From Research to Practice: Which Research Strategy Contributes More to Clinical Excellence? Comparing High-Volume versus High-Quality Biomedical Research

The question when and to what extent academic research can benefit society is of great interest to policy-makers and the academic community. Physicians in university hospitals represent a highly relevant test-group for studying the link between research and practice because they engage in biomedical academic research while also providing medical care of measurable quality. Physicians’ research contribution to medical practice can be driven by either high-volume or high-quality research productivity, as often pursuing one productivity strategy excludes the other. To empirically examine the differential contribution to medical practice of the two strategies, we collected secondary data on departments across three specializations (Cardiology, Oncology and Orthopedics) in 50 U.S.-based university hospitals served by 4,330 physicians. Data on volume and quality of biomedical research at each department was correlated with publicly available ratings of departments’ quality of care, demonstrating that high-quality research has significantly greater contribution to quality of care than high-volume research.     

Rangeland Fire Protection Associations in Great Basin Rangelands: A Model for Adaptive Community Relationships with Wildfire?

Widespread concern with the negative impacts of wildfire on human communities has spurred calls to foster more resilient and adaptable forms of community coexistence with fire. However, numerous institutional barriers work to perpetuate maladaptive individual and collective behaviors in many communities. Here we examine a unique institutional model in the remote U.S. West in which rural community members play active roles in responding to wildland fire under state-sanctioned Rangeland Fire Protection Associations. Our findings drawn from case studies of four associations in Idaho and Oregon suggest that the Rangeland Fire Protection Association model presents opportunities to leverage the motivations, skills, and knowledge of ranchers to inform effective fire response and create opportunities for learning and adaptation. At the same time, this model of coproduction presents challenges to the integration of formal and informal institutions.     

Leitbakteria of microbial biofilm communities causing occlusion of biliary stents

Biliary stents inserted to relieve obstructive jaundice caused by biliary or pancreatic malignancies inevitably become occluded by microbial growth in the form of diverse microbial community biofilms. The scarce information available on these communities is based on cultivation methods, but such methods usually provide distorted overviews of community composition, so commonalities and differences in biliary stent communities are uncertain. We extracted DNA and RNA from the microbial communities of 11 biliary stents explanted from nine patients in hospitals from two different countries, amplified 16S rRNA and rDNA sequences, analysed the amplicons by the single-strand conformation polymorphism (SSCP) method, and sequenced and deduced phylogenetic assignments of the major amplicons representing the major biofilm community members. We used a Modified Robbins Device (MRD) to study de novo development of a stent biofilm from a patient stent microbial community. Single-strand conformation polymorphism fingerprinting revealed the same six abundant bacterial species, here designated Leitbakteria, namely Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Enterobacter aerogenes, and two unculturable bacteria distantly related to E. coli and Shigella sonnei, in all of the stent biofilm communities. In the experimental biliary stent system, a sequential colonization of the stent surface was observed, with P. aeruginosa being the pioneer colonizer, followed by K. pneumoniae and one of the unculturable Leitbakteria, followed by the remainder of the community. The overview of microbial biofilm communities of biliary stents gained by the use of culture-independent methods revealed new unculturable bacteria as major members of biliary stent biofilms, and the diversity of the abundant members of the stent biofilms is considerably lower than suggested from earlier studies based on cultivation methods, and that communities from different stents from different patients in different countries are remarkably similar and have similar major members, the stent Leitbakteria.     

An isoclinal approach to the comparative statics of biological communities

An understanding of the comparative statics of biological communities is important both as a means of explaining the long-term effects of changes in environmental conditions, and as a framework for viewing community time trajectories. A general formulation of community dynamics is presented here which, given full information about a particular community's dynamic behavior, describes the impact of a change in environmental conditions on the community steady state. However, since such full information is often lacking in studies of biological communities, various approaches to partial information analysis of comparative statics are presented and compared, including a generalized protocol for isocline analysis. The suggested isocline protocol is shown to be a useful tool for both full and partial information analyses, as well as for both general and partial equilibrium studies. This work was supported over several years through funding from the International Biological Program, the Oregon State University Sea Grant College Program, the U.S. Environmental Protection Agency, the U.S. Forest Service, the Electric Power Research Institute, and the Northwest and Alaska Fisheries Center.     

The social structural basis of the organization of persons in memory

This paper summarizes and discusses three studies of patterns in the recall of persons in socially bounded communities. Individual sin three different communities (a graduate academic program, a religious fellowship, and a department in a formal organization) free-listed the names of persons in their respective communities. Results indicate that the individuals in each community share a common cognitive structure of community members that is based on the community’s social structure. These studies, combined with the results of other research, strongly suggest that persons are organized in memory according to social structural principles and that affiliation and dominance are the principal dimensions of social cognition. Suggestions are offered for future research to test the generality of these findings. An earlier version of this paper was presented at the 3rd European Conference on Social Network Analysis, June, 1993, in München (Munich), Germany. This research was supported by an Air Force Laboratory Graduate Fellowship awarded to the author by the U. S. Air Force Office of Scientific Research. Devon D. Brewer received his Ph.D. from the University of California, Irvine, and is currently a research consultant with the Social Development Research Group at the University of Washington. His research focuses on social networks, cognitive anthropology, and research methods.     

The community structure of sessile heterotrophic bacteria stressed by acid mine drainage

Microbial communities that developed on glass slides suspended in acid-polluted (pH=2.9) and nonpolluted (pH=6.5) but otherwise similar waters showed evidence of stress when suspended at the opposite station. Glucose incorporation was inhibited in both translocated communities, but the inhibition was not as severe and recovery of activity was faster for the acid-developed community as compared to the circumneutral community. The communities contained a substantially different set of members with little overlap. The range of pH values at which the members of the acid-developed community could function suggested that the members of that community were generalists, as opposed to narrowly constrained members of the community from the circumneutral station. Based on the proportion of test characters that received positive responses, the organisms from the acidic site were more general in their abilities (47.6% positive) as compared with the neutral counterparts (18.7% positive). The results support the concept that communities developed in extreme environments tend to be generalists, whereas those from mesic environments, due to the higher levels of competition present, tend to be specialists. Furthermore, the study of microbial communities in dynamic systems such as streams and reservoir inflows is facilitated by the use of solid surfaces which allow an assemblage of nontransient microbes to develop.     

Taxonomic and functional diversity of atrazine‐degrading bacterial communities enriched from agrochemical factory soil

Aims: To characterize atrazine‐degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. Methods and Results: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65–80% of ¹⁴C ring‐labelled atrazine. The presence of trzN‐atzBC‐trzD, trzN‐atzABC‐trzD and trzN‐atzABCDEF‐trzD gene combinations was determined by PCR. In all enriched communities, trzN‐atzBC genes were located on a 165‐kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α‐, β‐ and γ‐subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine‐degrading community members previously isolated from the same contaminated site. Conclusions: The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine‐catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine. Significance and Impact of the Study: This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long‐term contamination by s‐triazine compounds.     

Detritus-Dependent Development of the Microbial Community in an Experimental System: Qualitative Analysis by Denaturing Gradient Gel Electrophoresis

Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the “microbial loop.” To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.     

Investigation of the bacterial retting community of kenaf (Hibiscus cannabinus) under different conditions using next-generation semiconductor sequencing

The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 h from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources and having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria established themselves and in addition their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.     

Urban Neighborhoods and Depressive Symptoms in Late Middle Age

This study examines associations between multiple urban neighborhood characteristics (socioeconomic disadvantage, affluence, and racial/ethnic composition) and depressive symptoms among late middle aged persons and compares findings to those previously obtained for persons age 70 years and older. Survey data are from the Health and Retirement Study (HRS), a U.S. national probability sample of noninstitutionalized persons aged 51 to 61 years in 1992. Neighborhoods are 1990 U.S. census tracts. Hierarchical linear regression is used to estimate multilevel models. Depressive symptoms vary significantly across urban neighborhoods among late middle age persons. Neighborhood socioeconomic disadvantage is significantly associated with depressive symptoms, net of both individual-level sociodemographic and health variables. However, this association is contingent upon individual-level wealth in that persons with low wealth in the most disadvantaged neighborhoods report the most depressive symptoms. Unlike findings for older adults for whom neighborhood effects appear to be entirely compositional in nature, neighborhood context matters to subgroups of late middle age adults.     

16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community

Molecular methods are beginning to reveal inhabitants of natural microbial communities which have never before been cultured. Our approach involves selective cloning of naturally occurring 16S rRNA sequences as cDNA, and comparison of these sequences to a database which includes 16S rRNA sequences of isolated community members. We provide here an overview of the method and its potential for community analysis. A 16S rRNA sequence retrieved from the well-studied hot spring cyanobacterial mat in Octopus Spring (Yellowstone National Park) is shown as an example of one contributed by an uncultured member of the community.     

16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community

Abstract Molecular methods are beginning to reveal inhabitants of natural microbial communities which have nerver before been cultured. Our approach involves selective cloning of naturally occurring 16S rRNA sequences as cDNA, and comparison of these sequences to a database which includes 16S rRNA sequences of isolated community members. We provide here an overview of the method and its potential for community analysis. A 16S rRNA sequence retrieved from the well-studied hot spring cyanobacterial mat in Octopus Spring (Yellowstone National Park) is shown as an example of one contributed by an uncultured member of the community.     

A profile of the members of FASEB societies: NIH awards, degrees, and institutional affiliations, 1999.

Data from the FASEB Directory of Members and NIH were used to develop a statistical profile of the members of FASEB Societies. For the U.S.-based scientists (exclusive of retired and student members), the most frequently reported degree was a research doctorate (69. 6%). A substantial fraction, however, reported medical degrees (19. 2%) or both research and medical degrees (8.0%). The majority of members of FASEB Societies listed academic affiliations in the directory. Industrial affiliations were reported, however, in 9.7% of the entries with smaller fractions listing associations with hospitals, independent research institutes, and government agencies. Just over one-fourth of the members of FASEB Societies were principal investigators on NIH research grants. These investigators received one-half of all NIH grants and nearly 60% of the RO1 grants.     

Comparison of Free-Living and Particle-Associated Bacterial Communities in the Chesapeake Bay by Stable Low-Molecular-Weight RNA Analysis

Free-living and particle-associated bacterial communities in the Chesapeake Bay estuary were analyzed and compared by using acridine orange direct counts and low-molecular-weight (LMW) RNA analysis. Samples were taken from top and bottom waters at upper- and mid-bay sites in December 1992. Free-living bacteria dominated the bacterial numbers at all sampling sites, although particle-associated bacteria increased in areas with greater particle loads. LMW RNAs (5S rRNA and tRNA) obtained directly from free-living, particle-associated, and total bacterioplankton communities were analyzed by high-resolution electrophoresis. There were distinct differences in the migration distances between LMW RNAs of free-living and particle-associated communities taken from the same site, indicating that the two communities differ in composition. In addition, LMW RNA profiles differed minimally with depth for all of the communities examined, presumably because of vertical mixing. 5S rRNAs of free-living communities from the upper- and mid-bay regions differed considerably. Particle-associated RNAs, on the other hand, were very similar, suggesting consistent environmental conditions on particles that select for similar community members. Lastly, several isolated bacteria had 5S rRNAs that were not detected in their respective extracted community 5S rRNAs, indicating that these isolated organisms were not representative of dominant members.     

Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis.

Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the "microbial loop." To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.     

Landscape‐scale determinants of non‐native fish communities

Aim Predicting and preventing invasions depends on knowledge of the factors that make ecosystems susceptible to invasion. Current studies generally rely on non‐native species richness (NNSR) as the sole measure of ecosystem invasibility; however, species identity is a critical consideration, given that different ecosystems may have environmental characteristics suitable to different species. Our aim was to examine whether non‐native freshwater fish community composition was related to ecosystem characteristics at the landscape scale. Location United States. Methods We described spatial patterns in non‐native freshwater fish communities among watersheds in the Mid‐Atlantic region of the United States based on records of establishment in the U.S. Geological Survey’s Nonindigenous Aquatic Species Database. We described general relationships between non‐native species and ecosystem characteristics using canonical correspondence analysis. We clustered watersheds by non‐native fish community and described differences among clusters using indicator species analysis. We then assessed whether non‐native communities could be predicted from ecosystem characteristics using random forest analysis and predicted non‐native communities for uninvaded watersheds. We estimated which ecosystem characteristics were most important for predicting non‐native communities using conditional inference trees. Results We identified four non‐native fish communities, each with distinct indicator species. Non‐native communities were predicted based on ecosystem characteristics with an accuracy of 80.6%, with temperature as the most important variable. Relatively uninvaded watersheds were predicted to be invasible by the most diverse non‐native community. Main conclusions Non‐native species identity is an important consideration when assessing ecosystem invasibility. NNSR alone is an insufficient measure of invasibility because ecosystems with equal NNSR may not be equally invasible by the same species. Our findings can help improve predictions of future invasions and focus management and policy decisions on particular species in highly invasible ecosystems.     

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.     

Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.     

Estimating similarity of communities: a parametric approach to spatio‐temporal analysis of species diversity

Several stochastic models with environmental noise generate spatio‐temporal Gaussian fields of log densities for the species in a community. Combinations of such models for many species often lead to lognormal species abundance distributions. In spatio‐temporal analysis it is often realistic to assume that the same species are expected to occur at different times and/or locations because extinctions are rare events. Spatial and temporal β‐diversity can then be analyzed by studying pairs of communities at different times or locations defined by a bivariate lognormal species abundance model in which a single correlation occurs. This correlation, which is a measure of similarity between two communities, can be estimated from samples even if the sampling intensities vary and are unknown, using the bivariate Poisson lognormal distribution. The estimators are approximately unbiased, although each specific correlation may be rather uncertain when the sampling effort is low with only a small fraction of the species represented in the samples. An important characteristic of this community correlation is that it relates to the classical Jaccard‐ or the Sørensen‐indices of similarity based on the number of species present or absent in two communities. However, these indices calculated from samples of species in a community do not necessarily reflect similarity of the communities because the observed number of species depends strongly on the sampling intensities. Thus, we propose that our community correlation should be considered as an alternative to these indices when comparing similarity of communities. We illustrate the application of the correlation method by computing the similarity between temperate bird communities.