Showing papers by "Cornell University published in 1996"

Emergence of simple-cell receptive field properties by learning a sparse code for natural images

Abstract: The receptive fields of simple cells in mammalian primary visual cortex can be characterized as being spatially localized, oriented and bandpass (selective to structure at different spatial scales), comparable to the basis functions of wavelet transforms. One approach to understanding such response properties of visual neurons has been to consider their relationship to the statistical structure of natural images in terms of efficient coding. Along these lines, a number of studies have attempted to train unsupervised learning algorithms on natural images in the hope of developing receptive fields with similar properties, but none has succeeded in producing a full set that spans the image space and contains all three of the above properties. Here we investigate the proposal that a coding strategy that maximizes sparseness is sufficient to account for these properties. We show that a learning algorithm that attempts to find sparse linear codes for natural scenes will develop a complete family of localized, oriented, bandpass receptive fields, similar to those found in the primary visual cortex. The resulting sparse image code provides a more efficient representation for later stages of processing because it possesses a higher degree of statistical independence among its outputs.

Separable dual-space Gaussian pseudopotentials

Abstract: We present pseudopotential coefficients for the first two rows of the Periodic Table. The pseudopotential is of an analytic form that gives optimal efficiency in numerical calculations using plane waves as a basis set. At most, seven coefficients are necessary to specify its analytic form. It is separable and has optimal decay properties in both real and Fourier space. Because of this property, the application of the nonlocal part of the pseudopotential to a wave function can be done efficiently on a grid in real space. Real space integration is much faster for large systems than ordinary multiplication in Fourier space, since it shows only quadratic scaling with respect to the size of the system. We systematically verify the high accuracy of these pseudopotentials by extensive atomic and molecular test calculations. \textcopyright{} 1996 The American Physical Society.

Polymer Layered Silicate Nanocomposites

Abstract: Polymer nanocomposites with layered silicates as the inorganic phase (reinforcement) are discussed. The materials design and synthesis rely on the ability of layered silicates to intercalate in the galleries between their layers a wide range of monomers and polymers. Special emphasis is placed on a new, versatile and environmentally benign synthesis approach by polymer melt intercalation. In contrast to in-situ polymerization and solution intercalation, melt intercalation involves mixing the layered silicate with the polymer and heating the mixture above the softening point of the polymer. Compatibility with various polymers is accomplished by derivatizing the silicates with alkyl ammonium cations via an ion exchange reaction. By fine-tuning the surface characteristics nanodispersion (i. e. intercalation or delamination) can be accomplished. The resulting polymer layered silicate (PLS) nanocomposites exhibit properties dramatically different from their more conventional counterparts. For example, PLS nanocomposites can attain a particular degree of stiffness, strength and barrier properties with far less inorganic content than comparable glass- or mineral reinforced polymers and, therefore, they are far lighter in weight. In addition, PLS nanocomposites exhibit significant increase in thermal stability as well as self-extinguishing characteristics. The combination of improved properties, convenient processing and low cost has already led to a few commercial applications with more currently under development.

Turbulence, Coherent Structures, Dynamical Systems and Symmetry

Abstract: Preface Part I. Turbulence: 1. Introduction 2. Coherent structures 3. Proper orthogonal decomposition 4. Galerkin projection Part II. Dynamical Systems: 5. Qualitative theory 6. Symmetry 7. One-dimensional 'turbulence' 8. Randomly perturbed systems Part III. 9. Low-dimensional Models: 10. Behaviour of the models Part IV. Other Applications and Related Work: 11. Some other fluid problems 12. Review: prospects for rigor Bibliography.

Unreliable failure detectors for reliable distributed systems

Abstract: We introduce the concept of unreliable failure detectors and study how they can be used to solve Consensus in asynchronous systems with crash failures. We characterise unreliable failure detectors in terms of two properties—completeness and accuracy. We show that Consensus can be solved even with unreliable failure detectors that make an infinite number of mistakes, and determine which ones can be used to solve Consensus despite any number of crashes, and which ones require a majority of correct processes. We prove that Consensus and Atomic Broadcast are reducible to each other in asynchronous systems with crash failures; thus, the above results also apply to Atomic Broadcast. A companion paper shows that one of the failure detectors introduced here is the weakest failure detector for solving Consensus [Chandra et al. 1992].

Cyclophosphamide and Cisplatin Compared with Paclitaxel and Cisplatin in Patients with Stage III and Stage IV Ovarian Cancer

Abstract: Background Chemotherapy combinations that include an alkylating agent and a platinum coordination complex have high response rates in women with advanced ovarian cancer. Such combinations provide long-term control of disease in few patients, however. We compared two combinations, cisplatin and cyclophosphamide and cisplatin and paclitaxel, in women with ovarian cancer. Methods We randomly assigned 410 women with advanced ovarian cancer and residual masses larger than 1 cm after initial surgery to receive cisplatin (75 mg per square meter of body-surface area) with either cyclophosphamide (750 mg per square meter) or paclitaxel (135 mg per square meter over a period of 24 hours). Results Three hundred eighty-six women met all the eligibility criteria. Known prognostic factors were similar in the two treatment groups. Alopecia, neutropenia, fever, and allergic reactions were reported more frequently in the cisplatin–paclitaxel group. Among 216 women with measurable disease, 73 percent in the cisplatin–pacli...

Measurement of two-photon excitation cross sections of molecular fluorophores with data from 690 to 1050 nm

Abstract: Measurements of two-photon fluorescence excitation (TPE) spectra are presented for 11 common molecular fluorophores in the excitation wavelength range 690 nm < λ < 1050 nm. Results of excitation by ∼100-fs pulses of a mode-locked Ti:sapphire laser are corroborated by single-mode cw Ti:sapphire excitation data in the range 710 nm < λ < 840 nm. Absolute values of the TPE cross section for Rhodamine B and Fluorescein are obtained by comparison with one-photon-excited fluorescence, assuming equal emission quantum efficiencies. TPE action cross sections for the other nine fluorophores are also determined. No differences between one-photon- and two-photon-excited fluorescence emission spectra are found. TPE emission spectra are independent of excitation wavelength. With both pulsed and cw excitation the fluorescence emission intensities are strictly proportional to the square of the excitation intensity to within ±4% for excitation intensities sufficiently below excited-state saturation.

Bootstrap Confidence Intervals

Abstract: This article surveys bootstrap methods for producing good approximate confidence intervals. The goal is to improve by an order of magnitude upon the accuracy of the standard intervals $\hat{\theta} \pm z^{(\alpha)} \hat{\sigma}$, in a way that allows routine application even to very complicated problems. Both theory and examples are used to show how this is done. The first seven sections provide a heuristic overview of four bootstrap confidence interval procedures: $BC_a$, bootstrap-t , ABC and calibration. Sections 8 and 9 describe the theory behind these methods, and their close connection with the likelihood-based confidence interval theory developed by Barndorff-Nielsen, Cox and Reid and others.

Regional nitrogen budgets and riverine N & P fluxes for the drainages to the North Atlantic Ocean: Natural and human influences

Abstract: We present estimates of total nitrogen and total phosphorus fluxes in rivers to the North Atlantic Ocean from 14 regions in North America, South America, Europe, and Africa which collectively comprise the drainage basins to the North Atlantic. The Amazon basin dominates the overall phosphorus flux and has the highest phosphorus flux per area. The total nitrogen flux from the Amazon is also large, contributing 3.3 Tg yr-1 out of a total for the entire North Atlantic region of 13.1 Tg yr-1. On a per area basis, however, the largest nitrogen fluxes are found in the highly disturbed watersheds around the North Sea, in northwestern Europe, and in the northeastern U.S., all of which have riverine nitrogen fluxes greater than 1,000 kg N km-2 yr-1.

Lying in everyday life.

Abstract: In 2 diary studies of lying, 77 college students reported telling 2 lies a day, and 70 community members told 1. Participants told more self-centered lies than other-oriented lies, except in dyads involving only women, in which other-oriented lies were as common as self-centered ones. Participants told relatively more self-centered lies to men and relatively more other-oriented lies to women. Consistent with the view of lying as an everyday social interaction process, participants said that they did not regard their lies as serious and did not plan them much or worry about being caught. Still, social interactions in which lies were told were less pleasant and less intimate than those in which no lies were told.

Treatment of Septic Shock with the Tumor Necrosis Factor Receptor:Fc Fusion Protein

Abstract: Background A recombinant, soluble fusion protein that is a dimer of an extracellular portion of the human tumor necrosis factor (TNF) receptor and the Fc portion of IgG1 (TNFR:Fc) binds and neutralizes TNF-α and prevents death in animal models of bacteremia and endotoxemia. Methods To evaluate the safety and efficacy of TNFR:Fc in the treatment of septic shock, we conducted a randomized, double-blind, placebo-controlled, multicenter trial. A total of 141 patients were randomly assigned to receive either placebo or a single intravenous infusion of one of three doses of TNFR:Fc (0.15, 0.45, or 1.5 mg per kilogram of body weight). The primary end point was mortality from all causes at 28 days. Results There were 10 deaths among the 33 patients in the placebo group (30 percent mortality), 9 deaths among the 30 patients receiving the low dose of TNFR:Fc (30 percent mortality), 14 deaths among the 29 receiving the middle dose (48 percent mortality), and 26 deaths among the 49 receiving the high dose (53 percent...

Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators.

Abstract: ▪ Abstract The importance of accurate demographic information is reflected in the United States Constitution, Article 1, which provides for a decennial census of this country's human population. Bacteria also conduct a census of their population and do so more frequently, more efficiently, and as far we know, with little if any of the political contentiousness caused by human demographers. Many examples have been found of particular bacterial genes, operons, or regulons that are expressed preferentially at high cell densities. Many of these are regulated by proteins related to the LuxR and LuxI proteins of Vibrio fischeri, and by a diffusible pheromone called an autoinducer. LuxR and LuxI and their cognate autoinducer (3-oxohexanoyl homoserine lactone, designated VAI-1) provide an important model to describe the functions of this family of proteins. LuxR is a VAI-1 receptor and a VAI-1–dependent transcriptional activator, and LuxI directs the synthesis of VAI-1. VAI-1 diffuses across the bacterial envelop...

Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy

Abstract: Intrinsic, three-dimensionally resolved, microscopic imaging of dynamical structures and biochemical processes in living preparations has been realized by nonlinear laser scanning fluorescence microscopy. The search for useful two-photon and three-photon excitation spectra, motivated by the emergence of nonlinear microscopy as a powerful biophysical instrument, has now discovered a virtual artist's palette of chemical indicators, fluorescent markers, and native biological fluorophores, including NADH, flavins, and green fluorescent proteins, that are applicable to living biological preparations. More than 25 two-photon excitation spectra of ultraviolet and visible absorbing molecules reveal useful cross sections, some conveniently blue-shifted, for near-infrared absorption. Measurements of three-photon fluorophore excitation spectra now define alternative windows at relatively benign wavelengths to excite deeper ultraviolet fluorophores. The inherent optical sectioning capability of nonlinear excitation provides three-dimensional resolution for imaging and avoids out-of-focus background and photodamage. Here, the measured nonlinear excitation spectra and their photophysical characteristics that empower nonlinear laser microscopy for biological imaging are described.

Permutation Tests for Multiple Loci Affecting a Quantitative Character

Abstract: The problem of detecting minor quantitative trait loci (QTL) responsible for genetic variation not explained by major QTL is of importance in the complete dissection of quantitative characters. Two extensions of the permutation-based method for estimating empirical threshold values are presented. These methods, the conditional empirical threshold (CET) and the residual empirical threshold (RET), yield critical values that can be used to construct tests for the presence of minor QTL effects while accounting for effects of known major QTL. The CET provides a completely nonparametric test through conditioning on markers linked to major QTL. It allows for general nonadditive interactions among QTL, but its practical application is restricted to regions of the genome that are unlinked to the major QTL. The RET assumes a structural model for the effect of major QTL, and a threshold is constructed using residuals from this structural model. The search space for minor QTL is unrestricted, and RET-based tests may be more powerful than the CET-based test when the structural model is approximately true.

Partially Molten Middle Crust Beneath Southern Tibet: Synthesis of Project INDEPTH Results

Abstract: INDEPTH geophysical and geological observations imply that a partially molten midcrustal layer exists beneath southern Tibet. This partially molten layer has been produced by crustal thickening and behaves as a fluid on the time scale of Himalayan deformation. It is confined on the south by the structurally imbricated Indian crust underlying the Tethyan and High Himalaya and is underlain, apparently, by a stiff Indian mantle lid. The results suggest that during Neogene time the underthrusting Indian crust has acted as a plunger, displacing the molten middle crust to the north while at the same time contributing to this layer by melting and ductile flow. Viewed broadly, the Neogene evolution of the Himalaya is essentially a record of the southward extrusion of the partially molten middle crust underlying southern Tibet.

Expression of a Late Embryogenesis Abundant Protein Gene, HVA1, from Barley Confers Tolerance to Water Deficit and Salt Stress in Transgenic Rice

Abstract: A late embryogenesis abundant (LEA) protein gene, HVA1, from barley (Hordeum vulgare L.) was introduced into rice suspension cells using the Biolistic-mediated transformation method, and a large number of independent transgenic rice (Oryza sativa L.) plants were generated. Expression of the barley HVA1 gene regulated by the rice actin 1 gene promoter led to high-level, constitutive accumulation of the HVA1 protein in both leaves and roots of transgenic rice plants. Second-generation transgenic rice plants showed significantly increased tolerance to water deficit and salinity. Transgenic rice plants maintained higher growth rates than nontransformed control plants under stress conditions. The increased tolerance was also reflected by delayed development of damage symptoms caused by stress and by improved recovery upon the removal of stress conditions. We also found that the extent of increased stress tolerance correlated with the level of the HVA1 protein accumulated in the transgenic rice plants. Using a transgenic approach, this study provides direct evidence supporting the hypothesis that LEA proteins play an important role in the protection of plants under water-or salt-stress conditions. Thus, LEA genes hold considerable potential for use as molecular tools for genetic crop improvement toward stress tolerance.

Bedrock incision, rock uplift and threshold hillslopes in the northwestern Himalayas

Abstract: The topography of tectonically active mountain ranges reflects a poorly understood competition between bedrock uplift and erosion. Dating of abandoned river-cut surfaces in the northwestern Himalayas reveals that the Indus river incises through the bedrock at extremely high rates (2–12 mm yr-1). In the surrounding mountains, the average angles of hillslopes are steep and essentially independent of erosion rate, suggesting control by a common threshold process. In this rapidly deforming region, an equilibrium is maintained between bedrock uplift and river incision, with landsliding allowing hillslopes to adjust efficiently to rapid river down-cutting.

Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines.

Abstract: Advanced backcross QTL analysis is proposed as a method of combining QTL analysis with variety development. It is tailored for the discovery and transfer of valuable QTL alleles from unadapted donor lines (e.g., land races, wild species) into established elite inbred lines. Following this strategy, QTL analysis is delayed until the BC2 or BC3 generation and, during the development of these populations, negative selection is exercised to reduce the frequency of deleterious donor alleles. Simulations suggest that advanced backcross QTL analysis will be effective in detecting additive, dominant, partially dominant, or overdominant QTLs. Epistatic QTLs or QTLs with gene actions ranging from recessive to additive will be detected with less power than in selfing generations. QTL-NILs can be derived from advanced backcross populations in one or two additional generations and utilized to verify QTL activity. These same QTL-NILs also represent commercial inbreds improved (over the original recurrent inbred line) for one or more quantitative traits. The time lapse from QTL discovery to construction and testing of improved QTL-NILs is minimal (1-2 years). If successfully employed, advanced backcross QTL analysis can open the door to exploiting unadapted and exotic germplasm for the quantitative trait improvement of a number of crop plants.

Pivoted document length normalization

Abstract: Automatic information retrieval systems have to deal with documents of varying lengths in a text collection. Document length normalization is used to fairly retrieve documents of all lengths. In this study, we ohserve that a normalization scheme that retrieves documents of all lengths with similar chances as their likelihood of relevance will outperform another scheme which retrieves documents with chances very different from their likelihood of relevance. We show that the retrievaf probabilities for a particular normalization method deviate systematically from the relevance probabilities across different collections. We present pivoted normalization, a technique that can be used to modify any normalization function thereby reducing the gap between the relevance and the retrieval probabilities. Training pivoted normalization on one collection, we can successfully use it on other (new) text collections, yielding a robust, collectzorz independent normalization technique. We use the idea of pivoting with the well known cosine normalization function. We point out some shortcomings of the cosine function andpresent two new normalization functions--pivoted unique normalization and piuotert byte size normalization.

Transcriptional activation of the Cdk inhibitor p21 by vitamin D3 leads to the induced differentiation of the myelomonocytic cell line U937.

Abstract: The hormonal form of vitamin D, 1,25-dihydroxyvitamin D3, acting through its cognate nuclear receptor (vitamin D3 receptor, VDR) will induce myeloid leukemic cell lines to terminally differentiate into monocytes/macrophages. Because VDR acts by transcriptionally regulating responsive genes in a ligand-dependent manner, we sought target genes of the receptor that initiate, the differentiation process in response to ligand. We screened a cDNA library prepared from the myelomonocytic U937 cell line with probes generated from either 1,25-dihydroxyvitamin D3-treated or untreated cells. We report here that a candidate clone that hybridized differentially is the Cdk inhibitor p21WAF1, CIP1. Furthermore, we show that p21 is transcriptionally induced by 1,25-dihydroxyvitamin D3 in a VDR-dependent, but not p53-dependent, manner, and we identify a functional vitamin D response element in the p21 promoter. Transient overexpression of p21 and/or the related Cdk inhibitor p27 in U937 cells in the absence of 1,25-dihydroxyvitamin D3 results in the cell-surface expression of monocyte/macrophage-specific markers, suggesting that ligand-modulated transcriptional induction of the p21 gene facilitates the induced differentiation of this monoblastic cell line. We believe that this is the first report demonstrating that the ectopic overexpression of a Cdk inhibitor such as p21 or p27 directly leads to a terminal differentiation program.

Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP.

Abstract: Rapamycin, a potent immunosuppressive agent, binds two proteins: the FK506-binding protein (FKBP12) and the FKBP-rapamycin-associated protein (FRAP). A crystal structure of the ternary complex of human FKBP12, rapamycin, and the FKBP12-rapamycin-binding (FRB) domain of human FRAP at a resolution of 2.7 angstroms revealed the two proteins bound together as a result of the ability of rapamycin to occupy two different hydrophobic binding pockets simultaneously. The structure shows extensive interactions between rapamycin and both proteins, but fewer interactions between the proteins. The structure of the FRB domain of FRAP clarifies both rapamycin-independent and -dependent effects observed for mutants of FRAP and its homologs in the family of proteins related to the ataxia-telangiectasia mutant gene product, and it illustrates how a small cell-permeable molecule can mediate protein dimerization.

Structure and Dynamics of Polymer-Layered Silicate Nanocomposites

Abstract: The static and dynamic properties of polymer-layered silicate nanocomposites are discussed in the context of polymers in confined media. Despite the topological constraints imposed by the host lattice, mass transport of the polymer into the silicate layers (at least in the case of essentially non-polar polystyrene) appears to be unhindered and exhibits mobility similar to that of the pure polymer. However, both the local and global dynamics of the polymer in the hybrids are dramatically different from those in the bulk. On a local scale, intercalated polymer chains exhibit higher flexibility along their backbone along with a marked suppression (or even absence) of cooperative dynamics typically associated with the glass transition. On a global scale, relaxation of polymer chains either tethered to or in close proximity (<1 nm as in intercalated hybrids) to the host surface are dramatically altered and parallel those of other intrinsically anisotropic materials such as block copolymers and liquid crystals.

The weakest failure detector for solving consensus

Abstract: We determine what information about failures is necessary and sufficient to solve Consensus in asynchronous distributed systems subject to crash failures. In Chandra and Toueg [1996], it is shown that W, a failure detector that provides surprisingly little information about which processes have crashed, is sufficient to solve Consensus in asynchronous systems with a majority of correct processes. In this paper, we prove that to solve Consensus, any failure detector has to provide at least as much information as W. Thus, W is indeed the weakest failure detector for solving Consensus in asynchronous systems with a majority of correct processes.