High prevalence of bronchiectasis is linked to HTLV-1-associated inflammatory disease.

BACKGROUND: Human T-lymphotropic virus type 1 (HTLV-1), a retrovirus, is the causative agent of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T-cell leukaemia/lymphoma (ATLL). The reported association with pulmonary disease such as bronchiectasis is less certain. METHODS: A retrospective case review of a HTLV-1 seropositive cohort attending a national referral centre. The cohort was categorised into HTLV-1 symptomatic patients (SPs) (ATLL, HAM/TSP, Strongyloidiasis and HTLV associated inflammatory disease (HAID)) and HTLV-1 asymptomatic carriers (ACs). The cohort was reviewed for diagnosis of bronchiectasis. RESULT: 34/246 ACs and 30/167 SPs had been investigated for respiratory symptoms by computer tomography (CT) with productive cough +/- recurrent chest infections the predominant indications. Bronchiectasis was diagnosed in one AC (1/246) and 13 SPs (2 HAID, 1 ATLL, 10 HAM/TSP) (13/167, RR 19.2 95 % CI 2.5-14.5, p = 0.004) with high resolution CT. In the multivariate analysis ethnicity (p = 0.02) and disease state (p < 0.001) were independent predictors for bronchiectasis. The relative risk of bronchiectasis in SPs was 19.2 (95 % CI 2.5-14.5, p = 0.004) and in HAM/TSP patients compared with all other categories 8.4 (95 % CI 2.7-26.1, p = 0.0002). Subjects not of African/Afro-Caribbean ethnicity had an increased prevalence of bronchiectasis (RR 3.45 95 % 1.2-9.7, p = 0.02). CONCLUSIONS: Bronchiectasis was common in the cohort (3.4 %). Risk factors were a prior diagnosis of HAM/TSP and ethnicity but not HTLV-1 viral load, age and gender. The spectrum of HTLV-associated disease should now include bronchiectasis and HTLV serology should be considered in patients with unexplained bronchiectasis

A New Soldier-Producing Aphid Species, Pseudoregma baenzigeri, sp. nov., from Northern Thailand

Pseudoregma baenzigeri, sp. nov., is described from northern Thailand. This species forms dense, huge colonies on shoots of the bamboo Dendrocalamus sp., and produces many first-instar, pseudoscorpion-like soldiers. Alate sexuparae were found from the end of September to mid October. Two syrphids, Eupeodes sp. A (allied to E. confrater) and Dideoides chrysotoxoides, and the pyralid Dipha aphidivora were recorded as predators of P. baenzigeri. The aphids were also likely to be eaten by some rodents. The apterous adult, nymphs, soldier and alate sexupara of P. baenzigeri can be distinguished from those of the other congeners by the longer, conical ultimate rostral segment. A tentative key to the species of Pseudoregma living on bamboo is provided

Pyrimidine biosynthesis is not an essential function for trypanosoma brucei bloodstream forms

&lt;p&gt;Background: African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host, but it is unknown whether either process is essential to the parasite.&lt;/p&gt; &lt;p&gt;Methodology/Principal Findings: Pyrimidine requirements for growth were investigated using strictly pyrimidine-free media, with or without single added pyrimidine sources. Growth rates of wild-type bloodstream form Trypanosoma brucei brucei were unchanged in pyrimidine-free medium. The essentiality of the de novo pyrimidine biosynthesis pathway was studied by knocking out the PYR6-5 locus that produces a fusion product of orotate phosphoribosyltransferase (OPRT) and Orotidine Monophosphate Decarboxylase (OMPDCase). The pyrimidine auxotroph was dependent on a suitable extracellular pyrimidine source. Pyrimidine starvation was rapidly lethal and non-reversible, causing incomplete DNA content in new cells. The phenotype could be rescued by addition of uracil; supplementation with uridine, 2′deoxyuridine, and cytidine allowed a diminished growth rate and density. PYR6-5−/− trypanosomes were more sensitive to pyrimidine antimetabolites and displayed increased uracil transport rates and uridine phosphorylase activity. Pyrimidine auxotrophs were able to infect mice although the infection developed much more slowly than infection with the parental, prototrophic trypanosome line.&lt;/p&gt; &lt;p&gt;Conclusions/Significance: Pyrimidine salvage was not an essential function for bloodstream T. b. brucei. However, trypanosomes lacking de novo pyrimidine biosynthesis are completely dependent on an extracellular pyrimidine source, strongly preferring uracil, and display reduced infectivity. As T. brucei are able to salvage sufficient pyrimidines from the host environment, the pyrimidine biosynthesis pathway is not a viable drug target, although any interruption of pyrimidine supply was lethal.&lt;/p&gt

Morphological Transformations in the Magnetite Biomineralizing Protein Mms6 in Iron Solutions: A Small-Angle X-ray Scattering Study

Magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence of hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures

When, where and how osteoporosis-associated fractures occur: An analysis from the global longitudinal study of osteoporosis in women (GLOW)

Objective: To examine when, where and how fractures occur in postmenopausal women. Methods: We analyzed data from the Global Longitudinal Study of Osteoporosis in Women (GLOW), including women aged ≥55 years from the United States of America, Canada, Australia and seven European countries. Women completed questionnaires including fracture data at baseline and years 1, 2 and 3. Results: Among 60,393 postmenopausal women, 4122 incident fractures were reported (86% non-hip, non-vertebral [NHNV], 8% presumably clinical vertebral and 6% hip). Hip fractures were more likely to occur in spring, with little seasonal variation for NHNV or spine fractures. Hip fractures occurred equally inside or outside the home, whereas 65% of NHNV fractures occurred outside and 61% of vertebral fractures occurred inside the home. Falls preceded 68-86% of NHNV and 68-83% of hip fractures among women aged ≤64 to ≥85 years, increasing with age. About 45% of vertebral fractures were associated with falls in all age groups except those ≥85 years, when only 24% occurred after falling. Conclusion: In this multi-national cohort, fractures occurred throughout the year, with only hip fracture having a seasonal variation, with a higher proportion in spring. Hip fractures occurred equally within and outside the home, spine fractures more often in the home, and NHNV fractures outside the home. Falls were a proximate cause of most hip and NHNV fractures. Postmenopausal women at risk for fracture need counseling about reducing potentially modifiable fracture risk factors, particularly falls both inside and outside the home and during all seasons of the year. © 2013 Costa et al

U.S. academic libraries: understanding their web presence and their relationship with economic indicators

The final publication is available at Springer via http://dx.doi.org/10.1007/s11192-013-1001-0The main goal of this research is to analyze the web structure and performance of units and services belonging to U.S. academic libraries in order to check their suitability for webometric studies. Our objectives include studying their possible correlation with economic data and assessing their use for complementary evaluation purposes. We conducted a survey of library homepages, institutional repositories, digital collections, and online catalogs (a total of 374 URLs) belonging to the 100 U.S. universities with the highest total expenditures in academic libraries according to data provided by the National Center for Education Statistics. Several data points were taken and analyzed, including web variables (page count, external links, and visits) and economic variables (total expenditures, expenditures on printed and electronic books, and physical visits). The results indicate that the variety of URL syntaxes is wide, diverse and complex, which produces a misrepresentation of academic libraries’ web resources and reduces the accuracy of web analysis. On the other hand, institutional and web data indicators are not highly correlated. Better results are obtained by correlating total library expenditures with URL mentions measured by Google (r = 0.546) and visits measured by Compete (r = 0.573), respectively. Because correlation values obtained are not highly significant, we estimate such correlations will increase if users can avoid linkage problems (due to the complexity of URLs) and gain direct access to log files (for more accurate data about visits).Orduña Malea, E.; Regazzi, JJ. (2014). U.S. academic libraries: understanding their web presence and their relationship with economic indicators. Scientometrics. 98(1):315-336. doi:10.1007/s11192-013-1001-0S315336981Adecannby, J. (2011). Web link analysis of interrelationship between top ten African universities and world universities. Annals of library and information studies, 58(2), 128–138.Aguillo, I. F. (2009). Measuring the institutions’ footprint in the web. Library Hi Tech, 27(4), 540–556.Aguillo, I. F., Ortega, J. L., & Fernández, M. (2008). Webometric Ranking of World Universities: Introduction, methodology, and future developments. Higher education in Europe, 33(2/3), 234–244.Aguillo, I. F., Ortega, J. L., Fernandez, M., & Utrilla, A. M. (2010). Indicators for a webometric ranking of open Access repositories. Scientometrics, 82(3), 477–486.Arakaki, M., & Willet, P. (2009). Webometric analysis of departments of librarianship and information science: A follow-up study. Journal of information science, 35(2), 143–152.Arlitsch, K., & O’Brian, P. S. (2012). Invisible institutional repositories: Addresing the low indexing ratios of IR in Google Scholar. Library Hi Tech, 30(1), 60–81.Bar-Ilan, J. (1999). Search engine results over time—A case study on search engine stability”. Cybermetrics, 2/3. Retrieved February 18, 2013 from http://www.cindoc.csic.es/cybermetrics/articles/v2i1p1.html.Bar-Ilan, J. (2001). Data collection methods on the Web for informetric purposes: A review and analysis. Scientometrics, 50(1), 7–32.Bermejo, F. (2007). The internet audience: Constitution & measurement. New York: Peter Lang Pub Incorporated.Buigues-Garcia, M., & Gimenez-Chornet, V. (2012). Impact of Web 2.0 on national libraries. International Journal of Information Management, 32(1), 3–10.Chu, H., He, S., & Thelwall, M. (2002). Library and information science schools in Canada and USA: A Webometric perspective. Journal of education for Library and Information Science, 43(2), 110–125.Chua, Alton, Y. K., & Goh, D. H. (2010). A study of Web 2.0 applications in library websites. Library and Information Science Research, 32(3), 203–211.Gallego, I., García, I.-M., & Rodríguez, L. (2009). Universities’ websites: Disclosure practices and the revelation of financial information. The International Journal of Digital Accounting Research, 9(15), 153–192.Gomes, B. & Smith, B. T. (2003). Detecting query-specific duplicate documents. [Patent]. Retrieved February 18, 2013 from http://www.patents.com/Detecting-query-specific-duplicate-documents/US6615209/en-US .Harinarayana, N. S., & Raju, N. V. (2010). Web 2.0 features in university library web sites. Electronic Library, 28(1), 69–88.Lewandowski, D., Wahlig, H., & Meyer-Bautor, G. (2006). The freshness of web search engine databases. Journal of Information Science, 32(2), 131–148.Mahmood, K., & Richardson, J. V, Jr. (2012). Adoption of Web 2.0 in US academic libraries: A survey of ARL library websites. Program, 45(4), 365–375.Orduña-Malea, E., & Ontalba-Ruipérez, J-A. (2012). Selective linking from social platforms to university websites: A case study of the Spanish academic system. Scientometrics. (in press).Ortega, J. L., & Aguillo, I. F. (2009). Mapping World-class universities on the Web. Information Processing and Management, 45(2), 272–279.Ortega, José L. & Aguillo, Isidro F. (2009b). North America Academic Web Space: Multicultural Canada vs. The United States Homogeneity. In: ASIST & ISSI pre-conference symposium on informetrics and scientometrics.Phan, T., Hardesty, L., Sheckells, C., & George, A. (2009). Documentation for the academic libraries survey (ALS) public-use data file: Fiscal year 2008. Washington DC: National Center for Education Statistics. Institute of Education Sciences U.S. Department of Education.Qiu, J., Cheng, J., & Wang, Z. (2004). An analysis of backlinks counts and web impact factors for Chinese university websites. Scientometrics, 60(3), 463–473.Regazzi, J. J. (2012a). Constrained?—An analysis of U.S. Academic Libraries and shifts in spending, staffing and utilization, 1998–2008. College and Research Libraries, 73(5), 449–468.Regazzi, J. J. (2012b). Comparing Academic Library Spending with Public Libraries, Public K-12 Schools, Higher Education Public Institutions, and Public Hospitals Between 1998–2008. Journal of Academic Librarianship, 38(4), 205–216.Rousseau, R. (1999). Daily time series of common single word searches in AltaVista and NorthernLight. Cybermetrics, 2/3. Retrieved February 18, 2013 from http://www.cindoc.csic.es/cybermetrics/articles/v2i1p2.html .Sato, S., & Itsumura, H. (2011). How do people use open access papers in non-academic activities? A link analysis of papers deposited in institutional repositories. Library, Information and Media Studies, 9(1), 51–64.Scholze, F. (2007). Measuring research impact in an open access environment. Liber Quarterly: The Journal of European Research Libraries, 17(1–4), 220–232.Smith, A. G. (2011). Wikipedia and institutional repositories: An academic symbiosis? In: Proceedings of the ISSI 2011 conference. Durban, South Africa, 4–7 July 2011. 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HMDB: a knowledgebase for the human metabolome

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users

Flow cytometry as a rapid analytical tool to determine physiological responses to changing O2 and iron concentration by Magnetospirillum gryphiswaldense strain MSR-1

Magnetotactic bacteria (MTB) are a diverse group of bacteria that synthesise magnetosomes, magnetic membrane-bound nanoparticles that have a variety of diagnostic, clinical and biotechnological applications. We present the development of rapid methods using flow cytometry to characterize several aspects of the physiology of the commonly-used MTB Magnetospirillum gryphiswaldense MSR-1. Flow cytometry is an optical technique that rapidly measures characteristics of individual bacteria within a culture, thereby allowing determination of population heterogeneity and also permitting direct analysis of bacteria. Scatter measurements were used to measure and compare bacterial size, shape and morphology. Membrane permeability and polarization were measured using the dyes propidium iodide and bis-(1,3-dibutylbarbituric acid) trimethine oxonol to determine the viability and ‘health’ of bacteria. Dyes were also used to determine changes in concentration of intracellular free iron and polyhydroxylakanoate (PHA), a bacterial energy storage polymer. These tools were then used to characterize the responses of MTB to different O2 concentrations and iron-sufficient or iron-limited growth. Rapid analysis of MTB physiology will allow development of bioprocesses for the production of magnetosomes, and will increase understanding of this fascinating and useful group of bacteria