Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement

BACKGROUND: Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used to classify the same set of entities and methods allowing the comparison of the performance of two data sources or the determination of how well a given classification agrees with another are frequently needed, especially in the absence of a universally accepted "gold standard" classification. RESULTS: Here, we describe a novel measure – the Ranked Adjusted Rand (RAR) index. RAR differs from existing methods by evaluating the extent of agreement between any two groupings, taking into account the intercluster distances. This characteristic is relevant to evaluate cases of pairs of entities grouped in the same cluster by one method and separated by another. The latter method may assign them to close neighbour clusters or, on the contrary, to clusters that are far apart from each other. RAR is applicable even when intercluster distance information is absent for both or one of the groupings. In the first case, RAR is equal to its predecessor, Adjusted Rand (HA) index. Artificially designed clusterings were used to demonstrate situations in which only RAR was able to detect differences in the grouping patterns. A study with larger simulated clusterings ensured that in realistic conditions, RAR is effectively integrating distance and partition information. The new method was applied to biological examples to compare 1) two microbial typing methods, 2) two gene regulatory network distances and 3) microarray gene expression data with pathway information. In the first application, one of the methods does not provide intercluster distances while the other originated a hierarchical clustering. RAR proved to be more sensitive than HA in the choice of a threshold for defining clusters in the hierarchical method that maximizes agreement between the results of both methods. CONCLUSION: RAR has its major advantage in combining cluster distance and partition information, while the previously available methods used only the latter. RAR should be used in the research problems were HA was previously used, because in the absence of inter cluster distance effects it is an equally effective measure, and in the presence of distance effects it is a more complete one

Resonant nonlinear magneto-optical effects in atoms

In this article, we review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. We begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances, and contrast these effects with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultra-narrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.Comment: 51 pages, 23 figures, to appear in Rev. Mod. Phys. in Oct. 2002, Figure added, typos corrected, text edited for clarit

Coercivity enhancement in exchange biased systems driven by interfacial magnetic frustration

We report the temperature and cooling field dependence of the coercivity of exchange biased MnF2/Fe bilayers. When the antiferromagnetic surface is in a state of maximum magnetic frustration and the net exchange bias is zero, we observe a strong enhancement of the coercivity, which is proportional to the exchange coupling between the layers. Hence, the coercivity can be tuned in a reproducible and repeatable fashion in the same sample. We propose that a frustrated interface provides local energy minima which effectively pin the propagating domain walls in the ferromagnet, leading to an enhanced coercivity

Study of the relative humidity dependence of aerosol light-scattering in southern Spain

This investigation focuses on the characterisation of the aerosol particle hygroscopicity. Aerosol particle optical properties were measured at Granada, Spain, during winter and spring seasons in 2013. Measured optical properties included particle light-absorption coefficient (sap) and particle light-scattering coefficient (ssp) at dry conditions and at relative humidity (RH) of 85 +/- 10%. The scattering enhancement factor, f(RH=85%), had a mean value of 1.5 +/- 0.2 and 1.6 +/- 0.3 for winter and spring campaigns, respectively. Cases of high scattering enhancement were more frequent during the spring campaign with 27% of the f(RH=85%) values above 1.8, while during the winter campaign only 8% of the data were above 1.8. A Saharan dust event (SDE), which occurred during the spring campaign, was characterised by a predominance of large particles with low hygroscopicity. For the day when the SDE was more intense, a mean daily value of f(RH=85%)=1.3 +/- 0.2 was calculated. f(RH=85%) diurnal cycle showed two minima during the morning and afternoon traffic rush hours due to the increase in non-hygroscopic particles such as black carbon and road dust. This was confirmed by small values of the single-scattering albedo and the scattering Angstrom exponent. A significant correlation between f(RH=85%) and the fraction of particulate organic matter and sulphate was obtained. Finally, the impact of ambient RH in the aerosol radiative forcing was found to be very small due to the low ambient RH. For high RH values, the hygroscopic effect should be taken into account since the aerosol forcing efficiency changed from -13W/m2 at dry conditions to -17W/m2 at RH=85%.This work was supported by the Andalusia Regional Government through projects P10-RNM-6299 and P12-RNM-2409; by the Spanish Ministry of Economy and Competitiveness through projects CGL2010-18782, CSD2007-00067, CGL2011-13580-E/CLI and CGL2011-16124-E; and by EU through ACTRIS project (EU INFRA-2010-1.1.16-262254).G. Titos was funded by the program FPI of the Spanish Ministry of Economy and Competitiveness – Secretariat of Science, Innovation and Development under grant BES-2011-043721

Comparative assessment of phototherapy protocols for reduction of oxidative stress in partially transected spinal cord slices undergoing secondary degeneration

Background: Red/near-infrared light therapy (R/NIR-LT) has been developed as a treatment for a range of conditions, including injury to the central nervous system (CNS). However, clinical trials have reported variable or sub-optimal outcomes, possibly because there are few optimized treatment protocols for the different target tissues. Moreover, the low absolute, and wavelength dependent, transmission of light by tissues overlying the target site make accurate dosing problematic. Results: In order to optimize light therapy treatment parameters, we adapted a mouse spinal cord organotypic culture model to the rat, and characterized myelination and oxidative stress following a partial transection injury. The ex vivo model allows a more accurate assessment of the relative effect of different illumination wavelengths (adjusted for equal quantal intensity) on the target tissue. Using this model, we assessed oxidative stress following treatment with four different wavelengths of light: 450 nm (blue); 510 nm (green); 660 nm (red) or 860 nm (infrared) at three different intensities: 1.93 × 10¹⁶ (low); 3.85 × 10¹⁶ (intermediate) and 7.70 × 10¹⁶ (high) photons/cm²/s. We demonstrate that the most effective of the tested wavelengths to reduce immunoreactivity of the oxidative stress indicator 3-nitrotyrosine (3NT) was 660 nm. 860 nm also provided beneficial effects at all tested intensities, significantly reducing oxidative stress levels relative to control (p ≤ 0.05). Conclusions: Our results indicate that R/NIR-LT is an effective antioxidant therapy, and indicate that effective wavelengths and ranges of intensities of treatment can be adapted for a variety of CNS injuries and conditions, depending upon the transmission properties of the tissue to be treated.12 page(s

Tracking the spatial diffusion of influenza and norovirus using telehealth data: A spatiotemporal analysis of syndromic data

Background: Telehealth systems have a large potential for informing public health authorities in an early stage of outbreaks of communicable disease. Influenza and norovirus are common viruses that cause significant respiratory and gastrointestinal disease worldwide. Data about these viruses are not routinely mapped for surveillance purposes in the UK, so the spatial diffusion of national outbreaks and epidemics is not known as such incidents occur. We aim to describe the geographical origin and diffusion of rises in fever and vomiting calls to a national telehealth system, and consider the usefulness of these findings for influenza and norovirus surveillance. Methods: Data about fever calls (5- to 14-year-old age group) and vomiting calls (≥ 5-year-old age group) in school-age children, proxies for influenza and norovirus, respectively, were extracted from the NHS Direct national telehealth database for the period June 2005 to May 2006. The SaTScan space-time permutation model was used to retrospectively detect statistically significant clusters of calls on a week-by-week basis. These syndromic results were validated against existing laboratory and clinical surveillance data. Results: We identified two distinct periods of elevated fever calls. The first originated in the North-West of England during November 2005 and spread in a south-east direction, the second began in Central England during January 2006 and moved southwards. The timing, geographical location, and age structure of these rises in fever calls were similar to a national influenza B outbreak that occurred during winter 2005–2006. We also identified significantly elevated levels of vomiting calls in South-East England during winter 2005–2006. Conclusion: Spatiotemporal analyses of telehealth data, specifically fever calls, provided a timely and unique description of the evolution of a national influenza outbreak. In a similar way the tool may be useful for tracking norovirus, although the lack of consistent comparison data makes this more difficult to assess. In interpreting these results, care must be taken to consider other infectious and non-infectious causes of fever and vomiting. The scan statistic should be considered for spatial analyses of telehealth data elsewhere and will be used to initiate prospective geographical surveillance of influenza in England.

Reduction in biomass burning aerosol light absorption upon humidification: roles of inorganically-induced hygroscopicity, particle collapse, and photoacoustic heat and mass transfer

Smoke particle emissions from the combustion of biomass fuels typical for the western and southeastern United States were studied and compared under high humidity and ambient conditions in the laboratory. The fuels used were Montana ponderosa pine (<i>Pinus ponderosa</i>), southern California chamise (<i>Adenostoma fasciculatum</i>), and Florida saw palmetto (<i>Serenoa repens</i>). Information on the non-refractory chemical composition of biomass burning aerosol from each fuel was obtained with an aerosol mass spectrometer and through estimation of the black carbon concentration from light absorption measurements at 870 nm. Changes in the optical and physical particle properties under high humidity conditions were observed for hygroscopic smoke particles containing substantial inorganic mass fractions that were emitted from combustion of chamise and palmetto fuels. Light scattering cross sections increased under high humidity for these particles, consistent with the hygroscopic growth measured for 100 nm particles in HTDMA measurements. Photoacoustic measurements of aerosol light absorption coefficients revealed a 20% reduction with increasing relative humidity, contrary to the expectation of light absorption enhancement by the liquid coating taken up by hygroscopic particles. This reduction is hypothesized to arise from two mechanisms: (1) shielding of inner monomers after particle consolidation or collapse with water uptake; (2) the lower case contribution of mass transfer through evaporation and condensation at high relative humidity (RH) to the usual heat transfer pathway for energy release by laser-heated particles in the photoacoustic measurement of aerosol light absorption. The mass transfer contribution is used to evaluate the fraction of aerosol surface covered with liquid water solution as a function of RH

Cork : properties, capabilities and applications

Cork is a natural, renewable, sustainable raw material that has been used for many centuries. As a result of this very long term interest, the scientific literature on cork is extensive. The present review focuses on the chemical composition, physical and mechanical properties of cork and on its products and sub-products. The substantial efforts to fully characterise cork, as well as new developments and evolving research, are reviewed, beginning with its histology, growth and morphology (at macro- and microscales). The chemical structure is analysed in detail, covering both the materials that form the wall structure and the low molecular weight, extractable components. The unique properties of cork are discussed and correlated with current knowledge on morphology and chemical structure. Finally, the important industrial applications of cork are reviewed, in the context of research to provide cork with novel, high added-value applications