2-Transitivity is Insufficient for Local Testability

A basic goal in property testing is to identify a minimal set of features that make a property testable. For the case when the property to be tested is membership in a binary linear error-correcting code, Alon et al. (Trans Inf Theory, 51(11):4032–4039, 2005) had conjectured that the presence of a single low-weight codeword in the dual, and “2-transitivity” of the code (i.e., the code being invariant under a 2-transitive group of permutations on the coordinates of the code) suffice to get local testability. We refute this conjecture by giving a family of error-correcting codes where the coordinates of the codewords form a large field of characteristic two, and the code is invariant under affine transformations of the domain. This class of properties was introduced by Kaufman & Sudan (STOC, 2008) as a setting where many results in algebraic property testing generalize. Our result shows a complementary virtue: This family also can be useful in producing counterexamples to natural conjectures.     

The carbon-isotopic composition of Proterozoic carbonates: Riphean successions from northwestern Siberia (Anabar Massif, Turukhansk Uplift)

Thick carbonate-dominated successions in northwestern Siberia document secular variations in the C-isotopic composition of seawater through Mesoproterozoic and early Neoproterozoic (Early to early Late Riphean) time. Mesoproterozoic dolomites of the Billyakh Group, Anabar Massif, have delta 13C values that fall between 0 and -1.9 permil versus PDB, with values in the upper part of the succession (Yusmastakh Formation) consistently higher than those of the lower (Ust'-Il'ya and Kotuikan formations). Consistent with available biostratigraphic and radiometric data, delta 13C values for Billyakh carbonates compare closely with those characterizing early Mesoproterozoic carbonates (about 1600-1200 Ma) worldwide. In contrast, late Mesoproterozoic to early Neoproterozoic limestones and dolomites in the Turukhansk Uplift exhibit moderate levels of secular variation. Only the lowermost carbonates in the Turukhansk succession (Linok Formation) have delta 13C values that approximate Billyakh values. Higher in the Turukhansk succession, delta 13C values vary from -2.7 to +4.6 permil (with outliers as low as -5.0 permil interpreted as diagentically altered). Again, consistent with paleontological and radiometric data, these values compare well with isotopic values from 1200 to 850 Ma successions elsewhere. Five sections measured in different parts of the Turukhansk basin show nearly identical patterns of variation, confirming that carbonate delta 13C correlates primarily with time and not facies. The Siberian sections illustrate the potential of integrated biostratigraphic and chemostratigraphic data in the intra- and interbasinal correlation of Mesoproterozoic and early Neoproterozoic rocks.     

PET regularization by envelope guided conjugate gradients

The authors propose a new way to iteratively solve large scale ill-posed problems and in particular the image reconstruction problem in positron emission tomography by exploiting the relation between Tikhonov regularization and multiobjective optimization to obtain iteratively approximations to the Tikhonov L-curve and its corner. Monitoring the change of the approximate L-curves allows the authors to adjust the regularization parameter adaptively during a preconditioned conjugate gradient iteration, so that the desired solution can be reconstructed with a small number of iterations.     

Use of sky brightness measurements from ground for remote sensing of particulate polydispersions

The software code SKYEAD.pack for retrieval of aerosol size distribution and optical thickness from data of direct and diffuse solar radiation is described; measurements are carried out with sky radiometers in the wavelength range 0.369-1.048 μm. The treatment of the radiative transfer problem concerning the optical quantities is mainly based on the IMS (improved multiple and single scattering) method, which uses the delta-M approximation for the truncation of the aerosol phase function and corrects the solution for the first- and second-order scattering. Both linear and nonlinear inversion methods can be used for retrieving the size distribution. Improved calibration methods for both direct and diffuse radiation, the data-analysis procedure, the results from the proposed code, and several connected problems are discussed. The results can be summarized as follows: (a) the SKYRAD.pack code can retrieve the columnar aerosol features with accuracy and efficiency in several environmental situations, provided the input parameters are correctly given; (b) when data of both direct and diffuse solar radiation are used, the detectable radius interval for aerosol particles is approximately from 0.03 to 10 μm; (c) besides the retrieval of the aerosol features, the data-analysis procedure also permits the determination of average values for three input parameters (real and imaginary aerosol refractive index, ground albedo) from the optical data; (d) absolute calibrations for the sky radiometer are not needed, and calibrations for direct and diffuse radiation can be carried out with field data; (e) the nonlinear inversion gives satisfactory results in a larger radius interval, without the unrealistic humps that occur with the linear inversion, but the results strongly depend on the first-guess spectrum; (f) aerosol features retrieved from simulated data showed a better agreement with the given data for the linear inversion than for the nonlinear inversion.     

Amblyomma variegatum (Acari: Ixodidae): mechanism and control of arbovirus secretion in tick saliva

Saliva is considered to be the conduit by which pathogens are transmitted from blood-sucking arthropod vectors to their vertebrate hosts, but supporting evidence for this is fragmentary. To determine if Thogoto (THO) virus, a tick-borne member of the influenza virus family, is transmitted via tick saliva, and whether virus replication is a prerequisite for such transmission, two experimental conditions were compared: (1) "biological transmission" and (2) "mechanical transmission." In (1), THO virus was allowed to infect and replicate in a natural vector, Amblyomma variegatum: virus was detected in saliva collected from 3/22 (14%) ticks. In (2), virus was inoculated directly into the hemocoel with the drug used to induce salivation and saliva was collected immediately to preclude the possibility of virus replication: virus was detected in saliva collected from 31/170 (18%) ticks. The results demonstrate that THO virus is secreted in tick saliva and that virus can pass from the hemolymph to the salivary glands independently of viral replication within the tick. The comparatively low numbers of ticks that yielded virus-positive saliva samples together with the results from assays of serial saliva samples suggested that virus secretion may not be a continuous process during salivation. Ticks in which THO virus had established an infection showed an impaired secretory response compared with uninfected ticks and ticks used for mechanical transmission.     

Visual simulation of thermal fluid dynamics in a pressurized water reactor

We present a simulation and visualization system for a critical application—analysis of the thermal fluid dynamics inside a pressurized water reactor of a nuclear power plant when cold water is injected into the reactor vessel. We employ a hybrid thermal lattice Boltzmann method (HTLBM), which has the advantages of ease of parallelization and ease of handling complex simulation boundaries. For efficient computation and storage of the irregular-shaped simulation domain, we classify the domain into nonempty and empty cells and apply a novel packing technique to organize the nonempty cells. This method is implemented on a GPU cluster for acceleration. We demonstrate the formation of cold-water plumes in the reactor vessel. A set of interactive visualization tools, such as side-view slices, 3D volume rendering, thermal layers rendering, and panorama rendering, are provided to collectively visualize the structure and dynamics of the temperature field in the vessel. To the best of our knowledge, this is the first system that combines 3D simulation and visualization for analyzing thermal shock risk in a pressurized water reactor.     

Maximum likelihood, least squares, and penalized least squares for PET

The EM algorithm is the basic approach used to maximize the log likelihood objective function for the reconstruction problem in positron emission tomography (PET). The EM algorithm is a scaled steepest ascent algorithm that elegantly handles the nonnegativity constraints of the problem. It is shown that the same scaled steepest descent algorithm can be applied to the least squares merit function, and that it can be accelerated using the conjugate gradient approach. The experiments suggest that one can cut the computation by about a factor of 3 by using this technique. The results are applied to various penalized least squares functions which might be used to produce a smoother image.     

Treatment of acute lymphoblastic leukemia. 30 years' experience at St. Jude Children's Research Hospital

BACKGROUND: Therapy for childhood lymphoblastic leukemia has evolved during the past three decades, but key questions about what are the least toxic, most effective forms of treatment remain unanswered because of the lack of comprehensive follow-up information. METHODS: To assess long-term outcome in the series of clinical trials conducted at St. Jude Hospital, we compared the results of treatment typical of four eras: exploratory combination chemotherapy (era 1, 1962 to 1966; 91 patients), regimens for the control of meningeal leukemia (era 2, 1967 to 1979; 825 patients), limited intensification of therapy (era 3, 1979 to 1983; 428 patients), and extended intensification of therapy (era 4, 1984 to 1988; 358 patients). ("Intensification" refers to strategies of systemic chemotherapy that are more aggressive than conventional ones.) The major end points were survival and event-free survival; we also calculated the relative risk of treatment failure and the rate of relapse or death after treatment ended (post-treatment failure rate). RESULTS: The probability of event-free survival improved significantly in each successive era (P < 0.001 by the log-rank test), reaching 71 percent in era 4. There was a decrease of approximately 50 percent in the risk of treatment failure from one era to the next in each subgroup of patients defined according to different combinations of the leukocyte count, race, age, and sex. Leukemia appeared to be eradicated in patients who remained in complete remission for three years or more after treatment in era 4. The incidence of death due to nonleukemic causes remained 4 to 6 percent despite the trend toward more intensive treatment. An estimated 765 patients (45 percent) are long-term survivors; most of them (80 percent) have no health problems related to leukemia or its treatment. CONCLUSIONS: The development and successful application of preventive therapy for meningeal leukemia, followed by the intensification of systemic chemotherapy, has progressively improved the rate of cure of childhood lymphoblastic leukemia, with relatively few adverse sequelae.     

Effect of set-up error on the dose across the junction of matching cranial-spinal fields in the treatment of medulloblastoma

PURPOSE: The effect of systematic and stochastic setup error on the dose delivered to the gap region for the three field radiation treatment of medulloblastoma is studied. The consequences of such setup error is discussed. METHODS AND MATERIALS: The treatment of medulloblastoma is typically a 3 field technique, in which two lateral cranial fields are matched with a spine field. The x-ray dose delivered to the region between the matched fields depends upon the gap size. The choice of the gap width between the cranial and spinal fields is controversial. It is currently a compromise between minimizing the risk of dose hot spots to the spine, and the associated clinical complications, as well as the magnitude of cold spots (underdosing) across the gap, with the associated risk of disease recurrence. In this paper, we examine the effect of gap width with a moving junction, referred to as "field feathering", on the dose across the field junction for a 6MV photon beam. In addition, we have studied 129 portal films and 40 simulation films to assess the accuracy and precision of patient setup during treatment with a plan involving feathered fields. Selected landmarks observable on both portal and simulation films were identified and the variation in the distances to the field edges measured. The distribution of patient setup error was convoluted with the beam profiles for a 6MV linac. These convoluted field edges were used obtain dose profiles across the gap region as a function of gap separation. The consequences for therapy are discussed. In addition, analysis of patient setup error on an alternative treatment involving beam modifiers to broaden the beam penumbra is discussed. RESULTS: The magnitude of the spatial stochastic and systematic setup error was determined to be approximately three and two millimeters respectively. The dosimetric consequences of patient setup error lead to over and under dosing in the spinal gap region for the three field technique. The degree of under or over dose depends on the nature and magnitude of the patient setup error. CONCLUSIONS: The effect of patient setup error can lead to significant dosimetric errors in the dose to the gap region depending on the magnitude of the setup errors. The effective over and under dose can be compensated by the use beams modifiers such as a beam spoiler or vibrating jaws.     

Key exchange in IPSec: analysis of IKE

The IPSec (IP Security) protocol is a recently proposed standard of the Internet Engineering Task Force (IETF) for securing real-time communications on the Internet. The authors explain how its Internet Key Exchange (IKE) mechanism works and suggest improvements