Scientific Publishing: the Dilemma of Research Funding Organisations

Present changes in scientific publishing, especially those summarised by the term ‘Open Access' (OA), may ultimately lead to the complete replacement of a reader-paid to an author, or funding-paid, publication system. This transformation would shift the financial burden for scientific publishing from the Research Performing Organisations (RPOs), particularly from scientific libraries, universities, etc, to the Research Funding Organisations (RFOs). The transition phase is difficult; it leads to double funding of OA publications (by subscriptions and author-sponsored OA) and may thus increase the overall costs of scientific publishing. This may explain why - with a few exceptions - RFOs have not been at the forefront of the OA paradigm in the past. In 2008, the General Assembly of EUROHORCs, the European organisation of the heads of research councils, agreed to recommend to its member organisations at least a minimal standard of Open Access based on the Berlin Declaration of 2003 (green way of OA). In the long run, the publishing system needs some fundamental changes to reduce the present costs and to keep up its potential. In order to design a new system, all players have to cooperate and be ready to throw overboard some old traditions, lovable as they may b

Splotch: Visualizing Cosmological Simulations

We present a light and fast, public available, ray-tracer {\tt Splotch} software tool which supports the effective visualization of cosmological simulations data. We describe the algorithm it relies on, which is designed in order to deal with point-like data, optimizing the ray-tracing calculation by ordering the particles as a function of their ``depth'' defined as a function of one of the coordinates or other associated parameter. Realistic three-dimensional impressions are reached through a composition of the final color in each pixel properly calculating emission and absorption of individual volume elements. We describe several scientific as well as public applications realized with {\tt Splotch}. We emphasize how different datasets and configurations lead to remarkable different results in terms of the images and animations. A few of these results are available online.Comment: 19 Pages, 8 Figures, to appear in New Journal of Physics, Focus Issue on "Visualisation in Physics", edited by B. Sanders, T. Senden and V. Springe

Repetitive proteins from the flagellar cytoskeleton of African trypanosomes are diagnostically useful antigens

Trypanosome infection of mammalian hosts leads, within days, to a strong early response against a small, distinct number of parasite proteins. One of these proteins is the variable surface glycoprotein (VSG). Most of the others are apparently non-variable, intracellular trypanosome proteins. Two of these antigens I2 and I17 are now characterized at the molecular level. Both exhibit a highly repetitive amino acid sequence organization, but they show no sequence similarity either to each other or to any other proteins known to date. Preliminary serological analyses indicate that both allow the early, sensitive and specific detection of infections with different species of trypanosomatids, making them interesting candidates for the development of diagnostic tools for trypanosomiasis detectio

Cytoskeleton-associated antigens from African trypanosomes are recognized by self-reactive antibodies of uninfected mice

Serum from uninfected mice of different strains, as well as from germ-free animals, contains antibodies which react specifically with at least two trypanosomal proteins, I/6 and MARP1. These antibody populations are highly specific for the respective proteins, are of similar affinity as hyperimmune antibodies, and consist of IgM as well as IgG isotypes. Hyperimmune antibody raised against the cross-reacting trypanosomal protein I/6 detects a 60 kDa protein in mouse 3T6 cells, which is a component of the fibroblast cytoskeleto

Raw and Count Data Comparability of Hip-Worn ActiGraph GT3X+ and Link Accelerometers

To enable inter- and intrastudy comparisons it is important to ascertain comparability among accelerometer models. Purpose: The purpose of this study was to compare raw and count data between hip-worn ActiGraph GT3X+ and GT9X Link accelerometers. Methods: Adults (n = 26 (n = 15 women); age, 49.1 T 20.0 yr) wore GT3X+ and Link accelerometers over the right hip for an 80-min protocol involving 12–21 sedentary, household, and ambulatory/exercise activities lasting 2–15 min each. For each accelerometer, mean and variance of the raw (60 Hz) data for each axis and vector magnitude (VM) were extracted in 30-s epochs. A machine learning model (Montoye 2015) was used to predict energy expenditure in METs from the raw data. Raw data were also processed into activity counts in 30-s epochs for each axis and VM, with Freedson 1998 and 2011 count-based regression models used to predictMETs. Time spent in sedentary, light, moderate, and vigorous intensities was derived from predicted METs from each model. Correlations were calculated to compare raw and count data between accelerometers, and percent agreement was used to compare epoch-by-epoch activity intensity. Results: For raw data, correlations for mean acceleration were 0.96 T 0.05, 0.89 T 0.16, 0.71 T 0.33, and 0.80 T 0.28, and those for variance were 0.98 T 0.02, 0.98 T 0.03, 0.91 T 0.06, and 1.00 T 0.00 in the X, Y, and Z axes and VM, respectively. For count data, corresponding correlations were 1.00 T 0.01, 0.98 T 0.02, 0.96 T 0.04, and 1.00 T 0.00, respectively. Freedson 1998 and 2011 count-based models had significantly higher percent agreement for activity intensity (95.1% T 5.6% and 95.5% T 4.0%) compared with theMontoye 2015 raw data model (61.5% T 27.6%; P G 0.001). Conclusions: Count data were more highly comparable than raw data between accelerometers. Data filtering and/or more robust raw data models are needed to improve raw data comparability between ActiGraph GT3X+ and Link accelerometers

Reference Standards for Body Fat Measure Using GE Dual Energy X-Ray Absorptiometry in Caucasian Adults

Background Dual energy x-ray absorptiometry (DXA) is an established technique for the measurement of body composition. Reference values for these variables, particularly those related to fat mass, are necessary for interpretation and accurate classification of those at risk for obesityrelated health complications and in need of lifestyle modifications (diet, physical activity, etc.). Currently, there are no reference values available for GE-Healthcare DXA systems and it is known that whole-body and regional fat mass measures differ by DXA manufacturer. Objective To develop reference values by age and sex for DXA-derived fat mass measurements with GE-Healthcare systems. Methods A de-identified sample of 3,327 participants (2,076 women, 1,251 men) was obtained from Ball State University\u27s Clinical Exercise Physiology Laboratory and University of Wisconsin- Milwaukee\u27s Physical Activity & Health Research Laboratory. All scans were completed using a GE Lunar Prodigy or iDXA and data reported included percent body fat (%BF), fat mass index (FMI), and ratios of android-to-gynoid (A/G), trunk/limb, and trunk/leg fat measurements. Percentiles were calculated and a factorial ANOVA was used to determine differences in the mean values for each variable between age and sex. Results Normative reference values for fat mass variables from DXA measurements obtained from GE-Healthcare DXA systems are presented as percentiles for both women and men in 10- year age groups. Women had higher (p\u3c0.01) mean %BF and FMI than men, whereas men had higher (p\u3c0.01) mean ratios of A/G, trunk/limb, and trunk/leg fat measurements than women

Repetitive proteins from the flagellar cytoskeleton of African trypanosomes are diagnostically useful antigens

Trypanosome infection of mammalian hosts leads, within days, to a strong early response against a small, distinct number of parasite proteins. One of these proteins is the variable surface glycoprotein (VSG). Most of the others are apparently non-variable, intracellular trypanosome proteins. Two of these antigens I2 and I17 are now characterized at the molecular level. Both exhibit a highly repetitive amino acid sequence organization, but they show no sequence similarity either to each other or to any other proteins known to date. Preliminary serological analyses indicate that both allow the early, sensitive and specific detection of infections with different species of trypanosomatids, making them interesting candidates for the development of diagnostic tools for trypanosomiasis detection

Identification and characterization of two repetitive non-variable antigens from African trypanosomes which are recognized early during infection

The present paper describes two repetitive proteins representing common antigens of African trypanosomes which are non-variant and which are recognized early in infection by the host immune system. These antigens were identified by their ability to immunoreact with bovine serum taken during the early phase of a cyclic trypanosomal infection. Screening of a cDNA library from T. b. gambiense with such early infection serum identified a protein which contains a repetitive motif consisting of 68 amino acid repeat units (GM6). Immunofluorescence and immunogold electron microscopy revealed that GM6 is located on fibres which connect the microtubules of the membrane skeleton with the flagellum. A second repetitive antigen detected by this serum is MARP1 (microtubule-associated repetitive protein 1), a protein previously characterized in this laboratory as a high-molecular weight component of the membrane skeleton, which consists of more than 50 tandemly repeated, near-identical 38 amino acid repeat units. Beta-galactosidase fusion products of both proteins demonstrated a strong immunoreactivity with sera from T. b. brucei and T. congolense-infected cattle. The result from this preliminary immunological evaluation indicates a high immunodiagnostic sensititivy (90%) of the two recombinant antigens which make them interesting candidates for immunodiagnosis of trypanosomiasis in cattl