Defining eye-fixation sequences across individuals and tasks: the Binocular-Individual Threshold (BIT) algorithm

We propose a new fully automated velocity-based algorithm to identify fixations from eye-movement records of both eyes, with individual-specific thresholds. The algorithm is based on robust minimum determinant covariance estimators (MDC) and control chart procedures, and is conceptually simple and computationally attractive. To determine fixations, it uses velocity thresholds based on the natural within-fixation variability of both eyes. It improves over existing approaches by automatically identifying fixation thresholds that are specific to (a) both eyes, (b) x- and y- directions, (c) tasks, and (d) individuals. We applied the proposed Binocular-Individual Threshold (BIT) algorithm to two large datasets collected on eye-trackers with different sampling frequencies, and compute descriptive statistics of fixations for larger samples of individuals across a variety of tasks, including reading, scene viewing, and search on supermarket shelves. Our analysis shows that there are considerable differences in the characteristics of fixations not only between these tasks, but also between individuals

Quantitative-spatial assessment of soil contamination in S. Francisco de Assis due to mining activity of the Panasqueira mine (Portugal)

Through the years, mining and beneficiation processes produces large amounts of As-rich mine wastes laid up in huge tailings and open-air impoundments (Barroca Grande and Rio tailings) that are the main source of pollution in the surrounding area once they are exposed to the weathering conditions leading to the formation of AMD and consequently to the contamination of the surrounding environments, in particularly soils. In order to investigate the environmental contamination impact on S. Francisco de Assis (village located between the two major impoundments and tailings) agricultural soils, a geochemical survey was undertaken to assess toxic metals associations, related levels and their spatial distribution, and to identify the possible contamination sources. According to the calculated contamination factor, As and Zn have a very high contamination factor giving rise to 65.4 % of samples with a moderate to high pollution degree; 34.6 % have been classified as nil to very low pollution degree. The contamination factor spatial distribution put in evidence the fact that As, Cd, Cu, Pb, and Zn soils contents, downstream Barroca Grande tailing, are increased when compared with the local Bk soils. The mechanical dispersion, due to erosion, is the main contamination source. The chemical extraction demonstrates that the trace metals distribution and accumulation in S. Francisco de Assis soils is related to sulfides, but also to amorphous or poorly crystalline iron oxide phases. The partitioning study allowed understanding the local chemical elements mobility and precipitation processes, giving rise to the contamination dispersion model of the study area. The wind and hydrological factors are responsible for the chemical elements transport mechanisms, the water being the main transporter medium and soils as one of the possible retention media

Solvent-selective routing for centrifugally automated solid-phase purification of RNA

The final publication is available at Springer via https://doi.org/10.1007/s10404-014-1477-9.We present a disc-based module for rotationally controlled solid-phase purification of RNA from cell lysate. To this end, multi-stage routing of a sequence of aqueous and organic liquids into designated waste and elution reservoirs is implemented by a network of strategically placed, solvent-selective composite valves. Using a bead-based stationary phase at the entrance of the router, we show that total RNA is purified with high integrity from cultured MCF7 and T47D cell lines, human leucocytes and Haemophilus influenzae cell lysates. Furthermore, we demonstrate the broad applicability of the device through the in vitro amplification of RNA purified on-disc using RT-PCR and NASBA. Our novel router will be at the pivot of a forthcoming, fully integrated and automated sample preparation system for RNA-based analysis.Peer reviewe

Insecticide resistance in the sand fly, Phlebotomus papatasi from Khartoum State, Sudan

<p>Abstract</p> <p>Background</p> <p><it>Phlebotomus papatasi </it>the vector of cutaneous leishmaniasis (CL) is the most widely spread sand fly in Sudan. No data has previously been collected on insecticide susceptibility and/or resistance of this vector, and a first study to establish a baseline data is reported here.</p> <p>Methods</p> <p>Sand flies were collected from Surogia village, (Khartoum State), Rahad Game Reserve (eastern Sudan) and White Nile area (Central Sudan) using light traps. Sand flies were reared in the Tropical Medicine Research Institute laboratory. The insecticide susceptibility status of first progeny (F1) of <it>P. papatasi </it>of each population was tested using WHO insecticide kits. Also, <it>P. papatasi </it>specimens from Surogia village and Rahad Game Reserve were assayed for activities of enzyme systems involved in insecticide resistance (acetylcholinesterase (AChE), non-specific carboxylesterases (EST), glutathione-S-transferases (GSTs) and cytochrome p450 monooxygenases (Cyt p450).</p> <p>Results</p> <p>Populations of <it>P. papatasi </it>from White Nile and Rahad Game Reserve were sensitive to dichlorodiphenyltrichloroethane (DDT), permethrin, malathion, and propoxur. However, the <it>P. papatasi </it>population from Surogia village was sensitive to DDT and permethrin but highly resistant to malathion and propoxur. Furthermore, <it>P. papatasi </it>of Surogia village had significantly higher insecticide detoxification enzyme activity than of those of Rahad Game Reserve. The sand fly population in Surogia displayed high AChE activity and only three specimens had elevated levels for EST and GST.</p> <p>Conclusions</p> <p>The study provided evidence for malathion and propoxur resistance in the sand fly population of Surogia village, which probably resulted from anti-malarial control activities carried out in the area during the past 50 years.</p

Long-term decline of the Amazon carbon sink

Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades1, 2, with a substantial fraction of this sink probably located in the tropics3, particularly in the Amazon4. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity5. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale1, 2, and is contrary to expectations based on models6

Sadržaj toksičnih i esencijalnih metala u ljekovitom bilju koje raste u onečišćenim i neonečišćenim područjima u Makedoniji

The aim of this study was to determine and compare Ba, Cr, Cd, Fe, Sr, Pb, and Zn content in medicinal herbs Urtica dioica L., Taraxacum officinale, and Matricaria recutita growing in polluted and unpolluted areas of the Republic of Macedonia. The metal content was determined using inductively coupled plasma atomic emission spectroscopy (ICP-AES). In the unpolluted area of Mt. Plačkovica the metal content in Taraxacum officinale was in the descending order: Fe>Sr>Zn>Ba>Cr, while Pb and Cd were below the limit of detection. In the polluted area of Veles, the order was as follows: Fe>Zn>Sr>Pb>Ba>Cd>Cr. Our results suggest that quality assurance and monitoring of toxic metals is needed for plants intended for human use and consumption. Medicinal plants should be picked in areas free of any contamination sources.Cilj je ovoga istraživanja bio utvrditi i usporediti sadržaj Ba, Cr, Cd, Fe, Sr, Pb i Zn u ljekovitom bilju Urtica dioica L., Taraxacum offi cinale i Matricaria recutita koje raste u onečišćenome odnosno neonečišćenome području u Republici Makedoniji. Sadržaj metala utvrdili smo s pomoću atomske emisijske spektroskopije induktivno spregnutom plazmom (engl. inductively coupled plasma atomic emission spectroscopy, krat. ICP-AES). U neonečišćenome području planine Plačkovice, sadržaj metala u Taraxacum offi cinale kretao se kako slijedi: Fe>Sr>Zn>Ba>Cr, dok su Pb i Cd bili ispod granice detekcije. U onečišćenome području blizu talionice olova i cinka u Velesu redoslijed je bio ovakav: Fe>Zn>Sr>Pb>Ba>Cd>Cr. Naši rezultati upućuju na potrebu za osiguranjem kakvoće i praćenjem razina toksičnih metala u biljaka namijenjenih ljudskoj uporabi. Ljekovito bilje valja brati u područjima bez izvora onečišćenja

Restriction of HIV-1 Replication in Monocytes Is Abolished by Vpx of SIVsmmPBj

Background: Human primary monocytes are refractory to infection with the human immunodeficiency virus 1 (HIV-1) or transduction with HIV-1-derived vectors. In contrast, efficient single round transduction of monocytes is mediated by vectors derived from simian immunodeficiency virus of sooty mangabeys (SIVsmmPBj), depending on the presence of the viral accessory protein Vpx. Methods and Findings: Here we analyzed whether Vpx of SIVsmmPBj is sufficient for transduction of primary monocytes by HIV-1-derived vectors. To enable incorporation of PBj Vpx into HIV-1 vector particles, a HA-Vpr/Vpx fusion protein was generated. Supplementation of HIV-1 vector particles with this fusion protein was not sufficient to facilitate transduction of human monocytes. However, monocyte transduction with HIV-1-derived vectors was significantly enhanced after delivery of Vpx proteins by virus-like particles (VLPs) derived from SIVsmmPBj. Moreover, pre-incubation with Vpx-containing VLPs restored replication capacity of infectious HIV-1 in human monocytes. In monocytes of non-human primates, single-round transduction with HIV-1 vectors was enabled. Conclusion: Vpx enhances transduction of primary human and even non-human monocytes with HIV-1-derived vectors, only if delivered in the background of SIVsmmPBj-derived virus-like particles. Thus, for accurate Vpx function the presence of SIVsmmPBj capsid proteins might be required. Vpx is essential to overcome a block of early infection steps in primary monocytes