Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease.

PurposeAlterations in the urinary microbiome have been associated with urological diseases. The microbiome of patients with urethral stricture disease (USD) remains unknown. Our objective is to examine the microbiome of USD with a focus on inflammatory USD caused by lichen sclerosus (LS).MethodsWe collected mid-stream urine samples from men with LS-USD (cases; n = 22) and non-LS USD (controls; n = 76). DNA extraction, PCR amplification of the V4 hypervariable region of the 16S rRNA gene, and sequencing was done on the samples. Operational taxonomic units (OTUs) were defined using a > 97% sequence similarity threshold. Alpha diversity measurements of diversity, including microbiome richness (number of different OTUs) and evenness (distribution of OTUs) were calculated and compared. Microbiome beta diversity (difference between microbial communities) relationships with cases and controls were also assessed.ResultsFifty specimens (13 cases and 37 controls) produced a 16S rRNA amplicon. Mean sample richness was 25.9 vs. 16.8 (p = 0.076) for LS-USD vs. non-LS USD, respectively. LS-USD had a unique profile of bacteria by taxonomic order including Bacillales, Bacteroidales and Pasteurellales enriched urine. The beta variation of observed bacterial communities was best explained by the richness.ConclusionsMen with LS-USD may have a unique microbiologic richness, specifically inclusive of Bacillales, Bacteroidales and Pasteurellales enriched urine compared to those with non-LS USD. Further work will be required to elucidate the clinical relevance of these variations in the urinary microbiome

Ecological specialization and rarity indices estimated for a large number of plant species in France

International audienceThe biological diversity of the Earth is being rapidly depleted due to the direct and indirect consequences of human activities. Specialist or rare species are generally thought to be more extinction prone than generalist or common species. Testing this assumption however requires that the rarity and ecological specialization of the species are quantified. Many indices have been developed to classify species as generalists vs. specialists or as rare vs. common, but large data sets are needed to calculate these indices. Here, we present a list of specialization and rarity values for more than 2800 plant species of continental France, which were computed from the large botanical and ecological dataset SOPHY. Three specialization indices were calculated using species co-occurrence data. All three indices are based on (dis)similarity among plant communities containing a focal species, quantified either as beta diversity in an additive (Fridley et al., 2007 [6]) or multiplicative (Zeleny, 2008 [15]) partitioning of diversity or as the multiple site similarity of Baselga et al. (2007) [1]. Species rarity was calculated as the inverse of a species occurrence

Customer Perceptions of Diversity in Health Services: How Other Customers’ Race Influences Customer Perceptions

Using the Similarity Attraction perspective, this study examines racial diversity in health services. An initial review of the literature summarizes currently known findings related to the effects of Other Customers on Customer experiences in healthcare service settings. Two experimental studies, adopting Byrne and Nelson’s (1965) Similarity-Attraction perspective, test the effects of Customer-Other Customer Race (Black vs. White) interaction on Revisit Intentions and Customer Perceived Anxiety. Results indicate that Perceived Anxiety is not reduced by Customer-Other Customer race match (i.e., Black and Black, or White and White), though Other Customer Race (Black vs. White) drives Perceived Anxiety. Customer-Other Customer Race Match was also found to reduce Expected Satisfaction in high Service Failure cases

Seedling Emergence from Seed Banks in Ludwigia hexapetala-Invaded Wetlands: Implications for Restoration

Soil seed banks play a critical role in the maintenance of wetland plant communities and contribute to revegetation following disturbances. Analysis of the seed bank can therefore inform restoration planning and management. Emergence from seed banks may vary in response to hydrologic conditions and sediment disturbances. To assess the community-level impact of exotic Ludwigia hexapetala on soil seed banks, we compared differences in species composition of standing vegetation among invaded and non-invaded wetlands and the degree of similarity between vegetation and soil seed banks in northern California. To determine potential seed bank recruitment of L. hexapetala and associated plant species, we conducted a seedling emergence assay in response to inundation regime (drawdown vs. flooded) and sediment depth (surface vs. buried). Plant species richness, evenness, and Shannon’s H’ diversity were substantially lower in standing vegetation at L. hexapetala invaded sites as compared to non-invaded sites. Over 12 months, 69 plant taxa germinated from the seed banks, including L. hexapetala and several other exotic taxa. Seedling density varied among sites, being the highest (10,500 seedlings m−2) in surface sediments from non-invaded sites subjected to drawdown treatments. These results signal the need for invasive plant management strategies to deplete undesirable seed banks for restoration success

Small- scale structure of infaunal polychaete communities in an estuarine environment: Methodological approach

12 páginas, 3 figuras, 2 tablasThis study compares different methods for the estimation of minimal areas (viz. species/area curves, diversity/area curves, similarity/area curves, variance/mean ratio vs. area curves) as community structure descriptions. The comparisons are based upon two polychaete taxocoenoses from muddy and sandy habitats, located in a semienclosed shallow-water Mediterranean bay (Alfacs Bay, Ebro Delta, NW Mediterranean).The mud community appeared to be very homogeneous, with very low diversity. This community displayed high structural simplicity (related to various stress factors), and therefore, qualifies as a physically controlled community). The diversity index was stabilized for areas of 37 cm2, quantitative similarity (Kulcznski index) was higher than 0·7 for areas of 90 cm2, and density of individuals was stabilized for areas of 120 cm2. Therefore, and area of 120 cm2 is suggested as being representative of the community structure. However, it was impossible to define a qualitatively adequate sampling area ( more than 300cm2). The sand community displayed hig structural complexity, with hig species richness and high diversity. This community was characterized by high environmental stability and high variability of microhabitats, as is frequent in biologically accomodated communities. Tne number of individuals became homogeneous for areas of 600-1000 cm2, diversity was stabilized around 300 cm2 and a Kulczynski similarity index of 0·7 was alredy attained at areas of 1000cm2. Thus, a quantitatively representative sampling area of between 700 and 1000 cm2 was suggested. Moreover, the more general pattern of species distribution (with an important set of common species) was directly related to the relatively low qualitative minimal area (400 cm2)Peer reviewe

Aquatic bacterial assemblage structure in Pozas Azules, Cuatro Cienegas Basin, Mexico: Deterministic vs. stochastic processes

The aim of this study was to determine the contributions of stochastic vs. deterministic processes in the distribution of microbial diversity in four ponds (Pozas Azules) within a temporally stable aquatic system in the Cuatro Cienegas Basin, State of Coahuila, Mexico. A sampling strategy for sites that were geographically delimited and had low environmental variation was applied to avoid obscuring distance effects. Aquatic bacterial diversity was characterized following a culture-independent approach (16S sequencing of clone libraries). The results showed a correlation between bacterial beta diversity (1-Sorensen) and geographic distance (distance decay of similarity), which indicated the influence of stochastic processes related to dispersion in the assembly of the ponds’ bacterial communities. Our findings are the first to show the influence of dispersal limitation in the prokaryotic diversity distribution of Cuatro Cienegas Basin. [Int Microbiol 2015; 18(2):105-115]Keywords: bacterial assemblage structure · bacterial diversity · biogeography · inland waters· Cuatro Cienegas, Mexic

Multiculturalism, Colorblindness, and Prejudice: Examining How Diversity Ideologies Impact Intergroup Attitudes

The present research examined an underlying psychological process of the effect of diversity ideologies on prejudice among Whites. In one study, I tested whether colorblindness vs. multiculturalism affected perceptions of similarity vs. difference, outgroup perspective taking, and, in turn, prejudice. Using an experimental design, 341 total White participants from both an undergraduate (n = 151) and non-student adult sample (n = 190) were randomly assigned to a standard colorblind or multicultural condition. Participants then completed various measures of perceived similarities vs. differences (visual, interpersonal), outgroup perspective taking (egocentrism, perspective-taking scenario), and prejudice (explicit racial bias, symbolic racism). Results suggest the diversity ideology manipulation only had a significant effect on the outgroup perspective-taking scenario, but the direction of this effect was contrary to hypotheses and previous findings. Compared to colorblindness, multiculturalism significantly reduced participants’ likelihood of taking the perspective of a racial outgroup member, with additional mediation evidence suggesting this effect on reduced outgroup perspective taking, in turn, indirectly increased explicit racial bias and symbolic racism. Alternative explanations and additional research considerations are discussed

Similarity-based virtual screening using 2D fingerprints

This paper summarises recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of similarity coefficients demonstrates that the well-known Tanimoto coefficient remains the method of choice for the computation of fingerprint-based similarity, despite possessing some inherent biases related to the sizes of the molecules that are being sought. Group fusion involves combining the results of similarity searches based on multiple reference structures and a single similarity measure. We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available

Using Generic Summarization to Improve Music Information Retrieval Tasks

In order to satisfy processing time constraints, many MIR tasks process only a segment of the whole music signal. This practice may lead to decreasing performance, since the most important information for the tasks may not be in those processed segments. In this paper, we leverage generic summarization algorithms, previously applied to text and speech summarization, to summarize items in music datasets. These algorithms build summaries, that are both concise and diverse, by selecting appropriate segments from the input signal which makes them good candidates to summarize music as well. We evaluate the summarization process on binary and multiclass music genre classification tasks, by comparing the performance obtained using summarized datasets against the performances obtained using continuous segments (which is the traditional method used for addressing the previously mentioned time constraints) and full songs of the same original dataset. We show that GRASSHOPPER, LexRank, LSA, MMR, and a Support Sets-based Centrality model improve classification performance when compared to selected 30-second baselines. We also show that summarized datasets lead to a classification performance whose difference is not statistically significant from using full songs. Furthermore, we make an argument stating the advantages of sharing summarized datasets for future MIR research.Comment: 24 pages, 10 tables; Submitted to IEEE/ACM Transactions on Audio, Speech and Language Processin

Ultra accurate collaborative information filtering via directed user similarity

A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random-walks proposed in the Ref.7, the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3\% and 19.1\% for MovieLens and Netflix respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.Comment: 6 pages, 4 figure