cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks

Background: With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. Results: With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. Conclusions: This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services.SCI(E)CPCI-S(ISTP)[email protected]

PENYEMBUHAN PENYAKIT DIARE DAN INFEKSI LUKA DENGAN EKSTRAK DAUN KETUL (Bidens pilosa L)

Secara tradisional masyarakat dari setiap etnis sering menggunakan obat tradisional berbahan tumbuhan untuk mengobati penyakit yang menyerang manusia. Demikian halnya di desa Oelnasi Kecamatan Kupang Tengah Kabupaten Kupang masyarakat biasa meminum rebusan daun ketul (Bidens pilosa L) untuk menyembuhkan penyakit diare dan infeksi luka. Kepastian khasiat obat  rebusan daun ketul yang diambil dari Timor belum pernah dibuktikan secara ilmiah. Oleh karena itu penelitian untuk membuktikannya perlu dilakukan. Jenis penelitian ini adalah eksperimen laoboratoris dengan menggunakan Posttest Only Control Group Design yang terdiri dari empat perlakuan yang diulang tiga kali. Data dianalisis dengan anava satu arah dan dilanjutkan dengan uji beda nyata terkecil (BNT) dengan tingkat signifikansi 1%. Hasil penelitian menunjukkan bahwa ekstrak daun ketul (Bidens pilosa, L) dari Timor terbukti berkampuan menyembuhkan penyakit diare dan infeksi luka melalui indikator anti bakteri terhadap bakteri Escherichia coli dan Staphylococcus aureus secara In vitro dan level konsentrasi yang memiliki kemampuan penyembuhan tertinggi diare dan infeksi luka melalui indikator anti bakteri secara In vitro yaitu 75% dan 100% terhadap E.coli dan S.aureus 60% dan 80%. Kesimpulan dari penelitian ini yaitu bahwa ekstrak daun ketul (Bidans pilosa, L) terbukti dapat menyembuhkan penyakit diare dan infeksi luka melalui indikator anti bakteri terhadap E. coli dan S.aureus secara in vitro. Kemampuan penyembuhan penyakit diare dan infeksi luka terbaik melalui indikator antibateri ditemukan pada level konsentrasi ekstrak 75% dan  100% untuk bakteri E.coli dan 60% dan 80% untuk bakteri S.aurus. Hasil penelitian ini sangat penting untuk mendapatkan data akademis awal yang pasti terhadap kasiat obat tradisional berbahan Bidens pilosa,L dan untuk referensi peneliian farmakognosis lebih lanjut

Dynamics of Magnetic Flux Elements in the Solar Photosphere

The interaction of magnetic fields and convection is investigated in the context of the coronal heating problem. We study the motions of photospheric magnetic elements using filtergrams obtained at the Swedish Vacuum Solar Telescope at La Palma. We use potential-field modeling to extrapolate the magnetic and velocity fields to larger height. We find that the velocity in the chromosphere can be locally enhanced at the separatrix surfaces between neighboring flux tubes. The predicted velocities are several km/s, significantly larger than those of the photospheric flux tubes, which may have important implications for coronal heating. sComment: submitted to ApJ, 21 pages, 10 figure

Magnetic fields of opposite polarity in sunspot penumbrae

Context. A significant part of the penumbral magnetic field returns below the surface in the very deep photosphere. For lines in the visible, a large portion of this return field can only be detected indirectly by studying its imprints on strongly asymmetric and three-lobed Stokes V profiles. Infrared lines probe a narrow layer in the very deep photosphere, providing the possibility of directly measuring the orientation of magnetic fields close to the solar surface. Aims. We study the topology of the penumbral magnetic field in the lower photosphere, focusing on regions where it returns below the surface. Methods. We analyzed 71 spectropolarimetric datasets from Hinode and from the GREGOR infrared spectrograph. We inferred the quality and polarimetric accuracy of the infrared data after applying several reduction steps. Techniques of spectral inversion and forward synthesis were used to test the detection algorithm. We compared the morphology and the fractional penumbral area covered by reversed-polarity and three-lobed Stokes V profiles for sunspots at disk center. We determined the amount of reversed-polarity and three-lobed Stokes V profiles in visible and infrared data of sunspots at various heliocentric angles. From the results, we computed center-to-limb variation curves, which were interpreted in the context of existing penumbral models. Results. Observations in visible and near-infrared spectral lines yield a significant difference in the penumbral area covered by magnetic fields of opposite polarity. In the infrared, the number of reversed-polarity Stokes V profiles is smaller by a factor of two than in the visible. For three-lobed Stokes V profiles the numbers differ by up to an order of magnitude.Comment: 11 pages 10 figures plus appendix (2 pages 3 figures). Accepted as part of the A&A special issue on the GREGOR solar telescop

High Resolution Observations using Adaptive Optics: Achievements and Future Needs

Over the last few years, several interesting observations were obtained with the help of solar Adaptive Optics (AO). In this paper, few observations made using the solar AO are enlightened and briefly discussed. A list of disadvantages with the current AO system are presented. With telescopes larger than 1.5m are expected during the next decade, there is a need to develop the existing AO technologies for large aperture telescopes. Some aspects of this development are highlighted. Finally, the recent AO developments in India are also presented

Bisphosphonate nephrotoxicity

Bisphosphonates are valuable agents for the treatment of post-menopausal osteoporosis (PMO), hypercalcemia of malignancy, and osteolytic bone metastases. Oral bisphosphonates are used mainly to treat PMO and are not associated with significant nephrotoxicity. In contrast, nephrotoxicity is a significant potential limiting factor to the use of intravenous (IV) bisphosphonates, and the nephrotoxicity is both dose-dependent and infusion time-dependent. The two main IV bisphosphonates available to treat hypercalcemia of malignancy and osteolytic bone disease in the United States are zoledronate and pamidronate. Patterns of nephrotoxicity described with these agents include toxic acute tubular necrosis and collapsing focal segmental glomerulosclerosis, respectively. With both of these agents, severe nephrotoxicity can be largely avoided by stringent adherence to guidelines for monitoring serum creatinine prior to each treatment, temporarily withholding therapy in the setting of renal insufficiency, and adjusting doses in patients with pre-existing chronic kidney disease. In patients with PMO, zoledronate and pamidronate are associated with significantly less nephrotoxicity, which undoubtedly relates to the lower doses and longer dosing intervals employed for this indication. Ibandronate is approved in the US for treatment of PMO and in Europe for treatment of PMO and malignancy-associated bone disease. Available data suggest that ibandronate has a safe renal profile without evidence of nephrotoxicity, even in patients with abnormal baseline kidney function

The angular diameter of R Doradus: a nearby Mira-like star

We find the angular diameter of R Doradus to be 57 +/- 5 mas, exceeding that of Betelgeuse and implying that R Dor is larger in apparent size than every star except the Sun. R Dor is shown to be closely related to the Mira variables. We estimate an effective temperature of 2740 +/- 190 K, a distance of 61 +/- 7 pc, a luminosity of 6500 +/- 1400 Lsol and a radius of 370 +/- 50 Rsol. The characteristics of R Dor are consistent with it being near the edge of a Mira instability strip. We detect non-zero closure phases from R Dor, indicating an asymmetric brightness distribution. We also observed W Hya, a small-amplitude Mira, for which we find an angular diameter of 44 +/- 4 mas.Comment: MNRAS (accepted); 7 pages, LaTeX with necessary style file and PostScript figure

MECHANISTIC STUDIES OF CARBON DEPOSITION IN METHANE REDUCTION WITH IRON-BASED COMPOSITE PARTICLES

Chemical Looping Combustion (CLC) process has been widely considered to be clean energy conversion technology which utilizes an oxygen carrier to oxidize the fuel to H2O and separated CO2 efficiently. Therefore, the performance of the oxygen carrier (normally iron oxides) is critical to CLC. Although it has been found that the performances for reduction stage among these supported iron oxides are distinct from one to another, indicating complex iron oxide-support interaction, the understanding of these interactions including carbon deposition in methane reduction process remain limited, which could hamper the development of more efficient methane conversion system in CLC. Therefore, it is essential that a careful mechanistic study of methane reduction process be undertaken. In this study, efforts have been focused on understanding the mechanistic aspects of methane reduction process, among which carbon deposition and other key factors (such as supporting materials) to this process were carefully investigated. Iron oxides with three supporting materials, MgAl2O4, MgO and Al2O3, have been synthesized. Their combined reactivity, effect of supporting materials on the reaction, and corresponding reaction mechanisms have been studied using Thermogravimetric Analyzer (TGA), Brunauer-Emmett-Teller (BET), and Scanning Electron Microscope (SEM). It has been found that all three supported iron oxides, MgAl2O4, MgO and Al2O3, have the largest surface area and pore volume at point 4 (on TGA figure), where significant methane decomposition took place. The huge surface area and pore volume are believed to be largely attributed to the deposited carbon on solid samples. Correlations between the surface area (along with total pore volume) and the reaction pattern have been established by thoroughly analyzing results obtained from BET. During this stage of reduction, the MgO-supported iron oxides displayed the greatest reaction rate among all three synthesized particles. The reasons for the different behaviors may be attributed to the crystal structure change in the particles and different reaction pathways involved during redox reactions. Reactive sites in iron oxides are critical to the redox reactions, and they are closely related to the morphology of porous surface for the particles. Therefore, SEM was used to directly observe the morphological change of surfaces of unreacted and reacted particles among the reaction cycles.No embargoAcademic Major: Chemical Engineerin