Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches

We investigate the accuracy of different similarity approaches for clustering over two million biomedical documents. Clustering large sets of text documents is important for a variety of information needs and applications such as collection management and navigation, summary and analysis. The few comparisons of clustering results from different similarity approaches have focused on small literature sets and have given conflicting results. Our study was designed to seek a robust answer to the question of which similarity approach would generate the most coherent clusters of a biomedical literature set of over two million documents.We used a corpus of 2.15 million recent (2004-2008) records from MEDLINE, and generated nine different document-document similarity matrices from information extracted from their bibliographic records, including titles, abstracts and subject headings. The nine approaches were comprised of five different analytical techniques with two data sources. The five analytical techniques are cosine similarity using term frequency-inverse document frequency vectors (tf-idf cosine), latent semantic analysis (LSA), topic modeling, and two Poisson-based language models--BM25 and PMRA (PubMed Related Articles). The two data sources were a) MeSH subject headings, and b) words from titles and abstracts. Each similarity matrix was filtered to keep the top-n highest similarities per document and then clustered using a combination of graph layout and average-link clustering. Cluster results from the nine similarity approaches were compared using (1) within-cluster textual coherence based on the Jensen-Shannon divergence, and (2) two concentration measures based on grant-to-article linkages indexed in MEDLINE.PubMed's own related article approach (PMRA) generated the most coherent and most concentrated cluster solution of the nine text-based similarity approaches tested, followed closely by the BM25 approach using titles and abstracts. Approaches using only MeSH subject headings were not competitive with those based on titles and abstracts

Bladder inflammatory transcriptome in response to tachykinins: Neurokinin 1 receptor-dependent genes and transcription regulatory elements

Background Tachykinins (TK), such as substance P, and their neurokinin receptors which are ubiquitously expressed in the human urinary tract, represent an endogenous system regulating bladder inflammatory, immune responses, and visceral hypersensitivity. Increasing evidence correlates alterations in the TK system with urinary tract diseases such as neurogenic bladders, outflow obstruction, idiopathic detrusor instability, and interstitial cystitis. However, despite promising effects in animal models, there seems to be no published clinical study showing that NK-receptor antagonists are an effective treatment of pain in general or urinary tract disorders, such as detrusor overactivity. In order to search for therapeutic targets that could block the tachykinin system, we set forth to determine the regulatory network downstream of NK1 receptor activation. First, NK1R-dependent transcripts were determined and used to query known databases for their respective transcription regulatory elements (TREs). Methods: An expression analysis was performed using urinary bladders isolated from sensitized wild type (WT) and NK1R-/- mice that were stimulated with saline, LPS, or antigen to provoke inflammation. Based on cDNA array results, NK1R-dependent genes were selected. PAINT software was used to query TRANSFAC database and to retrieve upstream TREs that were confirmed by electrophoretic mobility shift assays. Results: The regulatory network of TREs driving NK1R-dependent genes presented cRel in a central position driving 22% of all genes, followed by AP-1, NF-kappaB, v-Myb, CRE-BP1/c-Jun, USF, Pax-6, Efr-1, Egr-3, and AREB6. A comparison between NK1R-dependent and NK1R-independent genes revealed Nkx-2.5 as a unique discriminator. In the presence of NK1R, Nkx2-5 _01 was significantly correlated with 36 transcripts which included several candidates for mediating bladder development (FGF) and inflammation (PAR-3, IL-1R, IL-6, α-NGF, TSP2). In the absence of NK1R, the matrix Nkx2-5_02 had a predominant participation driving 8 transcripts, which includes those involved in cancer (EYA1, Trail, HSF1, and ELK-1), smooth-to-skeletal muscle trans-differentiation, and Z01, a tight-junction protein, expression. Electrophoretic mobility shift assays confirmed that, in the mouse urinary bladder, activation of NK1R by substance P (SP) induces both NKx-2.5 and NF-kappaB translocations. Conclusion: This is the first report describing a role for Nkx2.5 in the urinary tract. As Nkx2.5 is the unique discriminator of NK1R-modulated inflammation, it can be imagined that in the near future, new based therapies selective for controlling Nkx2.5 activity in the urinary tract may be used in the treatment in a number of bladder disorders

Evaluation of thermal perception in schoolyards under Mediterranean climate conditions

The aim of this paper was to study qualitatively and quantitatively the thermal perception and corresponding heat stress conditions that prevail in two schoolyards in a coastal city in central Greece. For this purpose, meteorological parameters (i.e., wind speed, temperature, relative humidity, solar radiation) were recorded at 70 and 55 measuring points in the schoolyards, from 14:00 to 15:30 local time, during May and June of 2011. The measuring points were distributed so as to get measurements at points (a) directly exposed to the sun, (b) under the shadow of trees and building structures, and (c) near building structures. Cluster analysis was applied to group observations and revealed places that are microclimatically homogeneous. Thermal perception and heat stress conditions were assessed by means of the physiologically equivalent temperature (PET, °C), and the results are presented in relevant charts. The impact of material’s albedo, radiation’s reflection by structures and obstacles, and different tree species on thermal perception and heat stress conditions was also assessed. The analysis showed that trees triggered a reduction of incident solar radiation that ranged between 79 and 94 % depending on tree’s species, crown dimension, tree height, and leaf area. PET values were mainly affected by solar radiation and wind speed. Trees caused a reduction of up to 37 % in PET values, while a 1-m s−1 increase in wind speed triggered a reduction of 3.7–5.0 °C in PET value. The effective shading area in the two schoolyards was small, being 27.5 and 11 %. The results of this study could be exploited by urban planning managers when designing or improving the outdoor environment of a school complex. © 2015 IS

Unravelling institutional determinants affecting change in agriculture in West Africa

This paper compares lessons learned from nine studies that explored institutional determinants of innovation towards sustainable intensification of West African agriculture. The studies investigated issues relating to crop, animal, and resources management in Benin, Ghana, and Mali. The constraints addressed were agronomic or economic (e.g. low production, yield, quality, prices) and institutional (e.g. poor access to resources and constraining regulations) and were analysed using an array of research approaches. The studies showed that political ambitions to foster institutional change were often high (restoring the Beninese cotton sector and protecting Ghanaian farmers against fluctuating cocoa prices) and that the institutional change achieved was often remarkable. However, flexibility of institutions, co-evolution of technical and institutional change, and increased transparency are needed to make institutional change successful. The programme Convergence of Sciences – Strengthening Agricultural Innovation Systems encouraged interventions where needed and enabled researchers and stakeholders to acquire the change capacities required to identify the need and potential for change and to make change happen. More research is needed to design pathways towards sustainable intensification based on social and technological innovation. Policy-makers should create space for institutional experimentation and empower smallholder farmers in West Africa to create resilient, local food systems to feed burgeoning urban populations