation of results. Previous research on the effects of fixation target size and luminance on the control of fixation position rendered conflicting results, and no study has examined the effects of fixation target characteristics on square-wave jerks, the most common type of saccadic intrusion. Here we set out to determine the effects of fixation target size and luminance on the characteristics of microsaccades and square-wave jerks, over a large range of stimulus parameters. Human subjects fixated a circular target with varying luminance and size while we recorded their eye movements with an infrared video tracker (EyeLink 1000, SR Research). We detected microsaccades and SWJs automatically with objective algorithms developed previously. Microsaccade rates decreased linearly and microsaccade magnitudes increased linearly with target size. The percent of microsaccades forming part of SWJs decreased, and the time from the end of the initial SWJ saccade to the beginning of the second SWJ saccade (SWJ inter-saccadic interval; ISI) increased with target size. The microsaccadic preference for horizontal direction also decreased moderately with target size . Target luminance did not affect significantly microsaccades or SWJs, however. In the absence of a fixation target, microsaccades became scarcer and larger, while SWJ prevalence decreased and SWJ ISIs increased. Thus, the choice of fixation target can affect experimental outcomes, especially in human factors and in visual and oculomotor studies. These results have implications for previous and future research conducted under fixation conditions, and should encourage forthcoming studies to report the size of fixation targets to aid the interpretation and replication of their results.