Improved Algorithms for Approximate String Matching (Extended Abstract)

The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share. We designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s-|n-m|)min(m,n,s)+m+n) and linear space, where s is the edit distance between the two strings. This worst-case time bound sets the quadratic factor of the algorithm independent of the longest string length and improves existing theoretical bounds for this problem. The implementation of our algorithm excels also in practice, especially in cases where the two strings compared differ significantly in length. Source code of our algorithm is available at http://www.cs.miami.edu/\~dimitris/edit_distanceComment: 10 page

Providing insecticide treated bed nets in antiretroviral treatment clinics in Malawi: a pilot study

HIV infection and malaria, two of the most common and important health problems in sub-Saharan Africa, have been demonstrated to have interactive pathology. In Malawi, where malaria is endemic, and antiretroviral therapy (ART) delivery is scaling up, we piloted integration of long-lasting insecticide-treated bednets (ITN) provision in three ART clinics. In July 2006, 1,910 ITNs were delivered to pilot sites, and ART clinic staff personnel were briefed on ITN provision and use of a monitoring system. Sites were assessed using a structured questionnaire in December 2006. During the pilot period, 1,282 ITNs were distributed to patients. A large proportion (70%) of ART patients at these sites received pilot study ITNs. Site adherence to the monitoring system was variable. Seventeen patients were interviewed, 14 of whom were ART patients who had received ITNs; 11 of these (79%) had slept under the net the previous night. This pilot demonstrates the feasibility of ITN distribution to patients attending ART clinics in Malawi. Programmatic and policy considerations for national roll-out include the need to: 1) adopt a standardized monitoring system, 2) develop information, education, and communication materials, 3) develop in-service training for ART clinicians, and 4) identify systems for forecasting, procuring and distributing ITNs. Malawi Medical Journal Vol. 19 (3) 2007: pp. 111-11

HD 77407 and GJ 577: two new young stellar binaries detected with the Calar Alto Adaptive Optics system ALFA

We present the first results from our search for close stellar and sub-stellar companions to young nearby stars on the northern sky. Our infrared imaging observations are obtained with the 3.5 m Calar Alto telescope and the AO system ALFA. With two epoch observations which were separated by about one year, we found two co-moving companion candidates, one close to HD 77407 and one close to GJ 577. For the companion candidate near GJ 577, we obtained an optical spectrum showing spectral type M4.5; this candidate is a bound low-mass stellar companion confirmed by both proper motion and spectroscopy. We estimate the masses for HD 77407 B and GJ 577 B to be ~0.3 to 0.5 Msun and ~0.16 to 0.2 Msun, respectively. Compared to Siess al.(2000) models, each of the two pairs appears co-eval with HD 77407 A,B being 10 to 40 Myrs old and GJ 577 A,B being older than 100 Myrs. We also took multi-epoch high-resolution spectra of HD 77407 to search for sub-stellar companions, but did not find any with 3 Mjup as upper mass (msin(i)) limit (for up to 4 year orbits); however, we detected a long-term radial velocity trend in HD 77407 A, consistent with a ~ 0.3 Msun companion at ~ 50 AU separation, i.e. the one detected by the imaging. Hence, HD 77407 B is confirmed to be a bound companion to HD 77407 A. We also present limits for undetected, but detectable companions using a deep image of HD 77407 A and B, also observed with the Keck NIRC2 AO system; any brown dwarfs were detectable outside of 0.5 arcsec (17 AU at HD 77407), giant planets with masses from ~ 6.5 to 12 Mjup were detectable at > 1.5 arcsec.Comment: in pres

NICMOS Imaging of the HR 4796A Circumstellar Disk

We report the first near infrared (NIR) imaging of a circumstellar annular disk around the young (~8 Myr), Vega-like star, HR 4796A. NICMOS coronagraph observations at 1.1 and 1.6 microns reveal a ring-like symmetrical structure peaking in reflected intensity 1.05 arcsec +/- 0.02 arcsec (~ 70 AU) from the central A0V star. The ring geometry, with an inclination of 73.1 deg +/- 1.2 deg and a major axis PA of 26.8 deg +/- 0.6 deg, is in good agreement with recent 12.5 and 20.8 micron observations of a truncated disk (Koerner, et al. 1998). The ring is resolved with a characteristic width of less than 0.26 arcsec (17 AU) and appears abruptly truncated at both the inner and outer edges. The region of the disk-plane inward of ~60 AU appears to be relatively free of scattering material. The integrated flux density of the part of the disk that is visible (greater than 0.65 arcsec from the star) is found to be 7.5 +/- 0.5 mJy and 7.4 +/- 1.2 mJy at 1.1 and 1.6 microns, respectively. Correcting for the unseen area of the ring yields total flux densities of 12.8 +/- 1.0 mJy and 12.5 +/- 2.0 mJy, respectively (Vega magnitudes = 12.92 /+- 0.08 and 12.35 +/-0.18). The NIR luminosity ratio is evaluated from these results and ground-based photometry of the star. At these wavelengths Ldisk(lambda)/L*(lambda) = 1.4 +/- 0.2E-3 and 2.4 +/- 0.5E-3, giving reasonable agreement between the stellar flux scattered in the NIR and that which is absorbed in the visible and re-radiated in the thermal infrared. The somewhat red reflectance of the disk at these wavelengths implies mean particle sizes in excess of several microns, larger than typical interstellar grains. The confinement of material to a relatively narrow annular zone implies dynamical constraints on the disk particles by one or more as yet unseen bodies.Comment: 14 pages, 1 figure for associated gif file see: http://nicmosis.as.arizona.edu:8000/AAS99/FIGURE1_HR4796A_ApJL.gif . Accepted 13 January 1999, Astrophyical Journal Letter

Low-mass companions to Hyades stars

It is now well established that a large fraction of the low-mass stars are binaries or higher order multiples. Similarly a sizable fraction have giant planets. In contrast to these, the situation for brown dwarf companions is complicated: While close systems seem to be extremely rare, wide systems are possibly more common. In this paper, we present new results on a survey for low-mass companions in the Hyades. After measuring precisely the radial velocity of 98 Hyades dwarf stars for 5 years, we have selected all stars that show low-amplitude long-period trends. With AO-observations of these 14 stars we found companion candidates around nine of them, where one star has two companions. The two companions of HIP 16548 have masses between 0.07 to 0.08 Mo, and are thus either brown dwarfs or very low mass stars. In the case of HAN 172 we found a companion with a mass between 0.08 to 0.10 Mo, which is again between a star and a brown dwarf. The other seven stars all have stellar companions. In two additional cases, the RV-variations are presumably caused by stellar activity, and in another case the companion could be a short-period binary. The images of the remaining two stars are slightly elongated, which might imply that even these are binaries. Because at least 12 of the 14 stars showing low-amplitude RV trends turn out to have companions with a mass greater than 70 MJupiter, or are just active, we finally estimate the number of companions with masses between 10 MJupiter and 70 MJupiter within 8 AU of the host stars in the Hyades as less equal 2%.Comment: 10 pages, 10 figure

Long-Term Survival Rates after Resection for Locally Advanced Kidney Cancer: Memorial Sloan Kettering Cancer Center 1989 to 2012 Experience

Purpose: We analyzed the 23-year Memorial Sloan Kettering Cancer Center experience with surgical resection, and concurrent adrenalectomy and lymphadenectomy for locally advanced nonmetastatic renal cell carcinoma. Materials and Methods: We retrospectively reviewed the records of 802 patients who underwent nephrectomy with or without concurrent adrenalectomy or lymphadenectomy for locally advanced renal cell carcinoma, defined as stage T3 or greater and M0. Patients who received adjuvant treatment within 3 months of surgery or had fewer than 3 months of followup or bilateral renal masses at presentation were excluded from analysis. Five and 10-year progression-free and overall survival was estimated by the Kaplan-Meier method. Differences between groups were analyzed by the log rank test. Results: A total of 596 (74%) and 206 patients (26%) underwent radical and partial nephrectomy, respectively. Renal cell carcinoma progressed in 189 patients and 104 died of the disease. Median followup in patients without progression was 4.6 years. Symptoms at presentation, ASA (R) classification, tumor stage, histological subtype, grade and lymph node status were significantly associated with progression-free and overall survival. On multivariate analysis adrenalectomy use decreased with time but lymphadenectomy use increased (OR 0.82 vs 1.16 per year). Larger tumors were associated with a higher likelihood of concurrent adrenalectomy and lymphadenectomy. Conclusions: In our series of patients with locally advanced nonmetastatic renal cell carcinoma survival was favorable in those in good health who were asymptomatic at presentation with T3 tumors and negative lymph nodes. Further, there has been a trend toward more selective use of adrenalectomy and increased use of lymphadenectomy

Measurement of the internal magnetic field of plasmas using an alpha particle source

The internal magnetic fields of plasmas can be measured under certain conditions from the integrated v x B deflection of MeV alpha particles emitted by a small radioactive source. This alpha source and large-area alpha particle detector would be located inside the vacuum vessel but outside the plasma. Alphas with a typical energy of 5.5 MeV (241Am) can reach the center of almost all laboratory plasmas and magnetic fusion devices, so this method can potentially determine the q(r) profile of tokamaks or STs. Orbit calculations, background evaluations, and conceptual designs for such a vxB (or ''AVB'') detector are described

Absolute photometric calibration of IRAC: lessons learned using nine years of flight data

Significant improvements in our understanding of various photometric effects have occurred in the more than nine years of flight operations of the Infrared Array Camera aboard the Spitzer Space Telescope. With the accumulation of calibration data, photometric variations that are intrinsic to the instrument can now be mapped with high fidelity. Using all existing data on calibration stars, the array location-dependent photometric correction (the variation of flux with position on the array) and the correction for intra-pixel sensitivity variation (pixel-phase) have been modeled simultaneously. Examination of the warm mission data enabled the characterization of the underlying form of the pixelphase variation in cryogenic data. In addition to the accumulation of calibration data, significant improvements in the calibration of the truth spectra of the calibrators has taken place. Using the work of Engelke et al. (2006), the KIII calibrators have no offset as compared to the AV calibrators, providing a second pillar of the calibration scheme. The current cryogenic calibration is better than 3% in an absolute sense, with most of the uncertainty still in the knowledge of the true flux densities of the primary calibrators. We present the final state of the cryogenic IRAC calibration and a comparison of the IRAC calibration to an independent calibration methodology using the HST primary calibrators