Using Crowdsourcing to Evaluate Published Scientific Literature: Methods and Example

Systematically evaluating scientific literature is a time consuming endeavor that requires hours of coding and rating. Here, we describe a method to distribute these tasks across a large group through online crowdsourcing. Using Amazon''s Mechanical Turk, crowdsourced workers (microworkers) completed four groups of tasks to evaluate the question, “Do nutrition-obesity studies with conclusions concordant with popular opinion receive more attention in the scientific community than do those that are discordant?” 1) Microworkers who passed a qualification test (19% passed) evaluated abstracts to determine if they were about human studies investigating nutrition and obesity. Agreement between the first two raters'' conclusions was moderate (κ = 0.586), with consensus being reached in 96% of abstracts. 2) Microworkers iteratively synthesized free-text answers describing the studied foods into one coherent term. Approximately 84% of foods were agreed upon, with only 4 and 8% of ratings failing manual review in different steps. 3) Microworkers were asked to rate the perceived obesogenicity of the synthesized food terms. Over 99% of responses were complete and usable, and opinions of the microworkers qualitatively matched the authors'' expert expectations (e.g., sugar-sweetened beverages were thought to cause obesity and fruits and vegetables were thought to prevent obesity). 4) Microworkers extracted citation counts for each paper through Google Scholar. Microworkers reached consensus or unanimous agreement for all successful searches. To answer the example question, data were aggregated and analyzed, and showed no significant association between popular opinion and attention the paper received as measured by Scimago Journal Rank and citation counts. Direct microworker costs totaled $221.75, (estimated cost at minimum wage: $312.61). We discuss important points to consider to ensure good quality control and appropriate pay for microworkers. With good reliability and low cost, crowdsourcing has potential to evaluate published literature in a cost-effective, quick, and reliable manner using existing, easily accessible resources.     

Application of Fungal and Bacterial Production Methodologies to Decomposing Leaves in Streams

As leaves enter woodland streams, they are colonized by both fungi and bacteria. To determine the contribution of each of these microbial groups to the decomposition process, comparisons of fungal and bacterial production are needed. Recently, a new method for estimating fungal production based on rates of [(sup14)C]acetate incorporation into ergosterol was described. Bacterial production in environmental samples has been determined from rates of [(sup3)H]leucine incorporation into protein. In this study, we evaluated conditions necessary to use these methods for estimating fungal and bacterial production associated with leaves decomposing in a stream. During incubation of leaf disks with radiolabeled substrates, aeration increased rates of fungal incorporation but decreased bacterial production. Incorporation of both radiolabeled substrates by microorganisms associated with leaf litter was linear over the time periods examined (2 h for bacteria and 4 h for fungi). Incorporation of radiolabeled substrates present at different concentrations indicated that 400 nM leucine and 5 mM acetate maximized uptake for bacteria and fungi, respectively. Growth rates and rates of acetate incorporation into ergosterol followed similar patterns when fungi were grown on leaf disks in the laboratory. Three species of stream fungi exhibited similar ratios of rates of biomass increase to rates of acetate incorporation into ergosterol, with a mean of 19.3 (mu)g of biomass per nmol of acetate incorporated. Both bacterial and fungal production increased exponentially with increasing temperature. In the stream that we examined, fungal carbon production was 11 to 26 times greater than bacterial carbon production on leaves colonized for 21 days.     

Evaluation of management effectiveness in protected areas: Methodologies and results

Protected areas (PAs) play an important role in biodiversity conservation and the implementation of ambitious multilateral environmental agreements, like the 2010 targets of the Convention on Biological Diversity (CBD). In the CBD's Programme of Work on Protected Areas, it is requested that each country conduct management effectiveness evaluations of at least thirty percent of its PAs by 2010. This article compares the most common methodologies of PA management effectiveness evaluations, such as the Rapid Assessment and Prioritization of Protected Area Management (RAPPAM) Methodology, the Management Effectiveness Tracking Tool (METT) and UNESCO's Enhancing our Heritage (EoH) Toolkit. These and other methodologies can help to (1) examine overall effectiveness of PAs, (2) identify factors influencing the effectiveness and (3) determine common threats and their seriousness.However, the outcomes of major studies concerning overall effectiveness as well as success and failure factors for PA management are partially contradictory. Different results can be due to the approach (e.g. number and type of indicators or assessors included in the evaluation process) or to the individual context of the PA (e.g. age, region, IUCN category) and therefore these factors need to be considered when comparing results of management effectiveness studies.Research indicates that increased attention should be paid to regular monitoring of conservation activities in PAs including systematic social science studies with a socio-economic and socio-cultural focus. Unfortunately, the outcomes of the management effectiveness studies are not easily accessible and have not yet been widely shared or distributed among the conservation community.

     

海洋保护区管理与保护成效评估的方法与进展

全球物种多样性的持续下降使得生物多样性保护面临巨大挑战, 海洋生物多样性的保护任务尤其艰巨。海洋保护区是保护生物多样性的有效方式之一, 如何对其成效进行评估是当前研究热点。然而, 目前针对海洋保护区的评估体系较少, 而且评估指标多侧重于管理成效。近年来随着全球生物多样性监测网络和数据库的建立, 以及多种新技术(如遥感、声呐系统、卫星追踪、基因组学等)在海洋生物多样性监测中的应用, 使得从生态系统到基因水平的多层次连续监测成为可能。基于此, 建议未来我国海洋保护区成效评估应在充分利用新技术方法的基础上, 加强长期科学监测, 建立并完善生物多样性监测数据库和信息共享机制, 发展跨学科的综合保护成效评估体系, 加强基于生物多样性监测的保护成效评估。     

Characterization of a Novel Class of Interspersed LTR Elements in Primate Genomes: Structure, Genomic Distribution, and Evolution

Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus. Received: 29 September 1997 / Accepted: 16 January 1998     

Methodological Approaches to Evaluate Teratogenic Risk Using Birth Defect Registries: Advantages and Disadvantages

Background

Different approaches have been used in case-control studies to estimate maternal exposure to medications and the risk of birth defects. However, the performance of these approaches and how they affect the odds ratio (OR) estimates have not been evaluated using birth-defect surveillance programmes. The aim of this study was to evaluate the scope and limitations of three case-control approaches to assess the teratogenic risk of birth defects in mothers exposed to antiepileptic medications, insulin, or acetaminophen.

Methodology/Principal Findings

We studied 110,814 non-malformed newborns and 58,514 live newborns with birth defects registered by the Latin American Collaborative Study of Congenital Anomalies (ECLAMC) between 1967 and 2008. Four controls were randomly selected for each case in the same hospital and period, and three different control groups were used: non-malformed newborns (HEALTHY), malformed newborns (SICK), and a subgroup of SICK, only-exposed cases (OECA). Associations were evaluated using OR and Pearson''s chi-square (P<0.01). There were no concordance correlations between the HEALTHY and OECA designs, and the average OR differences ranged from 3.0 to 11.5 for the three evaluated medicines. The overestimations observed for HEALTHY design were increased as higher OR values were given, with a high and statistically significant correlation between the difference and the mean. On the contrary, the concordance correlations obtained between the SICK and OECA designs were quite good, with no significant differences in the average risks.

Conclusions

The HEALTHY design estimates the true population OR, but shows a high rate of false-positive results presumably caused by differential misclassification bias. This bias decreases with the increase of the proportion of exposed controls. SICK and OECA odds ratios cannot be considered a direct estimate of the true population OR except under certain conditions. However, the SICK and OECA designs could provide practical information to generate hypotheses about potential teratogens.     

Use of Microneurography to Evaluate Sympathetic Activity in Hypertension: A Brief Review

Muscle sympathetic nerve activity (MSNA) is an important variable in the study of autonomic activity in both normotensive and hypertensive subjects. It is measured directly from the peroneal nerve using microneurography. The technique is complex and difficult to learn, but yields accurate and direct information about sympathetic nerve impulses. MSNA provides not only greater reproducibility than other measures of sympathetic activity, but also a clearer and more consistent reflection of changes in sympathetic activity caused by changes in the subject's status or disease. This technique has been used primarily in basic research settings studying stress and hypertension. It has much potential to enhance our understanding of sympathetic nervous system activity and its role in applied psychophysiology and biofeedback.     

Contribution of Genome-Wide Association Studies to Scientific Research: A Pragmatic Approach to Evaluate Their Impact

The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets. We chose multiple sclerosis (MS) as a paradigm disease and assumed that, in pre-GWAS candidate-gene studies, the knowledge behind the choice of each gene reflected the understanding of the disease prior to the advent of GWAS. Importantly, this knowledge was based mainly on non-genetic, phenotypic grounds. We performed single-gene and pathway-oriented comparisons of old and new knowledge in MS by confronting an unbiased list of candidate genes in pre-GWAS association studies with those genes exceeding the genome-wide significance threshold in GWAS published from 2007 on. At the single gene level, the majority (94 out of 125) of GWAS-discovered variants had never been contemplated as plausible candidates in pre-GWAS association studies. The 31 genes that were present in both pre- and post-GWAS lists may be of particular interest in that they represent disease-associated variants whose pathogenetic relevance is supported at the phenotypic level (i.e. the phenotypic information that steered their selection as candidate genes in pre-GWAS association studies). As such they represent attractive therapeutic targets. Interestingly, our analysis shows that some of these variants are targets of pharmacologically active compounds, including drugs that are already registered for human use. Compared with the above single-gene analysis, at the pathway level GWAS results appear more coherent with previous knowledge, reinforcing some of the current views on MS pathogenesis and related therapeutic research. This study presents a pragmatic approach that helps interpret and exploit GWAS knowledge.     

Scarification and Cultural Resources: An Experiment to Evaluate Serotinous Lodgepole Pine Forest Regeneration Techniques

Abstract

The controlled analysis of the effects of natural resource management techniques on cultural resources has rarely been undertaken. Scarification is used by timber managers to mix soil and seed to insure proper regeneration in harvested areas. The effects of one scarification project on an artificial “site” are described and the resultant disturbance evaluated in light of its potential to affect cultural resources. Suggestions for meeting timber management goals while minimizing impacts on cultural resources are offered.     

Transport of Asparagine by Rat Brain Synaptosomes: An Approach to Evaluate Glutamine Accumulation

Isolated rat brain synaptosomes accumulated L-asparagine with a Km value of 348 microM and a Vmax value of 3.7 nmol/mg of protein/min at 28 degrees C. Uptake of L-asparagine was inhibited by the presence of L-glutamine, whereas transport of L-glutamine was blocked by L-asparagine. Alanine, serine, cysteine, threonine, and, in particular, leucine were also inhibitory whereas alpha-(methylamino)isobutyrate, ornithine, lysine, arginine, and glutamate were much less effective blockers. Transport of L-asparagine had a substantial sodium-dependent component, whereas that of the D-stereoisomer was almost unaffected by the presence or absence of the cation. L-Asparagine was accumulated to a maximal gradient, [L-Asn]i/[L-Asn]o, of 20-30, and this value was reduced to 5-6 by withdrawal of sodium or addition of high [KCI]. A plot of log [Na+]o/[Na+]i against the log [L-Asn]i/[L-Asn]o had a slope close to I, which indicates that a single sodium ion is transported inward with each asparagine molecule. It is postulated that uptake of L-asparagine occurs, to a large extent, in cotransport with Na+ and that it utilizes the sodium chemical gradient and the membrane electrical potential as the source of energy. The similarity between the L-asparagine and L-glutamine transport systems and the reciprocal inhibition of influx of the two amino acids suggest that the same mechanism is responsible for glutamine accumulation. This could explain the high [Gln]i maintained by the brain in vivo.     

Characterization of the Erythrocyte Sodium-Lithium Countertransporter: Limitations and Assumptions of Traditional and Kinetic Methodologies

The present work examined the key elements featuring in the various methods used to characterize the erythrocyte sodium-lithium countertransport. Effects of medium composition on lithium efflux were investigated in 20 subjects. Mean lithium efflux (mmol Li/l RBC.h) into a 150 mm sodium medium was significantly higher than efflux into a revised sodium-rich medium (149 mm) containing 1 mm Mg (0.335 ± 0.100 vs. 0.298 ± 0.085 respectively; P < 0.03). Mean lithium efflux into sodium-free media where sodium had been entirely replaced by magnesium, was significantly lower than efflux into a choline-based medium containing only 1 mm magnesium (0.088 ± 0.027 vs. 0.109 ± 0.034 respectively; P= 0.03). Sodium-lithium countertransport activity and the transporter's kinetic profile were measured simultaneously in 35 subjects using traditional choline-based and kinetic methodologies. There was a significant correlation between countertransport activity and maximal rate of turnover (V _max) (r= 0.62; P < 0.001); V _max values were consistently greater than their corresponding countertransport activities (P < 0.001). On subdividing the subject group into tertiles based on the Michaelis-Menten constant (k _m ) values (mm), <75, 75 − 150 and >150, the slopes of the regression lines for each group diminished progressively (0.64, 0.49 and 0.23 respectively), correlations within each group remained significant (P < 0.001, P < 0.001 and P < 0.02). No significant correlation was found between k _m values and countertransport activity (r= 0.035; P=ns). Increasing the number of points representing sodium concentrations within the range 0–150 mm, improved the confidence in the emerging estimates of V _max and k _m obtained by linear transformation. Comparison of kinetic data derived using four different analytical methods (two linear transformations, a nonlinear regression and a statistical method), showed no significant differences between the estimates yielded for either V _max (P= 0.88, ns) or k _m (P= 0.92, ns). This study has highlighted the critical roles of assay conditions and derivation techniques used when measuring sodium-lithium countertransport, emphasizing the need for standardization of the methodology. Received: 10 December 1996/Revised: 2 October 1997     

Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed

Methods for transfer of exogenous DNA into cells are essential for genetics and molecular biology, and the lack of effective methods hampers research on many different species of bacteria which have shown to be particularly recalcitrant to transformation. This review presents the progress on the development of methods for artificial transformation of bacteria with emphasis on different methodologies and the range of bacteria that can be transformed. The methods' strengths and weaknesses are described.     

Transcervical Ultrasonography Is Feasible to Visualize and Evaluate Base of Tongue Cancers

Background

Base of tongue (BOT) is a difficult subsite to examine clinically and radiographically. Yet, anatomic delineation of the primary tumor site, its extension to adjacent sites or across midline, and endophytic vs. exophytic extent are important characteristics for staging and treatment planning. We hypothesized that ultrasound could be used to visualize and describe BOT tumors.

Methods

Transcervical ultrasound was performed using a standardized protocol in cases and controls. Cases had suspected or confirmed BOT malignancy. Controls were healthy individuals without known malignancy.

Results

100% of BOT tumors were visualized. On ultrasound BOT tumors were hypoechoic (90.9%) with irregular margins (95.5%). Ultrasound could be used to characterize adjacent site involvement, midline extent, and endophytic extent, and visualize the lingual artery. No tumors were suspected for controls.

Conclusions

Ultrasonography can be used to transcervically visualize BOT tumors and provides clinically relevant characteristics that may not otherwise be appreciable.     

Sum of the Parts: Composition and Architecture of the Bacterial Extracellular Matrix

Bacterial biofilms are complex multicellular assemblies that exhibit resistance to antibiotics and contribute to the pathogenesis of serious and chronic infectious diseases. New approaches and quantitative data are needed to define the molecular composition of bacterial biofilms. Escherichia coli biofilms are known to contain polysaccharides and functional amyloid fibers termed curli, yet accurate determinations of biofilm composition at the molecular level have been elusive. The ability to define the composition of the extracellular matrix (ECM) is crucial for the elucidation of structure–function relationships that will aid the development of chemical strategies to disrupt biofilms. We have developed an approach that integrates non-perturbative preparation of the ECM with electron microscopy, biochemistry, and solid-state NMR spectroscopy to define the chemical composition of the intact and insoluble ECM of a clinically important pathogenic bacterium—uropathogenic E. coli. Our data permitted a sum-of-all-the-parts analysis. Electron microscopy revealed supramolecular shell-like structures that encapsulated single cells and enmeshed the bacterial community. Biochemical and solid-state NMR measurements of the matrix and constitutive parts established that the matrix is composed of two major components, curli and cellulose, each in a quantifiable amount. This approach to quantifying the matrix composition is widely applicable to other organisms and to examining the influence of biofilm inhibitors. Collectively, our NMR spectra and the electron micrographs of the purified ECM inspire us to consider the biofilm matrix not as an undefined slime, but as an assembly of polymers with a defined composition and architecture.     

Fish with Chips: Tracking Reef Fish Movements to Evaluate Size and Connectivity of Caribbean Marine Protected Areas

Coral reefs and associated fish populations have experienced rapid decline in the Caribbean region and marine protected areas (MPAs) have been widely implemented to address this decline. The performance of no-take MPAs (i.e., marine reserves) for protecting and rebuilding fish populations is influenced by the movement of animals within and across their boundaries. Very little is known about Caribbean reef fish movements creating a critical knowledge gap that can impede effective MPA design, performance and evaluation. Using miniature implanted acoustic transmitters and a fixed acoustic receiver array, we address three key questions: How far can reef fish move? Does connectivity exist between adjacent MPAs? Does existing MPA size match the spatial scale of reef fish movements? We show that many reef fishes are capable of traveling far greater distances and in shorter duration than was previously known. Across the Puerto Rican Shelf, more than half of our 163 tagged fish (18 species of 10 families) moved distances greater than 1 km with three fish moving more than 10 km in a single day and a quarter spending time outside of MPAs. We provide direct evidence of ecological connectivity across a network of MPAs, including estimated movements of more than 40 km connecting a nearshore MPA with a shelf-edge spawning aggregation. Most tagged fish showed high fidelity to MPAs, but also spent time outside MPAs, potentially contributing to spillover. Three-quarters of our fish were capable of traveling distances that would take them beyond the protection offered by at least 40–64% of the existing eastern Caribbean MPAs. We recommend that key species movement patterns be used to inform and evaluate MPA functionality and design, particularly size and shape. A re-scaling of our perception of Caribbean reef fish mobility and habitat use is imperative, with important implications for ecology and management effectiveness.