Do preparticipation clinical exams reduce morbidity and mortality for athletes?

Though clinical preparticipation exams (PPE) are recommended by experts and required in most states, we found no medium- or better-quality evidence that demonstrates they reduce mortality or morbidity. PPEs detect only a very small percentage of cardiac abnormalities among athletes who subsequently die suddenly (strength of recommendation [SOR]: C, case series study). PPEs are also unable to accurately identify athletes with exercise-induced bronchospasm (SOR: C, small cross-sectional study) and are poorly predictive of which athletes are at increased risk of orthopedic injuries (SOR: C, cross-sectional study)

Root density distribution and biomass allocation of co-occurring woody plants on contrasting soils in a subtropical savanna parkland

Background and aims: Root niche partitioning among trees/shrubs and grasses facilitates their coexistence in savannas, but little is known regarding root distribution patterns of co-occurring woody plants, and how they might differ on contrasting soils. Methods: We quantified root distributions of co-occurring shrubs to 2m on argillic and non-argillic soils. Results: Root biomass in the two shrub communities was 3- to 5- fold greater than that in the grassland community. Prosopis glandulosa, the dominant overstory species was deep-rooted, while the dominant understory shrub, Zanthoxylum fagara, was shallow-rooted (47% vs. 25% of root density at depths >0.4m). Shrubs on argillic soils had less aboveground and greater belowground mass than those on non-argillic soils. Root biomass and density on argillic soils was elevated at shallow (0.4m. Root density decreased exponentially with increasing distance from woody patch perimeters. Conclusions: Belowground biomass (carbon) pools increased markedly with grassland-to-shrubland state change. The presence/absence of a restrictive barrier had substantial effects on root distributions and above- vs. belowground biomass allocation. Differences in root distribution patterns of co-occurring woody species would facilitate their co-existence.NSF [BSR-9109240]; NASA [NAGW-2662]; NSF Doctoral Dissertation Improvement Grant [DEB/DDIG-1600790]; USDA/NIFA Hatch Project [1003961]; Sid Kyle Graduate Merit Assistantship from the Department of Ecosystem Science and Management; Tom Slick Graduate Research Fellowship from the College of Agriculture and Life Sciences, Texas AM University; Office of Graduate and Professional Studies at Texas AM University12 month embargo; first online: 11 March 2019This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

FastSpar: rapid and scalable correlation estimation for compositional data.

SUMMARY: A common goal of microbiome studies is the elucidation of community composition and member interactions using counts of taxonomic units extracted from sequence data. Inference of interaction networks from sparse and compositional data requires specialized statistical approaches. A popular solution is SparCC, however its performance limits the calculation of interaction networks for very high-dimensional datasets. Here we introduce FastSpar, an efficient and parallelizable implementation of the SparCC algorithm which rapidly infers correlation networks and calculates P-values using an unbiased estimator. We further demonstrate that FastSpar reduces network inference wall time by 2-3 orders of magnitude compared to SparCC. AVAILABILITY AND IMPLEMENTATION: FastSpar source code, precompiled binaries and platform packages are freely available on GitHub: github.com/scwatts/FastSpar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.

Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule, of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a to cap-f). H. influenzae type b (Hib) was historically responsible for the majority of invasive H. influenzae disease, and its prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccine era, nontypeable H. influenzae emerged as the most dominant group causing disease, but in recent years a resurgence of encapsulated H. influenzae strains has also been observed, most notably serotype a. Given the increasing incidence of encapsulated strains and the high frequency of Hib in countries without vaccination programs, there is growing interest in genomic epidemiology of H. influenzae Here we present hicap, a software tool for rapid in silico serotype prediction from H. influenzae genome sequences. hicap is written using Python3 and is freely available at https://github.com/scwatts/hicap under the GNU General Public License v3 (GPL3). To demonstrate the utility of hicap, we used it to investigate the cap locus diversity and distribution in 691 high-quality H. influenzae genomes from GenBank. These analyses identified cap loci in 95 genomes and confirmed the general association of each serotype with a unique clonal lineage, and they also identified occasional recombination between lineages that gave rise to hybrid cap loci (2% of encapsulated strains)

Episodic rainfall influences the distribution and abundance of the regular sea urchin Lytechinus variegatus in Saint Andrew Bay, northern Gulf of Mexico

The distribution and abundance of Lytechinus variegatus (Lamarck) were determined at three shallow-water stations in Saint Andrew Bay, FL, in the northern Gulf of Mexico. Populations were monitored at 4-mo intervals from Aug. 1997 to Aug. 1999 along 2- X 10-m transects, with four transects at each station. In Aug. 1997 individuals ranged in size from 15- to 63-mm diameter (mean = 38 mm; density= 1.4 individuals (ind.) m-2) at Station 1 (Stations 2 and 3 were not sampled on that date). By Oct. 1997 individuals at Station 1 ranged in size from 26 to 62 mm (mean = 48 mm; density = 0.6 ind. m-2), suggesting the growth of individuals within the population. At Station 2, individuals ranged between 50 and 70 mm (mean = 59 mm; densities = 1.0 ind. m-2) and at Station 3 between 30 and 79 mm (mean= 51 mm; densities = 1.4 ind, m-2) in Oct. 1997, indicating a population with no recent recruits. A mass mortality event was observed in April 1998 and was attributed to reduced salinities resulting from above-average rainfall in the previous month. Sea urchins were absent at Stations 1 and 2, whereas at Station 3 postdisturbance recruits were smaller (mean = 28 mm) and densities lower. Sea urchin tests were also observed at beach stations proximate to Stations 1 and 2. By July 1998 the populations had partially recovered at Stations 2 and 3 (densities = 0.6 and 1.1 ind. m-2, respectively), but test diameters were small at both stations. Test diameters had increased in Dec. 1998 at Station 3 when compared with those of July, but individuals at Station 2 showed overall smaller test diameters (mean = 28 mm), and densities had decreased again, presumably after another mass mortality caused by another major rainfall in Sep. In April 1999 test diameters had decreased further at Stations 2 and 3, indicating emigration or death of larger animals. We suggest that the shallow-water Saint Andrew Bay population of L. variegatus is reduced for several years at a time by episodic heavy rainfalls. This observation emphasizes the importance of density-independent processes controlling the distribution and abundance of marine organisms

Using Small-Scale Studies to Prioritize Threats and Guide Recovery of a Rare Hemiparasitic Plant: Cordylanthus rigidus ssp. littoralis

BACKGROUND: Recovering endangered species would benefit from identifying and ranking of the factors that threaten them. Simply managing for multiple positive influences will often aid in recovery; however, the relative impacts of multiple threats and/or interactions among them are not always predictable. We used a series of experiments and quantitative observational studies to examine the importance of five potential limiting factors to the abundance of a state-listed endangered hemiparasitic annual forb, Cordylanthus rigidus ssp. littoralis (C.r.l., California, USA): host availability, mammalian herbivores, insect seed predators, fire suppression, and exotic species. While this initial assessment is certainly not a complete list, these factors stem from direct observation and can inform provisional recommendations for management and further research. METHODOLOGY AND PRINCIPAL FINDINGS: Studies were conducted at five sites and included assessments of the influence of host availability, exotic species, exclusion of mammalian herbivores and insect seed predators on C.r.l. productivity, and simulated effects of fire on seed germination. C.r.l. was limited by multiple threats: individuals with access to host species produced up to three times more inflorescences than those lacking hosts, mammalian herbivory reduced C.r.l. size and fecundity by more than 50% and moth larvae reduced seed production by up to 40%. Litter deposition and competition from exotic plant species also appears to work in conjunction with other factors to limit C.r.l. throughout its life cycle. CONCLUSIONS AND SIGNIFICANCE: The work reported here highlights the contribution that a series of small-scale studies can make to conservation and restoration. Taken as a whole, the results can be used immediately to inform current management and species recovery strategies. Recovery of C.r.l. will require management that addresses competition with exotic plant species, herbivore pressure, and availability of preferred host species

Episodic Rainfall Influences the Distribution and Abundance of the Regular Sea Urchin Lytechinus variegatus in Saint Andrew Bay, Northern Gulf of Mexico

The distribution and abundance of Lytechinus variegatus (Lamarck) were determined at three shallow-water stations in Saint Andrew Bay, FL, in the northern Gulf of Mexico. Populations were monitored at 4-mo intervals from Aug. 1997 to Aug. 1999 along 2- X 10-m transects, with four transects at each station. In Aug. 1997 individuals ranged in size from 15- to 63-mm diameter (mean = 38 mm; density= 1.4 individuals (ind.) m-2) at Station 1 (Stations 2 and 3 were not sampled on that date). By Oct. 1997 individuals at Station 1 ranged in size from 26 to 62 mm (mean = 48 mm; density = 0.6 ind. m-2), suggesting the growth of individuals within the population. At Station 2, individuals ranged between 50 and 70 mm (mean = 59 mm; densities = 1.0 ind. m-2) and at Station 3 between 30 and 79 mm (mean= 51 mm; densities = 1.4 ind, m-2) in Oct. 1997, indicating a population with no recent recruits. A mass mortality event was observed in April 1998 and was attributed to reduced salinities resulting from above-average rainfall in the previous month. Sea urchins were absent at Stations 1 and 2, whereas at Station 3 postdisturbance recruits were smaller (mean = 28 mm) and densities lower. Sea urchin tests were also observed at beach stations proximate to Stations 1 and 2. By July 1998 the populations had partially recovered at Stations 2 and 3 (densities = 0.6 and 1.1 ind. m-2, respectively), but test diameters were small at both stations. Test diameters had increased in Dec. 1998 at Station 3 when compared with those of July, but individuals at Station 2 showed overall smaller test diameters (mean = 28 mm), and densities had decreased again, presumably after another mass mortality caused by another major rainfall in Sep. In April 1999 test diameters had decreased further at Stations 2 and 3, indicating emigration or death of larger animals. We suggest that the shallow-water Saint Andrew Bay population of L. variegatus is reduced for several years at a time by episodic heavy rainfalls. This observation emphasizes the importance of density-independent processes controlling the distribution and abundance of marine organisms

A multi-species modelling approach to examine the impact of alternative climate change adaptation strategies on range shifting ability in a fragmented landscape

An individual-based model of animal dispersal and population dynamics was used to test the effects of different climate change adaptation strategies on species range shifting ability, namely the improvement of existing habitat, restoration of low quality habitat and creation of new habitat. These strategies were implemented on a landscape typical of fragmentation in the United Kingdom using spatial rules to differentiate between the allocation of strategies adjacent to or away from existing habitat patches. The total area being managed in the landscape was set at realistic levels based on recent habitat management trends. Eight species were parameterised to broadly represent different stage structure, population densities and modes of dispersal. Simulations were initialised with the species occupying 20% of the landscape and run for 100 years. As would be expected for a range of real taxa, range shifting abilities were dramatically different. This translated into large differences in their responses to the adaptation strategies. With conservative (0.5%) estimates of the area prescribed for climate change adaptation, few species display noticeable improvements in their range shifting, demonstrating the need for greater investment in future adaptation. With a larger (1%) prescribed area, greater range shifting improvements were found, although results were still species-specific. It was found that increasing the size of small existing habitat patches was the best way to promote range shifting, and that the creation of new stepping stone features, whilst beneficial to some species, did not have such broad effect across different species

Coupled land use and ecological models reveal emergence and feedbacks in socio-ecological systems

Acknowledgements: This work was supported by an EPSRC Doctoral Training Centre grant (EP/G03690X/1). Supplementary material (Appendix ECOG‐04039 at ). Appendix 1.Peer reviewedPublisher PD

Correcting index databases improves metagenomic studies

AbstractAssessing the taxonomic composition of metagenomic samples is an important first step in understanding the biology and ecology of microbial communities in complex environments. Despite a wealth of algorithms and tools for metagenomic classification, relatively little effort has been put into the critical task of improving the quality of reference indices to which metagenomic reads are assigned. Here, we inferred the taxonomic composition of 404 publicly available metagenomes from human, marine and soil environments, using custom index databases modified according to two factors: the number of reference genomes used to build the databases, and the monophyletic strictness of species definitions. Index databases built following the NCBI taxonomic system were also compared to others using Genome Taxonomy Database (GTDB) taxonomic redefinitions. We observed a considerable increase in the rate of read classification using modified reference index databases as compared to a default NCBI RefSeq database, with up to a 4.4-, 6.4- and 2.2-fold increase in classified reads per sample for human, marine and soil metagenomes, respectively. Importantly, targeted correction for 70 common human pathogens and bacterial genera in the index database increased their specific detection levels in human metagenomes. We also show the choice of index database can influence downstream diversity and distance estimates for microbiome data. Overall, the study shows a large amount of accessible information in metagenomes remains unexploited using current methods, and that the same data analysed using different index databases could potentially lead to different conclusions. These results have implications for the power and design of individual microbiome studies, and for comparison and meta-analysis of microbiome datasets.</jats:p