Developing numerical libraries in Java

The rapid and widespread adoption of Java has created a demand for reliable and reusable mathematical software components to support the growing number of compute-intensive applications now under development, particularly in science and engineering. In this paper we address practical issues of the Java language and environment which have an effect on numerical library design and development. Benchmarks which illustrate the current levels of performance of key numerical kernels on a variety of Java platforms are presented. Finally, a strategy for the development of a fundamental numerical toolkit for Java is proposed and its current status is described.Comment: 11 pages. Revised version of paper presented to the 1998 ACM Conference on Java for High Performance Network Computing. To appear in Concurrency: Practice and Experienc

Circumstellar Disks revealed by HH/KK Flux Variation Gradients

The variability of young stellar objects (YSO) changes their brightness and color preventing a proper classification in traditional color-color and color magnitude diagrams. We have explored the feasibility of the flux variation gradient (FVG) method for YSOs, using $H$ and $K$ band monitoring data of the star forming region RCW\,38 obtained at the University Observatory Bochum in Chile. Simultaneous multi-epoch flux measurements follow a linear relation $F_{H}=\alpha + \beta \cdot F_{K}$ for almost all YSOs with large variability amplitude. The slope $\beta$ gives the mean $HK$ color temperature $T_{var}$ of the varying component. Because $T_{var}$ is hotter than the dust sublimation temperature, we have tentatively assigned it to stellar variations. If the gradient does not meet the origin of the flux-flux diagram, an additional non- or less-varying component may be required. If the variability amplitude is larger at the shorter wavelength, e.g. $\alpha < 0$, this component is cooler than the star (e.g. a circumstellar disk); vice versa, if $\alpha > 0$, the component is hotter like a scattering halo or even a companion star. We here present examples of two YSOs, where the $HK$ FVG implies the presence of a circumstellar disk; this finding is consistent with additional data at $J$ and $L$. One YSO shows a clear $K$-band excess in the $JHK$ color-color diagram, while the significance of a $K$-excess in the other YSO depends on the measurement epoch. Disentangling the contributions of star and disk it turns out that the two YSOs have huge variability amplitudes ($\sim 3-5$\,mag). The $HK$ FVG analysis is a powerful complementary tool to analyze the varying components of YSOs and worth further exploration of monitoring data at other wavelengths.Comment: 5 pages, 5 figures, accepted for publication in Astronomy and Astrophysic

High-intensity interval training combined with vibration and dietary restriction Improves body composition and blood lipids in obese adults: a randomized trial

This study aimed to compare the effect of high-intensity interval training (HIIT) with additional whole-body vibration (WBV) on body composition and lipid profile in obese/overweight adults on a hypocaloric diet. Forty adults were randomly assigned to (a) HIIT and vibration and hypocaloric diet (HIITWBV, n ¼ 13), (b) HIIT and diet (HIIT, n ¼ 14), and (c) diet only (control [CON], n ¼ 13). High-intensity interval training WBV participants trained 3 times per week for 8 weeks (6 sets 1 minute of HIIT, cycling at 90% heart rate peak followed by 1 minute of interset vibration, at a frequency of 18 Hz increasing until 25 Hz with a peak-to- peak displacement of 4 mm. Training volume increased 1 set every 2 weeks until 10 sets). The HIIT group performed HIIT training followed by 2 minutes of passive recovery, while the CON continued with their daily activities combined with calorie restriction. Body composition (body fat and fat-free mass) and biochemical indices (glucose, total cholesterol, high-density lipoprotein cholesterol, and triglycerides) were determined. Following 8 weeks, body fat was significantly reduced by 7.5% and both tri- glycerides and total cholesterol decreased in the HIITWBV group only ( 16.5% and 11.7% respectively). This study suggests that HIIT in combination with WBV and a hypocaloric diet can improve overall lipid profile in overweight/obese individual

Indomethacin decreases viscosity of gallbladder bile in patients with cholesterol gallstone disease

There is experimental evidence that inhibition of cyclooxygenase with nonsteroidal anti-inflammatory drugs may decrease cholesterol gall-stone formation and mitigate biliary pain in gall-stone patients. The mechanisms by which NSAIDs exert these effect are unclear. In a prospective, controlled clinical trial we examined the effects of oral indomethacin on the composition of human gall-bladder bile. The study included 28 patients with symptomatic cholesterol or mixed gallstones. Of these, 8 were treated with 3 × 25 mg indomethacin daily for 7 days prior to elective cholecystectomy while 20 received no treatment and served as controls. Bile and tissue samples from the gallbladder were obtained during cholecystectomy. Indomethacin tissue levels in the gallbladder mucosa, as assessed by HPLC, were 1.05±0.4 ng/mg wet weight, a concentration known to inhibit effectively cyclooxygenase activity. Nevertheless, no differences between the treated and untreated groups were found in the concentrations of biliary mucus glycoprotein (0.94±0.27 versus 0.93±0.32 mg/ml) or total protein (5.8±0.9 versus 6.4±1.3 mg/ml), cholesterol saturation (1.3±0.2 versus 1.5±0.2), or nucleation time (2.0±3.0 versus 1.5±2.0 days). However, biliary viscosity, measured using a low-shear rotation viscosimeter, was significantly lower in patients receiving indomethacin treatment (2.9±0.6 versus 5.6±1.2 mPa.s; P < 0.02). In conclusion, in man oral indomethacin decreases bile viscosity without alteration of bile lithogenicity or biliary mucus glycoprotein content. Since mucus glycoproteins are major determinants of bile viscosity, an alteration in mucin macromolecular composition may conceivably cause the indomethacin-induced decrease in biliary viscosity and explain the beneficial effects of nonsteroidal anti-inflammatory drugs in gallstone disease

Modelling photometric reverberation data -- a disk-like broad-line region and a potentially larger black hole mass for 3C120

We consider photometric reverberation mapping, where the nuclear continuum variations are monitored via a broad-band filter and the echo of emission line clouds of the broad line region (BLR) is measured with a suitable narrow-band (NB) filter. We investigate how an incomplete emission-line coverage by the NB filter influences the BLR size determination. This includes two basic cases: 1) a symmetric cut of the blue and red part of the line wings, and 2) the filter positioned asymmetrically to the line centre so that essentially a complete half of the emission line is contained in the NB filter. Under the assumption that the BLR size is dominated by circular Keplerian orbits, we find that symmetric cutting of line wings may lead to overestimating the BLR size by less than 5%. The case of asymmetric half-line coverage, similar as for our data of the Seyfert 1 galaxy 3C120, yields the BLR size with a bias of less than 1%. Our results suggest that any BLR size bias due to narrow-band line cut in photometric reverberation mapping is small and in most cases negligible. We used well sampled photometric reverberation mapping light curves with sharp variation features in both the continuum and the Hbeta light curves to determine the geometry type of the Hbeta BLR for 3C120. Modelling of the light curve, under the assumption that the BLR is essentially virialised, argues against a spherical geometry and favours a nearly face-on disk-like geometry with inclination i = 10 +/- 4 deg and extension from 22 to 28 light days. The low inclination may lead to a larger black hole mass than the derived when using the average geometry scaling factor f=5.5. We discuss deviations of Seyfert 1 galaxies from the M_BH - sigma relation.Comment: 9 pages, 11 figures, accepted for publication in Astronomy and Astrophysic

Positioning systems in Minkowski space-time: Bifurcation problem and observational data

In the framework of relativistic positioning systems in Minkowski space-time, the determination of the inertial coordinates of a user involves the {\em bifurcation problem} (which is the indeterminate location of a pair of different events receiving the same emission coordinates). To solve it, in addition to the user emission coordinates and the emitter positions in inertial coordinates, it may happen that the user needs to know {\em independently} the orientation of its emission coordinates. Assuming that the user may observe the relative positions of the four emitters on its celestial sphere, an observational rule to determine this orientation is presented. The bifurcation problem is thus solved by applying this observational rule, and consequently, {\em all} of the parameters in the general expression of the coordinate transformation from emission coordinates to inertial ones may be computed from the data received by the user of the relativistic positioning system.Comment: 10 pages, 7 figures. The version published in PRD contains a misprint in the caption of Figure 3, which is here amende

Delimitation of the Coastal Transition Zone in the Gulf of Guayaquil, Ecuador

The article presents a methodology for the delimitation of the coastal transition zone (CTZ) and the identification of zones with distinct soil properties in the Gulf of Guayaquil (GG), Ecuador. The Gulf was chosen as study area for its urban, economic and ecological potential, more in particular for its rich marine and agricultural resources, and biodiversity. Soil physical and chemical methods, such as soil salinity indices, physical and chemical parameters, coupled with multivariate analysis enabled the delimitation of the CTZ and the grouping of the studied soil transets in three clusters with distinct properties, located in the GG from the limit of the mangrove swamp. Whereas the average conductance in the swamp area is around 27.17 mS cm-1, inland to the isoline called the coastal transit zone soil salinity on average is 4 mS cm-1. The coastal transition zone has an average width of 4.2 km, which can be characterized by three clusters. Clusters 1 and 2 show similarities in their physical and chemical soil parameters, clearly different from the soil properties of cluster 3. The characteristics of each cluster is related to its location within the study area

The broad-line region and dust torus size of the Seyfert 1 galaxy PGC50427

We present the results of a three years monitoring campaigns of the $z = 0.024$ type-1 active galactic nucleus (AGN) PGC50427. Through the use of Photometric Reverberation Mapping with broad and narrow band filters, we determine the size of the broad-line emitting region by measuring the time delay between the variability of the continuum and the H$\alpha$ emission line. The H$\alpha$ emission line responds to blue continuum variations with an average rest frame lag of $19.0 \pm 1.23$ days. Using single epoch spectroscopy we determined a broad-line H$\alpha$ velocity width of 1020 km s$^{-1}$ and in combination with the rest frame lag and adoption a geometric scaling factor $f = 5.5$, we calculate a black hole mass of $M_{BH} \sim 17 \times 10^{6} M_{\odot}$. Using the flux variation gradient method, we separate the host galaxy contribution from that of the AGN to calculate the rest frame 5100\AA~ luminosity at the time of our monitoring campaign. The rest frame lag and the host-subtracted luminosity permit us to derive the position of PGC50427 in the BLR size -- AGN luminosity diagram, which is remarkably close to the theoretically expected relation of $R \propto L^{0.5}$. The simultaneous optical and NIR ($J$ and $K_{s}$) observations allow us to determine the size of the dust torus through the use of dust reverberation mapping method. We find that the hot dust emission ($\sim 1800K$) lags the optical variations with an average rest frame lag of $46.2 \pm 2.60$ days. The dust reverberation radius and the nuclear NIR luminosity permit us to derive the position of PGC50427 on the known $\tau - M{V}$ diagram. The simultaneus observations for the broad-line region and dust thermal emission demonstrate that the innermost dust torus is located outside the BLR in PGC50427, supporting the unified scheme for AGNs. (Abstract shortened, see the manuscript.)Comment: 11 pages, 23 figures, accepted for publication in Astronomy and Astrophysic

Relation of Gallbladder Motility to Viscosity and Composition of Gallbladder Bile in Patients with Cholesterol Gallstones

Background/Aims: Increased viscosity and supersaturation of cholesterol in gallbladder bile, as well as an impaired motility of the gallbladder, are considered to be important factors in the pathogenesis of cholesterol gallstones. However, the relation of these parameters has not yet been determined. Material and Methods: Bile viscosity (mPa.s) was measured by rotation viscosimetry and the composition of gallbladder bile was determined using standard methodology. Gallbladder motility was calculated as ejection fraction in percent of total volume 45 min after a test meal using ultrasonography in patients with gallstones prior to elective cholecystectomy. Results: The study included 35 patients with cholesterol gallstones. Viscosity of gallbladder bile ranged between 0.9 and 12.5 mPa.s (median 2.2 mPa.s) and an ejection fraction of the gallbladder of 55.4 +/- 18.3% (mean +/- SD) was determined. No significant correlation (r = 0.19, p < 0.2) between the 2 parameters could be calculated. Analysis of the composition of gallbladder bile revealed a positive correlation of all components to biliary viscosity but not to the motility of the gallbladder, with the exceptions of a negative correlation (r = 0.39, p < 0.02) between mucin concentration and the ejection fraction at 45 min after the test meal. Conclusions: The motility of the gallbladder appears to be unrelated to the viscosity of gallbladder bile or gallbladder bile composition. The negative correlation between the ejection fraction of the gallbladder and mucin concentration of gallbladder bile suggests that chronic inflammation of the gallbladder wall is associated with both an impaired motility of the gallbladder and increased mucin release into gallbladder bile. Copyright (C) 2009 S. Karger AG, Base

Evolution of asexual and sexual reproduction in the aspergilli

Aspergillus nidulans has long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genus Aspergillus, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings from Aspergillus, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction in A. nidulans was investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in the Pezizomycotina (e.g. AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (e.g. BrlA) had a more restricted distribution solely in the Eurotiomycetes, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of the Pezizomycotina. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of the A. nidulans abaA gene in Monascus ruber failed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of the Saccharomycotina supports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in the Pezizomycotina. Investigations were also made into the evolution of sex and sexuality in the aspergilli. MAT loci were identified from the heterothallic Aspergillus (Emericella) heterothallicus and Aspergillus (Neosartorya) fennelliae and the homothallic Aspergillus pseudoglaucus (=Eurotium repens). A consistent architecture of the MAT locus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement of MAT loci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made using A. clavatus as a representative ‘asexual’ species. It was possible to induce a sexual cycle in A. clavatus given the correct MAT1-1 and MAT1-2 partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexual reproduction might be possible in many supposedly asexual aspergilli and beyond, providing general insights into the nature of asexuality in fungi.National Natural Science Foundation of China 31601446National Research Foundation of Korea 2016010945Intelligent Synthetic Biology Center of Global Frontier Projects 2015M3A6A8065838Biotechnology and Biological Sciences Research CouncilGovernment of IraqMinisterio de Economía y Competitividad BIO2015-67148-