Non-Invasive Measurement of Frog Skin Reflectivity in High Spatial Resolution Using a Dual Hyperspectral Approach

Background:Most spectral data for the amphibian integument are limited to the visible spectrum of light and have been collected using point measurements with low spatial resolution. In the present study a dual camera setup consisting of two push broom hyperspectral imaging systems was employed, which produces reflectance images between 400 and 2500 nm with high spectral and spatial resolution and a high dynamic range.Methodology/Principal Findings:We briefly introduce the system and document the high efficiency of this technique analyzing exemplarily the spectral reflectivity of the integument of three arboreal anuran species (Litoria caerulea, Agalychnis callidryas and Hyla arborea), all of which appear green to the human eye. The imaging setup generates a high number of spectral bands within seconds and allows non-invasive characterization of spectral characteristics with relatively high working distance. Despite the comparatively uniform coloration, spectral reflectivity between 700 and 1100 nm differed markedly among the species. In contrast to H. arborea, L. caerulea and A. callidryas showed reflection in this range. For all three species, reflectivity above 1100 nm is primarily defined by water absorption. Furthermore, the high resolution allowed examining even small structures such as fingers and toes, which in A. callidryas showed an increased reflectivity in the near infrared part of the spectrum.Conclusion/Significance:Hyperspectral imaging was found to be a very useful alternative technique combining the spectral resolution of spectrometric measurements with a higher spatial resolution. In addition, we used Digital Infrared/Red-Edge Photography as new simple method to roughly determine the near infrared reflectivity of frog specimens in field, where hyperspectral imaging is typically difficult. © 2013 Pinto et al

Beehives, Booze and Suffragettes: The “Sad Case” of Ellen S. Tupper (1822–1888), the “Bee Woman” and “Iowa Queen Bee”

ELLEN S. TUPPER was a 19th century expert bee-keeper who was most active during and shortly after the end of the American Civil War. A vigorous writer and apiarist, primarily focused on business interests and opportunities, she became the first female editor of an entomological journal in 1869. Joining the mid-western suffragettes, who at this time were also strongly linked to the temperance societies, she was soon presented as a role model of a successful businesswoman the early feminist movement. Together with ANNIE NOWLIN SAVERY (1831-1891), a leading American suffragette of her time, she established the "Italian Bee Company". For a short period, ELLEN S. TUPPER successfully imported and distributed Italian queens and bees to an interested American audience, while she actively promoted bee keeping as a suitable endeavour for women. Her reports on successful fertilization of bee queens that were held in confinement sparked a lively and controversial discussion among entomologists not only in America but also in Europe. At the height of her career she became the first female lecturer in apiology and the first woman elected to serve as an officer in a national entomological society. At the same meeting more than 30 other suffragettes joined the "North American Beekeepers' Society". This was a symbolic and perhaps even defining moment of female activity in science during the 19th century. Her activities soon earned her nicknames such as "Iowa Queen Bee" or the "Bee Woman". However, financial difficulties put an end to most of her business endeavours. Her career as an apiarist and editor came to a disgraceful end when she was incarcerated for the forgery of notes presented at several banks, subsequently acquitted on the ground of insanity. The forgery trial though has overshadowed ELLEN S. TUPPER's legacy in the history of women in science: As a farmer's wife in one of the frontier towns of the Wild West, in a county, which on her first arrival did not even possess a printing press, she was able to start a successful and impressive career as an editress. With her work she and a few like-minded supporters practically single-handedly recruited more women for entomological societies than all other European and American societies and institutions in the 19th century together. For nearly two and a half decades she went on a stubborn and effective crusade to convince women to become bee-keepers

High-to-low CO2 acclimation reveals plasticity of the photorespiratory pathway and indicates regulatory links to cellular metabolism of Arabidopsis

Background: Photorespiratory carbon metabolism was long considered as an essentially closed and nonregulated pathway with little interaction to other metabolic routes except nitrogen metabolism and respiration. Most mutants of this pathway cannot survive in ambient air and require CO 2-enriched air for normal growth. Several studies indicate that this CO 2 requirement is very different for individual mutants, suggesting a higher plasticity and more interaction of photorespiratory metabolism as generally thought. To understand this better, we examined a variety of high- and low-level parameters at 1% CO 2 and their alteration during acclimation of wild-type plants and selected photorespiratory mutants to ambient air. Methodology and Principal Findings: The wild type and four photorespiratory mutants of Arabidopsis thaliana (Arabidopsis) were grown to a defined stadium at 1% CO 2 and then transferred to normal air (0.038% CO 2). All other conditions remained unchanged. This approach allowed unbiased side-by-side monitoring of acclimation processes on several levels. For all lines, diel (24 h) leaf growth, photosynthetic gas exchange, and PSII fluorescence were monitored. Metabolite profiling was performed for the wild type and two mutants. During acclimation, considerable variation between the individual genotypes was detected in many of the examined parameters, which correlated with the position of the impaired reaction in the photorespiratory pathway. Conclusions: Photorespiratory carbon metabolism does not operate as a fully closed pathway. Acclimation from high to low CO 2 was typically steady and consistent for a number of features over several days, but we also found unexpected short-term events, such as an intermittent very massive rise of glycine levels after transition of one particular mutant to ambient air. We conclude that photorespiration is possibly exposed to redox regulation beyond known substrate-level effects. Additionally, our data support the view that 2-phosphoglycolate could be a key regulator of photosynthetic-photorespiratory metabolism as a whole. © 2012 Timm et al

Discrepancies in autologous bone marrow stem cell trials and enhancement of ejection fraction (DAMASCENE): weighted regression and meta-analysis

Objective To investigate whether discrepancies in trials of use of bone marrow stem cells in patients with heart disease account for the variation in reported effect size in improvement of left ventricular function. Design Identification and counting of factual discrepancies in trial reports, and sample size weighted regression against therapeutic effect size. Meta-analysis of trials that provided sufficient information. Data sources PubMed and Embase from inception to April 2013. Eligibility for selecting studies Randomised controlled trials evaluating the effect of autologous bone marrow stem cells for heart disease on mean left ventricular ejection fraction. Results There were over 600 discrepancies in 133 reports from 49 trials. There was a significant association between the number of discrepancies and the reported increment in EF with bone marrow stem cell therapy (Spearman’s r=0.4, P=0.005). Trials with no discrepancies were a small minority (five trials) and showed a mean EF effect size of −0.4%. The 24 trials with 1-10 discrepancies showed a mean effect size of 2.1%. The 12 with 11-20 discrepancies showed a mean effect of size 3.0%. The three with 21-30 discrepancies showed a mean effect size of 5.7%. The high discrepancy group, comprising five trials with over 30 discrepancies each, showed a mean effect size of 7.7%. Conclusions Avoiding discrepancies is difficult but is important because discrepancy count is related to effect size. The mechanism is unknown but should be explored in the design of future trials because in the five trials without discrepancies the effect of bone marrow stem cell therapy on ejection fraction is zero

Spinach in Blunderland: How the myth that spinach is rich in iron became an urban academic legend

The claim that spinach contains a lot of iron is one of the longest standing myths in science. In recent decades, this early error though has become widely known to the public and several theories were proclaimed, how this misconception was born. The most famous one, known in many varieties and reported in numerous books and scientific journals, is that a simple decimal error occurred. More recently it was claimed that the story of the decimal error is itself a myth and that Popeye against popular belief originally did not eat spinach for its iron content. Unfortunately, not much is known on how urban academic legends and popular misbeliefs in medicine and natural sciences develop and how both facts and errors are popularized. Following an in-depth literature search, the article reports how spinach in the historical and publishing context became popularized as a healthy vegetable rich in iron and how and when this myth was debunked. Briefly, all previous analyses on the origin of the myth only told part of the story. Popularization of spinach as an iron rich vegetable fist occurred in the 1850s. The following propagation of the myth, however, was based on a complex interaction involving scientists, journalists and popular culture, which emphasizes that the impact of science and propagation of ideas is inadequately covered by classic citation links and networks

InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid

International audiencePlant phenotyping consists in the observation of physical and biochemical traits of plant genotypes in response to environmental conditions. Challenges , in particular in context of climate change and food security, are numerous. High-throughput platforms have been introduced to observe the dynamic growth of a large number of plants in different environmental conditions. Instead of considering a few genotypes at a time (as it is the case when phenomic traits are measured manually), such platforms make it possible to use completely new kinds of approaches. However, the data sets produced by such widely instrumented platforms are huge, constantly augmenting and produced by increasingly complex experiments, reaching a point where distributed computation is mandatory to extract knowledge from data. In this paper, we introduce InfraPhenoGrid, the infrastructure we designed and deploy to efficiently manage data sets produced by the PhenoArch plant phenomics platform in the context of the French Phenome Project. Our solution consists in deploying scientific workflows on a Grid using a middle-ware to pilot workflow executions. Our approach is user-friendly in the sense that despite the intrinsic complexity of the infrastructure, running scientific workflows and understanding results obtained (using provenance information) is kept as simple as possible for end-users

Difficulty in detecting discrepancies in a clinical trial report: 260-reader evaluation

Background: Scientific literature can contain errors. Discrepancies, defined as two or more statements or results that cannot both be true, may be a signal of problems with a trial report. In this study, we report how many discrepancies are detected by a large panel of readers examining a trial report containing a large number of discrepancies. Methods: We approached a convenience sample of 343 journal readers in seven countries, and invited them in person to participate in a study. They were asked to examine the tables and figures of one published article for discrepancies. 260 participants agreed, ranging from medical students to professors. The discrepancies they identified were tabulated and counted. There were 39 different discrepancies identified. We evaluated the probability of discrepancy identification, and whether more time spent or greater participant experience as academic authors improved the ability to detect discrepancies. Results: Overall, 95.3% of discrepancies were missed. Most participants (62%) were unable to find any discrepancies. Only 11.5% noticed more than 10% of the discrepancies. More discrepancies were noted by participants who spent more time on the task (Spearman’s ρ = 0.22, P < 0.01), and those with more experience of publishing papers (Spearman’s ρ = 0.13 with number of publications, P = 0.04). Conclusions: Noticing discrepancies is difficult. Most readers miss most discrepancies even when asked specifically to look for them. The probability of a discrepancy evading an individual sensitized reader is 95%, making it important that, when problems are identified after publication, readers are able to communicate with each other. When made aware of discrepancies, the majority of readers support editorial action to correct the scientific record

Frame rate required for speckle tracking echocardiography: A quantitative clinical study with open-source, vendor-independent software

Background Assessing left ventricular function with speckle tracking is useful in patient diagnosis but requires a temporal resolution that can follow myocardial motion. In this study we investigated the effect of different frame rates on the accuracy of speckle tracking results, highlighting the temporal resolution where reliable results can be obtained. Material and methods 27 patients were scanned at two different frame rates at their resting heart rate. From all acquired loops, lower temporal resolution image sequences were generated by dropping frames, decreasing the frame rate by up to 10-fold. Results Tissue velocities were estimated by automated speckle tracking. Above 40 frames/s the peak velocity was reliably measured. When frame rate was lower, the inter-frame interval containing the instant of highest velocity also contained lower velocities, and therefore the average velocity in that interval was an underestimate of the clinically desired instantaneous maximum velocity. Conclusions The higher the frame rate, the more accurately maximum velocities are identified by speckle tracking, until the frame rate drops below 40 frames/s, beyond which there is little increase in peak velocity. We provide in an online supplement the vendor-independent software we used for automatic speckle-tracked velocity assessment to help others working in this field

Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data

International audiencePlant high-throughput phenotyping aims at capturing the genetic variability of plant response to environmental factors for thousands of plants, hence identifying heritable traits for genomic selection and predicting the genetic values of allelic combinations in different environment. This first implies the automation of the measurement of a large number of traits to characterize plant growth, plant development and plant functioning. It also requires a fluent and versatile interaction between data and continuously evolving plant response models, that are essential in the analysis of the marker x environment interaction and in the integration of processes for predicting crop performance [1]. In the frame of the Phenome high throughput phenotyping infrastructure, we develop Phenomenal: a software framework dedicated to the analysis of high throughput phenotyping data and models. It is based on the OpenAlea platform [2] that provides methods and softwares for the modelling of plants, together with a user-friendly interface for the design and execution of scientific workflows. OpenAlea is also part of the InfraPhenoGrid infrastructure that allows high throughput computation and recording of provenance during the execution [3]. Figure 1: The 3D plant reconstruction and segmentation pipeline. Muti-view plants images from PhenoArch are binarised and used to reconstruct plants in3D. The 3D skeleton is extracted and separated into stem (central vertical elements) and leaves. 3D voxels are segmented by propagating skeleton segmentation

The Leaf Reticulate Mutant dov1 Is Impaired in the First Step of Purine Metabolism

Rosar C, Kanonenberg K, Nanda AM, et al. The Leaf Reticulate Mutant dov1 Is Impaired in the First Step of Purine Metabolism. Molecular Plant. 2012;5(6):1227-1241.A series of reticulated Arabidopsis thaliana mutants were previously described. All mutants show a reticulate leaf pattern, namely green veins on a pale leaf lamina. They have an aberrant mesophyll structure but an intact layer of bundle sheath cells around the veins. Here, we unravel the function of the previously described reticulated EMS-mutant dov1 (differential development of vascular associated cells 1). By positional cloning, we identified the mutated gene, which encodes glutamine phosphoribosyl pyrophosphate aminotransferase 2 (ATase2), an enzyme catalyzing the first step of purine nucleotide biosynthesis. dov1 is allelic to the previously characterized cia1-2 mutant that was isolated in a screen for mutants with impaired chloroplast protein import. We show that purine-derived total cytokinins are lowered in dov1 and crosses with phytohormone reporter lines revealed differential reporter activity patterns in dov1. Metabolite profiling unraveled that amino acids that are involved in purine biosynthesis are increased in dov1. This study identified the molecular basis of an established mutant line, which has the potential for further investigation of the interaction between metabolism and leaf development