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Observation of RNA polymerase clusters in a live zebrafish embryo

Data showing the distribution of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a live zebrafish embryo. Images were acquired by instant-SIM microscopy, Pol II Ser5P was marked by fluorescently labeled antibody fragments (Fab) provided by the laboratory of Hiroshi Kimura, Tokyo Institute of Technology. Data were processed using FIJI.

Association of oligopaint FISH labeled super-enhancers and genes with polymerase clusters (raw data, SE7-SE12)

This data set assesses the placement of different genomic regions relative to clusters formed by RNA polymerase II in zebrafish embryos. RNA polymerase was labeled by immunofluorescence, genomic regions by oligopaint DNA fluorescence in-situ hybridization (FISH). Microscopy images were acquired by instant-SIM microscopy, and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts. Raw image data for super enhancers SE7 to SE12

Association of oligopaint FISH labeled super-enhancers and genes with polymerase clusters

Effect of hexanediol treatment on clusters of RNA polymerase II in zebrafish embryo primary cell culture

This data set assesses changes in RNA polymerase II clusters upon treatment with 3% 1,6-hexanediol in zebrafish embryos. RNA polymerase was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.

opencc-zeroDec 2012View details →

Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes

Bayesian clustering methods have been widely used for studying species delimitation and genetic introgression. In order to test the effect of phylogenetic relationships and sampling scheme on the inferred clustering solution and on the performance of Bayesian clustering analysis, I simulated genotypes of the interfertile oak species Quercus robur, Quercus petraea, and Quercus pubescens and I run analyses using two popular software programs, STRUCTURE and BAPS. First, based on purebred simulations, I compared clustering solutions resulting from different sample size configurations. While clustering solution generally reflected the taxonomic relationships when equal samples of each species were included, spurious partition was inferred by STRUCTURE when some species were represented by larger and others by smaller samples. In very unbalanced configurations, STRUCTURE failed to identify the three species, even if three subpopulations were assumed. By contrast, BAPS could properly identify the three species under any sampling scheme. Second, based on simulations of purebreds and hybrids, I tested the performance of individual assignments with variable number of loci. This analysis showed that STRUCTURE can detect introgressed individuals more efficiently than BAPS. However, BAPS could assign purebreds more efficiently with a lower number of loci. Method performance also depended on phylogenetic relationships. In the case of Q. petraea, Q. pubescens, and their hybrids, method performance was lower due to their phylogenetic affinity. Inclusion of three instead of two species into the analysis led to reduction of performance, and to misclassification of hybrids, which often reflected the phylogenetic affinity between Q. petraea and Q. pubescens.

Data from: Improving rational use of ACTs through diagnosis-dependent subsidies: evidence from a cluster-randomized controlled trial in western Kenya

Background: More than half of artemisinin combination therapies (ACTs) consumed globally are dispensed in the retail sector where diagnostic testing is uncommon, leading to overconsumption and poor targeting. In many malaria-endemic countries, ACTs sold over-the-counter are available at heavily subsidized prices, further contributing to their misuse. Inappropriate use of ACTs can have serious implications for the spread of drug resistance and leads to poor outcomes for non-malaria patients treated with incorrect drugs. We evaluated the public health impact of an innovative strategy that targets ACT subsidies to confirmed malaria cases by coupling free diagnostic testing with a diagnosis-dependent ACT subsidy. Methods and Findings: We conducted a cluster-randomized controlled trial in 32 community clusters in western Kenya (population ~160,000). Eligible clusters had retail outlets selling ACTs and existing community health worker (CHW) programs and were randomly assigned 1:1 to control and intervention arms. In intervention areas, CHWs were available in their villages to perform malaria rapid diagnostic tests on demand for any individual >1 year of age experiencing a malaria-like illness. Malaria RDT positive individuals received a voucher for a discount on a quality-assured ACT, redeemable at a participating retail medicine outlet. In control areas, CHWs offered a standard package of health education, prevention and referral services. We conducted four population-based surveys, at baseline, 6 months, 12 months and 18 months, of a random sample of households with fever in the last 4 weeks to evaluate predefined, individual-level outcomes. The primary outcome was uptake of malaria diagnostic testing at 12 months. The main secondary outcome was rational ACT use, defined as the proportion of ACTs used by test-positive individuals. Analyses followed the intention-to-treat principle using generalized estimating equations to account for clustering with pre-specified adjustment for gender, age, education and wealth. All descriptive statistics and regressions were weighted to account for sampling design. Between July 2015 and May 2017, 32,404 participants were tested for malaria and 10,870 vouchers were issued. 7416 randomly-selected participants with recent fever from all 32 clusters were surveyed. The majority of recent fevers were in children under 18 years (62.9%, n=4653). The gender of enrolled participants was balanced in children (50.0%, n=2318 v 50.2%, n=2335), but more adult women were enrolled than men (78.0%, n=2139 v 22.0%, n=604). At baseline, 67.6% (n=1362) of participants took an ACT for their illness and 40.3% (n=810) of all participants took an ACT purchased from a retail outlet. At 12 months, 50.5% (n=454) in the intervention arm and 43.4% (n=389) in the control arm had a malaria diagnostic test for their recent fever (Adjusted Risk Difference=9 percentage points [pp], 95%CI: 2-15pp, p=0.015; Adjusted Risk Ratio=1.20, 95%CI:1.05-1.38, p=0.015). By 18-months, the ARR had increased to 1.25 (95%CI:1.09-1.44, p=0.005). Rational use of ACTs in the intervention area increased from 41.7% (n=279) at baseline to 59.6% (n=403) and was 40% higher in the intervention arm at 18 months (Adj RR 1.40, 95%CI: 1.19-1.64). While intervention effects increased between 12 and 18 months, we were not able to estimate longer-term impact of the intervention and could not independently evaluate the effects of the free testing and the voucher on uptake of testing. Conclusions: Diagnosis-dependent ACT subsidies and community-based interventions that include the private sector can have an important impact on diagnostic testing and population-wide rational use of ACTs. Targeting of the ACT subsidy itself to those with a positive malaria diagnostic test may also improve sustainability and reduce the cost of retail sector ACT subsidies.

opencc-zeroDec 2010View details →

Data from: Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements

Bilaterian animals have a Hox gene cluster essential for patterning the main body axis, and a ParaHox gene cluster. Comparison of Hox and ParaHox genes has led workers to postulate that both clusters originated from the duplication of an ancient cluster named ProtoHox, which contained up to four genes with at least the precursors of anterior and posterior Hox/ParaHox genes. However, the way in which genes diversified within the ProtoHox, Hox and ParaHox clusters remains unclear because no systematic study of non-bilaterian animals exists. Here we characterize the full Hox/ParaHox gene complements and genomic organization in two cnidarian species (Nematostella vectensis and Hydra magnipapillata), and suggest a ProtoHox cluster simpler than originally thought on the basis of three arguments. First, both species possess bilaterian-like anterior Hox genes, but their non-anterior genes do not appear as counterparts of either bilaterian central or posterior genes; second, two clustered ParaHox genes, Gsx and a gene related to Xlox and Cdx, are found in Nematostella vectensis; and third, we do not find clear phylogenetic support for a common origin of bilaterian Cdx and posterior genes, which might therefore have appeared after the ProtoHox cluster duplication. Consequently, the ProtoHox cluster might have consisted of only two anterior genes. Non-anterior genes could have appeared independently in the Hox and ParaHox clusters, possibly after the separation of bilaterians and cnidarians.

opencc-zeroDec 2015View details →

Data from: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function

CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12–13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies.

opencc-zeroDec 2011View details →

Data from: Genetic mapping identifies a major locus spanning P450 clusters associated with pyrethroid resistance in kdr-free Anopheles arabiensis from Chad

Prevention of malaria transmission throughout much of Africa is dependent on bednets that are impregnated with pyrethroid insecticides. Anopheles arabiensis is the major malaria vector in Chad and efforts to control this vector are threatened by the emergence of pyrethroid resistance. WHO bioassays revealed that An. arabiensis from Ndjamena is resistant to pyrethroids and dichlorodiphenyltrichloroethane (DDT) but fully susceptible to carbamates and organophosphates. No 1014F or 1014S kdr alleles were detected in this population. To determine the mechanisms that are responsible for resistance, genetic crosses were established between the Ndja strain and an insecticide susceptible population from Mozambique. Resistance was inherited as an autosomal trait and quantitative trait locus (QTL) mapping identified a single major locus on chromosome 2R, which explained 24.4% of the variance in resistance. This QTL is enriched in P450 genes including 25 cytochrome P450s in total. One of these, Cyp6p4 is 22-fold upregulated in the Ndja strain compared with the susceptible. Piperonyl butoxide (PBO) synergist and biochemical assays further support a role for P450s in conferring pyrethroid resistance in this population.

opencc-zeroApr 2020View details →

Data from: Species richness and patterns of overdispersion, clustering and randomness shape phylogenetic and functional diversity-area relationships in habitat islands

Aim: To evaluate how the area of habitat island systems influences multiple facets of diversity. Location: Southern Brazil. Taxon: Birds. Methods: Using an Information Theoretic approach, we compared the fit of 20 diversity–area relationship (DARs) models in three habitat island systems. We tested for the best-fit model, model-family, shape, and presence/absence of an asymptote. We used species richness (SR), Faith's phylogenetic diversity (PD) and Faith's functional diversity (FD) to assess species–area (SARs), phylogenetic (PDARs) and functional diversity–area relationships (FDARs). We controlled for the effect of SR in PD and FD via null models to assess PDARs and FDARs independently of SR and to explore the influence of phylogenetic and functional randomness, clustering and overdispersion. Results: PDARs and FDARs built with PD and FD resembled SARs and were all best fitted by convex or sigmoidal, upwards oriented, non-asymptotic models. Controlling for SR in diversity indices produced flat or downwards-oriented, weak PDARs and FDARs, which were best fitted by convex, non-asymptotic models or the linear model. Taxonomic diversity accumulated faster with area than functional diversity, which accumulated faster than phylogenetic diversity. Randomness and clustering patterns prevailed in shaping PDARs and FDARs relative to overdispersion. Main conclusions: Controlling for SR in PD and FD affects DARs patterns and the strength of the relationships. Irrespective of this influence of SR, a few simple models of the power and exponential model-families best fit DARs. Model parameters reveal differences in the response of each facet of diversity to increases in area, highlighting the complementary nature of DARs. When considered independently of SR, both PDAR and FDAR patterns largely reflect the broad variation of phylogenetic and functional diversity in small islands. It is therefore likely that the ecological processes that promote phylogenetic and functional overdispersion and clustering operate at contrasting spatial scales.

opencc-zeroSep 2019View details →

Data from: Cluster analysis successfully identifies clinically meaningful knee valgus moment patterns: frequency of early peaks reflects sex-specific ACL injury incidence

Background: Biomechanical studies of ACL injury risk factors frequently analyze only a fraction of the relevant data, and typically not in accordance with the injury mechanism. Extracting a peak value within a time series of relevance to ACL injuries is challenging due to differences in the relative timing and size of the peak value of interest. Aims/hypotheses: The aim was to cluster analyze the knee valgus moment time series curve shape in the early stance phase. We hypothesized that 1a) There would be few discrete curve shapes, 1b) there would be a shape reflecting an early peak of the knee valgus moment, 2a) youth athletes of both sexes would show similar frequencies of early peaks, 2b) adolescent girls would have greater early peak frequencies. Methods: N = 213 (39% boys) youth soccer and team handball athletes (phase 1) and N = 35 (45% boys) with 5 year follow-up data (phase 2) were recorded performing a change of direction task with 3D motion analysis and a force plate. The time series of the first 30% of stance phase were cluster analyzed based on Euclidean distances in two steps; shape-based main clusters with a transformed time series, and magnitude based sub-clusters with body weight normalized time series. Group differences (sex, phase) in curve shape frequencies, and shape-magnitude frequencies were tested with chi-squared tests. Results: Six discrete shape-clusters and 14 magnitude based sub-clusters were formed. Phase 1 boys had greater frequency of early peaks than phase 1 girls (38% vs 25% respectively, P < 0.001 for full test). Phase 2 girls had greater frequency of early peaks than phase 2 boys (42% vs 21% respectively, P < 0.001 for full test). Conclusions: Cluster analysis can reveal different patterns of curve shapes in biomechanical data, which likely reflect different movement strategies. The early peak shape is relatable to the ACL injury mechanism as the timing of its peak moment is consistent with the timing of injury. Greater frequency of early peaks demonstrated by Phase 2 girls is consistent with their higher risk of ACL injury in sports.

opencc-zeroDec 2016View details →

Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus. We found that a genomic region consistently governs variation in several of the traits that distinguish these contrasting forms. Additionally, some of the taxon specific traits controlled by this QTL cluster have evolved repeatedly during the adaptation to the same habitats, suggesting that it could mediate divergence between locally adapted forms. This cluster contains footprints of divergent natural selection across the range of S. lautus, which suggests that it could have been instrumental for the rapid diversification of this species.

Data from: Single-dose oral ciprofloxacin prophylaxis as a response to a meningococcal meningitis epidemic in the African meningitis belt: a three-arm, open-label, cluster-randomized trial

Background: Antibiotic prophylaxis for contacts of meningitis cases is not recommended during outbreaks in the African meningitis belt. We assessed the effectiveness of single-dose oral ciprofloxacin administered to household contacts and in village-wide distributions on the overall attack rate (AR) in an outbreak of meningococcal meningitis. Methods and findings: In this 3-arm, open-label, cluster-randomized trial during a meningococcal meningitis outbreak in Madarounfa District, Niger, villages notifying a suspected case were randomly assigned (1:1:1) to standard care (the control arm), single-dose oral ciprofloxacin for household contacts within 24 hours of case notification, or village-wide distribution of ciprofloxacin within 72 hours of first case notification. The primary outcome was the overall AR of suspected meningitis after inclusion. A random sample of 20 participating villages was enrolled to document any changes in fecal carriage prevalence of ciprofloxacin-resistant and extended-spectrum beta-lactamase (ESBL)–producing Enterobacteriaceae before and after the intervention. Between April 22 and May 18, 2017, 49 villages were included: 17 to the control arm, 17 to household prophylaxis, and 15 to village-wide prophylaxis. A total of 248 cases were notified in the study after the index cases. The AR was 451 per 100,000 persons in the control arm, 386 per 100,000 persons in the household prophylaxis arm (t test versus control p = 0.68), and 190 per 100,000 persons in the village-wide prophylaxis arm (t test versus control p = 0.032). The adjusted AR ratio between the household prophylaxis arm and the control arm was 0.94 (95% CI 0.52–1.73, p = 0.85), and the adjusted AR ratio between the village-wide prophylaxis arm and the control arm was 0.40 (95% CI 0.19‒0.87, p = 0.022). No adverse events were notified. Baseline carriage prevalence of ciprofloxacin-resistant Enterobacteriaceae was 95% and of ESBL-producing Enterobacteriaceae was >90%, and did not change post-intervention. One limitation of the study was the small number of cerebrospinal fluid samples sent for confirmatory testing. Conclusions: Village-wide distribution of single-dose oral ciprofloxacin within 72 hours of case notification reduced overall meningitis AR. Distributions of ciprofloxacin could be an effective tool in future meningitis outbreak responses, but further studies investigating length of protection, effectiveness in urban settings, and potential impact on antimicrobial resistance patterns should be carried out.

Data from: Genetic evidence of female kin clusters in a continuous population of a solitary carnivore, the Eurasian lynx

Large terrestrial carnivores can sometimes display strong family bonds affecting the spatial distribution of related individuals. We studied the spatial genetic relatedness and family structure of female Eurasian lynx, continuously distributed in southern Finland. We hypothesized that closely related females form matrilineal assemblages, clustering together with relatives living in the neighboring areas. We evaluated this hypothesis using tissue samples of 133 legally harvested female lynx (from year 2007 to 2015), genotyped with 23 microsatellite markers, and tested for possible spatial genetic family structure using a combination of Bayesian clustering, spatial autocorrelation, and forensic genetic parentage analysis. The study population had three potential family genetic clusters, with a high degree of admixture and geographic overlap, and showed a weak but significant negative relationship between pairwise genetic and geographic distance. Moreover, parentage analysis indicated that 64% of the females had one or more close relatives (sister, mother, or daughter) within the study population. Individuals identified as close kin consistently assigned to the same putative family genetic cluster. They also were sampled closer geographically than females on average, although variation was large. Our results support the possibility that Eurasian lynx forms matrilineal assemblages, and comparisons with males are now required to further assess this hypothesis.

opencc-zeroAug 2019View details →

Data from: Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities

Objective: Our objective was to develop and test a new concept (affinity) analogous to multimorbidity of chronic conditions for individuals at census tract level in Memphis, TN. The use of affinity will improve the surveillance of multiple chronic conditions and facilitate the design of effective interventions. Methods: We used publicly available chronic condition data (Center for Disease Control and Prevention (CDC) 500 Cities project), socio-demographic data (U.S. Census Bureau) and demographics data (Environmental Systems Research Institute; ESRI). We examined the geographic pattern of the affinity of chronic conditions using global Moran's I and Getis-Ord Gi statistics and its association with socio-economic disadvantage (poverty, unemployment, and crime) using robust regression models. We also used the most common behavioral factor, smoking, and other demographic factors (percent of the male population, percent of the population 67 years and over and total population size) as control variables in the model. Results: A geo-distinctive pattern of clustered chronic affinity associated with socio-economic deprivation was observed. Statistical results confirmed that neighborhoods with higher rates of crime, poverty, and unemployment were associated with an increased likelihood of having a higher affinity among major chronic conditions. With the inclusion of smoking in the model, however, only the crime prevalence was statistically significantly associated with the chronic affinity. Conclusion: Chronic affinity disadvantages were disproportionately accumulated in socially disadvantaged areas. We showed links between commonly co-observed chronic diseases at the population level and systematically explored the complexity of affinity and socio-economic disparities. Our affinity score, based on publicly available datasets, served as a surrogate for multimorbidity at the population level, which may assist policymakers and public health planners to identify urgent hot spots for chronic disease and allocate clinical, medical and healthcare resources efficiently.

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.

opencc-zeroSep 2019View details →

Data from: The Fear Reduction Exercised Early (FREE) approach to management of low back pain in general practice: a pragmatic cluster-randomised controlled trial

Background: Effective and cost-effective primary care treatments for low back pain (LBP) are required to reduce the burden of the world's most disabling condition. This study aimed to compare the clinical effectiveness and cost-effectiveness of the Fear Reduction Exercised Early (FREE) approach to LBP (intervention) with usual general practitioner (GP) care (control). Methods and findings: This pragmatic, cluster-randomised controlled trial with process evaluation and parallel economic evaluation was conducted in the Hutt Valley, New Zealand. Eight general practices were randomly assigned (stratified by practice size) with a 1:1 ratio to intervention (4 practices; 34 GPs) or control group (4 practices; 29 GPs). Adults presenting to these GPs with LBP as their primary complaint were recruited. GPs in the intervention practices were trained in the FREE approach, and patients presenting to these practices received care based on the FREE approach. The FREE approach restructures LBP consultations to prioritise early identification and management of barriers to recovery. GPs in control practices did not receive specific training for this study, and patients presenting to these practices received usual care. Between 23 September 2016 and 31 July 2017, 140 eligible patients presented to intervention practices (126 enrolled) and 110 eligible patients presented to control practices (100 enrolled). Patient mean age was 46.1 years (SD 14.4), and 46% were female. The duration of LBP was less than 6 weeks in 88% of patients. Primary outcome was change from baseline in patient participant Roland Morris Disability Questionnaire (RMDQ) score at 6 months. Secondary patient outcomes included pain, satisfaction, and psychosocial indices. GP outcomes included attitudes, knowledge, confidence, and GP LBP management behaviour. There was active and passive surveillance of potential harms. Patients and outcome assessors were blind to group assignment. Analysis followed intention-to-treat principles. A total of 122 (97%) patients from 32 GPs in the intervention group and 99 (99%) patients from 25 GPs in the control group were included in the primary outcome analysis. At 6 months, the groups did not significantly differ on the primary outcome (adjusted mean RMDQ score difference 0.57, 95% CI −0.64 to 1.78; p = 0.354) or secondary patient outcomes. The RMDQ difference met the predefined criterion to indicate noninferiority. One control group participant experienced an activity-related gluteal tear, with no other adverse events recorded. Intervention group GPs had improvements in attitudes, knowledge, and confidence compared with control group GPs. Intervention group GP LBP management behaviour became more guideline concordant than the control group. In cost-effectiveness, the intervention dominated control with lower costs and higher Quality-Adjusted Life Year (QALY) gains. Limitations of this study were that although adequately powered for primary outcome assessment, the study was not powered for evaluating some employment, healthcare use, and economic outcomes. It was also not possible for research nurses (responsible for patient recruitment) to be masked on group allocation for practices. Conclusions: Findings from this study suggest that the FREE approach improves GP concordance with LBP guideline recommendations but does not improve patient recovery outcomes compared with usual care. The FREE approach may reduce unnecessary healthcare use and produce economic benefits. Work participation or health resource use should be considered for primary outcome assessment in future trials of undifferentiated LBP.

opencc-zeroDec 2013View details →

Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands

Field elm (Ulmus minor) is a riparian tree that grows in rare, small populations scattered along temporary watercourses in the Balearic Islands, nowadays mostly covered with Mediterranean vegetation. Agriculture and farming on the fertile land along the periodically flooded plains have reduced the elm populations to sparse tree lines along the creek beds. The presence of field elm in this very anthropic landscape has led some authors to consider it as an introduced species in the Balearics. However, pollen data suggest these elms may be the remains of larger populations experiencing continuous population shrinkage during the Holocene, and hence be native to the isles. In this paper, we apply genetic markers to assess whether field elm is or is not indigenous to the Balearic Islands. We compare the genetic variation in nine nuclear microsatellites of six Balearic populations (three in each of the largest islands, Majorca and Minorca) with that of three natural Iberian populations located in two regions, one geologically (Baetic mountains, SE Iberia) and another historically (Catalonia, NE Iberia) related to the islands. Principal coordinates analysis and Bayesian clustering methods reveal a strong genetic differentiation of the Balearic populations from the Iberian ones, and even among islands, which support their native origin. Genotypic variation in the islands is very low and clonal reproduction is very high compared with the mainland, as it is frequently observed in populations of clonal species where sexual reproduction is limited. We discuss the practical implications of these findings for the conservation of elm genetic resources of these findings.

opencc-zeroOct 2019View details →

Data from: Factors that can affect the spatial positioning of large and small individuals in clusters of sit-and-wait predators

Shadow competition, the interception of prey by sit-and-wait predators closest to the source of prey arrival, is prevalent in clusters of sit-and-wait predators. Peripheral positions in the cluster receive more prey and should thus be more frequently occupied. Models predicting spatial positioning in groups, however, usually ignore variability among group members. Here, I used a simulation model to determine conditions under which small and large sit-and-wait predators, which differ in their attack range, should differ in their spatial positions in the cluster. Small predators occupied peripheral positions more frequently than large predators at the simulation beginning, while the opposite held true as time advanced. Due to the large and small attack range of large and small predators respectively, small predators mistakenly relocated away from peripheral positions, while large predators did not relocate fast enough from inferior central positions. Any factor that moderated the frequent relocations of small predators or had the opposite effect on large predators assisted small or large predators respectively to reach the more profitable peripheral positions. Furthermore, any factor elevating shadow competition led to longer occupation of the periphery by large predators. This model may explain why sit-and-wait predators are not homogenously distributed in space according to size.