gebhart/patrepeval huggingface dataset:
A contour-based approach to multisensor image registration (1995)

Image registration is concerned with the establishment of correspondence between images of the same scene. One challenging problem in this area is the registration of multispectral/multisensor images. In general, such images have different gray level characteristics, and simple techniques such as those based on area correlations cannot be applied directly. On the other hand, contours representing region boundaries are preserved in most cases. The authors present two contour-based methods which use region boundaries and other strong edges as matching primitives. The first contour matching algorithm is based on the chain-code correlation and other shape similarity criteria such as invariant moments. Closed contours and the salient segments along the open contours are matched separately. This method works well for image pairs in which the contour information is well preserved, such as the optical images from Landsat and Spot satellites. For the registration of the optical images with synthetic aperture radar (SAR) images, the authors propose an elastic contour matching scheme based on the active contour model. Using the contours from the optical image as the initial condition, accurate contour locations in the SAR image are obtained by applying the active contour model. Both contour matching methods are automatic and computationally quite efficient. Experimental results with various kinds of image data have verified the robustness of the algorithms, which have outperformed manual registration in terms of root mean square error at the control points.
A Semantic Analysis of the Design Space of Input Devices (1990)

A bewildering variety of devices for communication from humans to computers now exists on the market. In this article, we propose a descriptive framework for analyzing the design space of these input devices. We begin with Buxton's (1983) idea that input devices are transducers of physical properties in one, two, or three dimensions. Following Mackinlay's semantic analysis of the design space for graphical presentations, we extend this idea to more comprehensive descriptions of physical properties, space, and transducer mappings. In our reformulation, input devices are transducers of any combination of linear and rotary, absolute and relative, position and force, in any of the six spatial degrees of freedom. Simple input devices are described in terms of semantic mappings from the transducers of physical properties into the parameters of the applications. One of these mappings, the resolution function, allows us to describe the range of possibilities from continuous devices to discrete devices, including possibilities in between. Complex input controls are described in terms of hierarchical families of generic devices and in terms of composition operators on simpler devices. The description that emerges is used to produce a new taxonomy of input devices. The taxonomy is compared with previous taxonomies of Foley, Wallace, and Chan (1984) and of Buxton (1983) by reclassifying the devices previously analyzed by these authors. The descriptive techniques are further applied to the design of complex mouse-based virtual input controls for simulated three-dimensional (3D) egocentric motion. One result is the design of a new virtual egocentric motion control.
Chaff: engineering an efficient SAT solver (2002)

Boolean Satisfiability is probably the most studied of combinatorial optimization/search problems. Significant effort has been devoted to trying to provide practical solutions to this problem for problem instances encountered in a range of applications in Electronic Design Automation (EDA), as well as in Artificial Intelligence (AI). This study has culminated in the development of several SAT packages, both proprietary and in the public domain (e.g. GRASP, SATO) which find significant use in both research and industry. Most existing complete solvers are variants of the Davis-Putnam (DP) search algorithm. In this paper we describe the development of a new complete solver, Chaff, which achieves significant performance gains through careful engineering of all aspects of the search - especially a particularly efficient implementation of Boolean constraint propagation (BCP) and a novel low overhead decision strategy. Chaff has been able to obtain one to two orders of magnitude performance improvement on difficult SAT benchmarks in comparison with other solvers (DP or otherwise), including GRASP and SATO.
How Revenue Assurance and Yield Insurance Stack Up: A Cost Comparison (2015)

What percentage of expected revenue would be assured to agricultural producers if government yield insurance was transformed into a revenue assurance type of safety net program? Recent interest in a potential dual federal crop insurance program that would offer producers the option of yield or revenue insurance at the same level of U.S. government subsidy prompts this question.
Synergism through direct covalent bonding between agents: A strategy for rational design of chemotherapeutic combinations (1990)

Self-assembling chemotherapeutic agents are mixtures of relatively nontoxic precursors that can combine chemically under physiological conditions to form products with greater cytotoxic and/or antimicrobial activity than either of the precursors. Combinations that form products more rapidly in or near the target (tumor, pathogen, virally infected cell) than in normal tissues will exhibit target-selective synergism, thus exhibiting an antitarget selectivity that is greater than the selectivities of the product (e.g., a hydrazone) and of either precursor (e.g., a hydrazine derivative or ketone) used singly. This paper describes the target-selective cytotoxic synergism of a cationic aldehyde (A) and a cationic acylhydrazine (B) containing a triarylalkylphosphonium moiety against Ehrlich ascites carcinoma cells (ELA) in culture, in addition to reviewing previous work on self-assembling cytotoxins. The synergism between A and B is carcinoma selective when the ELA cells (the target) are compared to CV-1, an untransformed African green monkey kidney epithelial line. Like tetraphenylphosphonium and rhodamine 123, which are selectively concentrated in ELA cells relative to CV-1, A, B and the hydrazone C resulting from their reaction are lipophilic delocalized cations that selectively inhibit ELA growth relative to CV-1 growth. The hydrazone C is more growth inhibitory than either A or B for both cell lines. A combination of A with an unreactive analogue of B and a combination of B with an unreactive analogue of A did not synergistically inhibit ELA proliferation. The degree of synergism is greater against the ELA cells than against the CV-1 cells. These data, together with hydrazone formation kinetics, suggest that A and B are both concentrated together selectively inside the ELA due to the transmembrane potentials, reacting inside the ELA cells at a higher velocity than inside the CV-1 cells to form the more growth-inhibitory hydrazone C.
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL (1998)

TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. The databases are accessible via WWW:http://transfac.gbf.de/TRANSFAC orhttp://www.bionet.nsc.ru/TRRD
Medium‐density particleboards from rice husks and soybean protein concentrate (2007)

Abstract Rice husks are a valuable agricultural residue produced worldwide with potential applications as a wood substitute in particleboard manufacturing. In this work, the feasibility of producing medium‐density particleboards based on waste rice husks bonded with environmentally friendly adhesives from soybean protein concentrate was analyzed. The mechanical properties, internal bond strength, and water resistance of the obtained panels bonded with the homemade soybean protein concentrate adhesives were compared to those of boards glued with commercial adhesives such as phenol–formaldehyde and urea–formaldehyde resins. An alkaline treatment improved the gluing ability of the soybean protein concentrate. The mechanical properties of the alkali‐treated soybean protein concentrate were comparable to those determined for panels with urea–formaldehyde. The lower water resistance of the alkali‐treated soybean protein concentrate particleboards, compared with that of the formaldehyde‐based resins, was counterbalanced by the advantage of being more environmentally sound, which makes them suitable for applications for which the requirements for water resistance are not stringent. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Critical illness myopathy: A direct role for endotoxin* (2008)

Department of Clinical Neurological Sciences, The University of Western Ontario, London, Ontario, Canada
c-Jun Has Multiple Enhancing Activities in the Novel Cross Talk between the Androgen Receptor and Ets Variant Gene 1 in Prostate Cancer (2007)

The multiple transcriptional roles of c-Jun are shown in a novel cross-talk between the androgen receptor (AR) and its new target gene, Ets variant gene 1 (ETV1). In this report, we show that c-Jun can mediate AR induction of ETV1 expression independent of c-Jun transactivation function. Interestingly, c-Jun can transactivate the cloned ETV1 promoter also in the absence of ligand-activated AR, suggesting two mechanisms by which c-Jun can induce ETV1 expression. In addition, both wild-type c-Jun and a transactivation-deficient mutant can enhance the transcriptional activity of ETV1, as measured by both reporter gene assay and endogenous expression of matrix metalloproteinase genes, well-known targets of Ets proteins. Overexpression of the c-Jun mutant protein also led to increased prostate cancer cell invasion. Immunoprecipitation and immunocytochemistry experiments showed copurification and colocalization of c-Jun with AR or ETV1, suggesting that c-Jun acts on AR or ETV1 via a physical association. Collectively, these results, together with a parallel overexpression of ETV1, c-Jun, and AR in prostate tumors, imply that c-Jun plays a pivotal role in the pathway that connects ligand-activated AR to elevated ETV1 expression, leading to enhanced expression of matrix metalloproteinases and prostate cancer cell invasion.
A sequestered pool of aminoacyl-tRNA in mammalian cells. (1992)

We have recently proposed that aminoacyl-tRNA is channeled during protein synthesis in vivo--i.e., it is directly transferred among the components of the protein-synthesizing machinery and does not mix with aminoacyl-tRNA molecules introduced from outside the cell. To understand the structural basis for these functional properties, we have examined the disposition of aminoacyl-tRNA within the cell. To do this we have developed a Chinese hamster ovary (CHO) permeabilized-cell system using the plant glycoside saponin. We show, using a mixture of free 14C-labeled amino acids and 3H-labeled aminoacyl-tRNAs, that 14C-labeled aminoacyl-tRNAs synthesized endogenously from the free amino acids are preferentially sequestered within the cell, whereas their exogenous 3H counterparts distribute between the inside and outside of the cell based solely on the relative volumes of the two compartments. Furthermore, the endogenous 14C-labeled aminoacyl-tRNA population is resistant to pancreatic ribonuclease action, whereas the 3H molecules are rapidly degraded. We conclude, based on these observations, that aminoacyl-tRNAs synthesized in vivo are continually associated with components of the protein synthesis machinery and are thereby retained within the permeabilized cell and are also protected from RNase action. These data provide independent evidence for the channeling model of protein biosynthesis.
Modulation of immune dysfunction during murine leukaemia retrovirus infection of old mice by dehyroepiandrosterone sulphate (DHEAS) (1997)

Ageing, leukaemia and acquired immune deficiency syndrome (AIDS) are conditions with dysregulated cytokine production. As dehydroepiandrosterone sulphate (DHEAS) restored normal cytokine production in old mice its effects on retrovirally infected old mice were investigated. Retrovirus infection and ageing-induced immune dysfunction. Murine retrovirus-infected old C57BL/6 female mice consumed 0.22 or 0.44 microgram of DHEAS/mouse/day beginning 2 weeks postinfection for 10 weeks. DHEAS largely prevented the retrovirus-induced reduction in T-cell and B-cell mitogenesis. DHEAS supplement prevented loss of cytokines [interleukin-2 (IL-2) and interferon-gamma] secretion by mitogen-stimulated splenocytes representing T helper 1 (Th1) cell phenotypes. It also suppressed the retrovirus-induced, excessive production of cytokines (IL-6 and IL-10) by Th2 cells. The highest dose of DHEAS reduced IL-6 production by splenocytes from uninfected old mice by 75% while increasing their IL-2 secretion by nearly 50%. Thus immune dysfunction induced by ageing, even when exacerbated by murine retrovirus infection, was largely prevented by DHEAS.
Reduction of Sintering during Annealing of FePt Nanoparticles Coated with Iron Oxide (2005)

FePt/iron oxide core/shell nanoparticles are synthesized by a two step polyol process with 1,2-hexadecanediol as the reducing reagent. Monodispersed 2.6-nm FePt nanoparticles are first obtained by reduction of iron(III) acetylacetonate and platinum(II) acetylacetonate. These preformed FePt nanoparticles are then used as seeds and an iron oxide shell is formed in the second synthesis step. The role of the iron oxide shell on sintering of FePt nanoparticles is investigated. Annealing studies show that these FePt/iron oxide core/shell structures are stable after annealing at 550 °C for 30 min at which 2.6-nm FePt nanoparticles without oxide shell coating start to sinter. Low-temperature magnetic hysteresis behavior of the annealed core/shell nanoparticles suggests exchange coupling between the magnetically hard FePt core and the magnetically soft iron oxide shell.
Uptake of 18F-Fluorocholine, 18F-FET, and 18F-FDG in C6 Gliomas and Correlation with 131I-SIP(L19), a Marker of Angiogenesis (2007)

One day after intravenous injection, (131)I-SIP(L19) displayed a very high tumor-to-cortex ratio, which may be used in the diagnostic work-up of brain tumor patients. Of the 3 investigated (18)F tracers, (18)F-fluorocholine and (18)F-FET correlated better with the pattern of (131)I-SIP(L19) uptake than did (18)F-FDG. Whether this means that (18)F-fluorocholine and (18)F-FET are better suited than (18)F-FDG to monitor antiangiogenic therapy should be investigated in future studies.
Complexity of Inflammatory Responses in Endothelial Cells and Vascular Smooth Muscle Cells Determined by Microarray Analysis (2002)

To better understand the molecular basis of vascular cell system behavior in inflammation, we used gene expression microarrays to analyze the expression of 7,075 genes and their response to IL-1beta and TNFalpha in cultures of coronary artery endothelium and smooth muscle derived from a single coronary artery. The most noticeable difference between the cell types was the considerably greater magnitude and complexity of the transcriptional response in the endothelial cells. Two hundred and nine genes were regulated in the endothelium and only 39 in vascular smooth muscle. Among the 209 regulated genes in the endothelium, 99 have not been previously associated with endothelial cell activation and many implicate the endothelium in unconventional roles. For example, the induced genes include several that have only been associated with leukocyte function (e.g., IL-7 receptor, EBI-3 receptor) and others related to antiviral and antibacterial defense (e.g., oligoadenylate synthetase, LMP7, toll-like receptor 4, complement component 3). In addition, 43 genes likely to participate in signal transduction (eg. IL-18 receptor, STK2 kinase, STAF50, ANP receptor, VIP receptor, RAC3, IFP35) were regulated providing evidence that a major effect of TNFalpha and IL-1beta is to alter the potential of the endothelial cell to respond to various other external stimuli.
Transcriptional Profiling After Bile Duct Ligation Identifies PAI-1 as a Contributor to Cholestatic Injury in Mice * (2005)

Extrahepatic cholestasis leads to complex injury and repair processes that result in bile infarct formation, neutrophil infiltration, cholangiocyte and hepatocyte proliferation, extracellular matrix remodeling, and fibrosis. To identify early molecular mechanisms of injury and repair after bile duct obstruction, microarray analysis was performed on liver tissue 24 hours after bile duct ligation (BDL) or sham surgery. The most upregulated gene identified encodes plasminogen activator inhibitor 1 (PAI-1, Serpine 1), a protease inhibitor that blocks urokinase plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) activity. Because PAI-1, uPA, and tPA influence growth factor and cytokine processing as well as extracellular matrix remodeling, we evaluated the role of PAI-1 in cholestatic liver injury by comparing the injury and repair processes in wild-type (WT) and PAI-1-deficient (PAI-1-/-) mice after BDL. PAI-1-/- mice had fewer and smaller bile infarcts, less neutrophil infiltration, and higher levels of cholangiocyte and hepatocyte proliferation than WT animals after BDL. Furthermore, PAI-1-/- mice had higher levels of tPA activation and mature hepatocyte growth factor (HGF) after BDL than WT mice, suggesting that PAI-1 effects on HGF activation critically influence cholestatic liver injury. This was further supported by elevated levels of c-Met and Akt phosphorylation in PAI-1-/- mice after BDL. In conclusion, PAI-1 deficiency reduces liver injury after BDL in mice. These data suggest that inhibiting PAI-1 might attenuate liver injury in cholestatic liver diseases.
[The differentiation antigen of trophoblast expressed on trophoblastic neoplasms (choriocarcinoma and hydatidiform mole) detected by monoclonal antibodies]. (1986)

To analyse the differentiation and malignant transformation of human trophoblasts, attempts were made to establish monoclonal antibodies (MoAbs) that react with cells at a certain stage of the trophoblast differentiation process. Two MoAbs, TM7-3 and TM3-8, were obtained by immunizing BALB/c mice with a human choriocarcinoma cell line, BeWo. In the cellular radioimmunoassay with 125I-labelled F(ab')2 of goat anti-mouse IgG, they reacted with nine out of ten choriocarcinoma cell lines and five of sixteen non-choriocarcinoma cell lines but not with twenty-six lymphoblastoid cell lines tested. Immunofluorescence and immunoperoxidase stainings showed that these MoAbs reacted predominantly with cytotrophoblast-like, but not syncytiotrophoblast-like components in the tissue of choriocarcinoma or hydatidiform mole, in the normal chorionic villi, cytotrophoblasts were very weakly positive but syncytiotrophoblasts were negative, and in a variety of normal tissues tested, only a part of the urinary tubules of kidney and the ducts of pancreas reacted to these MoAbs. These results suggest that TM7-3 and TM3-8 detect a differentiation antigen of human trophoblasts, which appears to increase with the malignant transformation of cytotrophoblasts. Thus, TM7-3 and TM3-8 may be useful in the study of human trophoblast differentiation.
P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila. (1989)

We describe a new approach for identifying and studying genes involved in Drosophila development. Single copies of an enhancer detector transposon, P[1ArB], have been introduced into flies at many different genomic locations. The beta-galactosidase reporter gene in this construct is influenced by a wide range of genomic transcriptional regulatory elements in its vicinity. Our results suggest that a significant proportion of these regulatory sequences are control elements of nearby Drosophila genes. These genes need not be disrupted for their regulatory elements to be identified by P[1ArB]. The P[1ArB] transposon has been designed to facilitate both rapid cloning and deletion analysis of genomic sequences into which it inserts. Therefore, the enhancer detection system is an efficient method of screening for genes primarily on the basis of their expression pattern and then rapidly analyzing those of particular interest at the molecular and genetic levels.
Cyclic mechanical strain‐induced proliferation and migration of human airway smooth muscle cells: role of EMMPRIN and MMPs (2005)

Airway smooth muscle (ASM) proliferation and migration are major components of airway remodeling in asthma. Asthmatic airways are exposed to mechanical strain, which contributes to their remodeling. Matrix metalloproteinase (MMP) plays an important role in remodeling. In the present study, we examined if the mechanical strain of human ASM (HASM) cells contributes to their proliferation and migration and the role of MMPs in this process. HASM were exposed to mechanical strain using the FlexCell system. HASM cell proliferation, migration and MMP release, activation, and expression were assessed. Our results show that cyclic strain increased the proliferation and migration of HASM; cyclic strain increased release and activation of MMP-1, -2, and -3 and membrane type 1-MMP; MMP release was preceded by an increase in extracellular MMP inducer; Prinomastat [a MMP inhibitor (MMPI)] significantly decreased cyclic strain-induced proliferation and migration of HASM; and the strain-induced increase in the release of MMPs was accompanied by an increase in tenascin-C release. In conclusion, cyclic mechanical strain plays an important role in HASM cell proliferation and migration. This increase in proliferation and migration is through an increase in MMP release and activation. Pharmacological MMPIs should be considered in the pursuit of therapeutic options for airway remodeling in asthma.
An efficient algorithm for finding dominant trapping sets of LDPC codes (2010)

This paper presents an efficient algorithm for finding the dominant trapping sets of a low-density parity-check (LDPC) code. This algorithm can be used to estimate the error floor of LDPC codes or to be part of the apparatus to design LDPC codes with low error floors. The algorithm is initiated with a set of short cycles as the input. The cycles are then expanded recursively to dominant trapping sets of increasing size. At the core of the algorithm lies the analysis of the graphical structure of dominant trapping sets and the relationship of such structures to short cycles. The algorithm is universal in the sense that it can be used for an arbitrary graph and that it can be tailored to find other graphical objects, such as absorbing sets and Zyablov-Pinsker (ZP) trapping sets, known to dominate the performance of LDPC codes in the error floor region over different channels and for different iterative decoding algorithms. Simulation results on several LDPC codes demonstrate the accuracy and efficiency of the proposed algorithm. In particular, the algorithm is significantly faster than the existing search algorithms for dominant trapping sets.