Swelfe: a detector of internal repeats in sequences and structures

Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results

Prevalencia de microfilariasis en la población humana de Iquitos y zonas peri urbanas, Loreto, Perú

Los estudios de filariasis podrían ayudarnos a identificar casos febriles de etiología desconocida en los establecimientos de Salud. Se realizó un estudio epidemiológico, descriptivo, observacional, transversal y prospectivo; determinando la prevalencia de microfilariasis, relacionándola con las características epidemiológicas como sexo, edad y fiebre. Se procesaron 755 muestras. La microfilariasis fue detectada mediante microscopia simple, la prueba de Knott y Gota Gruesa fueron modificados por los autores. Se determinó una prevalencia de 6,2 %, encontrándose  Mansonella ozzardi  (2,0%) y una especie atípica, designada como Microfilaria sp. (4,1%); y la confección por ambas especies (0,1%). Las personas infectadas por Microfilaria sp., desarrollaban actividades en zona urbana; encontrándose una  frecuencia alta en mujeres de 4 a 12 años, procedentes de los distritos de San Juan, Iquitos y Punchana. Las infecciones por M. ozzardi  fueron  frecuentes en pacientes febriles del género masculino, de 22 a 39 años, procedentes del distrito de Belén, cuya actividad principal se desarrolla mayormente  en el campo.  Se encontró pobladores infectados con microfilarias en la ciudad de Iquitos y zonas peri urbanas; resultados que justifican investigaciones para determinar si el parásito Microfilaria sp., está causando síndromes clínicos y definir los ciclos de transmisión

A striking correspondence between the dynamics generated by the vector fields and by the scalar parabolic equations

The purpose of this paper is to enhance a correspondence between the dynamics of the differential equations $\dot y(t)=g(y(t))$ on $\mathbb{R}^d$ and those of the parabolic equations $\dot u=\Delta u +f(x,u,\nabla u)$ on a bounded domain $\Omega$. We give details on the similarities of these dynamics in the cases $d=1$, $d=2$ and $d\geq 3$ and in the corresponding cases $\Omega=(0,1)$, $\Omega=\mathbb{T}^1$ and dim($\Omega$)$\geq 2$ respectively. In addition to the beauty of such a correspondence, this could serve as a guideline for future research on the dynamics of parabolic equations

Internal kinematics of spiral galaxies in distant clusters IV. Gas kinematics of spiral galaxies in intermediate redshift clusters and in the field

(Abridged) We trace the interaction processes of galaxies at intermediate redshift by measuring the irregularity of their ionized gas kinematics, and investigate these irregularities as a function of the environment (cluster versus field) and of morphological type (spiral versus irregular). Our sample consists of 92 distant galaxies. 16 cluster (z~0.3 and z~0.5) and 29 field galaxies (mean z=0.44) of these have velocity fields with sufficient signal to be analyzed. We find that the fraction of galaxies that have irregular gas kinematics is remarkably similar in galaxy clusters and in the field at intermediate redshifts. The distribution of the field and cluster galaxies in (ir)regularity parameters space is also similar. On the other hand galaxies with small central concentration of light, that we see in the field sample, are absent in the cluster sample. We find that field galaxies at intermediate redshifts have more irregular velocity fields as well as more clumpy and less centrally concentrated light distributions than their local counterparts. Comparison with a SINS sample of 11 z ~ 2 galaxies shows that these distant galaxies have more irregular gas kinematics than our intermediate redshift cluster and field sample. We do not find a dependence of the irregularities in gas kinematics on morphological type. We find that two different indicators of star formation correlate with irregularity in the gas kinematics. More irregular gas kinematics, also more clumpy and less centrally concentrated light distributions of spiral field galaxies at intermediate redshifts in comparison to their local counterparts indicate that these galaxies are probably still in the process of building their disks via mechanisms such as accretion and mergers. On the other hand, they have less irregular gas kinematics compared to galaxies at z ~ 2.Comment: Accepted for publication in A&A, high resolution version available at http://www.astro.rug.nl/~kutdemir/13262/13262_hr.p

The physical properties of star forming galaxies in the low redshift universe

(modified) We present a comprehensive study of the physical properties of \~10^5 galaxies with measurable star formation in the SDSS. By comparing physical information extracted from the emission lines with continuum properties, we build up a picture of the nature of star-forming galaxies at z<0.2. We take out essentially all aperture bias using resolved imaging, allowing an accurate estimate of the total SFRs in galaxies. We determine the SFR density to be 1.915^{+0.02}_{-0.01}(rand.)^{+0.14}_{-0.42} (sys.) h70 10^{-2} Msun/yr/Mpc^3 at z=0.1 (for a Kroupa IMF) and we study the distribution of star formation as a function of various physical parameters. The majority of the star formation in the low redshift universe takes place in moderately massive galaxies (10^10-10^11 Msun), typically in HSB disk galaxies. Roughly 15% of all star formation takes place in galaxies that show some sign of an active nucleus. About 20% occurs in starburst galaxies. We show that the present to past-average star formation rate, the Scalo b-parameter; is almost constant over almost three orders of magnitude in mass, declining only at M*>10^10 Msun. The volume averaged b parameter is 0.408^{+0.005}_{-0.002} (rand).^{+0.029}_{-0.090} (sys.) h70^{-1}. We use this value constrain the star formation history of the universe. In agreement with other work we find a correlation between $b$ and morphological type, as well as a tight correlation between the 4000AA break (D4000) and b. We discuss how D4000 can be used to estimate b parameters for high redshift galaxies.Comment: Accepted for MNRAS. Replaced with accepted version. A section on comparison with other methods of SFR estimation added and various updates have been made. The main results are almost unchange

The effects of dilution and mixed layer depth on deliberate ocean iron fertilization : 1-D simulations of the southern ocean iron experiment (SOFeX)

Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 71 (2008): 112-130, doi:10.1016/j.jmarsys.2007.07.002.To better understand the role of iron in driving marine ecosystems, the Southern Ocean Iron Experiment (SOFeX) fertilized two surface water patches with iron north and south of the Antarctic Polar Front Zone (APFZ). Using 1-D coupled biological-physical simulations, we examine the biogeochemical dynamics that occurred both inside and outside of the fertilized patches during and shortly after the SOFeX field campaign. We focus, in particular, on three main issues governing the biological response to deliberate iron fertilization: the interaction among phytoplankton, light, macro-nutrient and iron limitation; dilution and lateral mixing between the fertilized patch and external, unfertilized waters; and the effect of varying mixed layer depth on the light field. At the patch south of the APFZ, sensitivity simulations with no dilution results in the maximum bloom magnitude, whereas dilution with external water extends the development of the north patch bloom by relieving silicon limitation. In model sensitivity studies for both sites, maximum chlorophyll concentration and dissolved inorganic carbon depletion inside the fertilized patches are inversely related to mixed layer depth, similar to the patterns observed across a number of iron fertilization field experiments. Our results suggest that Southern Ocean phytoplankton blooms resulting from natural or deliberate iron fertilization will tend to become iron-light co-limited unless the mixed layer depth is quite shallow.This work was supported by NASA grant NAG5-12520 from the NASA Ocean Biogeochemistry Program

Essential fatty acids for premenstrual syndrome and their effect on prolactin and total cholesterol levels: a randomized, double blind, placebo-controlled study

<p>Abstract</p> <p>Objective</p> <p>To evaluate the effectiveness and safety of polyunsaturated fatty acids for the treatment of the premenstrual syndrome (PMS) using a graded symptom scale and to assess the effect of this treatment on basal plasma levels of prolactin and total cholesterol.</p> <p>Methods</p> <p>A randomized, double-blind, placebo-controlled study was conducted with 120 women with PMS divided into three groups and treated with 1 or 2 grams of the medication or placebo. Symptoms were recorded over a 6-month period using the Prospective Record of the Impact and Severity of Menstruation (PRISM) calendar. Total cholesterol and prolactin levels were measured. Analysis of variance (ANOVA), Pearson's chi-square test, Wilcoxon's nonparametric signed-rank test for paired samples and the Mann-Whitney nonparametric test for independent samples were used in the statistical analysis.</p> <p>Results</p> <p>There were no differences in age, marital status, schooling or ethnicity between the groups. In the group treated with 1 gram of the medication, a significant reduction was found when the median PRISM score recorded in the luteal phase at baseline (99) was compared with the median score recorded in the 3^rdmonth (58) and in the 6^thmonth of evaluation (35). In the 2-gram group, these differences were even more significant (baseline score: 98; 3^rdmonth: 48; 6^thmonth: 28). In the placebo group, there was a significant reduction at the 3^rdbut not at the 6^thmonth (baseline: 96.5; 3^rdmonth: 63.5; 6^thmonth: 62). The difference between the phases of the menstrual cycle was greater in the 2-gram group compared to the group treated with 1 gram of the medication. There were no statistically significant differences in prolactin or total cholesterol levels between baseline values and those recorded after six months of treatment.</p> <p>Conclusion</p> <p>The difference between the groups using the medication and the placebo group with respect to the improvement in symptomatology appears to indicate the effectiveness of the drug. Improvement in symptoms was higher when the 2-gram dose was used. This medication was not associated with any changes in prolactin or total cholesterol levels in these women.</p

Gas flows, star formation and galaxy evolution

In the first part of this article we show how observations of the chemical evolution of the Galaxy: G- and K-dwarf numbers as functions of metallicity, and abundances of the light elements, D, Li, Be and B, in both stars and the interstellar medium (ISM), lead to the conclusion that metal poor HI gas has been accreting to the Galactic disc during the whole of its lifetime, and is accreting today at a measurable rate, ~2 Msun per year across the full disc. Estimates of the local star formation rate (SFR) using methods based on stellar activity, support this picture. The best fits to all these data are for models where the accretion rate is constant, or slowly rising with epoch. We explain here how this conclusion, for a galaxy in a small bound group, is not in conflict with graphs such as the Madau plot, which show that the universal SFR has declined steadily from z=1 to the present day. We also show that a model in which disc galaxies in general evolve by accreting major clouds of low metallicity gas from their surroundings can explain many observations, notably that the SFR for whole galaxies tends to show obvious variability, and fractionally more for early than for late types, and yields lower dark to baryonic matter ratios for large disc galaxies than for dwarfs. In the second part of the article we use NGC 1530 as a template object, showing from Fabry-Perot observations of its Halpha emission how strong shear in this strongly barred galaxy acts to inhibit star formation, while compression acts to stimulate it.Comment: 20 pages, 10 figures, to be presented at the "Penetrating Bars through Masks of Cosmic Dust" conference in South Africa, proceedings published by Kluwer, Eds. D.L. Block, K.C. Freeman, I. Puerari, & R. Groes

Changing outcomes following pelvic exenteration for locally advanced and recurrent rectal cancer

Background Pelvic exenteration for locally advanced rectal cancer (LARC) and locally recurrent rectal cancer (LRRC) is technically challenging but increasingly performed in specialist centres. The aim of this study was to compare outcomes of exenteration over time. Methods This was a multicentre retrospective study of patients who underwent exenteration for LARC and LRRC between 2004 and 2015. Surgical outcomes, including rate of bone resection, flap reconstruction, margin status and transfusion rates, were examined. Outcomes between higher- and lower-volume centres were also evaluated. Results Some 2472 patients underwent pelvic exenteration for LARC and LRRC across 26 institutions. For LARC, rates of bone resection or flap reconstruction increased from 2004 to 2015, from 3.5 to 12.8 per cent, and from 12.0 to 29.4 per cent respectively. Fewer units of intraoperative blood were transfused over this interval (median 4 to 2 units; P = 0.040). Subgroup analysis showed that bone resection and flap reconstruction rates increased in lower- and higher-volume centres. R0 resection rates significantly increased in low-volume centres but not in high-volume centres over time (low-volume: from 62.5 to 80.0 per cent, P = 0.001; high-volume: from 83.5 to 88.4 per cent, P = 0.660). For LRRC, no significant trends over time were observed for bone resection or flap reconstruction rates. The median number of units of intraoperative blood transfused decreased from 5 to 2.5 units (P < 0.001). R0 resection rates did not increase in either low-volume (from 51.7 to 60.4 per cent; P = 0.610) or higher-volume (from 48.6 to 65.5 per cent; P = 0.100) centres. No significant differences in length of hospital stay, 30-day complication, reintervention or mortality rates were observed over time. Conclusion Radical resection, bone resection and flap reconstruction rates were performed more frequently over time, while transfusion requirements decreased