Scanner calibration revisited

<p>Abstract</p> <p>Background</p> <p>Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (<it>BMC Bioinformatics</it>, 2005, <b>6</b>, Art. No. S11 Suppl. 2.) reported usage of a Full Moon BioSystems slide for calibration. Inspired by the Shi et al. work, we have calibrated microarray scanners in our previous research. We were puzzled however, that most of the signal intensities from a biological sample fell below the sensitivity threshold level determined by the calibration slide. This conundrum led us to re-investigate the quality of calibration provided by the Full Moon BioSystems slide as well as the accuracy of the analysis performed by Shi et al.</p> <p>Methods</p> <p>Signal intensities were recorded on three different microarray scanners at various photomultiplier gain levels using the same calibration slide from Full Moon BioSystems. Data analysis was conducted on raw signal intensities without normalization or transformation of any kind. Weighted least-squares method was used to fit the data.</p> <p>Results</p> <p>We found that initial analysis performed by Shi et al. did not take into account autofluorescence of the Full Moon BioSystems slide, which led to a grossly distorted microarray scanner response. Our analysis revealed that a power-law function, which is explicitly accounting for the slide autofluorescence, perfectly described a relationship between signal intensities and fluorophore quantities.</p> <p>Conclusions</p> <p>Microarray scanners respond in a much less distorted fashion than was reported by Shi et al. Full Moon BioSystems calibration slides are inadequate for performing calibration. We recommend against using these slides.</p

Abundance and local-scale processes contribute to multi-phyla gradients in global marine diversity

Among themost enduring ecological challenges is an integrated theory explaining the latitudinal biodiversity gradient, including discrepancies observed at different spatial scales. Analysis of Reef Life Survey data for 4127 marine species at 2406 coral and rocky sites worldwide confirms that the total ecoregion richness peaks in low latitudes, near +15 degrees N and -15 degrees S. However, although richness at survey sites is maximal near the equator for vertebrates, it peaks at high latitudes for large mobile invertebrates. Site richness for different groups is dependent on abundance, which is in turn correlated with temperature for fishes and nutrients for macroinvertebrates. We suggest that temperature-mediated fish predation and herbivory have constrained mobile macroinvertebrate diversity at the site scale across the tropics. Conversely, at the ecoregion scale, richness responds positively to coral reef area, highlighting potentially huge global biodiversity losses with coral decline. Improved conservation outcomes require management frameworks, informed by hierarchical monitoring, that cover differing site- and regional-scale processes across diverse taxa, including attention to invertebrate species, which appear disproportionately threatened by warming seas

Bilateral gluteal abscesses and myofibrosis complicating intramuscular pentazocine abuse: a case report

BACKGROUND: There is paucity of reports on the musculoskeletal complications of pentazocine abuse in Nigeria.The aim was to report a case of bilateral gluteal abscesses and myofibrosis as a consequence of parenteral pentazocine abuse.CASE SUMMARY: We report a case of a 39 year old housewife who presented with bilateral gluteal pyomyositis and myofibrosis following intramuscular pentazocine abuse.The patient had received parental pentazocine for pain relief for about 3 weeks seven years ago.She gradually developed dependence on this drug and received increasing doses of this drug by self injection on both buttocks. She subsequently developed bilateral gluteal abscesses and myofibrosis that was treated by surgical drainage,debridement,wound dressing and antibiotics.CONCLUSION: Pentazocine abuse should be considered a differential diagnosis in cases of multiple gluteal abscesses.Clinicians should be cautious in the use of pentazocine as routine painkillers.KEYWORDS: Pentazocine abuse,gluteal abscesses,Nigeria

Engaging Diverse Students in Statistical Inquiry: A Comparison of Learning Experiences and Outcomes of Under-Represented and Non-Underrepresented Students Enrolled in a Multidisciplinary Project-Based Statistics Course

Introductory statistics needs innovative, evidence-based teaching practices that support and engage diverse students. To evaluate the success of a multidisciplinary, project-based course, we compared experiences of under-represented (URM) and non-underrepresented students in 4 years of the course. While URM students considered the material more difficult than non-URM students, URM students demonstrated similar levels of increased confidence in applied skills and interest in follow up courses as non-URM students. URM students were found to be twice as likely as non-URM students to report that their interest in conducting research increased. Increasing student confidence and interest gives all students a welcoming place at the table that will afford the best hope for achieving the kind of statistical literacy necessary for interdisciplinary research

Chromatic sensitivity of neurones in area MT of the anaesthetised macaque monkey compared to human motion perception

Abstract We recorded activity from neurones in cortical motion-processing areas, middle temporal area (MT) and middle posterior superior temporal sulcus (MST), of anaesthetised and paralysed macaque monkeys in response to moving sinewave gratings modulated in luminance and chrominance. The activity of MT and MST neurones was highly dependent on luminance contrast. In three of four animals isoluminant chromatic modulations failed to activate MT/MST neurones significantly. At low luminance contrast a systematic dependence on chromaticity was revealed, attributable mostly to residual activity of the magnocellular pathway. Additionally, we found indications for a weak Scone input, but rod intrusion could also have made a contribution. In contrast to the activity of MT and MST neurones, speed judgments and onset amplitude of evoked optokinetic eye movements in human subjects confronted with equivalent visual stimuli were largely independent of luminance modulation. Motion of every grating (including isoluminant) was readily visible for all but one observer. Similarity with the activity of MT/ MST cells was found only for motion-nulling equivalent luminance contrast judgments at isoluminance. Our results suggest that areas MT and MST may not be involved in the processing of chromatic motion, but effects of central anaesthesia and/or the existence of intra-and inter-species differences must also be considered

The anti-fibrotic effect of inhibition of TGFβ-ALK5 signalling in experimental pulmonary fibrosis in mice is attenuated in the presence of concurrent γ-herpesvirus infection.

Journal ArticleTGFβ-ALK5 pro-fibrotic signalling and herpesvirus infections have been implicated in the pathogenesis and exacerbation of pulmonary fibrosis. In this study we addressed the role of TGFβ-ALK5 signalling during the progression of fibrosis in a two-hit mouse model of murine γ-herpesvirus 68 (MHV-68) infection on the background of pre-existing bleomycin-induced pulmonary fibrosis. Assessment of total lung collagen levels in combination with ex vivo micro-computed tomography (µCT) analysis of whole lungs demonstrated that MHV-68 infection did not enhance lung collagen deposition in this two-hit model but led to a persistent and exacerbated inflammatory response. Moreover, µCT reconstruction and analysis of the two-hit model revealed distinguishing features of diffuse ground-glass opacities and consolidation superimposed on pre-existing fibrosis that were reminiscent of those observed in acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF). Virally-infected murine fibrotic lungs further displayed evidence of extensive inflammatory cell infiltration and increased levels of CCL2, TNFα, IL-1β and IL-10. Blockade of TGFβ-ALK5 signalling attenuated lung collagen accumulation in bleomycin-alone injured mice, but this anti-fibrotic effect was reduced in the presence of concomitant viral infection. In contrast, inhibition of TGFβ-ALK5 signalling in virally-infected fibrotic lungs was associated with reduced inflammatory cell aggregates and increased levels of the antiviral cytokine IFNγ. These data reveal newly identified intricacies for the TGFβ-ALK5 signalling axis in experimental lung fibrosis, with different outcomes in response to ALK5 inhibition depending on the presence of viral infection. These findings raise important considerations for the targeting of TGFβ signalling responses in the context of pulmonary fibrosis.MRCNovartis CASE studentshi

Rapid turnover of tissue nitrogen of primary consumers in tropical freshwaters

Abstract Stable isotopes are widely used as time-integrating tracers of trophic interactions, but turnover rates of isotopes in animal tissues remain poorly understood. Here, we report nitrogen (N) isotope turnover rates in tissues of four primary consumer species: Ancistrus triradiatus armored catfish (muscle, fins, and whole blood), Tarebia granifera snails (muscle), and Rana palmipes tadpoles (muscle) from a Venezuelan river, and Lavigeria grandis snails (muscle) from Lake Tanganyika, East Africa. Turnover was estimated from the dilution of a 15 N label introduced into consumer tissues by feeding on 15 N-enriched periphyton. Muscle turnover rates were rapid (0.5-3.8% per day), and were attributable to metabolic replacement of N as well as growth in catfish and snails. N turnover in catfish muscle decreased with size, and fin tissue turned over more rapidly than whole blood or muscle, though the difference was not significant. Our results indicate that stable isotope signatures of these tropical species could change markedly within weeks following a shift in diet. However, generalization across taxa or latitudes is complicated by the strong sizedependence of isotope turnover rates. The enrichmentdilution approach outlined here may facilitate measurement of isotopic turnover in a wide variety of consumers under field conditions

Inside-Out Evacuation of Transitional Protoplanetary Disks by the Magneto-Rotational Instability

How do T Tauri disks accrete? The magneto-rotational instability (MRI) supplies one means, but protoplanetary disk gas is typically too poorly ionized to be magnetically active. Here we show that the MRI can, in fact, explain observed accretion rates for the sub-class of T Tauri disks known as transitional systems. Transitional disks are swept clean of dust inside rim radii of ~10 AU. Stellar coronal X-rays ionize material in the disk rim, activating the MRI there. Gas flows from the rim to the star, at a rate limited by the depth to which X-rays ionize the rim wall. The wider the rim, the larger the surface area that the rim wall exposes to X-rays, and the greater the accretion rate. Interior to the rim, the MRI continues to transport gas; the MRI is sustained even at the disk midplane by super-keV X-rays that Compton scatter down from the disk surface. Accretion is therefore steady inside the rim. Blown out by radiation pressure, dust largely fails to accrete with gas. Contrary to what is usually assumed, ambipolar diffusion, not Ohmic dissipation, limits how much gas is MRI-active. We infer values for the transport parameter alpha on the order of 0.01 for GM Aur, TW Hyd, and DM Tau. Because the MRI can only afflict a finite radial column of gas at the rim, disk properties inside the rim are insensitive to those outside. Thus our picture provides one robust setting for planet-disk interaction: a protoplanet interior to the rim will interact with gas whose density, temperature, and transport properties are definite and decoupled from uncertain initial conditions. Our study also supplies half the answer to how disks dissipate: the inner disk drains from the inside out by the MRI, while the outer disk photoevaporates by stellar ultraviolet radiation.Comment: Accepted to Nature Physics June 7, 2007. The manuscript for publication is embargoed per Nature policy. This arxiv.org version contains more technical details and discussion, and is distributed with permission from the editors. 10 pages, 4 figure

Enhanced clay formation key in sustaining the Middle Eocene Climatic Optimum

The Middle Eocene Climatic Optimum (around 40 million years ago) was a roughly 400,000-year-long global warming phase associated with an increase in atmospheric CO2 concentrations and deep-ocean acidifcation that interrupted the Eocene’s long-term cooling trend. The unusually long duration, compared with early Eocene global warming phases, is puzzling as temperature-dependent silicate weathering should have provided a negative feedback, drawing down CO2 over this timescale. Here we investigate silicate weathering during this climate warming event by measuring lithium isotope ratios (reported as δ7 Li), which are a tracer for silicate weathering processes, from a suite of open-ocean carbonate-rich sediments. We fnd a positive δ7 Li excursion—the only one identifed for a warming event so far —of ~3‰. Box model simulations support this signal to refect a global shift from congruent weathering, with secondary mineral dissolution, to incongruent weathering, with secondary mineral formation. We surmise that, before the climatic optimum, there was considerable soil shielding of the continents. An increase in continental volcanism initiated the warming event, but it was sustained by an increase in clay formation, which sequestered carbonate-forming cations, short-circuiting the carbonate–silicate cycle. Clay mineral dynamics may play an important role in the carbon cycle for climatic events occurring over intermediate (i.e., 100,000 year) timeframes