Journals
2011 EN
Abhaya V. Kulkarni · Brittany Aziz · Iffat Shams
+1 more
Background Author self-citation contributes to the overall citation count of an article and the impact factor of the journal in which it appears. Little is known, however, about the extent of self-citation in the general clinical medicine literature. The objective of this study was to determine the extent and temporal pattern of author self-citation and the article characteristics associated with author self-citation. Methodology/Principal Findings We performed a retrospective cohort study of articles published in three high impact general medical journals ( JAMA , Lancet , and New England Journal of Medicine ) between October 1, 1999 and March 31, 2000. We retrieved the number and percentage of author self-citations received by the article since publication, as of June 2008, from the Scopus citation database. Several article characteristics were extracted by two blinded, independent reviewers for each article in the cohort and analyzed in multivariable linear regression analyses. Since publication, author self-citations accounted for 6.5% (95% confidence interval 6.3–6.7%) of all citations received by the 328 articles in our sample. Self-citation peaked in 2002, declining annually thereafter. Studies with more authors, in cardiovascular medicine or infectious disease, and with smaller sample size were associated with more author self-citations and higher percentage of author self-citation (all p≤0.01). Conclusions/Significance Approximately 1 in 15 citations of articles in high-profile general medicine journals are author self-citations. Self-citation peaks within about 2 years of publication and disproportionately affects impact factor. Studies most vulnerable to this effect are those with more authors, small sample size, and in cardiovascular medicine or infectious disease.
Public Library of Science
Journals
2011 EN
James Stegen · Allen H. Hurlbert
Understanding the influences of dispersal limitation and environmental filtering on the structure of ecological communities is a major challenge in ecology. Insight may be gained by combining phylogenetic, functional and taxonomic data to characterize spatial turnover in community structure (β-diversity). We develop a framework that allows rigorous inference of the strengths of dispersal limitation and environmental filtering by combining these three types of β-diversity. Our framework provides model-generated expectations for patterns of taxonomic, phylogenetic and functional β-diversity across biologically relevant combinations of dispersal limitation and environmental filtering. After developing the framework we compared the model-generated expectations to the commonly used “intuitive” expectation that the variance explained by the environment or by space will, respectively, increase monotonically with the strength of environmental filtering or dispersal limitation. The model-generated expectations strongly departed from these intuitive expectations: the variance explained by the environment or by space was often a unimodal function of the strength of environmental filtering or dispersal limitation, respectively. Therefore, although it is commonly done in the literature, one cannot assume that the strength of an underlying process is a monotonic function of explained variance. To infer the strength of underlying processes, one must instead compare explained variances to model-generated expectations. Our framework provides these expectations. We show that by combining the three types of β-diversity with model-generated expectations our framework is able to provide rigorous inferences of the relative and absolute strengths of dispersal limitation and environmental filtering. Phylogenetic, functional and taxonomic β-diversity can therefore be used simultaneously to infer processes by comparing their empirical patterns to the expectations generated by frameworks similar to the one developed here.
Public Library of Science
Journals
2011 EN
Balázs Könnyű · Tamás Czárán
The chemical machinery of life must have been catalytic from the outset. Models of the chemical origins have attempted to explain the ecological mechanisms maintaining a minimum necessary diversity of prebiotic replicator enzymes, but little attention has been paid so far to the evolutionary initiation of that diversity. We propose a possible first step in this direction: based on our previous model of a surface-bound metabolic replicator system we try to explain how the adaptive specialization of enzymatic replicator populations might have led to more diverse and more efficient communities of cooperating replicators with two different enzyme activities. The key assumptions of the model are that mutations in the replicator population can lead towards a) both of the two different enzyme specificities in separate replicators: efficient “specialists” or b) a “generalist” replicator type with both enzyme specificities working at less efficiency, or c) a fast-replicating, non-enzymatic “parasite”. We show that under realistic trade-off constraints on the phenotypic effects of these mutations the evolved replicator community will be usually composed of both types of specialists and of a limited abundance of parasites , provided that the replicators can slowly migrate on the mineral surface. It is only at very weak trade-offs that generalists take over in a phase-transition-like manner. The parasites do not seriously harm the system but can freely mutate, therefore they can be considered as pre-adaptations to later, useful functions that the metabolic system can adopt to increase its own fitness.
Public Library of Science
Journals
2011 EN
Purnima Kumar · Michael R. Brooker · Scot E. Dowd
+1 more
Pyrosequencing of 16S rRNA genes allows for in-depth characterization of complex microbial communities. Although it is known that primer selection can influence the profile of a community generated by sequencing, the extent and severity of this bias on deep-sequencing methodologies is not well elucidated. We tested the hypothesis that the hypervariable region targeted for sequencing and primer degeneracy play important roles in influencing the composition of 16S pyrotag communities. Subgingival plaque from deep sites of current smokers with chronic periodontitis was analyzed using Sanger sequencing and pyrosequencing using 4 primer pairs. Greater numbers of species were detected by pyrosequencing than by Sanger sequencing. Rare taxa constituted nearly 6% of each pyrotag community and less than 1% of the Sanger sequencing community. However, the different target regions selected for pyrosequencing did not demonstrate a significant difference in the number of rare and abundant taxa detected. The genera Prevotella , Fusobacterium , Streptococcus , Granulicatella , Bacteroides , Porphyromonas and Treponema were abundant when the V1–V3 region was targeted, while Streptococcus , Treponema , Prevotella , Eubacterium , Porphyromonas , Campylobacer and Enterococcus predominated in the community generated by V4–V6 primers, and the most numerous genera in the V7–V9 community were Veillonella , Streptococcus , Eubacterium , Enterococcus , Treponema , Catonella and Selenomonas . Targeting the V4–V6 region failed to detect the genus Fusobacterium , while the taxa Selenomonas , TM7 and Mycoplasma were not detected by the V7–V9 primer pairs. The communities generated by degenerate and non-degenerate primers did not demonstrate significant differences. Averaging the community fingerprints generated by V1–V3 and V7–V9 primers providesd results similar to Sanger sequencing, while allowing a significantly greater depth of coverage than is possible with Sanger sequencing. It is therefore important to use primers targeted to these two regions of the 16S rRNA gene in all deep-sequencing efforts to obtain representational characterization of complex microbial communities.
Public Library of Science
Journals
2011 EN
Eliana Alves · M. Amparo F. Faustino · João P. C. Tomé
+6 more
Background Photodynamic antimicrobial chemotherapy (PACT) combines light, a light-absorbing molecule that initiates a photochemical or photophysical reaction, and oxygen. The combined action of these three components originates reactive oxygen species that lead to microorganisms' destruction. The aim was to evaluate the efficiency of PACT on Vibrio fischeri : 1) with buffer solution, varying temperature, pH, salinity and oxygen concentration values; 2) with aquaculture water, to reproduce photoinactivation (PI) conditions in situ . Methodology/Principal Findings To monitor the PI kinetics, the bioluminescence of V. fischeri was measured during the experiments. A tricationic meso -substituted porphyrin (Tri-Py + -Me-PF) was used as photosensitizer (5 µM in the studies with buffer solution and 10–50 µM in the studies with aquaculture water); artificial white light (4 mW cm −2 ) and solar irradiation (40 mW cm −2 ) were used as light sources; and the bacterial concentration used for all experiments was ≈10 7 CFU mL −1 (corresponding to a bioluminescence level of 10 5 relative light units - RLU). The variations in pH (6.5–8.5), temperature (10–25°C), salinity (20–40 g L −1 ) and oxygen concentration did not significantly affect the PI of V. fischeri , once in all tested conditions the bioluminescent signal decreased to the detection limit of the method (≈7 log reduction). The assays using aquaculture water showed that the efficiency of the process is affected by the suspended matter. Total PI of V. fischeri in aquaculture water was achieved under solar light in the presence of 20 µM of Tri-Py + -Me-PF. Conclusions/Significance If PACT is to be used in environmental applications, the matrix containing target microbial communities should be previously characterized in order to establish an efficient protocol having into account the photosensitizer concentration, the light source and the total light dose delivered. The possibility of using solar light in PACT to treat aquaculture water makes this technology cost-effective and attractive.
Public Library of Science
Journals
2011 EN
Nathan Pankratz · Alexandra Dumitriu · Kurt N. Hetrick
+10 more
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2 . PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-valuessmaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
Public Library of Science
Journals
2011 EN
Alessandra Balduini · Stefania Badalucco · Mariateresa Pugliano
+5 more
Background Ph-negative myeloproliferative neoplasms (MPNs) are clonal disorders that include primary myelofibrosis (PMF), polycythemia vera (PV) and essential thrombocythemia (ET). Although the pathogenesis of MPNs is still incompletely understood, an involvement of the megakaryocyte lineage is a distinctive feature. Methodology/Principal Findings We analyzed the in vitro megakaryocyte differentiation and proplatelet formation in 30 PMF, 8 ET, 8 PV patients, and 17 healthy controls (CTRL). Megakaryocytes were differentiated from peripheral blood CD34 + or CD45 + cells in the presence of thrombopoietin. Megakaryocyte output was higher in MPN patients than in CTRL with no correlation with the JAK2 V617F mutation. PMF-derived megakaryocytes displayed nuclei with a bulbous appearance, were smaller than ET- or PV-derived megakaryocytes and formed proplatelets that presented several structural alterations. In contrast, ET- and PV-derived megakaryocytes produced more proplatelets with a striking increase in bifurcations and tips compared to both control and PMF. Proplatelets formation was correlated with platelet counts in patient peripheral blood. Patients with pre-fibrotic PMF had a pattern of megakaryocyte proliferation and proplatelet formation that was similar to that of fibrotic PMF and different from that of ET. Conclusions/Significance In conclusion, MPNs are associated with high megakaryocyte proliferative potential. Profound differences in megakaryocyte morphology and proplatelet formation distinguish PMF, both fibrotic and prefibrotic, from ET and PV.
Public Library of Science
Journals
2011 EN
Elizabeth M. Robinson · Delbert L. Smee · Geoffrey C. Trussell
Predators can strongly influence prey populations and the structure and function of ecosystems, but these effects can be modified by environmental stress. For example, fluid velocity and turbulence can alter the impact of predators by limiting their environmental range and altering their foraging ability. We investigated how hydrodynamics affected the foraging behavior of the green crab ( Carcinus maenas ), which is invading marine habitats throughout the world. High flow velocities are known to reduce green crab predation rates and our study sought to identify the mechanisms by which flow affects green crabs. We performed a series of experiments with green crabs to determine: 1) if their ability to find prey was altered by flow in the field, 2) how flow velocity influenced their foraging efficiency, and 3) how flow velocity affected their handling time of prey. In a field study, we caught significantly fewer crabs in baited traps at sites with fast versus slow flows even though crabs were more abundant in high flow areas. This finding suggests that higher velocity flows impair the ability of green crabs to locate prey. In laboratory flume assays, green crabs foraged less efficiently when flow velocity was increased. Moreover, green crabs required significantly more time to consume prey in high velocity flows. Our data indicate that flow can impose significant chemosensory and physical constraints on green crabs. Hence, hydrodynamics may strongly influence the role that green crabs and other predators play in rocky intertidal communities.
Public Library of Science
Journals
2011 EN
Benjamin I. Ruttenberg · Scott L. Hamilton · Sheila Walsh
+5 more
In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ∼10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management.
Public Library of Science
Journals
2011 EN
Georges Natsoulis · John Bell · Hua Xu
+8 more
We have developed an integrated strategy for targeted resequencing and analysis of gene subsets from the human exome for variants. Our capture technology is geared towards resequencing gene subsets substantially larger than can be done efficiently with simplex or multiplex PCR but smaller in scale than exome sequencing. We describe all the steps from the initial capture assay to single nucleotide variant (SNV) discovery. The capture methodology uses in-solution 80-mer oligonucleotides. To provide optimal flexibility in choosing human gene targets, we designed an in silico set of oligonucleotides, the Human OligoExome, that covers the gene exons annotated by the Consensus Coding Sequencing Project (CCDS). This resource is openly available as an Internet accessible database where one can download capture oligonucleotides sequences for any CCDS gene and design custom capture assays. Using this resource, we demonstrated the flexibility of this assay by custom designing capture assays ranging from 10 to over 100 gene targets with total capture sizes from over 100 Kilobases to nearly one Megabase. We established a method to reduce capture variability and incorporated indexing schemes to increase sample throughput. Our approach has multiple applications that include but are not limited to population targeted resequencing studies of specific gene subsets, validation of variants discovered in whole genome sequencing surveys and possible diagnostic analysis of disease gene subsets. We also present a cost analysis demonstrating its cost-effectiveness for large population studies.
Public Library of Science