Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments.

We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.

Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar.

The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions-content now foundational to the growing WeDigBio event.

Asymptotic confidence intervals for the Pearson correlation via skewness and kurtosis.

When bivariate normality is violated, the default confidence interval of the Pearson correlation can be inaccurate. Two new methods were developed based on the asymptotic sampling distribution of Fisher's z' under the general case where bivariate normality need not be assumed. In Monte Carlo simulations, the most successful of these methods relied on the (Vale & Maurelli, 1983, Psychometrika, 48, 465) family to approximate a distribution via the marginal skewness and kurtosis of the sample data. In Simulation 1, this method provided more accurate confidence intervals of the correlation in non-normal data, at least as compared to no adjustment of the Fisher z' interval, or to adjustment via the sample joint moments. In Simulation 2, this approximate distribution method performed favourably relative to common non-parametric bootstrap methods, but its performance was mixed relative to an observed imposed bootstrap and two other robust methods (PM1 and HC4). No method was completely satisfactory. An advantage of the approximate distribution method, though, is that it can be implemented even without access to raw data if sample skewness and kurtosis are reported, making the method particularly useful for meta-analysis. Supporting information includes R code.

Radiology examination as a diagnostic aid in presentations with wide differential diagnoses: Case report of new Hodgkin's lymphoma on a background of poorly controlled HIV.

Hodgkin's lymphoma and disseminated Mycobacterium avium complex (MAC) infection share similar clinical features; both may affect human immunodeficiency virus (HIV)-positive individuals. We discuss a patient with poorly controlled HIV-infection presenting with chest sepsis, dyspnoea and weight loss. Whilst the initial working diagnosis was that of MAC infection, pathology results had not met diagnostic criteria. Lymph node biopsy instead revealed classical Hodgkin's lymphoma. We discuss the role of radiological examination in cases of diagnostic uncertainty.

Pain relief by touch: a quantitative approach.

Pain relief by touch has been studied for decades in pain neuroscience. Human perceptual studies revealed analgesic effects of segmental tactile stimulation, as compared to extrasegmental touch. However, the spatial organisation of touch-pain interactions within a single human dermatome has not been investigated yet. In 2 experiments we tested whether, how, and where within a dermatome touch modulates the perception of laser-evoked pain. We measured pain perception using intensity ratings, qualitative descriptors, and signal detection measures of sensitivity and response bias. Touch concurrent with laser pulses produced a significant analgesia, and reduced the sensitivity in detecting the energy of laser stimulation, implying a functional loss of information within the ascending Aδ pathway. Touch also produced a bias to judge laser stimuli as less painful. This bias decreased linearly when the distance between the laser and tactile stimuli increased. Thus, our study provides evidence for a spatial organisation of intrasegmental touch-pain interactions.

Eutrophic lichens respond to multiple forms of N: implications for critical levels and critical loads research.

Epiphytic lichen communities are highly sensitive to excess nitrogen (N), which causes the replacement of native floras by N-tolerant, "weedy" eutrophic species. This shift is commonly used as the indicator of ecosystem "harm" in studies developing empirical critical levels (CLE) for ammonia (NH3) and critical loads (CLO) for N. To be most effective, empirical CLE and/or CLO must firmly link lichen response to causal pollutant(s), which is difficult to accomplish in field studies in part because the high cost of N measurements limits their use. For this case study we synthesized an unprecedented array of atmospheric N measurements across 22 long-term monitoring sites in the Los Angeles Basin, California, USA: gas concentrations of NH3, nitric acid (HNO3), nitrogen dioxide, and ozone (n = 10 sites); N deposition in throughfall (n = 8 sites); modeled estimates of eight different forms of N (n = 22 sites); and nitrate deposition accumulated on oak twigs (n = 22 sites). We sampled lichens on black oak (Quercus kelloggii Newb.), and scored plots using two indices of eutroph (N tolerant species) abundance to characterize the community-level response to N. Our results contradict two common assertions about the lichen-N response: (1) that eutrophs respond specifically to NH3 and (2) that the response necessarily depends upon the increased pH of lichen substrates. Eutroph abundance related significantly but weakly to NH3 (r2 = 0.48). Total N deposition as measured in canopy throughfall was by far the best predictor of eutroph abundance (r2 = 0.94), indicating that eutrophs respond to multiple forms of N. Most N variables had significant correlations to eutroph abundance (r2 = 0.36-0.62) as well as to each other (r2 = 0.61-0.98), demonstrating the risk of mistaken causality in CLE/CLO field studies that lack sufficient calibration data. Our data furthermore suggest that eutroph abundance is primarily driven by N inputs, not substrate pH, at least at the high-pH values found in the basin (4.8-6.1). Eutroph abundance correlated negatively with trunk bark pH (r2 = 0.43), exactly the opposite of virtually all previous studies of eutroph behavior. This correlation probably results because HNO3 dominates N deposition in our study region.

Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States.

Molecular methodologies were used to investigate fungal assemblages of biological soil crusts (BSCs) from arid lands in the southwestern United States. Fungal diversity of BSCs was assessed in a broad survey that included the Chihuahuan and Sonoran deserts as well as the Colorado Plateau. At selected sites samples were collected along kilometer-scale transects, and fungal community diversity and composition were assessed based on community rRNA gene fingerprinting using PCR-denaturing gradient gel electrophoresis (DGGE). Individual phylotypes were characterized through band sequencing. The results indicate that a considerable diversity of fungi is present within crusted soils, with higher diversity being recovered from more successionally mature BSCs. The overwhelming majority of crust fungi belong to the Ascomycota, with the Pleosporales being widespread and frequently dominant. Beta diversity patterns of phylotypes putatively representing dominant members of BSC fungal communities suggest that these assemblages are specific to their respective geographic regions of origin.

X-ray emission current scaling experiments for compact single-tungsten-wire arrays at 80-nanosecond implosion times.

We report the results of a series of current scaling experiments with the Z accelerator for the compact, single, 20-mm diameter, 10-mm long, tungsten-wire arrays employed for the double-ended hohlraum ICF concept [M. E. Cuneo, Plasma Phys. Controlled Fusion 48, R1 (2006)]. We measured the z -pinch peak radiated x-ray power and total radiated x-ray energy as a function of the peak current, at a constant implosion time tau_{imp}=80ns . Previous x-ray emission current scaling for these compact arrays was obtained at tau_{imp}=95ns in the work of Stygar [Phys. Rev. E 69, 046403 (2004)]. In the present study we utilized lighter single-tungsten-wire arrays. For all the measurements, the load hardware dimensions, materials, and array wire number (N=300) were kept constant and were the same as the previous study. We also kept the normalized load current spatial and temporal profiles the same for all experiments reported in this work. Two different currents, 11.2+/-0.2MA and 17.0+/-0.3MA , were driven through the wire arrays. The average peak x-ray power for these compact wire arrays increased by 26%+/-7%to158+/-26TW at 17+/-0.3MA from the 125+/-24TW obtained at a peak current of 18.8+/-0.5MA with tau_{imp}=95ns . The higher peak power of the faster implosions may possibly be attributed to a higher implosion velocity, which in turn improves the implosion stability, and/or to shorter wire ablation times, which may lead to a decrease in trailing mass and trailing current. Our results show that the scaling of the radiated x-ray peak power and total radiated x-ray energy scaling with peak drive current to be closer to quadratic than the results of Stygar We find that the x-ray peak radiated power is P_{r} proportional, variantI;{1.57+/-0.20} and the total x-ray radiated energy E_{r} proportional, variantI;{1.9+/-0.24} . We also find that the current scaling exponent of the power is sensitive to the inclusion of a single data point with a peak power at least 1.9sigma below the average. If we eliminate this particular shot from our analysis (shot 1608), the power and energy scaling becomes closer to quadratic. Namely, we find that the dependence on the peak load current of the peak x-ray radiated power and the total x-ray radiated energy become P_{r} proportional, variantI;{1.71+/-0.10} and E_{r} proportional, variantI;{2.01+/-0.21} , respectively. In this case, the power scaling exponent is different by more than 2sigma from the previously published results of Stygar Larger data sets are likely required to resolve this uncertainty and eliminate the sensitivity to statistical fluctuations in any future studies of this type. Nevertheless, with or without the inclusion of shot 1608, our results with tau_{imp}=80ns fall short of an I2 scaling of the peak x-ray radiated power by at least 2sigma . In either case, the results of our study are consistent with the heuristic wire ablation model proposed by Stygar (P_{r} proportional, variantI;{1.5}) . We also derive an empirical predictive relation that connects the power scaling exponent with certain array parameters.

Life in extreme environments: survival strategy of the endolithic desert lichen Verrucaria rubrocincta.

Verrucaria rubrocincta Breuss is an endolithic lichen that inhabits caliche plates exposed on the surface of the Sonoran Desert. Caliche surface temperatures are regularly in excess of 60 degrees C during the summer and approach 0 degrees C in the winter. Incident light intensities are high, with photosynthetically active radiation levels typically to 2,600 micromol/m(2) s(-1) during the summer. A cross-section of rock inhabited by V. rubrocincta shows an anatomical zonation comprising an upper micrite layer, a photobiont layer containing clusters of algal cells, and a pseudomedulla embedded in the caliche. Hyphae of the pseudomedulla become less numerous with depth below the rock surface. Stable carbon and oxygen isotopic data for the caliche and micrite fall into two sloping, well-separated arrays on a delta(13)C-delta(18)O plot. The delta(13)C(PDB) of the micrite ranges from 2.1 to 8.1 and delta(18)O(SMOW) from 25.4 to 28.9, whereas delta(13)C(PDB) of the caliche ranges from -4.7 to 0.7 and delta(18)O(SMOW) from 23.7 to 29.2. The isotopic data of the micrite can be explained by preferential fixing of (12)C into the alga, leaving local (13)C enrichment and evaporative enrichment of (18)O in the water. The (14)C dates of the micrite range from recent to 884 years b.p., indicating that "dead" carbon from the caliche is not a significant source for the lichen-precipitated micrite. The endolithic growth is an adaptation to the environmental extremes of exposed rock surfaces in the hot desert. The micrite layer is highly reflective and reduces light intensity to the algae below and acts as an efficient sunscreen that blocks harmful UV radiation. The micrite also acts as a cap to the lichen and helps trap moisture. The lichen survives by the combined effects of biodeterioration and biomineralization. Biodeterioration of the caliche concomitant with biomineralization of a protective surface coating of micrite results in the distinctive anatomy of V. rubrocincta.

The relation of H2 S release to SO2 , fumigation of lichens.

Hydrogen sulphide emission in lichens as a response to low concentration SO2 , fumigation was investigated. In an open flow-through system several lichen species were fumigated with 36 ppb SO2 , Two species were also fumigated with higher concentrations (72, 119, 122 and 198 ppb SO2 ,). Hydrogen sulphide emission was monitored concurrently by cryogenic trapping and analysis with gas chromatography. All tested species increased H, S emission significantly in response to fumigation with 36 ppb SO2 . Parmelina tiliacea (L.) Hale and Cladina rangiferina (L.) Wigg. released significantly more H2 S (0.098±0.015 and 0.073±0.013 pmol H2 S g-1 d. wt s-1 , respectively) than Parmelina quercina (Ach.) Hale, Ramalina menziesii Tayl. and Parmelia sulcata Tayl. (0.028 ± 0.01, 0.025±0.014 and 0.023±0.013 pmol H2 S g-1 d. wt s-1 , respectively). Release of H2 S in Hypogymnia physodes was enhanced by increasing SO2 concentrations up to 72 ppb SO2 . No significant difference in H2 S emission in the dark vs. in the light was found. Generally, no correlation was found between photosynthetic activity and H2 S emission for the tested species. Uptake of SO2 was similar for all species, at 24.7 ± 5.6 pmol SO2 g-1 d. wt s-1 in 36 ppb SO2 and increasing at greater SO2 concentrations. Therefore, H2 S-S release represents only 0.11-0.74% of SO2 -S uptake.

Photosynthetic patterns of Cetraria cucullata (Bell.) Ach. at Anaktuvuk Pass, Alaska.

The daily photosynthetic patterns of Cetraria cucullata were followed over the 1976 summer period at Anaktuvuk Pass, Alaska. With the exception of rainy peroids, the lichen exhibited a strong diurnal pattern with peak photosynthetic activity occurring between 0300 and 0700 h. This correllated with periods of maximal lichen water retention and the presence of direct solar radiation. When the lichen was moist, a strong gradient in photosynthetic activity was observed with no activity in the lichen bases and maximal activity in the lichen tips.